Each of the top level terms in this file is the root term of an independent controlled vocabulary
The PSI MI schema defines short labels for controlled vocabulary terms
The correct use of these vocabularies in the PSI Molecular Interaction XML schema is
The last accession number used in this file is stored in a separate file,
The maintenance of this file is ensured by Luana Licata luana.licata@uniroma2.it and Sandra Orchard orchard@ebi.ac.uk
coverage: This file collect controlled vocabularies describing different aspects of molecular interactions.
formalized in a mapping file available at http://www.psidev.info/files/validator/xml/MI-CVMapping.xml.
mapping an element of the PSI Molecular Interaction XML schema.
psi-mi.lastac. It MUST be updated when this file is updated.
publisher: This file is published by the PSI MI working group see http://psidev.info/MI
short labels are reported as PSI-MI-short synonyms that are created when a term is more than 20 characteres long.
Protein feature description from UniProtKB
Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions.
Method to determine the molecules involved in the interaction.
Method to determine the features of the proteins involved in the interaction.
This class of approaches is characterised by the use of affinity resins as tools to purify molecule of interest (baits) and their binding partners. The baits can be captured by a variety of high affinity ligands linked to a resin - for example, antibodies specific for the bait itself, antibodies for specific tags engineered to be expressed as part of the bait or other high affinity binders such as glutathione resins for GST fusion proteins, metal resins for histidine-tagged proteins.
This approach is used to identify the residues that are involved in an interaction. Several variants of the native protein are prepared by sequentially mutating each residue of interest to an alanine. The mutated proteins are expressed and probed in the binding assay.
A specific antibody for the molecule of interest (bait) is available, this is used to generate a high affinity resin to capture the endogenous bait present in a sample.
A specific antibody for the molecule of interest is not available, therefore the bait protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient and specific antibodies or a specific ligand are available.
In this class of methodologies, the molecules to be tested are presented ordered in an array format (typically at high density) on planar supports. The characteristics and chemical nature of the planar support can vary. This format permits the simultaneous assay, in controlled conditions, of several thousand proteins/peptides/nucleic acids for different functions, for instance their ability to bind any given molecule.
The protein of interest is presented on the outer membrane of Gram negative bacteria by expressing it as a fusion partner to peptide signals that direct heterologous proteins to the cell surface. For instance, a single chain Fv (scFv) antibody fragment, consisting of the variable heavy and variable light domains from two separate anti-digoxin monoclonal antibodies, was displayed on the outer membrane of Escherichia coli by fusing it to an Lpp-OmpA. Similar systems have also been developed for gram positive bacteria. Fluorescence-activated cell sorting (FACS), is used to specifically select clones displaying a protein binding to scFv-producing cells.
Beta-galactosidase activity can be used to monitor the interaction of chimeric proteins. Pairs of inactive beta gal deletion mutants are capable of complementing to restore activity when fused to interacting protein partners. Critical to the success of this system is the choice of two poorly complementing mutant moieties, since strongly complementing mutants spontaneously assemble and produce functional beta-gal activity detectable in absence of any fused protein fragment.
This strategy is based on a protein fragment complementation assay (PCA) of the enzyme TEM-1 beta-lactamase. The approach includes a simple colorimetric in vitro assays using the cephalosporin nitrocefin and assays in intact cells using the fluorescent substrate CCF2/AM. The combination of in vitro colorimetric and in vivo fluorescence assays of beta-lactamase in mammalian cells permits a variety of sensitive and high-throughput large-scale applications.
In this variation of the FRET assay the donor fluorophore is replaced by a luciferase (typically Renilla luciferase). In the presence of its substrate, the luciferase catalyses a bioluminescent reaction that excites the acceptor fluorophore through a resonance energy transfer mechanism. As with FRET the energy transfer occurs only if the protein fused to the luciferase and the one fused to the acceptor fluorophore are in close proximity (10-100 Angstrom).
bioluminescence resonance energy transfer
The application of physical principles and methods to biological experiments.
Adenylate cyclase is encoded by the cyaA gene and contains a catalytic domain which can be proteolytically cleaved into two complementary fragments, T25 and T18, which remain associated in the presence of calmodulin in a fully active ternary complex. In the absence of calmodulin, the mixture of the two fragments does not exhibit detectable activity, suggesting that the two fragments do not associate. When expressed in an adenylate cyclase-deficient E. coli strain (E. coli lacks calmodulin or calmodulin-related proteins), the T25 and T18 fragments fused to putative interacting proteins are brought into close association which result in cAMP synthesis. The level of reconstructed adenylate cyclase can be estimated by monitoring the expression of a cAMP dependent reporter gene. The T25 tagged protein is generally regarded as the bait, the T18 as the prey.
Circular dichroism (CD) is observed when optically active molecules absorb left and right hand circularly polarized light slightly differently. Linearly polarized light can be viewed as a superposition of two components of circularly polarized light of equal amplitude and phase but opposite handness. When this light passes through an optically active sample the two polarized components are absorbed differently. The difference in left and right handed absorbance A(l)- A(r) is the signal registered in CD spectra. This signal displays distinct features corresponding to different secondary structures present in peptides, proteins and nucleic acids. The analysis of CD spectra can therefore yield valuable information about the secondary structure of biological macromolecules and the interactions among molecules that influence their structure.
Proteins contain endogenous fluorophores such as tryptophan residue and heme or flavins groups. Protein folding and protein-protein interaction can be studied by monitoring changes in the tryptophan environment detected by changes in its intrinsic fluorescence. Changes in the fluorescence emission spectrum on complex formation can occur either due to a shift in the wavelength of maximum fluorescence emission or by a shift in fluorescence intensity caused by the mixing of two proteins. The interaction of two proteins causes a shift in the fluorescence emission spectrum relative to the sum of the individual fluorescence spectra, resulting in a difference spectrum [F (complex)-2 F (sum)], which is a measurable effect of the interaction. Loss of fluorescence signal from a substrate can be used to measure protein cleavage.
The classical two-hybrid system is a method that uses transcriptional activity as a measure of protein-protein interaction. It relies on the modular nature of many site-specific transcriptional activators (GAL 4) , which consist of a DNA-binding domain and a transcriptional activation domain. The DNA-binding domain serves to target the activator to the specific genes that will be expressed, and the activation domain contacts other proteins of the transcriptional machinery to enable transcription to occur. The two-hybrid system is based on the observation that the two domains of the activator need to be non-covalently brought together by the interaction of any two proteins. The application of this system requires the expression of two hybrid. Generally this assay is performed in yeast cell, but it can also be carried out in other organism. The bait protein is fused to the DNA binding molecule, the prey to the transcriptional activator.
In this approach an antibody, specific for the molecule of interest (bait) or any tag expressed within a fusion protein, is used to separate the bait from a molecular mixture or a cell lysate and to capture its ligand simultaneously. The partners that bind to the bait molecule retained by the resin can then be eluted and identified. The antibody may be free or bound to a matrix during this process.
Microscopy technique in which a beam of electrons is transmitted through a sample to form an image. Samples can be purified molecules, for which no staining is required in order to detect interaction, or tissue/cells. In the latter case, during the treatment for microscope analysis a tissue section is incubated with high-specificity antibodies coupled to heavy metals (e.g. gold). Any tissue section can then be analysed by electron microscopy to localise the target proteins within the cell. This method supports very high resolution colocalisation of different molecules in a cell.
Two proteins can be localised to cell compartments, in the same experiment, if they are expressed as chimeric proteins fused to distinct proteins fluorescing at different wavelengths (Green Fluorescent Protein and Red Fluorescent Protein for example). Using a confocal microscope the two proteins can be visualized in living cells and it can be determined whether they have the same subcellular location. Fluorescence microscopy of cells expressing a GFP fusion protein can also demonstrate dynamic processes such as its translocation from one subcellular compartment to another. OBSOLETE: use imaging technique (MI:0428) and specific probe as feature of each interacting protein.
colocalization by fluorescent probes cloning
The subcellular location of a protein can be demonstrated by treating cells fixed on a microscope slide with an antibody specific for the protein of interest. A secondary antibody conjugated with a reactive enzyme (e.g. horseradish peroxidase) is then added. Following a washing step to remove the unbound secondary ligand, a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme and can then be visualised by standard microscopic techniques. OBSOLETE since combination of Interaction Detection Method and Interaction Type.Consider using the Interaction Detection Method imaging techniques (MI:0428) coupled with Interaction Type colocalisation (MI:0403) and Participant detection immunostaining (MI:0422) instead.
Techniques enabling the identification of the subcellular localisation of a protein or complex. Two different proteins show a similar distribution in the cell are said to co-localise. Obsolete since combination of Interaction Detection Method and Interaction Type. OBSOLETE. Consider using imaging techniques (MI:0428) as interaction detection method coupled with colocalisation (MI:0401) as interaction type and predetermined (MI:0396) as participant detection.
colocalization/visualisation technologies
Text mining is used to support interactions which have been determined by other methods.
Approaches designed to separate cell components on the basis of their physicochemical properties. The observation that two or more proteins copurify in one or several conditions is taken as an indication that they form a molecular complex. OBSOLETE since too non-specific. Consider use of cosedimentation (MI:0027) or comigration in non denaturing gel electrophoresis (MI:0404) or affinity chromatography technologies (MI:0004) or molecular sieving (MI:0071) or for unspecific cases biochemical (MI:0401).
Pairs of multiple alignments of orthologous sequences are used to identify potential interacting partners as proteins that show covariation of their residue identities between different species. Proteins displaying inter-protein correlated mutations during evolution are likely to be interacting proteins due to co-adapted evolution of their protein interacting interfaces.
Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact.
The ultracentrifuge can be used to characterise and/or purify macromolecules in solution according to their mass and hydrodynamic properties. Sedimentation studies provide information about the molecular weight and shape of a molecule. It is also possible to measure the association state of the sample. Both the mass of a molecule and its shape, that influences the friction forces and diffusion that counterbalances gravity, determine the sedimentation speed.
Sedimentation through a density gradient measures the sedimentation rate of a mixture of proteins through either a glycerol or sucrose gradient. Two interacting proteins will sediment mostly as a complex at concentrations above the binding constant. By varying the concentration of one or both of the complex constituents and taking into account the dilution of the species during sedimentation, one can reasonably accurately estimate the binding constant.
cosedimentation through density gradient
Analysis of complexes obtained by input of energy or chemical treatments, or by introducing cysteines followed by oxidation to promote the formation of covalent bonds among molecules in close proximity.
Cross-linking agents induce the formation of covalent bonds among proteins that are neighbours. The cross-linker may be a bifunctional molecule having two reactive ends linked by a spacer, often containing a disulfide bond. When a reducing agent is added the disulfide bridge is cleaved, the cross-linked pairs are released and can be identified. There are various classes of cross-linkers, the most common are those having photoreactive groups that become reactive fluorophores when activated by UV light thereby resulting in photolabeling the cross-linked moieties.
protein cross-linking with a bifunctional reagent
The strategy to determine the complete amino acid sequence of a protein by mass spectrometry relies on the generation of a nested set of fragments differing by one amino acid. This reveals the identity of the residue that has been removed at each degradation step by measuring the mass difference of fragments differing of one residue. Peptide fragments can be obtained by protease treatment combined with the fragmentation promoted by collision (or other methods) within a tandem mass spectrometer. This approach can be carried out with LC MS/MS (Liquid Chromatography Tandem Mass Spectrometry), nanoESI MS/MS (nanoElectrospray Ionisation tandem mass spectrometry), or FTMS (Fourier Transform mass spectrometry) instruments.
de novo protein sequencing by mass spectrometry
In this approach, once a molecule is demonstrated to participate in an interaction, several deletion derivatives are produced and tested in the binding assay to identify the minimal fragment (domain) that can still support the interaction.
All the methods that permit the physical linking of a protein/peptide to its coding sequence. As a consequence affinity purification of the displayed peptide results in the genetic enrichment of its coding sequence. By these technologies genes encoding a peptide with desired binding properties can be selected over an excess of up to 1012 unrelated molecules.
Predicts the structure of a molecular complex from the unbound structures of its components. The initial approach in the majority of docking procedures is based largely on the 'rigid-body' assumption, whereby the proteins are treated as solid objects. Initial scoring of a complex is based on geometric fit or surface complementarity. This generally requires some knowledge of the binding site to limit the number of solutions.
The rosetta stone, or domain fusion procedure, is based on the assumption that proteins whose homologues in other organisms happen to be fused into a single protein chain are likely to interact or to be functionally related.
This approach uses a protein interaction network of a given organism to infer interaction in another organism using information about the interacting region. The regions or domains involved in interactions are clustered if they share sequence similarity and have common interacting partners. The resulting domain profiles are then used to screen the proteome of another organism and domain-domain interactions are inferred. Ultimately, an inferred protein interaction map is built in this second organism.
In dynamic light scattering, particle diffusion in solution gives rise to fluctuations in the intensity of the scattered light on the microsecond scale. The hydrodynamic radius of the particles can be easily calculated.
In this procedure the N-terminus amino acid is cleaved from a polypeptide and identified by high-pressure liquid chromatography. The cycle is repeated on the ever-shortening polypeptide until all the residues are identified. On average only 20-30 consecutive cycles can be performed and lead to amino acid identification. Longer polypeptides or full length proteins must be cleaved by specific protease before Edman degradation and their sequences built by fragment overlapping.
Electron microscopy methods provide insights into the structure of biological macromolecules and their supramolecular assemblies. Resolution is on average around 10 Angstroms but can reach the atomic level when the samples analysed are 2D crystals. Different types of samples can be analysed by electron microscopy: crystals, single particles like viruses, macromolecular complexes or entire cells and tissue sections. Samples can be chemically fixed or vitrified by rapid freezing in liquid ethane, and then transferred into the electron microscope. Data collection consists of the recording of electron diffraction data (2D crystals) and images. Depending on the type of sample, different approaches are used to analyse and merge images and electron diffraction data.
A combination of NMR and EPR. The lines in the EPR spectrum that are caused by coupling of an unpaired electron nearby nuclei change in intensity when these nuclei are excited at their NMR frequency.
EPR (also called ESR, Electron Spin Resonance) spectroscopy is analogous to NMR, but is based on the excitation of unpaired electrons instead of nuclei. Unpaired (single) electrons are only found in radicals and some metal ions (paramagnetic species); the EPR spectrum provides information about the environment and mobility of the paramagnetic species. The magnetic interaction of two paramagnetic centres in a protein can be used to calculate the distance between them; this allows studies of the movements and interactions of protein segments. In proteins without any intrinsic unpaired electrons it is possible to attach a radical probe (spin label). Stable nitroxide radicals can be bound to amino acid residues, in analogy with fluorescent probes. In combination with site directed mutagenesis this method is used in particular to study structure and assembly of membrane proteins, by measuring with EPR whether an amino acid is in a polar or non polar environment.
A form of spectroscopy in which the absorption of microwave by a sample in a strong magnetic field is used to study atoms or molecules with unpaired electrons.
Methods based on laboratory experiments to determine an interaction.
Predictive algorithms that rely on the information obtained by experimental results.
Proteins are fractionated by PAGE (SDS-polyacrylamide gel electrophoresis), transferred to a nitrocellulose membrane and tested for the ability to bind to a protein, a peptide, or any other ligand. Cell lysates can also be fractionated before gel electrophoresis to increase the sensitivity of the method for detecting interactions with rare proteins. Denaturants are removed during the blotting procedure, which allows many proteins to recover (or partially recover) activity. However, if biological activity is not recoverable, the proteins can be fractionated by a non denaturing gel system. This variation of the method eliminates the problem of activity regeneration and allows the detection of binding when the presence of a protein complex is required for binding. The protein probe can be prepared by any one of several procedures, while fusion affinity tags greatly facilitate purification. Synthesis in E. coli with a GST fusion, epitope tag, or other affinity tag is most commonly used. The protein of interest can then be radioactively labelled, biotinylated, or used in the blotting procedure as an unlabeled probe that is detected by a specific antibody.
Filamentous phages (M13, f1, fd) have been extensively used to develop and implement the technology of phage display. Repertoires of relatively short peptides of random amino acid sequences or cDNA libraries have been constructed and searched successfully. Most experiments have taken advantage of the ability to assemble phages decorated with hybrid versions of the receptor protein pIII or of the major coat protein pVIII. Both systems allow the display of foreign peptides by fusion to the amino-terminus of the capsid protein but differ in the number of peptide copies that can be displayed on each phage particle. Display libraries of very diverse protein fragments have been constructed by fusing either genomic or cDNA fragments to gene III or gene VIII.
A method in which separation depends upon the ability of one participant to bind to a filter or membrane which the other participants do not. Molecules interacting with the bound molecule will also be retain on the filter. For example, proteins expressed by different clones of an expression library are bound to a nitrocellulose membrane, by colony (bacterial library) or plaque (phage library) blotting. A labelled protein can then be used as a probe to identify clones expressing proteins that interact with the probe. Interactions occur on the nitrocellulose filters. The method is highly general and therefore widely applicable. A variety of approaches can be used to label the ligand, alternatively the ligand can be detected by a specific antibody.
The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: flag-tagged (MI:0518) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
Techniques based upon the measurement of the emission of one or more photons by a molecule activated by the absorption of a quantum of electro-magnetic radiation. Typically the emission, which is characterised by a wavelength that is longer than the one of excitatory radiation, occurs within 10-8 seconds.
FCS monitors the random motion of fluorescently labelled molecules inside a defined volume irradiated by a focused laser beam. These fluctuations provide information on the rate of diffusion or diffusion time of a particle and this is directly dependent on the particle mass. As a consequence, any increase in the mass of a biomolecule, e.g. as a result of an interaction with a second molecule, is readily detected as an increase in the diffusion time of the particle. From these results the concentration of the different molecules can be calculated as well as their binding constant.
Because of the long lifetimes of excited fluorescent molecules (nanoseconds), fluorescence can be used to monitor the rotational motion of molecules, which occurs on this timescale. This is accomplished experimentally by excitation with plane-polarized light, followed by measurement of the emission at parallel and perpendicular planes. Since rotational correlation times depend on the size of the molecule, this method can be used to measure the binding of two proteins because the observed polarization increase when a larger complex is formed. A fluorescence anisotropy experiment is normally carried out with a protein bearing a covalently added fluorescent group, which increases both the observed fluorescence lifetime of the excited state and the intensity of the fluorescent signal. Residue modification can be assessed by addition of an antibody which binds to the modified residue and alters the molecular weight of the complex. A variation of this technique has been used to show interaction of a DNA binding protein with another protein. In this case the DNA rather than protein is fluorescently labelled.
Cells in suspension flow through a laser beam, the scattered light or emitted fluorescence is measured, filtered and converted to digital values. Cells can be sorted according to their properties. Using flow cytometry, any fluorescent or light scattering experiment can be carried out on entire cells. With this instrument, interactions occurring either on cell surfaces or in any other subcellular location can be studied by using suitable fluorescent labels.
FRET is a quantum mechanical process involving the radiationless transfer of energy from a donor fluorophore to an appropriately positioned acceptor fluorophore. The fluorophores are genetically fused to the protein in analysis and cotransfected. Three basic conditions must be fulfilled for FRET to occur between a donor molecule and acceptor molecule. First, the donor emission spectrum must significantly overlap the absorption spectrum of the acceptor. Second, the distance between the donor and acceptor fluorophores must fall within the range 20 to 100 Angstrom. Third, the donor and acceptor fluorophores must be in favourable orientations.
Sequencing occurs during the course of the experiment. DNA sequencing is the process of determining the nucleotide order of a given DNA fragment. Thus far, most DNA sequencing has been performed using the chain termination method developed by Frederick Sanger. This technique uses sequence-specific termination of a DNA synthesis reaction using modified nucleotide substrates. However, new sequencing technologies such as Pyrosequencing are generating the majority of data.
Gene pairs that show a conserved topological neighbourhood in many prokaryotic genomes are considered by this approach to encode interacting or functionally related proteins. By measuring the physical distance of any given gene pair in different genomes, interacting partners are inferred.
Methods that require fully sequenced genomes either because they are based on the comparison of genome topology or on the identification of orthologous sequences in different genomes.
The bait protein is expressed and purified as a fusion to the glutathione S-tranferase protein. The bait protein is normally attached to a glutathione sepharose resin or alternatively to a support containing an anti-GST antibody. OBSOLETE redundant term. Map to feature type : gst-tagged (MI:0519) and Interaction detection method: pull down (MI:0096).
The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemaglutinin protein) for which antibodies are commercially available. OBSOLETE redundant term. Map to feature type : ha-tagged (MI:0520) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
The bait protein is expressed and purified fused to an amino or carboxyterminal tail containing a variable number of histidines. The bait protein is normally attached to a metal (usually nickel) resin. OBSOLETE redundant term. Map to feature type : his-tagged (MI:0521) and Interaction detection method: pull down (MI:0096).
The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies. OBSOLETE redundant term. Map to feature type: his-tagged (MI:0521) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
Computational methods to predict an interaction.
Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties.
Isothermal titration calorimetry (ITC) measures directly the energy associated with a chemical reaction triggered by the mixing of two components. A typical ITC experiment is carried out by the stepwise addition of one of the reactants (~10-6 L per injection) into the reaction cell (~1mL) containing the second reactant. The chemical reaction occurring after each injection either releases or absorbs heat (qi) proportional to the amount of ligand that binds to the protein with a characteristic binding enthalpy (DH). As modern ITC instruments operate on the heat compensation principle, the instrumental response (measured signal) is the amount of power (microcalories per second) necessary to maintain constant the temperature difference between the reaction and the reference cells. Because the amount of uncomplexed protein available progressively decreases after each successive injection, the magnitude of the peaks becomes progressively smaller until complete saturation is achieved. The difference between the concentration of bound ligand in the ith and (i-1)th injections depends on the binding constant Ka and the total ligand injected. The calculations depend on the binding model (number of substrates). Analysis of the data yields DH and DG = -RTlnKa. The entropy change is obtained by using the standard thermodynamic expression DG = DH-TDS.
Morphologically classified as one of the siphoviridae, lambda is a temperate bacteriophage of E.coli, with a double-stranded DNA genome. It has an icosahedral head attached to a flexible helical tail. Both the tail protein pV and the head protein pD have been used for displaying (C or N terminally) foreign peptides on the viral capsid.
Dynamic and static laser light scattering probes the size, shape, and structure of biological macromolecules or of their assemblies. A beam is focused on an optically clear cylindrical cell containing the sample. Most of the light passes directly through the sample. A small portion of the light is scattered; the scattered light intensity containing information about the scattering particle is detected at an angle (typically in the range 15-180degrees) from the direction of the incident beam.
Mass spectrometry can be used to characterise chemical modifications within peptides. One approach consists in the observation of a mass difference when a sample is treated with an enzyme that can specifically remove a peptide modification, for instance a phosphatase. The mass difference corresponds to the mass of the chemical group covalently linked to a residue. Such experiments carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) do not allow the mapping of the modification site within the sequence, whereas any tandem mass spectrometer (LC MS/MS Liquid Chromatography Tandem Mass Spectrometry, nanoESI MS/MS nanoElectrospray Ionisation tandem mass spectrometry, FTMS Fourier Transform mass spectrometry) provide such information. A second approach consists of the direct mass measurement of the ionized chemical group dissociated from the residue within a tandem mass spectrometer. Both approaches need a prior enrichment of the modified peptide population in the samples with IMAC (Immobilized Metal Affinity Chromatography)or specific anti-modification antibodies.
Mass spectrometric approaches to the study of macromolecular complexes permits the identification of subunit stoichiometry and transient associations. By preserving complexes intact in the mass spectrometer, mass measurement can be used for monitoring changes in different experimental conditions, or to investigate how variations of collision energy affect their dissociation.
Protein modifications can be identified by gel electrophoresis since any change in the mass and/or the charge of the protein can alter its mobility in PAGE. Although this method does not allow the unequivocal identification of the type of modification that has caused the shift, it is possible, by combining this approach with more direct methods, to correlate the extent of the shift to a specific modification.
In sizing columns (gel filtration), the elution position of a protein or of a complex depends on its Stokes radius. Molecules with a radius that is smaller than the bead size are retained and retarded by the interaction with the matrix. The observation that two proteins, loaded on a sieving column, elute in a fraction(s) corresponding to a MW that is larger than the MW of either protein may be taken as an indication that the two proteins interact. Furthermore this technique provides a conceptually simple method for evaluating the affinity of the interaction.
Western blot assay carried out using monospecific antibodies produced in the supernatant of a cell line obtained by fusing a lymphocyte B to a myeloma cell line or selected by phage display technology.
This method relies on the covalent coupling of mRNA to the nascent polypeptide. The mRNA (natural or artificial) is first covalently linked to a short DNA linker carrying a puromycin moiety. The mRNA mixture is then translated in vitro. When the ribosome reaches the RNA-DNA junction the ribosome stalls and the puromycin moiety enters the peptidyltransferase site of the ribosome and forms a covalent linkage to the nascent polypeptide. As a result the protein and the mRNA are covalently joined and can be isolated from the ribosome and purified. In the current protocol, a cDNA strand is then synthesised to form a less sticky RNA-DNA hybrid and these complexes are finally used for affinity selection. As in most display approaches, several selections cycles (3-6) are sufficient to enrich for mRNAs encoding ligand proteins.
Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding.
The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem. OBSOLETE redundant term. Map to feature type: myc-tagged (MI:0522) and Interaction detection method: anti tag coimmunoprecipitation (MI:0007).
Neural networks are trained on the properties of residues belonging to a cluster of residues that are neighbours in space on protein surface. The predictor permits the inference of the residues that are likely to be on an interaction interface.
Nuclear magnetic resonance (NMR) is an effect whereby magnetic nuclei in a magnetic field absorb and re-emit electromagnetic (EM) energy. Certain atomic nuclei, and in particular hydrogen, have a magnetic moment or spin; i.e., they have an intrinsic magnetisation, like a bar magnet. The spin aligns along the strong magnetic field, but can be changed to a misaligned excited state in response to applied radio frequency (RF) pulses of electromagnetic radiation. When the excited hydrogen nuclei relax to their aligned state, they emit RF radiation, which can be measured and displayed as a spectrum. The nature of the emitted radiation depends on the environment of each hydrogen nucleus, and if one nucleus is excited, it will influence the absorption and emission of radiation by other nuclei that lie close to it. It is consequently possible, by an ingenious elaboration of the basic NMR technique known as two-dimensional NMR, to distinguish the signals from hydrogen nuclei in different amino acid residues and to identify and measure the small shifts in these signals that occur when these hydrogen nuclei lie close enough to interact: the size of such a shift reveals the distance between the interacting pair of hydrogen atoms. In this way NMR can give information about the distances between the parts of the interacting molecule. NMR provides information about interacting atoms thereby permitting to obtain information about macromolecular structure and molecular interactions.
Identification of a nucleotide sequence. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
Experimental methods that could not be assigned to the other large group of technologies. OBSOLETE use biochemical (MI:0401) instead.
Genes are recognised by hybridization of a probe with a fragment of the gene sequence.
partial DNA sequence identification by hybridization
The peptide synthesis methods offer numerous opportunities to synthesise and subsequently screen large arrays of synthetic peptides on planar cellulose supports. Discrete spots are arranged as arrays on membrane sheets where each spot is individually accessed by manual or automated delivery of the appropriate reagent solutions. Over the past few years protein-protein recognition, peptide-metal ion interactions, peptide-nucleic acid binding, enzymatic modification of peptides experiments, have been explored using synthetic peptide arrays on planar support.
This approach leads to protein identification by matching peptide masses, as measured by mass spectrometry, to the ones calculated from in silico fragmentation of a protein sequence database. A peptide mixture from a tryptic digest is analysed by MALDI-MS (Matrix-assisted laser desorption ionization mass spectrometry). The list of peptide masses obtained by MALDI MS is automatically compared to the calculated masses of the predicted peptide fragments for each entry in the database. High mass accuracy is very important in order to obtain a statistically significant and unambiguous match This method is best applied to completely sequenced genomes and well characterised proteomes. However, depending on the data quality, proteins that are highly homologous to already characterised proteins (greater than 80 to 90% sequence identity) can also be identified. The retrieved sequence are evaluated by mass accuracy of the peptides, matching of additional peptide masses in the MALDI spectrum after accounting for common modifications such as oxidation, acrylamidation of cysteine and missed cleavages and the use of secondary information (apparent isoelectric point and molecular weight). If any ambiguity about the identification by MALDI-MS still exists, the results must verified by an other identification method. Peptide mass fingerprint is generally carried out with a MALDI-TOF (Matrix-assisted laser desorption ionization time-of-flight ) instrument but can also be achieved ESI-TOF (Electrospray Ionisation time-of-flight) or LC-MS (Liquid Chromatography-Mass Spectrometry) mass spectrometer.
When one of the partners participates in the interaction with a relatively short peptide fragment, it is often convenient to precisely identify the minimal region that supports the interaction by synthesising a series of overlapping peptides and by testing them in the binding assay. Synthetic peptides that are identical with peptides synthesised in vivo are useful experimental tools for such studies. Peptides are routinely synthesised in a test tube from monomeric amino acids by condensation reactions that form peptide bonds. Peptides are constructed sequentially by coupling the C-terminus of a monomeric amino acid to the N-terminus of the growing peptide. To prevent unwanted reactions involving the amino groups and carboxyl groups of the side chains during the coupling steps, a protecting (blocking) group is attached to the side chains. Without these protecting groups, branched peptides would be generated. In the last steps of synthesis, the side chain-protecting groups are removed and the peptide is cleaved from the resin on which synthesis occurs.
Peptide sequences or entire proteins can be displayed on phage capsids by fusion to coat proteins to generate a library of fusion phages each displaying a different peptide. Such a library can then be exploited to identify specific phages that display peptides that bind to any given bait molecule for instance an antibody. The selection is performed by a series of cycles of affinity purification known as panning. The bait protein, immobilized on a solid support (plastic, agarose, sepharose, magnetic beads and others) is soaked in the phage mixture and that phage that remains attached to the bait is amplified and carried through a further affinity purification step. Each cycle results in an approximately 1,000-fold enrichment of specific phage and after a few selection rounds (2-4), DNA sequencing of the tight-binding phage reveals only a small number of sequences. Phage display panning experiments can be carried out either on libraries of peptides of random amino acid sequence or on libraries of displaying natural peptides obtained by inserting cDNA fragments into the phage vector (cDNA libraries). Libraries have been assembled on several different phages (Fd, Lambda or T7).
The phylogenetic profile of a protein stores information about the presence and the absence of that protein in a set of genomes. By clustering identical or similar profiles, proteins with similar functions and potentially interacting are identified.
Western blot assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest.
Methods based on natural language processing to detect possible interactions between proteins (direct physical interactions or indirect genetic interactions). This includes the detection of non ambiguous protein or gene names and analysis of the relation expressed in a sentence among them.
Sequences can be identified in a DNA mixture by launching a PCR (Polymerase Chain Reaction) controlled by sequence specific primers. Such reaction starts only when the hybridization of the primer with a complementary sequence occurs.
The protein array technology allows the screening of biochemical activities or binding abilities of hundreds or thousands of protein samples in parallel. After synthesis and purification by high-throughput methodologies, the proteins are printed onto the chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with labelled molecules to identify proteins that bind to the bait.
In the protein-fragment complementation assay, the proteins of interest ("Bait" and "Prey") are covalently linked at the genetic level to incomplete fragments of a third protein (known as the "reporter") and are expressed in vivo, Interaction between the "bait" and the "prey" proteins brings the fragments of the "reporter" protein in close enough proximity to allow them to reform and become the functional reporter protein. Typically enzymes which confer resistance to antibiotics, such as Dihydrofolate reductase or Beta-lactamase, or proteins that give colorimetric or fluorescent signals are used. The Bait protein is generally the protein under study and the methods are readily adaptable to highthroughput mode.
Used to separate and/or analyse complex mixtures. The components to be separated are distributed between two phases: a stationary phase (bed) and a mobile phase which percolates through the stationary bed. The nature of the two phases determines the separation criteria exploited by the column such as affinity, ionic charges, size or hydrophobicity of the molecules under analysis. Each type of column can be implemented with the mobile phase under atmospheric or high pressure condition. In this later case columns are designated as High Pressure Liquid Chromatography (HPLC).
Protein In Situ Array is a method by which protein arrays are rapidly generated in one step directly from DNA, by cell-free protein expression and simultaneous in situ immobilisation at a surface. Individual genes or fragments are produce by PCR or RT-PCR depending on the source of genetic material using properly designed primers. The PISA is generated by cell-free protein synthesis using coupled transcription and translation to produce a tagged protein, the reaction being carried out on a surface to which the protein adheres as soon as it is synthesised.
Single amino acid identification along a protein sequence.
A wide range of dyes have been used over the years to visualise proteins in polyacrylamide gels - Coomasie Blue and silver-staining being two classical methods. Fluorescent dyes such as Nile Red and SYPRO Orange are now increasingly used due to their superior dynamic range. Use of non-denaturing gels can allow visualisation of protein protein interactions. Several dyes can be used to specifically indicate residue modification, however this methodology will give no information as the number of residues modified or their position within the protein sequence. Examples include the use of acid fuscian or the fluorescent dansyl hydrazine to show protein glycosylation.
ProteinChip(r) Array technology is a surface-enhanced laser desorption/ionization (SELDI) approach (Ciphergen Biosystems Inc. Fremont, CA, USA) for sample fractionation accomplished by retentate chromatography. Retentate chromatography is performed on ProteinChip Arrays with varying chromatographic properties (e.g. anion exchange, cation exchange, metal affinity and reverse phase). By utilising arrays with differing surface chemistries in parallel and in series, a complex mixture of proteins, as from cells or body fluids, can be resolved into subsets of proteins with common properties. Specific analytes can also be examined by using preactivated arrays to which a bait molecule (such as an antibody or biotinylated DNA) is immobilized and a solution containing the binding partner(s) is presented to the array. This array-based immunoprecipitation or protein-binding experiment has been used with good success to study DNA-binding proteins, receptor-ligand interactions, and protein complexes. Any ligand retained on a SELDI chip can directly be identified by mass spectrometry.
proteinchip(r) on a surface-enhanced laser desorption/ionization
A specific affinity chromatography method where a molecule of interest (bait) is bound to a column, often via an affinity tag expressed as a protein fusion (GST, HIS tag and others) or chemically linked to the bait molecule . The molecule may be expressed or synthesised and purified first, often in an heterologous system, bound to the matrix at high concentration and then challenged with a solution or cellular extract containing the candidate partner molecules. Alternatively, a multi-molecular complex may be adsorbed to the resin and the retained binding molecules subsequently identified.
In this complementation approach the bait can be any membrane protein (for example a receptor or a channel protein), the prey is cloned as a fusion protein of any cDNA from a library and the coding sequence of cytoplasmic RAS (cdc25 in yeast). If the bait and the prey interact, RAS is recruited close to the membrane and can activate cell growth. This procedure must take place in cells having a mutated RAS (Cdc25-2 yeast strain having a temperature sensitive mutation of RAS) to avoid constitutive growth activation.
This method permits the coupling of phenotype to genotype via the formation of a non-covalent ternary complex between mRNAs and their encoded polypeptides while they are translated in an in vitro system. As a first step a cDNA library is constructed that encodes chimeric proteins in which the natural proteins or protein domains are fused to a C-terminal tether. As a consequence when the mRNA is translated in vitro the domain can fold while the tether is still in the ribosomal tunnel. Furthermore this chimeric mRNAs lack a stop codon, thus preventing release of the mRNA and the polypeptide from the ribosome. High concentrations of magnesium and low temperature further stabilise the ternary complex. Similarly to phage display, these complexes can be used directly to select for nucleic acids encoding proteins with desired properties.
SPA relies upon the fact that a beta particle emitted from a radioisotope decay can excite a fluorophore only when it is at a very short distance in water solution (few micrometers). The ligand is labelled with a radioactive atom and its potential partner is fixed to fluorophore containing beads, the emitted fluorescence proving their interaction can be measured in a scintillation counter. The scintillator measures only the amount of bound radiolabelled ligand. Competition experiment with cold competitor can be done to estimate the binding affinities (50% inhibitory concentration [IC50], cold ligand versus labelled ligand). Loss of signal can also be used to measure substrate cleavage by an enzyme, and labelled antibodies used to titrate the degree of modified residue present.
Multiple alignments of orthologous sequences in the same species and their corresponding phylogenetic trees are built. Every phylogenetic tree is computed as a matrix of distances between all possible interacting pairs. The covariation of the distance matrices reveals interacting pairs.
Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs.
This approach leads to protein identification by combining mass measurement and short amino acid sequence information obtained by tandem mass spectrometry. This information is then used to automatically find the best match in a sequence database. A mixture of peptides derived from a protease digestion is analysed by nanoelectrospray LC-MS/MS (Liquid Chromatography Tandem Mass Spectrometer or nanoESI MS/MS) mass spectrometry. Electrospray mass spectrometry cannot be applied to dilute samples and is affected by high salt. As a consequence peptides, normally extracted from acrylamide gels by in situ proteolysis, are desalted and concentrated on a microcolumn followed by elution into a capillary used for nanoelectrospray tandem mass spectrometry. A first mass spectrum (Normal mass spectrum or Q1 mass spectrum) gives information about the masses of all the peptides. Peptides observed in the normal mass spectrum are isolated in turn and dissociated into fragments by collision with gas molecules within the mass spectrometer. Some of the fragments obtained from a peptide constitute a nested set, differing by one amino acid, and the mass difference between them allows assignment of a partial sequence. The masses of the fragments define the position of the partial sequence in the peptide. Together with the cleavage specificity of the protease used to cleave the protein, and mass information such sequence tag provides much higher search specificity to match the a database entry. The procedure is repeated with several peptides from the digest, resulting in multiple identifications of the same protein or identification of several proteins from the peptide mixture. Unknown proteins can easily be identified by using the high specificity of the peptide sequence tag for searches in most sequence databases including EST or genome databases.
A standard procedure to identify DNA fragments containing specific gene sequences. In this procedure i) a genome is fragmented using a restriction enzyme ii) the generated fragments are separated by electrophoresis iii) the fragments are transferred to a membrane iv)the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
In static light scattering, the average intensity of scattered light at multiple angles is measured. The data yield information on particle molecular weight, particle size and shape, and particle-particle interactions.
Methods based on 3D structure information.
Surface patches are built using 6 criteria: solvation potential, residue interface propensity, hydrophobicity, planarity, protrusion and accessible surface area. Protein structures having similar patches are likely to have the same interactions.
This method measures formation of complex by monitoring changes in the resonance angle of light impinging on a gold surface as a result of changes in the refractive index of the surface. A ligand of interest (small molecule, peptide, protein, sugar, lipid, nucleic acid) is immobilized on a gold surface, and the interacting partner is injected in buffer flow over it. Biomolecules that interact with the immobilized ligand are retained on the surface, and alter the resonance angle of impinging light as a result of the change in refractive index brought about by the increased biomolecule mass retained on the surface. Since all the biomolecules belonging to the same class have the same refractive index and since there is a linear correlation between resonance angle shift and biomolecule concentration near the surface, this allows one to measure changes in concentration at the surface as a consequence of interaction. Furthermore, this is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation.
T7 is a double stranded DNA bacteriophage with a thin-walled icosahedral capsid, ~550 Angstrom in diameter, which is decorated by 415 copies of the capsid protein, the product of gene 10. gp10 can tolerate insertions at the carboxyterminus without loosing its ability to be inserted into functional phage capsids. Both low density and high density display (albeit only with short peptides) can be achieved.
Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1.
The TAP method involves the fusion of the TAP tag (encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A) to the target protein and the introduction of the construct into the host cell or organism, maintaining the expression of the fusion protein at, or close to, its natural level. The fusion protein and associated components are recovered from cell extracts by affinity selection on an IgG matrix. After washing, the TEV protease is added to release the bound material. The eluate is incubated with calmodulin-coated beads in the presence of calcium. This second affinity step is required to remove the TEV protease as well as traces of contaminants remaining after the first affinity selection. After washing, the bound material is released with EGTA. This two steps purification steps ensures a highly selective complex purification of the tapped protein (first round of selection on the protein A, a high affinity tag) under mild condition (non denaturant pH or conditions required to remove the tag). OBSOLETE redundant term. Map to feature type: tap tagged (MI:0524) and as interaction detection method tandem affinity purification (MI:0676).
Text mining methods can be used to predict or confirm interactions by automated processing of scientific literature. Co-occurrence in the same sentence of an abstract of gene products labels are analysed to evaluate whether it represents a valid evidence of an interaction.
The gene for DHFR is rationally dissected into two fragments called F[1,2] and F[3]. Two proteins or protein domains that are thought to bind to each other can then be fused to either of the two DHFR fragments. Reconstitution of enzyme activity can be monitored in vivo by cell survival in DHFR-negative cells grown in the absence of nucleotides. A fluorescence assay can also be carried out taking advantage of fMTX binding to reconstituted DHFR. The basis of this assay is that complementary fragments of DHFR, when expressed and reassembled in cells, will bind with high affinity (Kd 5 540 pM) to fMTX in a 1:1 complex. fMTX is retained in cells by this complex, whereas the unbound fMTX is actively and rapidly transported out of the cells. Survival depends only on the number of molecules of DHFR reassembled.
The split-ubiquitin system provides a method for examining the interactions of membrane proteins. In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety ("Cub", residues 35-76) and an N-terminal ubiquitin moiety ("Nub", residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases. Upon bait-prey interaction, Nub and Cub-moieties assemble, reconstituting the split-ubiquitin. The reconstituted split-ubiquitin molecule is recognized by ubiquitin specific proteases, which cleave off the reporter protein, allowing it to induce the transcription of reporter genes.
Western blot is a procedure to identify and quantify proteins. A mixture of protein is first submitted to an electrophoresis in denaturing condition and then electro-transferred from the gel to a membrane. The membrane is then incubated with a primary antibody specific for a given protein or a specific residue modification in the sample under analysis. A secondary antibody, radiolabelled or fused to fluorophore or to a chromogenic enzyme, targets the first antibody and allows the visualisation of the protein band on the membrane.
Analysis of a diffraction pattern generated by a single crystal. X-rays have a wavelength, typically around 1 Angstrom (the diameter of a hydrogen atom). If a narrow parallel beam of X-rays is directed at a sample of a pure protein, most of the X-rays will pass straight through it. A small fraction, however, will be scattered by the atoms in the sample. If the sample is a well-ordered crystal, the scattered waves will reinforce one another at certain points and will appear as diffraction spots when the X-rays are recorded by a suitable detector. The position and intensity of each spot in the X-ray diffraction pattern contain information about the position and nature of the atoms in the crystal. The three-dimensional structure of a large molecule can be deduced from the electron-density map of its crystal. In recent years X-ray diffraction analysis has become increasingly automated, and now the slowest step is likely to be the production of suitable macromolecule crystals. This requires high concentration of very pure macromolecule and empirical searching for the proper crystallization conditions.
The proteins are displayed on the surface of the yeast S. cerevisiae by fusion to signal sequences for protein secretion. This method is limited by the low efficiency of the yeast display system but can take full advantage of exploiting cell sorting methods (FACS) to isolate cells that display molecules with desired binding properties.
Property of a subsequence that may interfere with the binding of a molecule.
A region of a molecule or a component of a complex identified as being involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner.
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event.
Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
Residue covalent modifications occurring in the specific protein form involved in an interaction. OBSOLETE remap to MOD:00000.
Residue modification. OBSOLETE remap to MOD:00394.
Residue modification. OBSOLETE remap to MOD:00050.
Residue modification. OBSOLETE remap to MOD:00359.
alpha-acetylamino-delta-guanidinovaleric acid
Residue modification. OBSOLETE remap to MOD:00780.
Residue modification. OBSOLETE remap to MOD:00051.
Residue modification. OBSOLETE remap to MOD:00052.
(R)-2-acetylamino-3-sulfanylpropanoic acid
Residue modification. OBSOLETE remap to MOD:00054.
Residue modification. OBSOLETE remap to MOD:00053.
Residue modification. OBSOLETE remap to MOD:00055.
Residue modification. OBSOLETE remap to MOD:00781.
Residue modification. OBSOLETE remap to MOD:00056.
(2S,3S)-2-acetylamino-3-methylpentanoic acid
Residue modification. OBSOLETE remap to MOD:00782.
Residue modification. OBSOLETE remap to MOD:00057.
Residue modification. OBSOLETE remap to MOD:00064.
(S)-2-amino-6-(acetylamino)hexanoic acid
Residue modification. OBSOLETE remap to MOD:00058.
(S)-2-acetylamino-4-(methylsulfanyl)butanoic acid
2-acetylamino-4-(methylthio)butanoic acid
Residue modification. OBSOLETE remap to MOD:00784.
Residue modification. OBSOLETE remap to MOD:00059.
(2S)-1-acetyl-2-pyrrolidinecarboxylic acid
Residue modification. OBSOLETE remap to MOD:00060.
(S)-2-acetylamino-3-hydroxypropanoic acid
Residue modification. OBSOLETE remap to MOD:00061.
(2S,3R)-2-acetylamino-3-hydroxybutanoic acid
Residue modification. OBSOLETE remap to MOD:00785.
Residue modification. OBSOLETE remap to MOD:00062.
(S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid
Residue modification. OBSOLETE remap to MOD:00063.
Residue modification. OBSOLETE remap to MOD:00674.
Residue modification. OBSOLETE remap to MOD:00091.
Residue modification. OBSOLETE remap to MOD:00493.
Residue modification. OBSOLETE remap to MOD:00030.
(S)-2-formylamino-4-(methylsulfanyl)butanoic acid
2-formylamino-4-(methylthio)butanoic acid
Residue modification. OBSOLETE remap to MOD:00428.
Residue modification. OBSOLETE remap to MOD:01155.
Residue modification. OBSOLETE remap to MOD:00111.
(R,E,E)-2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylsulfanyl)propanoic acid
2-amino-3-(3,7,11-trimethyl-2,6,10-dodecatrienylthio)propanoic acid
Residue modification. OBSOLETE remap to MOD:00113.
(R,E,E,E)-2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylsulfanyl)propanoic acid
2-amino-3-(3,7,11,15-tetramethyl-2,6,10,14-hexadecatetraenylthio)propanoic acid
Residue modification. OBSOLETE remap to MOD:00069.
(R)-2-hexadecanoylamino-3-sulfanylpropanoic acid
2-hexadecanoylamino-3-mercaptopropanoic acid
Residue modification. OBSOLETE remap to MOD:00115.
(R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid
2-amino-3-(hexadecanoylthio)propanoic acid
Residue modification. OBSOLETE remap to MOD:00068.
Residue modification. OBSOLETE remap to MOD:00087.
(S)-2-amino-6-(tetradecanoylamino)hexanoic acid
Residue modification. OBSOLETE remap to MOD:00427.
Residue modification. OBSOLETE remap to MOD:00070.
Residue modification. OBSOLETE remap to MOD:00071.
Residue modification. OBSOLETE remap to MOD:00077.
(S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid
Residue modification. OBSOLETE remap to MOD:00237.
(2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid
Residue modification. OBSOLETE remap to MOD:00080.
Residue modification. OBSOLETE remap to MOD:00081.
(S)-2-aminopentanedioic acid 5-methyl ester
Residue modification. OBSOLETE remap to MOD:00085.
Residue modification. OBSOLETE remap to MOD:00084.
(S)-2-amino-6-dimethylaminohexanoic acid
Residue modification. OBSOLETE remap to MOD:00083.
(S)-2-amino-6-(trimethylammonio)hexanoic acid
Residue modification. OBSOLETE remap to MOD:00073.
(S)-2-methylamino-4-(methylsulfanyl)butanoic acid
2-methylamino-4-(methylthio)butanoic acid
Residue modification. OBSOLETE remap to MOD:00074.
(S)-2-methylamino-3-phenylpropanoic acid
Residue modification. OBSOLETE remap to MOD:00696.
Residue modification. OBSOLETE remap to MOD:00227.
(S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid
alpha-amino-delta-phosphonoguanidinovaleric acid
Residue modification. OBSOLETE remap to MOD:00042.
(S)-2-aminobutanedioic 4-phosphoric anhydride
Residue modification. OBSOLETE remap to MOD:00043.
(R)-2-amino-3-(phosphonosulfanyl)propanoic acid
Residue modification. OBSOLETE remap to MOD:00046.
(S)-2-amino-3-(phosphonooxy)propanoic acid
2-amino-3-hydroxypropanoic acid 3-phosphate
2-amino-3-hydroxypropanoic acid 3-phosphate;O-phosphonoserine;O3-phosphoserine
Residue modification. OBSOLETE remap to MOD:00047.
(2S,3R)-2-amino-3-phosphonooxybutanoic acid
2-amino-3-hydroxybutanoic acid 3-phosphate
Residue modification. OBSOLETE remap to MOD:00048.
(S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate
Residue modification. OBSOLETE remap to MOD:00032.
Residue modification. OBSOLETE remap to MOD:00031.
Residue modification. OBSOLETE remap to MOD:00530.
Residue modification. OBSOLETE remap to MOD:01169.
Residue modification. OBSOLETE remap to MOD:00179.
(S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid
L-glutamyl 5-glycerophosphorylethanolamine
L-glutamyl 5-glycerylphosphorylethanolamine
glutamyl 5-glycerylphosphorylethanolamine
Residue modification. OBSOLETE remap to MOD:00126.
(S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid
Residue modification. OBSOLETE remap to MOD:00125.
(S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid
Residue modification. OBSOLETE remap to MOD:00129.
(S)-2-amino-6-[(2E,4E,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)-2,4,6,8-nonatetraenylidene]aminohexanoic acid
Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein. OBSOLETE remap to MOD:00134.
Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead.
Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues.
Irreversible reaction that can affect A,R,N,D,C,Q,E,G,H,I,L,K,M,F,P,S,T,W,Y or V residues. It involves the addition of an amide group from a glycine to the target residue.
Covalent bond breakage in a molecule leading to the formation of smaller molecules.
Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners.
Physical interaction mediated by covalent bond rearrangement. OBSOLETE use covalent binding (MI:0195) instead.
N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues.
S-farnesyl-L-cysteined is cleaved and returns a C residue.
N6-formyl-L-lysine is cleaved and returns a K residue.
S-geranylgeranyl-L-cysteine is cleaved and returns a C residue.
N6-myristoyl-L-lysine is cleaved and returns a K residue.
S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine are cleaved and return C,K,T or S residues.
Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues.
Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading.
Reversible reaction that can affect C residue.
Reaction that can affect K or G residues. Reside is functionalised with a formyl group.
An effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E
A genetic interaction refers to an unexpected phenotype not easily explained by combining the effects of individual genetic variants (7).
A quantitative genetic interaction definition has two components: a quantitative phenotypic measure and a neutrality function that predicts the phenotype of an organism carrying two noninteracting mutations. Interaction is then defined by deviation of a double-mutant organism's phenotype from the expected neutral phenotype.
More generally, a genetic interaction can be defined as the difference between an experimentally measured double-mutant phenotype and an expected double-mutant phenotype, the latter of which is predicted from the combination of the single-mutant effects, assuming the mutations act independently.
Two genes A and B 'genetically interact' when the phenotype generated as the result of mutations in both genes (double mutant ab) is unexpectedly not just a combination of the phenotypes of the two single mutants a and b.
Attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).Reversible reaction that can affect C residue.
Irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues. Hydroxylation is the first step in the oxidative degeneration of organic compounds.
Covalent or non covalent binding of lipid group on a protein residue.
Cleavage of a lipid group covalently bound to a protein residue.
The covalent attachment of a methyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Irreversible reaction that can affect A,G,M,F,P,C,R,N,Q,E,H,or K residues.
Irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid. Reaction that can affect K or G residues.
Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead.
Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues.
Reversible reaction that can affect D,C,H,S,T,Y,R residues.
Interaction among molecules that can be direct or indirect. OBSOLETE: splitted to 'association' MI:0914 and 'physical association' MI:0915. For remapping consider the experimental setting of an interaction. For bulk remapping a possible criteria is to whatever physical interaction that has among its participant a bait should become 'association' MI:0914 the others can become 'physical association' MI:0915. Two hybrid interactions are an expection and can be 'physical association' MI:0915.
Death phenotype observed on cells carrying combination of two independently silent mutations. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell.
A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate.
A molecule is estimated to be expressed at lower levels than in physiological condition.
The method combines a modified chromatin immunoprecipitation (ChIP) procedure, with DNA microarray analysis. Cells are fixed with formaldehyde, harvested, and disrupted by sonication. The DNA fragments cross-linked to a protein of interest are enriched by immunoprecipitation with a specific antibody. After reversal of the cross-links, the enriched DNA is amplified and labeled with a fluorescent dye (Cy5) by using a ligation-mediatedpolymerase chain reaction (LM-PCR). In parallel a sample of DNA that is not enriched by immunoprecipitation is subjected to LM-PCR in the presence of a different fluorophore (Cy3), and both immunoprecipitation (IP)-enriched and unenriched pools of labeled DNA were hybridized to a single DNA microarray containing a set of intergenic sequences. The ratio of the Cy5 to Cy3 fluorescence intensities measured at each DNA element in the microarray provided a measure of the extent of binding of the transcription factor to the corresponding genomic locus.
Stable complexes and their component proteins can be separated on the basis of their net charge by ion-exchange chromatography. If a protein has a net positive charge at pH 7, it will usually bind to a column of beads containing carboxylate groups, and can then be eluted by increasing the concentration of sodium chloride or another salt in the eluting buffer by competition of sodium ions with positively charged groups on the protein for binding to the column. Protein that have a low density of net positive charge will tend to emerge first, followed by those having a higher charge density. Positively charged complexes or proteins (cationic proteins) can be separated on negatively charged carboxymethyl-cellulose (CM-cellulose) columns. Conversely, negatively charged complexes or proteins (anionic proteins) can be separated by chromatography on positively charged diethylaminoethyl-cellulose (DEAE-cellulose) columns.
Reverse phase chromatography operates on the basis of hydrophilicity and lipophilicity. The stationary phase consists of silica based packings with n-alkyl chains covalently bound. For example, C-8 signifies an octyl chain and C-18 an octadecyl ligand in the matrix. The more hydrophobic the matrix on each ligand, the greater is the tendency of the column to retain hydrophobic moieties. Thus hydrophilic compounds elute more quickly than do hydrophobic compounds.
Protein complementation assay performed by dissecting a cytoplasmic protein activity and restoring it through the two hybrid proteins interaction. OBSOLETE remap to MI:0090 protein complementation assay
OBSOLETE remap to MI:0090 protein complementation assay.
The MAPPIT(mammalian protein-protein interaction Trap) is a screening method for protein-protein interaction in mammalian cells, based on the reconstitution of a membrane STAT (signal transducers and activators of transcription) receptor. The bait protein is fused to a STAT recruitment-deficient receptor and the prey protein to a functional STAT recruitment sites. In such a configuration, a given baitprey interaction restores a STAT-dependent responses leading to the expression of a reporter gene. This system, enable to demonstrate not only protein interaction but also modification-independent and tyrosine phosphorylation- dependent interactions.
mammalian protein protein interaction trap
Protein complementation assay performed by dissecting a transcription factor activity (DNA binding domain and transcription activation domain) its restoration through the two hybrid proteins interaction that lead to a reporter gene expression.
A stable set of interacting protein and DNA that can be copurified and operate as a functional unit.
Molecule labelled with 131 radio isotope of iodine atoms.
Molecule labelled with the radio isotope 14 of carbon atoms.
Molecule labelled with the radio isotope 32 of phosphorus atoms.
Molecule labelled with the radio isotope 33 of phosphorus atoms.
Molecules labelled with isotope 3 of hydrogen atoms.
Biotin, a 244 Dalton vitamin found in tissue and blood, binds with high affinity to avidin and streptavidin protein. Since biotin is a relatively small molecule, it can be conjugated to many proteins or nucleic acids without significantly altering their biological activity. Biotinylation reagents are available for targeting a variety of specific functional groups, including primary amines, sulfhydryls, carboxyls and carbohydrates that lead to nucleotides or amino acid biotinilation.
The protein under study is expressed as a fusion with a labelling protein, having either fluorescence properties or an enzymatic activity that facilitates its purification, identification, localisation or quantification.
Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference.
Reference to the master sequence from which this isoform has been derived.
Collection of functional complexes within Reactome - a knowledgebase of biological processes. http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome.
Collection of protein within the Reactome database - a knowledgebase of biological processes. http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome.
CABRI cell lines catalogue available at. http://www.cabri.org/
New EBI Web Taxonomy. http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942
The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications. http://www.ebi.ac.uk/RESID/index.html
A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/
A genomic region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
Reference pointing to a protein object from its genomic or nucleic acid sequence.
Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences.
One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number.
This term refers to methods that aim at interfering with the activity of a specific gene by altering the gene regulatory or coding sequences. This goal can be achieved either by a classical genetic approach (random mutagenesis followed by phenotype characterization and genetic mapping) or by a reverse genetics approach where a gene of interest is modified by directed mutagenesis.
This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself.
RNA interference (RNAi) is a post-transcriptional gene silencing method reproducing a naturally occurring phenomena. RNAi is the process whereby double-stranded RNA (dsRNA) induces the sequence-specific degradation of homologous mRNA. RNAi or dsRNA-induced silencing phenomena are present in evolutionarily diverse organisms, e.g., nematodes, plants, fungi, and trypanosomes. The mechanisms by which RNAi works is initiated by a progressive cleavage of dsRNA into 21 to 23 nucleotide (nt) short interfering RNAs (siRNAs). These native siRNA duplexes are then incorporated into a protein complex called RNA-induced silencing complex (RISC). ATP-dependent unwinding of the siRNA duplex generates an active RISC complex. Guided by the antisense strand of siRNA, the active RISC complex recognizes and cleaves the corresponding mRNA.
This approach is based on the observation that expression of RNA that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
Intracellular or extracellular expression of antibodies is used to target specific gene products in order to inactivate them. Most of the times the antibody scaffold need s to reengineered for efficient expression and solubility in the cytoplasm. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
This approach is based on the expression of peptides that bind to specific target proteins thereby interfering with their activity. In a standard approach the interfering peptide is expressed by genetic fusion to a stable protein scaffold. Interfering peptides can also be introduced into cells by fusing them to proteins or peptides (homeodomains, Tat protein.) having the property of penetrating the cell membrane. The peptide-carrier fusion protein is either synthesized chemically or produced in vivo, normally in bacteria. When the purified fusion protein is added to a cell culture, it penetrates the cell membrane thereby permitting the fused peptide to interfere with its target protein. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
Protein activity is inhibited by small inorganic molecules (drugs) that specifically bind to their targets. Recently this classical pharmacological approach is sometime referred to as 'chemical genetics'. OBSOLETE as such method can be described using the biological role inhibitor (MI:0586).
A supressed gene mutation cause of an altered phenotype that is reverted to wild type phenotype when cell also carry a suppressor gene with a specific mutation or altered expression level. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793.
A given (suppressed) mutation phenotype is reverted by a supressor gene mutation. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'mutated gene' MI:0804.
Knocked out gene is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock out' MI:0788.
A mutation is the partial suppressor of a mutant phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'knock down' MI:0789.
An altered expression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
Overexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'over expressed' MI:0506.
Level of over/underexpression scales the 'extend' of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'expression level alteration' MI:0803.
Underexpression is the suppressor of a phenotype. OBSOLETE: remap to CV intraction type 'suppressive interaction' MI:0793 and genetic experimental form 'under expressed' MI:0223.
Two silent mutations show an altered phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794.
Two silent mutations show a conditional synthetic lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (lethal FBcv:0000351)
Two silent mutations show a temperature sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description (FBcv:0000310 'temperature conditional')
conditional synthetic lethal temperature-sensitivity
Two silent mutations show altered growth effect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
Two silent mutations show growth defect when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
Two silent mutations show growth increase when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description ( FBcv:0000427 'cell growth defective')
Blue native PAGE (BN-PAGE) permits a high-resolution separation of multi-protein complexes under native conditions. Blue native (BN)-PAGE is a charge shift method, in which the electrophoretic mobility of a complex is determined by the negative charge of the bound Coomassie dye and the size and shape of the complex. Coomassie does not act as a detergent and preserves the structure of complexes. Importantly, the resolution of BN-PAGE is much higher than that of other methods such as gel filtration or sucrose-gradient ultracentrifugation. Combined with other pre-purifications or dialysis steps this method permits the analysis of multi-protein complexes of whole cellular lysates by BN-PAGE.
Descriptor of type of nomenclature used to describe interactor.
A name used to represent an ORF in a completely sequenced genome or chromosome. It is generally based on a prefix representing the organism and a number which usually represents the sequential ordering of genes on the chromosome. Depending on the genome sequencing center, numbers are attributed only to protein-coding genes, or also to pseudogenes, or also to tRNAs and other features.
For instance HI0934, Rv3245c, At5g34500, YER456W.
A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system.
For instance MtCY277-28c, SYGP-ORF50, SpBC2F12-04, C06E1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames.
Method by which molecule is delivered or engineered into a cell.
Method for temporarily permeabilising cell membranes so as to facilitate the entry of large or hydrophilic molecules (as in transfection). A brief (ca 1 msec) electric pulse is given with potential gradients of about 700V/cm.
A cassette coding for a protein tag is inserted by homologous recombination onto the genomic copy of an open reading frame. The advantage of this delivery method is that the resulting engineered protein is expressed under its natural promoter control. OBSOLETE redundant term. Map to feature type : tag (MI:0507).
Molecule introduced into a cell via an external organism, usually a virus or bacteria.
The insertion of a substance into a cell through a microneedle. To extrude the substances through the very fine needle tip, either hydrostatic pressure (pressure injection) or electric currents (ionophoresis) is employed.
Introducing DNA into eukaryotic cells, such as animal cells, is called transfection. Transfection typically involves opening transient "holes" or gates in cells to allow the entry of extracellular molecules, typically supercoiled plasmid DNA, but also siRNA, among others. Transfection differs from transformation since the DNA is not generally incorporated into the cell's genome, it is only transiently expressed.
Molecular species involved in the interaction.
Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level.
A stable set of interacting proteins that can be copurified and operate as a functional unit.
A macromolecular complex containing both protein and RNA molecules.
Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes.
Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages.
Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine.
Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine.
Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link.
Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing.
A heterogeneous mixture of RNA molecules with a rapid turnover rate that occurs in cell nuclei during protein synthesis; it is the form of RNA synthesized in eukaryotes by RNA polymerase II, which is translated into protein.
Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains.
The low molecular weight RNAs that specifically bind amino acids by aminoacetylation to form aminoacyl tRNA and which possess a special nucleotide triplet, the anticodon.
A linear polymer of amino acids joined by peptide bonds in a specific sequence.
Chains of amino acids joined by peptide bonds. Distinction between peptides, oligopeptides and polypeptides is arbitrarily by length; a polypeptide is perhaps more than 15 residues.
Molecule not part of or directly encoded by the genome, encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity.
Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level.
Defines whether molecule is endogenously expressed or has in any way been altered, in sequence or expression level, from its native state. For a complete description of the experimental molecule form use the orthogonal CVs expression level, delivery method, and sample process.
Molecule has been added into system from an external source or altered within the cell.
Unaltered endogenous molecule in its naturally occurring state.
Describes sequence positions resolution of a given participant feature. In PSI schema this CV is associated with the start and end position of a feature range.
Term describing the last amino acid of a peptide chain.
Position within the sequence clearly defined.
Partially determined sequence position known to be in a location higher than a given position.
Partially determined sequence position known to be in a position lower than a given position.
Describes a sequence position known to be in a certain range, where the exact position is unclear.
For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'.
Term describing a completely unknown or unspecified sequence position.
Term describing the first amino acid of a peptide chain.
Mixture of protein forms where N-terminus has been progressively truncated.
Indicates the sample context in which each interacting molecule is presented to its partner.
Mixed population of cDNAs (complementaryDNA) made from mRNA from a defined source, usually a specific cell type. This term should be associated only to nucleic acid interactors not to their proteins product. For instance in 2h screening use living cells (MI:0349) as sample process.
Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components.
Name assigned to a molecule by the authors within a paper that may differ from the reference database.
Set of terms to describe the participant experimental treatment and status. This term groups a number of orthologous short controlled vocabularies delivery method, expression level, molecular source, and sample process. Each participant can then be annotated with a maximum of 4 terms selected from each short list.
Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis.
Molecule is observed within in a living cell.
Molecule has undergone one or more purification steps to isolate it from the cellular environment.
The author states a molecule is completely pure, i.e. no other molecular species are present.
The author states a molecule is only partially purified, i.e. other molecular species also known to be present.
Qualifier to describe the type of information a cross-reference is pointing to.
Cross reference pointing to a Gene Ontology -'cellular component' term.
Cross reference pointing to a Gene Ontology -'molecular function' term.
Reference to the corresponding object in another database. Correspondence may be complete or partial.
For instance this qualifier, in an interaction entry, can be associated to a cross reference to the same interaction in an other database.
identical object in an external resource
Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment.
Used to indicate the PMID from which the experimental data is extracted.
Cross reference pointing to a Gene Ontology -'cellular process' term.
Reference to the corresponding object in another database (like identity xref qualifier) but the identifier used in the external database is a secondary identifier or former accession number.
Related object within the same database or pointing to an external database.
Evidence based on human assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
Evidence based on the author of a paper assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
Evidence based on a curator assumption, either when the complete experimental support is not available or when the results are extended by homology to closely related orthologues sequences.
Molecule under study is fused to an enzyme, for example alkaline phosphatase, and measure of enzyme activity can be taken as indicative of presence of protein.
Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
The green fluorescent protein of organisms such as the bioluminescent jellyfish Aequorea victoria can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
Yellow fluorescent protein from species such as Vibrio fischeri can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
The method is based on the repression of a reporter gene activity by two LexA DNA binding domains with different binding specificities. LexA is a transcription factor with an N-terminal DNA binding/activation domain (DBAct) and a C-terminal dimerization domain. LexA dimerization is required to repress transcription efficiently. The discovery of LexA DNA binding domains that bind to different DNA sequence enabled the development of this system.
This assay allow identification of interactions in the inner membrane of E. coli. by using a chimeric construct ToxR-TM-MBP composed of the N-terminal DNA binding/transcriptional activation domain of ToxR (a dimerization dependant transcription factor) fused to a transmembrane domain of interest (TM) and a monomeric periplasmic anchor (the maltose binding protein). Association of the two TM results in the ToxR-mediated activation of a reporter gene such as CAT (chloroamphenicol acetyltransferase activity). The level of CAT expression indicates the strength of TM association. CAT expression can then be tested and quantify by measuring CAM resistance with disk diffusion assay or CAT activity assays on cell-free extracts.
Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium.
Cell lysates are partially fractionated to isolate a specific subcellular fraction.
Dye coupled to a molecule allowing its identification isolation and monitoring.
The organic polymethine cyanine dyes which, depending on structure, cover the spectrum from IR to UV.s. Their emission range is such that background fluorescence is often reduced. In addition these molecules can be linked directly to specific locations in synthetically produced nucleic acids.
The organic cyanine Cy3 emits maximally at 570 nm.
The organic cyanine Cy5 emits maximally at 670 nm.
Fluorescein isothiocyanate is a yellow-green coloured low molecular weight dye which couples to proteins via reaction with primary amine groups at high pH. FITC is excitable at 488nm, close to its absorption maximum at 494nm, and produces maximum fluorescence emission around 520nm.
Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
Molecules labelled with isotope 13 of carbon atoms.
Molecules labelled with isotope 15 of nytrogen atoms.
Molecules labelled with isotope 2 of hydrogen atoms.
Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction).
Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds.
All Alexa dyes are fluorescent iodoacetamide dyes that can be conjugated with the primary amines of biomolecules. All Alexa dyes and their conjugates are more fluorescent and more photostable than the commonly used dyes. The numbers in the Alexa names indicate the approximate excitation wavelength maximum in nm).
Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm.
Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm.
Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm.
Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm.
Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm.
Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm.
Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm.
Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s).
Two-hybrid screening can be done in a colony array format, in which each colony expresses a defined pair of proteins. Because the particular protein pair expressed in each colony is defined by its position in the array, positive signals identify interacting proteins without further characterization, thus obviating the need for DNA purification and sequencing. The interrogation of a two-hybrid colony array usually involves a mating strategy in which every DNA binding domain hybrid (the bait) is tested against all activation domain hybrids (the preys) in a grid pattern. Arrays usually use full-length open reading frames.
In the pooling strategy sets of either both bait and prey hybrid vectors are mated or, more commonly, individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners. The pooling of both baits and prey molecules is now a rarely used technique as the pooling of baits often leads to misleading results.
Individual baits are mated against pools of random fragmented preys. The usage of degenerated fragment allows identification of the minimal protein region required for the interaction. Since multiple clones that encode overlapping regions of protein are often identified, the minimal domain for interaction may be readily apparent from the initial screen.
Techniques which depend upon the strength of the interaction between two entities.
The application of chemical principles and methods to biological experiments to demonstrate an interaction.
Chromatin immunoprecipitation (ChIP) is a powerful approach that allows one to define the interaction of factors with specific chromosomal sites in living cells. An antibody against a protein suspected of binding a given cis-element is used to immunoprecipitate fragmented chromatin fragments. Cells or tissue may first be briefly treated with an agent such formaldehyde to crosslink proteins to DNA. Nucleic acids are then identified by sequencing, for example polymerase chain reaction analysis of the immunoprecipitate with primers flanking the cis-element or next-generation sequencing techniques
Coincident occurrence of molecules in a given subcellular fraction observed with a low resolution methodology from which a physical interaction among those molecules cannot be inferred.
A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a non-denaturing gel.
comigration in non denaturing gel electrophoresis
Competitive binding experiments measure equilibrium binding of a single concentration of ligand at various concentrations of an unlabeled competitor. Analysis of these data gives the affinity of the receptor for the competitor.
Measures the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
Interaction between molecules that are in direct contact with each other.
Covalent bond mediated by 2 sulfur atoms.
Experimental method used to identify the region of a nucleic acid involved in an interaction with a protein. One sample of a radiolabeled nucleic acid of known sequence is submitted to partial digestion. A second sample is incubated with its interacting partner and then is submitted to the same partial digestion. The two samples are then analyzed in parallel by electrophoresis on a denaturing acrylamide gel. After autoradiography the identification of the bands that correspond to fragments missing from the lane loaded with the second sample reveals the region of the nucleic acid that is protected from nuclease digestion upon binding. OBSOLETE because redundant with MI:0417 'footprinting' combined with interactor type MI:0319 'DNA' replace by:MI:0417
Three-dimensional (3D) reconstruction of single, transparent objects from a collection of projection images recorded with a transmission electron microscope. It offers the opportunity to obtain 3D information on structural cellular arrangements with a high resolution.
Following non-covalent binding of a purified primary ligand to a solid phase, a blocking reagent is added to prevent any non-specific binding. A specific antigen is then allowed to bind to the primary ligand. Unbound antigen is removed by washing and a secondary antibody conjugated to an enzyme (e.g. horseradish peroxidase) is added. Following a washing step to remove unbound secondary ligand, the extent to which a chromogenic substrate (e.g. 3,3', 5,5' tetramethyl benzidine chromogen [TMB]) is converted to a soluble coloured product by the conjugated enzyme in a given time is determined by spectrophotometry using a standard microplate absorbance reader. A similar type of approach can be utilized to detect enzymatic activities. The substrate, attached to a solid phase is incubated in the presence of the enzyme and the enzymatic modification is monitored by an antibody that is specific for the modified substrate (for instance a phosphorylated protein).
The EMSA supershift is a EMSA experiment carried out using a third lane loaded with the radiolabeled nucleic acid, a protein mixture and an antibody for a specific protein. If an extra retardation is observed, this is due to the formation of a larger complex including the antibody. By this approach, at least one protein of the complex is directly identified.
electrophoretic mobility supershift assay
This method proves the interaction between a nucleic acid and a protein partner. On the same electrophoresis gel 1 lane is loaded with a nucleic acid of known sequence, a second lane is loaded with the same nucleic acid together with a purified protein (or a protein mixture). The nucleic acid is often radio-labelled to enable visualisation by autoradiography. Comparison of the nucleic acid migration in the two lanes enables the retardation of the nucleic acid due to its interaction with a protein to be observed.
terms aiming to represent biochemical reactions referring to their resulting product modifications.
Participants are enzyme or substrate in a biochemical reaction.
Fluorescent microscopy uses a high intensity light to illuminate the sample. This light excites fluorescence species in the sample, which then emit light of a longer wavelength. A fluorescent microscope also produces a magnified image of the sample, but the image is based on the second light source -- the light emanating from the fluorescent species -- rather than from the light originally used to illuminate, and excite, the sample.
Footprinting analysis is used to identify regions of molecules involved in binding other macromolecules and therefore protected from the effects of degradative enzymes, chemical treatment or other deleterious treatments.
methods supporting genetic interactions. OBSOLETE as too unspecific use Genetic interference instead MI:0254.
Measures the catalysis of the reaction: GTP + H2O = GDP + phosphate.
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being added from close proximity on the phosphorylated substrate due to the action of the kinase.
kinase homogeneous time resolved fluorescence
Antibody mediated participant identification.
Method using an antibody coupled with some colouring agent to detect a specific protein within a cell or tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
Substrate protein radio-labelled by kinase transferring an isotope of phosphate from the nucleotide. Substrate isolated by gel electrophoresis and radio-labelling confirmed by autoradiography.
Catalysis of the transfer of a phosphate group, usually from ATP, to a protein substrate.
Relies on the radiolabelling of a peptide substrate immobilized on a scintillant coated SPA-bead. The kinase transfers a phosphate isotope from the nucleotide to the substrate.
Light visible microscopy uses environmental light to illuminate the sample and produce a magnified image of the sample.
Methods that provide images of molecules at various resolution depending on the technology used.
A sequence range within a molecule identified as being absolutely required for an interaction. The sequence may or may not be in direct physical contact with the interaction partner.
Nucleic acids are incubated with purified proteins or a protein mixture and then exposed to a chemical cross-linking agent that may be activated by UV light exposure. The eventual complexes can be identified by sequencing or autoradiography if the nucleic acid is radio-labelled and the sequence is known. The proteins involved in the complex can be recognized by specific antibodies or by retrieving the original protein mixture and carrying further analysis on it.
Deprecated terms. OBSOLETE term replaced by the default OBO class 'Obsolete'.
Protein-DNA complementation assay where a single promoter act as bait and is screened against a library of prey transcription factors.
partial protein sequence identification.
partial identification of protein sequence
Measures the catalysis of the reaction: a phosphosubstrate + H2O = a substrate + phosphate.
Measures the enzymatic hydrolysis of a peptide bond within a peptide or protein substrate.
Protein footprinting is a technique for identifying structural changes modulated by protein-ligand binding, and mapping protein-ligand interfaces This technique involves attaching cutting reagents randomly to amino acid residue (e.g. lysine or cysteine) on the proteins surface and then using this lysine-labelled protein to cleave polypeptide backbone of the other protein at exposed residues adjacent to its binding site.
Two hybrid assay performed with a third protein component co-transfected into a recombinant yeast strain together with a bait and a prey construct. Negative control shows that the interaction between the bait and the prey do not occur when the third protein is not co-transfected.
In vivo reconstruction of specific RNA-proteins interactions. The DNA binding and transcription activator domains of GAL4 are brought together via the interaction of recombinant RNA. The first hybrid protein contains the DNA binding domain of GAL4 fused to RevM10 (a mutated RNA binding protein of HIV-1 that binds specifically to the Rev responsive element RRE of the env gene). A recombinant RNA contains the RRE sequence and a target RNA sequence X. The second hybrid protein contains the activation domain of GAL4 fused to protein Y tested for its ability to bind the target RNA X. If this interaction occurs the three hybrid reconstructs GAL4 and the transcription of a reporter gene is activated.
A technique used to detect genetic interactions between 2 (or more) genes in a sporulating organism by scoring a large population of haploid spores for a phenotype and correlating the phenotype with the presence of single vs double (multiple) mutations. A diploid heterozygous organism harbouring mutations in two (or more) genes is induced to sporulate. Resulting spores are meiotic segregants that are haploid and are either wild type or mutant at each locus. Spores are scored for a phenotype, such as loss of viability.
Saturation binding experiments measure specific ligand binding at equilibrium at various concentrations of the ligand. Analysis of these data can determine receptor number and affinity.
Identification of genetic interactions by generation of an organism harbouring mutations in 2 or more genes and scoring for a phenotype, such as loss of viability, that is not observed for any of the mutations in isolation.
Binding will occur when this sequence range is present within a molecule or part of a molecule. This region will contain the direct binding region but may be longer.
Interaction concerning ubiquitin that is covalently attached to any Lys residue of its interaction partner. OBSOLETE remap to ubiquitination reaction (MI:0220) or describe ubiquitine as a participant on the interaction using physical interaction (MI:0218) or covalent binding (MI:0195) as interaction type.
Database citation list names of databases commonly used to cross reference interaction data. http://purl.obolibrary.org/obo/clo.owl
Databases acting as a source of literature information.
PubMed is designed to provide access to citations from biomedical literature. The data can be found at both NCBI PubMed and Europe PubMed Central. http://www.ncbi.nlm.nih.gov/pubmed http://europepmc.org
A database describing a feature on a molecule.
The objective of Gene Ontology (GO) is to provide controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products. http://www.ebi.ac.uk/GO
InterPro combines a number of databases (referred to as member databases) that use different methodologies and a varying degree of biological information on well-characterised proteins to derive protein signatures that predict family membership and domain composition of naive protein sequences. https://www.ebi.ac.uk/interpro/
The Conserved Domain Database may be used to identify the conserved domains present in a protein sequence. http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. http://www.sanger.ac.uk/Software/Pfam
PIRSF is a classification system based on evolutionary relationship of whole proteins. http://pir.georgetown.edu/pirwww/dbinfo/pirsf.shtml
PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family. http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
The ProDom protein domain database consists of an automatic compilation of homologous domains. http://protein.toulouse.inra.fr/prodom.html
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles. http://us.expasy.org/prosite/
SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain. http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/
SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. http://smart.embl-heidelberg.de/
TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, Hidden Markov Models (HMMs) and annotation. http://www.tigr.org/TIGRFAMs
MMDB (Molecular Modeling DataBase), is a subset of three-dimensional structures obtained from the Protein Data Bank. http://www.ncbi.nlm.nih.gov/Structure
The RCSB PDB provides a variety of tools and resources for studying the structures of biological macromolecules and their relationships to sequence, function, and disease. http://www.pdb.org/
Databases that contain experimental or predictive molecular interaction data.
The Biomolecular Interaction Network Database (BIND) is a collection of records documenting molecular interactions. http://www.blueprint.org/bind
The General Repository for Interaction Datasets (BioGRID) is a database of genetic and physical interactions. http://thebiogrid.org
The MIPS Comprehensive Yeast Genome Database (CYGD) aims to present information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis. http://mips.gsf.de/proj/yeast/CYGD. http://mips.gsf.de/genre/proj/mpact
The database of interacting protein (DIP) database stores experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. http://dip.doe-mbi.ucla.edu/
EcoCyc is a bioinformatics database that describes the genome and the biochemical machinery of E. coli K12 MG1655. http://ecocyc.org/
The Reactome project is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology. http://www.reactome.org/
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome. http://www.hprd.org/
INTerAction database (IntAct) provides an open source database and toolkit for the storage, presentation and analysis of molecular interactions. http://www.ebi.ac.uk/intact
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a knowledge base for systematic analysis of gene functions, linking genomic information with higher order functional information and also supplies information about chemical compounds, enzyme molecules and enzymatic reactions. http://www.genome.ad.jp/kegg/
The Molecular INTeraction database (MINT) is a relational database designed to store interactions between biological molecules. http://mint.bio.uniroma2.it
The Protein Data Bank in Europe - the European project for the collection, management and distribution of data about macromolecular structures, derived in part from the Protein Data Bank (PDB). http://www.ebi.ac.uk/pdbe/
Database of molecules participating in molecular interactions.
A definitive, freely available database of Chemical compounds of Biological Interest (ChEBI). http://www.ebi.ac.uk/chebi/
DDBJ EMBL GenBank Nucleotide Sequence Database Collaboration exchange new and updated data on a daily basis to achieve optimal synchronisation. http://www.ebi.ac.uk/embl/Contact/collaboration
Ensembl is a joint project between the EMBL-EBI and the Wellcome Trust Sanger Institute that aims at developing a system that maintains automatic annotation of large eukaryotic genomes. http://www.ensembl.org
LocusLink provides a single query interface to curated sequence and descriptive information about genetic loci. http://www.ncbi.nlm.nih.gov/LocusLink/
FlyBase is a comprehensive database for information on the genetics and molecular biology of Drosophila. http://flybase.org
Mouse Genome Informatics (MGI) provides integrated access to data on the genetics, genomics, and biology of the laboratory mouse. http://www.informatics.jax.org/
Online Mendelian Inheritance in Man (OMIM) is a catalogue of human genes and genetic disorders, with links to literature references, sequence records, maps, and related databases. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM
The Reference Sequence (RefSeq) collection aims to provide a comprehensive, integrated, non-redundant set of sequences, including genomic DNA, transcript (RNA), and protein products, for a number of organisms. http://www.ncbi.nlm.nih.gov/RefSeq/
Rfam is a large collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. http://www.sanger.ac.uk/Software/Rfam/
The Rat Genome Database (RGD) curates and integrates rat genetic and genomic data. http://rgd.mcw.edu/
SGD is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae. http://www.yeastgenome.org/
UniProt Archive (UniParc) is part of UniProt project. It is a non-redundant archive of protein sequences derived from many sources. http://www.ebi.ac.uk/uniparc/
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. http://www.uniprot.org
WormBase is the central worm database that houses the gene reports, locus reports, translation reports, expression pattern data and genome browser. http://www.wormbase.org/
Database that originally provided the interaction record for exchange purposes.
Describes the location of the experiment. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
Results generated by predictive bioinformatics approaches rather than experimental data. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
Experiments performed with participants removed from the cellular environment e.g. cell extracts, isolated proteins. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
Experiment undertaken within a cellular environment, although this may not be the natural host of the proteins in the study. OBSOLETE as a full host organisms description is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
Literally, in place i.e. the protein is in its natural environment during the experiment. OBSOLETE as a full host organisms is recommended using tax id == -1 as convention to refer to 'in vitro' interaction.
Role played by the participant within the experiment.
Molecule experimentally treated to capture its interacting partners.
Molecule role in an experimental setting that does not have an embedded asymmetry.
Molecule experimentally identified as being captured by a given bait.
Role not specified or not applicable to the data.
Physiological role of an interactor in a cell or in vivo environment, which is reproduced in the current experiment.
Molecule catalyzing a modification on its interacting partner.
Molecule that is the target of its binding partner catalytic activity.
Molecule that makes intramolecular interactions.
The form of a molecule that was actually used to experimentally demonstrate the interaction, that may differ from the sequence described by the identifying accession number.
A molecule is estimated to be expressed at higher levels than in physiological condition.
Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
Measures the release of radiolabelled acetic acid from a pre-labeled molecule.
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Relies on a fluorescence energy donor and acceptor being removed from close proximity on the phosphorylated substrate due to the action of the phosphatase.
phosphatase homogeneous time resolved fluorescence
Methods based on the exceptionally long fluorescence lifetime characteristics of certain fluorophores, which allows the elimination of the effects of background fluorescence. Uses nonradiative energy transfer or quenching between fluorescent lanthanide chelates and different acceptors to measure reaction rates.
Measures quenching of the nonradiative energy transfer between fluorescent long-lifetime lanthanide chelates and different acceptors. Fluorescence donor and acceptor are on the same peptide molecule and separated by the action of the protease.
protease homogeneous time resolved fluorescence
Samples run on a gelatine containing gels under non-reducing condition, gels then incubated under conditions in which the enzyme is active. Gels are stained with coomasie and gelatine-free regions of the gel taken as a measure of enzyme activity.
Measures the amount of radiolabel released into the medium when enzyme is added onto a film of isotope-labelled collagen.
Substrate pre-radiolabelled either synthetically or through the action of a kinase transferring an isotope of phosphate from a nucleotide. Substrate then exposed to phosphate under assay conditions. Substrate isolated by gel electrophoresis and loss of radiolabelling confirmed by autoradiography.
Measures the catalysis of the transfer of a methyl group to an acceptor molecule.
Measures the transfer of a radiolabelled methyl group of a donor, for example S-adenosyl-L-methionine (SAM) to a carboxyl group of an acceptor.
A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule.
The protein of interest is expressed as a fusion to the peptide DYKDDDDKV for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
The protein is expressed and purified as a fusion to the glutathione S-tranferase protein.
The protein of interest is expressed as a fusion to the peptide YPYDVPDYA (a fragment of the influenza hemagglutinin protein) for which antibodies are commercially available.
The protein of interest is expressed as a fusion to a poly-His tail. This permits purification by chromatography over a metal column or by binding to commercially available anti poly-His antibodies.
The protein of interest is expressed as a fusion to the peptide EUKLISEED (a fragment of the Myc oncogene protein) for which antibodies are commercially available. Sometimes multiple copies of the peptide are fused in tandem.
The protein of interest is expressed as a fusion to the peptide MASMTGGQQMG for which antibodies are commercially available.
Tag encoding a calmodulin binding peptide, a TEV cleavage site, and the Staphylococcus aureus Protein A fused to a target protein. The tag allows two purification steps ensuring a highly selective purification of the tagged protein.
calmodulin binding peptide plus protein a tag
The protein of interest is expressed as a fusion to the peptide GKPIPNPLLGLDST for which antibodies are commercially available.
Residue modification. OBSOLETE remap to MOD:00723.
Residue modification. OBSOLETE remap to MOD:00752.
Residue modification. OBSOLETE remap to MOD:00177.
(S)-2-amino-5-([imino([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)methyl]amino)pentanoic acid
N(omega)-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-arginine
N(omega)-alpha-D-ribofuranosyl-L-arginine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
Residue modification. OBSOLETE remap to MOD:00178.
(R)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]sulfanyl)propanoic acid
S-L-cysteine alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
S-alpha-D-ribofuranosyl-L-cysteine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
Residue modification. OBSOLETE remap to MOD:00300.
(S)-2-amino-5-poly[2'-adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with 1alpha-D-ribofuranosyl]oxy-5-oxopentanoic acid
Residue modification. OBSOLETE remap to MOD:00242.
(S)-2-amino-3-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]oxy)-propanoic acid Formula
O3-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-serine
O3-alpha-D-ribofuranosyl-L-serine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
Residue modification. OBSOLETE remap to MOD:00236.
(S)-2-amino-4-([adenosine 5'-(trihydrogen diphosphate) 5'->5'-ester with alpha-D-ribofuranosyl]amino)-4-oxobutanoic acid
N4-[alpha-D-ribofuranoside 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)]-L-asparagine
N4-alpha-D-ribofuranosyl-L-asparagine 5'->5'-ester with adenosine 5'-(trihydrogen diphosphate)
Residue modification. OBSOLETE remap to MOD:00693.
Residue modification. OBSOLETE remap to MOD:00131.
Residue modification. OBSOLETE remap to MOD:00163.
Residue modification. OBSOLETE remap to MOD:00164.
Residue modification. OBSOLETE remap to MOD:00332.
Residue modification. OBSOLETE remap to MOD:00160.
Residue modification. OBSOLETE remap to MOD:00818.
Residue modification. OBSOLETE remap to MOD:00172.
Residue modification. OBSOLETE remap to MOD:00167.
Residue modification. OBSOLETE remap to MOD:00168.
Residue modification. OBSOLETE remap to MOD:00169.
Residue modification. OBSOLETE remap to MOD:00170.
Residue modification. OBSOLETE remap to MOD:00171.
Residue modification. OBSOLETE remap to MOD:00173.
Residue modification. OBSOLETE remap to MOD:01110.
Residue modification. OBSOLETE remap to MOD:00663.
Artificial residue modification enabling studies of cysteine binding status. OBSOLETE remap to MOD:00660.
Residue modification. OBSOLETE remap to MOD:00041.
(S)-3-amino-1,1,3-propanetricarboxylic acid
Residue modification. OBSOLETE remap to MOD:00461.
Residue modification. OBSOLETE remap to MOD:00235.
(R)-2-amino-3-nitrososulfanyl-propanoic acid
Residue modification. OBSOLETE remap to MOD:00181.
(S)-2-amino-3-(4-sulfooxyphenyl)propanoic acid
2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-sulfate
Residue modification due to a cross-link between a lysine and a glycine from the sumo (Small Ubiquitin-related MOdifier) protein. OBSOLETE remap to MOD:01149.
(S)-2-amino-6-[(aminoacetyl)amino]hexanoic acid
Residue modification. OBSOLETE remap to MOD:00890.
Gln-Lys cross-link catalyzed by a transglutaminase.
Involves the addition of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
Reaction catalyzed by PNGase, a deglycosylating enzyme that promotes the hydrolysis of the beta-aspartylglycosylamine bond of aspargine-linked glycopeptides and glycoproteins.
The covalent attachment of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer. Reaction that can affect Ser, Thr, Cys, Arg, and Asn residues. This reaction is known to be reversible in the case of Asn substrate.
Residue modification. OBSOLETE remap to MOD:00438.
Residue modification. OBSOLETE remap to MOD:00440.
Residue modification. OBSOLETE remap to MOD:00665.
Residue modification. OBSOLETE remap to MOD:00658.
Residue modification. OBSOLETE remap to MOD:00078.
(S)-2-amino-5-[(imino(methylamino)methyl)amino]pentanoic acid
Residue modification due to a cross-link between a lysine and a glycine from the Nedd8 protein family. OBSOLETE remap to MOD:01150.
Reversible reaction that create a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
Reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
Cleavage of the G-K bond and release of the SUMO ubiquitin like proteins.
Cleavage of the G-K bond and release of the NEDD8 ubiquitin like proteins. Deneddylation, which removes the NEDD8 moiety, requires the isopeptidase activity of the COP9 signalosome.
Covalent modification of a polypeptide occuring during its maturation or its proteolytic degradation.
Any process by which a pre-mRNA or mRNA molecule is cleaved at specific sites or in a regulated manner.
Covalent bond breakage of a DNA molecule leading to the formation of smaller fragments.
Region of a molecule whose mutation or deletion totally disrupts an interaction strength or rate (in the case of interactions inferred from enzymatic reaction)..
Identifier of a publication prior to pubmed indexing.
Alliance for Cellular Signaling (AfCS -Nature) store yeast 2-hybrid Interaction data and expression data. Information and data are freely available to all. http://www.signaling-gateway.org
Method to identify domain-domain interactions within the same resolved structure. Domains are first projected onto a pdb structure and then the distance between all pairs of residues in different domains are calculated. When the distance between 2 residues is below the non covalent bond threshold, the corresponding pair of domains is predicted to interact.
Group of method taking advantage of 3D structure to calculate and infer the feature of interacting molecules.
The protein is expressed and purified as a fusion to the glutathione maltose-binding protein (MBP). The MBP-fusion protein can be purified by affinity chromatography using an amylose resin.
Any molecule that is able to transfer an electron to another chemical species.
Molecule to which an electron may be transferred from an electron donor.
A gene whose genetic perturbation suppresses the phenotype resulting from a different genetic perturbation.
A gene whose genetic perturbation phenotype is suppressed by a different genetic perturbation.
Fluorophore which emits electromagnetic radiation of given wavelength.
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific donor fluorophore, then re-emiting its own characteristic fluorescence.
IntEnz is the name for the Integrated relational Enzyme database and is the official version of the Enzyme Nomenclature. The Enzyme Nomenclature comprises recommendations of the Nomenclature Committee of the International Union of Bio chemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions. IntEnz is supported by NC-IUBMB and contains enzyme data curated and approved by this committee. The database IntEnz is available at. http://www.ebi.ac.uk/intenz
Molecule inhibiting an interaction by interacting with one or more of its participants.
Molecule being identified as target of an inhibitor. OBSOLETE as term is deprecated to describe the target of an inhibitor that can have any other biological role.
Group of methods based on complementation assay where a third participant is shown to be necessary for the binding of a given bait prey pair. The molecule fused to the DNA binding domain is the bait, that fused to the transcriptional activator is the prey.
Protein sample collected by in vitro translation of its mRNA taking advantage of purified translation machinery.
Collection of topics describing the free text stored as an attribute value.
The experimental condition text description, should contain information about the organisms hosting the interaction.
Web resource that allows the investigation of protein interactions in the Protein Data Bank structures at the level of Pfam domains and amino acid residues. iPfam is available on the Web for browsing at. http://www.sanger.ac.uk/Software/Pfam/iPfam/
Xref pointing to a GO process term describing the start and end location of a migrating molecule, for instance see GO:0006611, 'protein-nucleus export'.
Xref pointing to a GO compartment term describing the start location of a migrating molecule.
Xref pointing to a GO compartment term describing the end location of a migrating molecule.
Free text description of all the tags and artificial process undergone by a molecule during an experiment.
The feature text description may include information about the feature detection method.
The feature constraint free text will specificity whether a biological feature is shown to be possible (just observed) or required (experimentally demonstrated to be necessary for an interaction).
Text pointing to a specific paper figure legend where the experimental evidences for an interaction are to be found.
Two silent mutations show a nutrition sensitive lethal phenotype when they co-occur on the same cell. OBSOLETE: remap to CV intraction type 'synthetic interaction' MI:0794 and external CV for phenotype description.
conditional synthetic lethal nutrition-sensitivity
The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data.
Binding sites are identified by altered reactivity of a complex to a chemical treatment compared to the unbound molecules. Residues in close contact with the binding partner are protected from chemical modification. When these chemicals are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
Dimethylsulphate (DMS) is the most commonly used chemical to study DNA-protein interactions. DMS induces methylation of guanine residues so DNA interaction with protein binding to AT rich sequences or to the phosphate backbone may be not detected by DMS footprinting. However as DMS diffuses across membrane it can also be used for in vivo footprinting. The experiment involves the treatment with DMS of two DNA samples with identical sequence, one protein bound and the other naked. The two samples are treated with piperidine to induce chemical cleavage of the DMS modified guanine residues followed by digestion with restriction enzymes. Once labelled the samples are run in parallel on a gel to visualize the pattern of nested fragments sharing a common end generated by restriction enzyme(or PCR primer extension) and a variable end guanine dependent. The missing bands of the protein bound sample correspond to the guanine residues protected from modification by an interaction.
Potassium permanganate bind to single-stranded pyrimidine residues, it is commonly used to detect promoters opening regions in vivo. KMnO4 treatment of cells, followed by treatment with piperidine, followed by either PCR and/or acrylamide gel electrophoresis allows detection of interaction between transcription factor and the DNA sequence under their control.
Binding sites are identified by altered reactivity of a complex to an enzymatic probe compared to the unbound molecules. Residues in close contact with the binding partner are protected from cleavage by the enzyme. When these enzymes are administrated to intact cells, the pattern of protection from the probes identifies the location of DNA-protein or protein-protein interactions in vivo.
Deoxyribonuclease I (DNase I) does not have high specificity for given sequences or residues, thus footprinting with DNase I permits the exact delineation of the protein-DNA binding site. Moreover DNase I, can be used for in vivo footprinting by treating intact cells with permeabilising drugs. In this latter case DNase I in vivo footprinting allow studies of the chromatin structure in genomic DNA.
These RNA molecules are relatively short (less than 200 nucleotides each), and there are five of them (U1, U2, U4, U5, and U6) involved in the major form of pre-mRNA splicing. Known as snRNAs (small nuclear RNAs), each is complexed with at least seven protein subunits to form a snRNP (small nuclear ribonucleoprotein). These snRNPs form the core of the spliceosome.
RNA that is transcribed from the DNA of the nucleolus and is found, together with characteristic proteins, in the ribosomes.
The small nucleolar RNAs, are stable RNA contained in the nucleoli and these RNAs exist as snoRNA: protein complexes called snoRNPs (also called 'snorps'). The snoRNPs function is in the maturation of ribosomal RNA and other RNAs, by: creating two types of modified nucleotides, (2'-O-methylated nucleotides and pseudouridine), and mediating endonucleolytic cleavages of pre-rRNA.
Ribonucleic acid used in RNAi study. These RNA have the reverse complementary sequence of a target gene's mRNA transcript and inhibit its expression.
Small (300 nucleotides) stable RNAs transcribed by RNA pol III that are part of the signal-recognition particle (SRP). This particle comprises one RNA and six proteins bound to the RNA. SRP function is to assist secretory proteins sorting in the endoplasmic reticulum (ER). SRP is a cytosolic particle that transiently binds to the ER signal sequence of a nascent protein, to the large ribosomal unit, and to the SRP receptor in the ER membrane.
Comment for public view. This attribute can be associated to interaction, experiment, CV term, an organism and any participant.
Biological function of a participant or of an interaction.
URL/Web address describing an experiment, an interaction, a Cv term or an organism.
Search engine URL associated to Cv Database terms.
Example generally associated to Cv terms. Test.
The interaction has a known or demonstrated disease association.
Warning about errors or grounds for confusion. Can be associated to an interaction, experiment, CV term or any participant.
Refers to the metabolic or signalling pathway involving an interaction or a complex.
Search URL to retrieve an external entry in ASCII format. Generally associated to Cv Database terms.
Confidence classification assigned by the author of the publication to a specific interaction.
Description of confidence assessment method generally associated to the experiment.
The interaction between the proteins or the formation of a complex is disrupted by a biological molecule or by a modification of the interactors.
Reaction occurs at a faster rate in the presence of this compound or molecule i.e. the molecule directly physically co-operates with the interaction. Reaction may not occur at all in the absence of this molecule.
Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that stimulates an interaction, potentially by causing modification of one or more of the interactors.
Any chemical applied externally to cells or any type of environmental condition, such as hypoxia, that inhibits an interaction, potentially by alteration of amount or binding affinity of one or more of the interactors.
Modifications of the standard experimental method described in the CV.
Regular Expression used to check the validity of cross references' identifier. Attribute generally associated to terms in Cv Database.
Information on the complex being annotated. Attribute generally associated to an interaction.
Comments on the 3D structure. This attribute is generally associated to an interaction.
Free R-Factor and working R-Factor for the quality of the crystallographic model. This attribute is generally associated to an interaction.
Resolution of the 3D structure. This attribute is generally associated to an interaction.
Information about how the data was processed. This attribute is used mainly for large scale experiment.
E-mail address to contact the author or organisation which has produced the data. This attribute is generally associated to an experiment.
Free text notes on how to contact the author or organisation which has produced the data This attribute is generally associated to an experiment.
List of authors associated to a publication. This attribute is generally associated to an experiment.
Participant isoform's comment. This attribute can be attached to interactions or participants.
Post translational modification required for an interaction to occur.
Post translational modification occurs subsequently to an interaction.
Parameter for enzymatic or binding kinetic studies.
Molar concentration of an antagonist which produces 50% of the maximum possible inhibitory response for that antagonist. Note this measure depends on the specific antagonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ic50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
Molar concentration of an agonist which produces 50% of the maximum possible response for that agonist. Note this measure depends on the specific agonist used and upon experimental conditions, notably temperature, pH and solution composition (e.g., salts, chelating agents and others). Thus the ec50 is a relative measure and its values can be compared only when sharing the same experimental setting. Unit Molar.
Equilibrium constant for dissociation of an inhibitor. Unit Molar.
Michaelis-Menten constant: concentration of substrate at which the reaction rate is equal to half the maximal rate (i.e. Km={s} when Vo=1/2Vmax). Unit Molar.
The number of substrate molecules converted to product in a given unit of time, on a single enzyme molecule when the enzyme is saturated with substrate. Unit per second, or s-1.
The equilibrium dissociation constant of a receptor/ligand or proteinA/proteinB complex. Unit Molar (generally M-1).
Controlled vocabulary for kinetic constant units.
Molarity is the number of moles of solute dissolved in one liter of solution. The units, therefore are moles per liter, specifically it's moles of solute per liter of solution. These units are abbreviated as M and it means moles per liter (not just moles).
The second is the duration of 9 192 631 770 periods of the radiation corresponding to the transition between the two hyperfine levels of the ground state of the cesium-133 atom. The second was originally defined as 1/86 400 mean solar day until astronomers discovered that the mean solar day is actually not constant.
10E-3 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
10E-6 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
10E-9 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
10E-12 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
10E-15 moles per liter of solution. OBSOLETE: term redundant with the schema exponent attribute of the parameter.
A protein of interest (the bait) is fused to the full-length bacteriophage lambda repressor protein (lambdacI, 237 amino acids), containing the amino terminal DNA-binding domain and the carboxylterminal dimerization domain. The corresponding target (prey) protein is fused to the N-terminal domain of the alfa-subunit of RNA polymerase (248 amino acids). The bait is tethered to the lambda operator sequence upstream of the reporter promoter through the DNA-binding domain of lambdacI. When the bait and prey interact, they recruit and stabilize the binding of RNA polymerase at the promoter and activate the transcription of the HIS3 reporter gene. Due to the tendency of both the lambda repressor protein and the N-terminal domain of the alfa-subunit of RNA polymerase to dimerize, this system might not be optimal for the analysis of proteins that self-associate unless their interaction with other protein partners depends on the oligomerization.
Peptide whose sequence is experimentally identified and can lead to a full protein identification.
RNA and cDNA constructs with variable central sequences and a constant flanking region are collected in a complex library. The library is then screened to select either specific binding partners of a bait molecule (generally a protein) or particular enzymatic activities of the nucleic acid molecules themselves. The selected nucleic acids are amplified using the constant flanking regions to increase their abundance. Cycles of selection-amplification can be repeated to increase the specificity of the targets that, at the end, are individually identified by sequencing.
systematic evolution of ligands by exponential enrichment
MudPIT is a method for rapid and large-scale protein identification by multidimensional liquid chromatography associated with tandem mass spectrometry. The chromatography step consists of strong cation exchange material back-to-back with reversed phase material inside fused silica capillaries. The peptides bound to the cation-exchange resin are freed by the gradually increasing salt concentration of the buffer and are subsequently retained by the reversed phase resin. Increasing buffers hydrophobicity progressively elute peptides from the reversed phase packing directly into the mass spectrometer. Typically this mass spectrometer will be a tandem electrospray, so peptides undergo ionization in the liquid phase, are separated in a primary mass spectrometer, analysed in the second mass spectrometer and identified.
multidimensional protein identification technology
Experimental method by which a feature is detected or identified.
Feature detection based on computational analysis.
experimental participant identification.
IMEx primary identifier that is assigned to an experiment record by the database that created the record in the context of IMEx consortium. The identifiers are unique across all member database as they are all generated by a centralized key-assigner. http://imex.sourceforge.net/
A confocal is a standard epifluorescence microscope with improvement essentially coming from the rejection of out-of-focus light interference. Confocal imaging system achieves this by two strategies: a) by illuminating a single point of the specimen at any one time with a focused beam, so that illumination intensity drops off rapidly and b) by the use of blocking a pinhole aperture in a conjugate focal plane to the specimen so that light emitted away from the point in the specimen being illuminated is blocked from reaching the detector. Only the light from the single point illuminated of the specimen passing through the image pinhole is detected by a photodetector. Usually a computer is used to control the sequential scanning of the sample and to assemble the image for display onto a video screen.
Attribute name of annotation associated to an interaction element.
Attribute name of annotation associated to an experiment element.
Attribute name of annotation associated to a participant element.
Attribute name of annotation associated to a CV term.
Attribute name of annotation associated to a feature element.
Attribute name of annotation associated to an organism element.
International Molecular Interaction Exchange.
This annotation topic should contain information about antibodies when specific antibodies (monoclonal or polyclonal raised against specific regions of the proteins or purified in a specific manner) have been used.
This annotation topic will be used to store information about the cDNA library. If a name is available this should be reported along with a short description of the library.
Alternative names to describe a complex.
Describe a cross reference pointing to a peptide parent sequence.
IPI provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases. IPI is updated monthly in accordance with the latest data released by the primary data sources.
Tandem affinity purification allows rapid purification under native conditions of complexes, even when expressed at their natural level. Prior knowledge of complex composition or function is not required. The TAP method requires fusion of the a multiple tag, either N- or C-terminally, to the target (or bait) protein of interest. The multiple tag allows two steps purification steps ensuring a highly selective complex purification.
A tandem tag consists of the concatenation of simple distinct tags that is engineered to be cloned as a unique element onto a sequence of interest. Note that when a protein is fused to many simple tags that are inserted individually and possibly in different sequence positions these should be reported as independent features.
A microarray consisting of antibodies spotted on a solid support in appropriate orientation is incubated with a biological sample (or antigen). Some proteins are captured by the antibodies in the array. Protein of forming complexes on the array are identified according to their prior labelling (tag, ELISA, biotin and others).
A sequence of adenine nucleotides that is added to the 3' end of some primary transcript messenger RNA molecules in eukaryotes during post-transcriptional processing. The added tail is believed to confer stability to the molecule.
DNA that consists of only one chain of nucleotides rather than the two base pairing strands found in DNA in the double helix form.
DNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
A cofactor is a small molecule required for the catalysis of an enzyme.
Database collecting nucleic or amino acid sequences mainly derived from genomic or mRNA sequencing.
Molecule required for an observed binary interaction to occur. This molecule may act as stabilizer of any of the interaction partners or may act as a bridge molecule between them but the method does not provide resolution or evidence to demonstrate its actual molecular function (i.e.Mudpit, tri hybrid etc).
Publication or document describing the originating resource where an interaction, or other curated information, was first described.
Yet to be identified interaction detection method associated with interaction data imported from a third party database. This database may have potentially different standards of curation.
Protein having well characterized fluorescence excitation and emission spectra used as fusion with a protein under study to facilitate its localisation or identification.
Part of a transcription factor responsible for the binding of gene regulatory region prior to their transcription. Such tags are generally used in two hybrid experiments where they are fused to a bait polypeptide tested for its ability to interact with a prey fused to an activation domain tag.
Part of a transcription factor responsible for the activation of DNA transcription. Such tags are generally used in two hybrid experiments where they are fused to a prey polypeptide tested for its ability to interact with a bait fused to a DNA binding domain tag.
Part of the yeast transcription factor GAL4 (amino acids 766-881) specifically responsible for DNA transcription activation.
Full viral protein vp16 exclusively responsible for preferential transcriptional activation of viral genes. Activation requires the formation of a complex with the host cell transcription factor.
B42 is an acidic sequence of 89 residues derived from Escherichia coli acting as weak transcription activation domain. When use in two hybrid experiments, the weakness of B42 as activator increases the sensitivity of the interaction detection.
Part of the yeast transcription factor GAL4 (amino acids 11-38) specifically responsible for DNA binding of a 17 base-pair long sequence in the upstream activating sequence of galactose-induced genes.
Amino terminal (1-220) part of the Escherichia coli lexA repressor, binding to 16 base pair palindromic DNA sequences.
Antibody array where proteins retained by the arrayed antibodies are identified using a detector antibody. The detector antibody is either modified with a directly detectable label (enzyme, fluorescent molecule, isotope, etc.), or it is biotinylated for detection after subsequent probing with labeled streptavidin.
Measures the catalysis of the transfer of a free nucleotidyl group to a nucleic acid chain.
Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template or primer.
Measures the catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
Measures the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1). Catalyzes RNA-template-directed extension of the 3'- end of a DNA strand by one deoxynucleotide at a time.
Measures the catalysis of the reaction: nucleoside triphosphate + RNA (n) = diphosphate + RNA (n+1); uses an RNA template.
The process by which a DNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent DNA strand.
The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. www.pantherdb.org/
The Gene3D database provides a combined structural, functional and evolutionary view of the protein world. It is focused on providing structural annotation for protein sequences without structural representatives--including the complete proteome sets of over 240 different species. http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
Method by which nucleic acids are delivered or engineered into a cell.
Western blot assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag for which efficient antibodies are available. The antibody may be either monoclonal or polyclonal.
Transformation is the genetic alteration of a cell resulting from the introduction, uptake and expression of foreign genetic material incorporated into the cell's genome (DNA or RNA).
Immunostaining assay performed when specific antibodies for the protein of interest are not available. Therefore the protein is expressed as a hybrid protein fused to a tag peptide/protein for which efficient antibodies are available. The anti tag antibody may be either monoclonal or polyclonal.
A monospecific antibody for the protein of interest is available, this is used to detect a specific protein within a cell or tissue sample.
Immunostaining assay carried out using a mixture of different antibodies that represent the immune response, normally in an experimental animal, to the protein of interest. These antibodies are used to detect the protein within a cell or tissue sample.
Stable introduction and expression of nucleic acid carried out by treatment with divalent cation.
nucleic acid transformation by treatment with divalent cation
Electroporation, or electropermeabilization, is a significant increase in the electrical conductivity and permeability of the cell plasma membrane caused by externally applied electrical field. It is usually used in molecular biology as a way of introducing some substance inside the cell, such as loading it with a molecular probe, a drug that can change cell's function, or a piece of coding DNA.
Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases nucleic acids.
Nucleic acid entrance into cells that does not involved specific treatments but rely on natural cellular processes.
Transduction is the process by which bacterial DNA is moved from one bacterium to another by a virus.
Bacterial conjugation is the transfer of genetic material between bacteria through cell-to-cell contact. Bacterial conjugation is often incorrectly regarded as the bacterial equivalent of sexual reproduction or mating. It is not actually sexual, as it does not involve the fusing of gametes and the creation of a zygote. It is merely the transfer of a conjugative plasmid from a donor cell to a recipient
Entrance of molecules into cells that does not involved specific treatments but relies on natural cellular processes.
Lipofection (or liposome transfection) is a technique used to inject genetic material into a cell by means of liposomes which are vesicles that can easily merge with the cell membrane since they are both made of a phospholipid bilayer.
Transient introduction and expression of nucleic acid carried out by treatment with chemicals.
Transient introduction and expression of nucleic acid carried out by treatment with calcium phosphate.
calcium phosphate nucleic acid transfection
Nucleic acid introduced into a cell via an external organism, usually a virus or bacteria..
Method by which proteins are delivered into a cell.
Method for temporarily permeabilising cell membranes in order to facilitate the entry of a protein.
Microinjection refers to the process of using a micro needle to insert substances at a microscopic level into a single living cell. It is a simple mechanical process in which an extremely fine micro needle penetrates the cell membrane and sometimes the nuclear envelope and releases proteins.
Proteins are delivered into cells by treatment with cationic lipids.
protein delivery by cationic lipid treatment
Protein introduced into a cell via an external organism, usually a virus or bacteria.
Yeast strains are generated in which expression of DB-X/AD-Y or DBPX hybrid proteins is toxic under particular conditions (negative selection). Under these conditions, dissociation of an interaction should provide a selective advantage thereby facilitating detection: a few growing yeast colonies in which DB-X/AD-Y (or DBPX/binding site) fail to interact should be identified among many nongrowing colonies containing interacting DB-X/AD-Y or DBPX/binding site.
Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), E. coli B42 acidic sequence as the activation domain (AD), and two reporters, lacZ and LEU2, each containing upstream LexA binding elements.
A chimeric protein consisting of the GAL4 DNA-binding domain (aa 1-147 of GAL4) and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) can specifically activate transcription of a reporter gene located downstream ofGAL4 DNA binding sites and the E1B minimal promoter. Similarly, two chimeric proteins, one encoding a chimeric GAL4 protein and the other encoding a chimeric VP16 protein, can activate the reporter gene, if the domains fused to the GAL4 and VP16 sequences can complex with appropriate conformation. However, if the domains fused to the GAL4 and VP16 sequences do not interact specifically to form a + complex that reconstitutes GAL4 function, the reporter gene cannot be activated.
This strategy uses a luciferase enzyme fused to proteins of interest, which are then coexpressed with individual epitope-tagged partners in mammalian cells. Their interactions are determined by performing an enzymatic assay on anti-tag immunoprecipitates.
luminescence based mammalian interactome mapping
PubChem provides information on the biological activities of small molecules. http://pubchem.ncbi.nlm.nih.gov/
The aim of 3D Repertoire is to determine the structures of all amenable complexes in a cell at medium or high resolution, which will later serve to integrate in toponomic and dynamic analyses of protein complexes in a cell. Complex models, EM pictures, expression and purification protocols obtained in the project will be collected in a database connected to the PDB repository.
The red fluorescent protein derived from, for example, marine anemone Discosoma striata and reef corals belonging to the class Anthozoacan can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
The cyan fluorescent protein derived from Anthozoa reef coral can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
Variation of the green fluorescent protein derived from the bioluminescent jellyfish Aequorea victoria, can be fused to individual proteins which then acquire fluorescence excitation and emission spectra virtually identical to those of the native.
Tag derived from the transactivating (Tat) protein of human immunodeficiency virus 1 (HIV-1) that can enter cells efficiently when added exogenously in tissue culture. The Tat tag can carry other molecules into cells, by fusion of Tat peptides (residues 1-72 or 37-72,) to any molecule under study. Tat-mediated uptake may allow the delivery of macromolecules previously thought to be impermeable to living cells.
Proteins entrance into cells that does not involved specific treatments but rely on natural cellular processes.
database storing sequences detected by peptide identification methods.
PRIDE is a public repository of protein and peptide identifications for the proteomics community. http://www.ebi.ac.uk/pride/
Membrane shuttling peptide derived from the Drosophila homeobox protein Antennapedia: RQIKIWFQNRRMKWKK
The peptides named CPPs vary greatly in size, amino acid sequence, and charge, but share the common feature that they have the ability to rapidly translocate the plasma membrane and enable delivery to the cytoplasm or nucleus.
PeptideAtlas addresses these needs by identifying peptides by tandem mass spectrometry (MS/MS), statistically validating those identifications and then mapping identified sequences to the genomes of eukaryotic organisms. http://www.peptideatlas.org/
Global Proteome Machine aim to improve the quality of analysis, make the results portable and to provide a common platform for testing and validating proteomics results. http://www.thegpm.org
Descriptor of an experimental form involved in a genetic interaction
The gene has been completely removed e.g. by genetic engineering
The gene expression has been significantly reduced compared to wild-type by introduction of an external substance, e.g. by RNA interference.
The gene function has been partially improved compared to wild-type by altering its sequence.
The gene function has been partially reduced compared to wild-type by altering its sequence e.g. a temperature sensitive mutant.
The gene function has been antagonized by a mutation in another copy of the gene.
The gene function has been abolished by mutation, though the type of mutation is not known.
An effect in which two genetic perturbations, when combined, result in a mutant phenotype that is not observed (or minimally observed) as a result of any of the individual perturbations. wt = a = b = E (not=) ab
aphenotypic diverging genetic interaction
synthetic genetic interaction (sensu inequality)
synthetic genetic interaction defined by inequality
An effect in which individual perturbations of different genes and their combination result in the same mutant phenotype, to the same degree of severity/penetrance. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a = b = ab != wt where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
A, B, and the AB combination all have the same effect on the WT background (2 inequalities).
Another subtype of alleviating interaction, 'coequal' interaction, is defined by single- and double-mutant strains that exhibit fitness values that are indistinguishable from one another (19).
Lastly, we observed ten gene pairs for which the MMS sensitivity of the single- and double-deletion strains was statistically indistinguishable (Sxy = Sx = Sy). These interactions, which we call ‘coequal’, are related to‘complementary gene action’, ‘complementary epistasis’ or ‘asynthetic’ relationship types that have been previously described18,30,31.
asynthetic genetic interaction (sensu inequality)
isophenotypic masking genetic interaction
An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than the most severe phenotype of the original perturbations, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab <= wt [E = a*] OR wt <= ab < a* [E = a*] where 'a*' is the most severe observed phenotype value of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
suppressive genetic interaction (sensu inequality)
An effect in which individual perturbations of two different genes result in different mutant phenotypes, and the resulting phenotype of their combination (the double mutant) is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively or quantitatively different phenotypes.
epistatic genetic interaction (sensu inequality)
The phenotype resulting from genetic perturbation of A has an effect only in the b background, or the b mutant has an effect only in the a background. a has an effect only in the b background, or the b mutant has an effect only in the a background. E. g., WT = a > ab > b or WT > a > b > ab.
conditional genetic interaction (sensu inequality)
conditional genetic interaction defined by inequality
Single-mutant phenotype effects combine to give a double-mutant effect different from the wild type and different from single mutant effect. For instance, WT < a = b < ab, b < WT = ab < a, WT < a < b < ab, b < WT < ab < a, and all additional inequalities obtained by interchanging a and b, or reversing the effect of both a and b.
additive genetic interaction (sensu inequality)
additive genetic interaction defined by inequality
The phenotype resulting from genetic perturbation of B shows opposing effects in the WT and a backgrounds (for example, b > WT and ab < a); or, a shows opposing effects in the WT and b backgrounds, but not both. E.g., WT > a > ab > b.
single nonmonotonic genetic interaction (sensu inequality)
single nonmonotonic genetic interaction defined by inequality
The phenotype resulting from genetic perturbation of both A and B show opposing effects in the WT background and the background with the other mutant gene. E.g., WT >= ab > a >= b
double nonmonotonic genetic interaction (sensu inequality)
double nonmonotonic genetic interaction defined by inequality
The A genetic perturbation enhances the phenotype of the B perturbation, or vice versa (e.g. WT = A < B < AB or WT = B < A < AB). This could be conditional or additive by the above scheme. OBSOLETE: remap to MI:0933 'negative genetic interaction'
Synthesis rate of a molecule under investigation differs from its naturally occurring expression level in a cell.
The gene is mutated in some unknown manner
The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. http://www.wwpdb.org/
PDBj(Protein Data Bank Japan) maintains the database for the protein structures with financial assistance from the Institute for Bioinformatics Research and Development of Japan Science and Technology Corporation(BIRD-JST), collaborating with the Research Collaboration for Structural Bioinformatics(RCSB) and the MSD in the European Bioinformatics Institute(MSD-EBI) in EU. All three organizations serve as deposition, data processing and distribution sites. http://www.pdbj.org/
The interaction of two or more molecules is determined by their very close proximity or the overlap of their respective bands in a gel.
A method allowing the detection of strong interactions between two or more molecules as running, all of them, within a single band in a denaturing gel.
The bimolecular fluorescence complementation (BiFC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two non- fluorescent fragments of a protein fluorophore such as green fluorescent protein (GFP) or its derivatives. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional flourophore that can be identified through fluorescence spectroscopy or microscopy.
green fluorescence protein complementation assay
bimolecular fluorescence complementation
In this approach, once a molecule is demonstrated to participate in an interaction, several substitution mutants are produced and tested in the binding assay to identify the residues which identity is crucial for the interaction.
In this approach, once a molecule is demonstrated to participate in an interaction, several insertion derivatives are produced and tested in the binding assay to detect the regions that are important for the interaction.
The protein is expressed and purified as a fusion to the calmoduling-binding protein. The fusion protein can be purified by affinity chromatography using a calmodulin resin.
Upon binding of two proximity probes (usually antibodies conjugated to DNA) to the same target protein complex, the oligonucleotides on the proximity probes are brought close together. These antibody-conjugated oligonucleotides hybridize to two connector oligonucleotides that are ligated to form a circular DNA molecule. This newly formed DNA-molecule can be amplified by rolling circle amplification. The resulting single-stranded DNA-molecule collapses into a bundle, which is detectable through hybridization of fluorescently labeled complementary oligonucleotides.
In protease accessibility laddering (PAL) tagged proteins are purified on magnetic beads in their natively folded state. While attached to the beads, proteins are probed with proteases. Proteolytic fragments are eluted and detected by immunoblotting with antibodies against the tag (e.g., Protein A, GFP, and 6xHis).
Molecule whose sequence identity is derived from their molecular weight
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker.
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with silver.
molecular weight estimation by silver staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with comassie dye.
molecular weight estimation by coomasie staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with bromide dyes.
molecular weight estimation by bromide staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with sybr dyes.
molecular weight estimation by sybr staining
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining by autoradiography.
molecular weight estimation by autoradiography
Molecule whose sequence identity is derived from their molecular weight after a comigration in a gel with molecular weight marker and staining of the molecules with Hoechst dyes.
molecular weight estimation by hoechst staining
Feature detection not verified in the context of an experiment but assumed from external or previous experimental evidence(s).
Analysis of a diffraction pattern generated by an isotropic sample composed of many randomly oriented crystals.
Analysis of the diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using X-ray.
Method where the internal structure of a sample is derived from the intensity distribution of the scattered monochromatic X-ray beam at very low scattering angles.
X-ray Tomography is a branch of X-ray microscopy. A series of projection images are used to calculate a three dimensional reconstruction of an object. The technique has found many applications in materials science and later in biology and biomedical research. In terms of the latter, the National Center for X-ray Tomography (NCXT) is one of the principle developers of this technology, in particular for imaging whole, hydrated cells.
Subpart of a polyprotein that is naturally cleaved in vivo.
This qualifier is used for hybrid or composite molecules with more than one cross-reference to parent molecules.
List of tissue used as topic in UniProt RC line. http://www.expasy.org/cgi-bin/lists?tisslist.txt
Ontology of cell types. http://obo.sourceforge.net/cgi-bin/detail.cgi?cell
A protein modification that is effectively either one half of a cystine cross-link, or a cysteine residue with one hydrogen atom or proton removed
Experimental method by which radiolabel is detected by exposure to a photographic emulsion forming a pattern on the film.
Association rate constant or rate of complex formation. Unit MOLE per SECOND (M-1 s-1)
Dissociation rate constant measuring the stability of a complex. Unit SECOND (s-1)
Temperature at which interaction was determined. Unit KELVIN (K)
The kelvin (K) is the SI unit of thermodynamic temperature. It is defined by taking the fixed numerical value of the Boltzmann constant k to be 1.380649×10-23 when expressed in the unit J·K-1, which is equal to kg·m2·s-2·K-1, where the kilogram, metre and second are defined in terms of h, c and caesium frequency. It is equivalent to -273.15°C / -459.67°F.
Per mole per second, unit for association rate constant.
Molecule stimulating an interaction by interacting with one or more of the participants.
Measures the rate of a phosphate transfer between two molecules.
Any molecule that is able to transfer a phosphate group to another chemical species.
Molecule to which a phosphate group may be transferred from a phosphate donor.
Reaction where a phosphate is transferred between two proteins of a phosphorelay system.
Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest.
Paramagnetic molecule (1-oxyl-2,2,5,5-tetramethylpyrroline- 3-methyl)-methanethiosulfonate. that can be covalently attached to any cysteine aminoacid producing a nitroxide side chain designated R1.
Dansyl is the acronym of 5-dimethylaminonaphthalene-1-sulfonyl radical group reacting with any NH2 groups.
5-dimethylaminonaphthalene-1-sulfonyl tag
Molecule labelled with 125 radio isotope of iodine atoms.
The NCBI taxonomy database indexes over 55 000 organisms that are represented in the sequence databases with at least one nucleotide or protein sequence. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group of organisms. Searches of the NCBI taxonomy may be made on the basis of whole or partial organism names, and direct links to organisms commonly used in biological research are also provided. The Taxonomy Browser can also be used to display the number of nucleic acid sequences, protein sequences, and protein structures available for organisms included in the branch. From the data display for a particular organism, one can retrieve and download the sequence data for that organism, or protein 3D structure data if available. http://www.ncbi.nlm.nih.gov/Taxonomy/
ENCODE (the Encyclopedia Of DNA Elements) seeks to identify all protein-coding genes. The current ENCODE data set is derived from 1% of the human genome and has been selected for analysis in the pilot phase of the project. http://www.genome.gov/10005107
GenBank Identifier or GI numbers for proteins.
GenBank Identifier or GI numbers for nucleotide.
An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase
An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule.
An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule.
A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore.
Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength.
Method involving consecutive coimmunoimmunoprecipitations on the same sample, a control where an interaction is detected, and other CoIPs where the sample is previously treated with a specific antibody that precipitates a candidate interactor and leads to the suppression of an interaction or a change in composition of a complex.
A single-molecule technique that measures the behavior of a molecular complex under stretching or torsional mechanical force.
The protein A is a bacterial cell wall isolated from Staphylococcus aureus that binds to mammalian IgGs mainly through Fc regions. The protein A can be use to retaint antibodies or as fusion tag of a protein under analysis.
The ZZ tag is a tag made out of two tandem repeats of the Protein A IgG binding domain.
Thiol-reactive lanthanide complexes have been synthesized that are luminescent when bound to terbium and/or europium. The Tb3+-DTPA-cs124-EMCH complexes consist of a diethylenetriaminepentaacetate (DTPA) chelate covalently joined through one amide bond to a chromophore, carbostyril 124, and via a second amide bond to a maleimide, bromoacetamide, or pyridyldithio moiety. This label can be Site-specific attached to both proteins and DNA.
A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms. http://www.brenda-enzymes.info
Pair of fluorophores attached to the same molecule used in a fret experiment to observe the details of conformational changes.
Molecule whose sequence identity is not checked after the interaction but its presence is detected through its tag.
The molecule is produced fused to a tag containing a fluorophore, such as GFP tagged to a recombinant protein, or a fluorophore has been chemically attached to the molecule. Subsequence observation or measurement of fluorescence is used to identify the presence of the molecule in an interaction.
Identifier assigned when the record was created by a source database.
Measures the catalysis of the hydrolysis of an methyl group from a substrate molecule.
The cleavage of a methyl group from a polypeptide. Methylation is generally an irreversible reaction except in mamalian.
The atomic force microscope (AFM) is a very high-resolution type of scanning probe microscope, with demonstrated resolution of fractions of a nanometer, more than 1000 times better than the optical diffraction limit. The AFM was invented by Binnig, Quate and Gerber in 1986, and is one of the foremost tools for imaging, measuring and manipulating matter at the nanoscale.The term 'microscope' in the name is actually a misnomer because it implies looking, while in fact the information is gathered by feeling out the surface with a mechanical feeler. http://en.wikipedia.org/wiki/Atomic_force_microscope
Annotation of a published paper which has been externally requested.
Targeted curation dataset grouping experiments by topic or dataset origin.
Data directly submitted by the authors to a database prior to publication.
Measures the catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
Measures the catalysis of the hydrolysis of ATP+ H2O = ADP + phosphate.
Catalysis of the hydrolysis of a nucleoside triphosphate into a nucleoside diphosphate plus phosphate.
Catalysis of the hydrolisis of ATP+ H2O = ADP + phosphate.
Catalysis of the hydrolisis of GTP+ H2O = GDP + phosphate.
Epitope tag derived from vesicular stomatitis virus (VSV) glycoprotein. The tag sequence is YTDIEMNRLGK and many antibodies against it are commercially available.
Name and details of a journal from which paper has been taken.
In histone acetylation the histones are acetylated on lysine residues in the N-terminal tail as part of gene regulation. Typically, these reactions are catalyzed by enzymes with "histone acetyltransferase" (HAt)
During a SANS experiment a beam of neutrons is directed at a sample. The neutrons are elastically scattered by a sample and the resulting scattering pattern is analyzed to provide information about the size, shape and orientation of some component of the sample.
Measures the catalysis of the addition of an acetyl group to a target molecule.
Qdot are nanocrystals fluorophores . Nanocrystals a are extremely efficient materials for generating and they have a highly customizable surface for directing their bioactivity, producing a fluorescent probe that outperforms traditional dyes in many fluorescence applications.
Analysis of diffraction pattern of a partially ordered sample composed of fibers oriented parallel to each other using neutron beam.
Assay where at least one molecule under analysis is bound to a solid surface, such as a microplate wall or the sides of a tube, the other reactants being free in solution.
Analysis of diffraction pattern using neutron beam
Analysis of diffraction pattern using electron beam.
This method uses Renilla luciferase (Rluc)-based protein fragment complementation assay (PCA) that is designed specifically to investigate dynamic protein complexes (association and dissociation). It is chose to generate a PCA based on the Rluc, which is, because of its simplicity and sensitivity, a widely used bioluminescence reporter. The general scheme for construction and detection of the Rluc-PCA PKA sensor consists of fusing complementary fragments of Rluc to the regulatory (Reg) and catalytic (Cat) PKA subunits of PKA.
Renilla luciferase, is an enzyme of the sea pansy catalyzing the oxidation of the coelenterazine pigment) that produces light. Renilla luciferase produces a blue light of 480nm.
Catalogue of covalent modification of, or a change resulting in an alteration of the measured molecular mass of, a peptide or protein amino acid residue.
Molecule that is reported to self-interact but the experimental condition does not allow to resolve whether the interaction is intramolecular (true self interaction) or intermolecular (homodimer).
pIII is one of the minor coat proteins that decorates in five copies the emerging tip of filamentous phage. Similarly to pVIII pIII also tolerates peptide insertions at the amino-terminus. The sequences to be displayed can either be encoded in the phage copy of the coat gene or in an extra pIII gene copy carried on a phagemid. In the first case 5 copies o the hybrid proteins are displayed while in the latter only a few capsid display one copy and the majority display none. Because of the low copy number pIII display is often referred to as low valency display.
pVIII is the major coat protein of filamentous phage. Its amino-terminus is exposed to solvent and tolerates the insertion of relatively large peptide fragments. By inserting the peptide coding sequence into the phage copy of the pVIII gene up to 3000 copies of the hybrid proteins can be displayed along the phage capsid. Alternatively the hybrid protein can be encoded on a phagemid that is incorporated in a virus like particle by infection with a helper phage. In this latter case one obtains a chimeric capsid where hybrid proteins are interspersed at different density in an otherwise wild type coat. Because of the high copy number pVIII display is also referred to as high valency display.
Exposed amino acid residues undergo a rapid exchange of a specific radio-isotope e.g. hydrogen/deuterium. Residues involved in a molecular interaction are protected from this exchange and exhibit a much slower rate of exchange. This method of binding range identification must be coupled to NMR or mass spectrometry technologies in order to detect the radio-isotope exchange.
Any process by which an RNA molecule is cleaved at specific sites or in a regulated manner.
The microbial protein-protein interactions database (MPDIB) aims to collect and provide all known physical prokaryotic interactions. Note as of 2013, this database is no longer active, but all IMEx curation was imported and is now maintained by the IntAct database (www.ebi.ac.uk/intact).
A polysaccharide is a complex polymer of carbohydrate monormers. They are polymers made up of many monosaccharides joined together by glycosidic bonds. They are therefore very large, often branched, macromolecules.
AlphaScreen relies on the use of Donor and Acceptor beads that are coated with a layer of hydrogel providing functional groups for bioconjugation. When a biological interaction between molecules brings the beads into proximity, a cascade of chemical reactions is initiated to produce a greatly amplified signal. Upon laser excitation, a photosensitizer in the Donor bead converts ambient oxygen to a more excited singlet state. The singlet state oxygen molecules diffuse across to react with a chemiluminescer in the Acceptor bead that further activates fluorophores contained within the same bead. The fluorophores subsequently emit light at 520-620 nm. In the absence of a specific biological interaction, the singlet state oxygen molecules produced by the Donor bead go undetected without the close proximity of the Acceptor bead. AlphaScreen has successfully been developed for enzyme assays (kinase, helicase, protease, ...), interaction assays (ligand/receptor, protein/protein, protein/DNA), immunoassays, and GPCR functional assays (cAMP, IP3).
amplified luminescent proximity homogeneous assay
The protein of interest is expressed as a fusion to the peptide DTYRYI for which antibodies are commercially available.
Statement about the native/denatured conformation of the protein.
Altered conformation state of the protein as a result of heat or chemical modification resulting in a changed structure of the protein.
State of the protein without interference i.e. the natural form.
Covalent bond breakage of a nucleic acid molecule leading to the formation of smaller fragments.
A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed.
N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond.
N -Succinimidyl 3-(2-pyridyldithio)-propionate
Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable and membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester that will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm.
Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate
Interaction between molecules that may participate in formation of one, but possibly more, physical complexes. Often describes a set of molecules that are co-purified in a single pull-down or coimmunoprecipitation but might participate in formation of distinct physical complexes sharing a common bait.
Interaction between molecules within the same physical complex. Often identified under conditions which suggest that the molecules are in close proximity but not necessarily in direct contact with each other.
Yeast two-hybrid system using Escherichia coli LexA amino acids 1-202 as the DNA-binding domain (BD), and a transcriptional activation domain from the herpes simplex virus protein VP16 (either aa 411-490 or aa 411-455) that can specifically activate transcription of a reporter gene located downstream.
Knowledgebase of the extracellular matrix storing experimentally determined interactions involving extracellular biomolecules. It includes protein-protein, protein-polysaccharide, and protein-lipid interactions. https://matrixdb.univ-lyon1.fr
Molecule which emits active chemical groups, electrons or ions that are transfered to an acceptor molecule.
Molecule able to receive active chemical groups, electrons or ions from a donor molecule.
Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
This array technology allows the screening of binding abilities of hundreds or thousands of biomolecules (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) printed onto the gold-coated chip by using an instrument (micro-arrayer) that is capable of spotting liquid samples in a reproducible manner onto a planar support. The ordered protein array can then be probed with a non-labelled sample (small molecule, peptide, protein, sugar, lipid, nucleic acid, and their fragments) to identify the baits that can bind to it. This is done in real time, allowing direct measurement of both the on-rate and the off-rate and of the affinity constant of complex formation on each spot.
Experimental evidence supporting an interaction curated and released under the IMEx agreement.
iRefIndex provides an index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index allows the user to search for a protein and retrieve a non-redundant list of interactors for that protein. iRefIndex uses the Sequence Global Unique Identifier (SEGUID) to group proteins and interactions into redundant groups. This method allows users to integrate their own data with the iRefIndex in a way that ensures proteins with the exact same sequence will be represented only once. http://irefindex.uio.no/
Camjedb is a comprehensive database for information on the genome of Campylobacter jejuni. http://www.sanger.ac.uk/Projects/C_jejuni/
Post translational modification observed on a protein in the context of an interaction.
This fluorescent label is a small ligand membrane-permeant and nonfluorescent until it binds with high affinity and specificity to the tetracysteine domain. Such in situ labeling adds much less mass than does green fluorescent protein and offers greater versatility in attachment sites as well as potential spectroscopic and chemical properties.
IAEDANS is fluorescent tag that bind to cysteines. IAEDANS is the acronyme of (5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid) with free SH groups.
(5((((2-iodoacetyl)amino)ethyl)amino)-naphthalene-1-sulfonic acid)
Biomolecules are mixed in a buffer and the resulting mixture is passed through a filter. Large aggregates are retained on the filter and the pariticipants may then be identified.
A standard procedure to identify RNA fragments containing specific sequences. In this procedure RNA fragments are separated by electrophoresis, the fragments are transferred to a membrane and the membrane is incubated with a radio labelled probe that hybridises any complementary subsequence.
Two genes A and B present an genetic interaction defined by inequality if the phenotypes of the two single mutants a and b, the double mutant ab and the wild-type WT can be measured quantitatively and described relative to each other by an inequality relationship.
genetic interaction defined by inequality
The observation that, when tested, no interaction was observed between two or more genes, for a given phenotype. In other words, the phenotype of the combined perturbations a and b result in the expected phenotype.
noninteractive genetic interaction (sensu inequality)
noninteractive genetic interaction defined by inequality
An effect in which two genetic perturbations, when combined, result in a phenotype that is more severe/penetrant than expected given the phenotypes of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E <= wt OR wt <= E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
OBSOLETE: An effect in which the observed phenotype of individual perturbations and/or the double perturbation collectively exhibit values both greater than AND less than wild type (on the same scale). Alternatively, this could describe a scenario in which individual perturbations result in qualitatively different phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b [ab != E] OR With respect to two qualitatively different phenotypes, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates qualitatively different phenotypes.
An effect in which two genetic perturbations, when combined, result in a phenotype that is less severe/penetrant than would be expected from the original phenotypes, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E < ab <= wt OR wt <= ab < E where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
The Electron Microscopy Data Bank (EMDB) contains experimentally determined three-dimensional maps and associated experimental data and files. https://www.ebi.ac.uk/emdb
This peptide is a 314 to 319 amino acids fragment of the middle T antigen of mouse polymavirus. Glu-Glu epitope peptide.
Characterization of viscoelastic properties of biomolecule solution is used to infer interactions between molecules.
Fluorescence label used to monitor the presence of a protein.
Fluorescein-5-maleimide is one of the most popular fluorescent dyes for thiol modifications of proteins at cysteine residues that either are intrinsically present or result from reduction of cystines. Unlike iodoacetamides, maleimides do not react with histidines and methionines under physiological conditions.
Binds to an interacting molecule in competition with other interaction candidates, for example at a shared binding site.
Based on NCBO Taxonomy but adapted for UniProt http://www.uniprot.org/taxonomy/
'Study of interactions by an analytical technique based on measurements of mass-to-charge ratio of charged particles in a mass spectrometer.
Mass spectroscopy based measurement of the rate and/or extent of the hydrogen/deuterium exchange.
mass spectrometry study of hydrogen/deuterium exchange
An oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
oxidoreductase activity electron transfer reaction
Combines on-chip in-vitro protein synthesis with an in situ microfluidic affinity assay. Co-spotted DNA microarray containing a linear template encoding the proteins is aligned and bonded with a microfluidic device that creates chambers in the array chip. The experiment consists of three main stages: (i) an antibody that recognizes the bait protein or a specific tag is deposited on a circular area inside each individual chamber; (ii) proteins are expressed in vitro by transcription and translation of DNA spotted on the chip; (iii) the bait is immobilized on the chamber surface by the antibody and the chamber is washed, retaining only interacting bait-prey pairs.
Binding of proteins bound to beads leads to a measurable aggregation of the beads.
A brief description (such as temp, pH) of the conditions under which a kinetic measurment has been performed.
Experiments monitoring interactions of GTP-GDP exchange factors with their cognate GTPases.
Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate.
Reference to the master sequence from which this chain has been derived.
Deprecated IMEx identifiers should be exchanged in IMEx records and stored as cross reference with this qualifier.
Interaction inferred by monitoring polymerization/depolymerization of an interactor
An assessment of the depth and extent to which a paper has been curated
Assessment of the depth to which a paper has been curated
Assessment to the extent of interactions captured in this paper
All interactions which can be ascribed to an unambiguous identified in this paper have been captured.
Not all interactions which can be ascribed to an unambiguous identified in this paper have been captured.
Paper has been curated to full IMEx specifications
Paper has been curated to meet MIMIx specifications
Minimal interaction data has been extracted from the paper
The protein of interest is expressed with a StrepII fusion peptide Ser-Ala-Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (SAWSHPQFEK).
A specific pull down method where the protein of interest (bait) is endogenously expressed with at least two affinity tags (GFP, FLAG or others). The bait is purified in parallel using different purification protocols in contrast to tandem affinity purification (TAP) (publication currently in press).
Subset of spectroscopy that deals with the infrared region of the electromagnetic spectrum.
Two-dimensional infrared correlation spectroscopy analysis is the application of 2D correlation analysis on infrared spectra. 2D IR spectroscopy probes molecular structures by means of vibrational frequencies, couplings, and transition dipole angles.
Ultraviolet-visible spectroscopy or ultraviolet-visible spectrophotometry (UV-Vis or UV/Vis) involves the spectroscopy of photons in the UV-visible region. This means it uses light in the visible and adjacent (near ultraviolet (UV) and near infrared (NIR)) ranges.
ChEMBL focuses on mapping the interactions of small molecules binding to their macromolecular targets.
A biosensor is a device for the detection of an analyte that combines a biological component with a physicochemical detector component
BLI is an optical analytical technique that analyzes the interference pattern of white light reflected from two surfaces: a layer of immobilized protein on the biosensor tip, and an internal reference layer
InChIKeys consist of 14 characters resulting from a hash of the connectivity information of the InChI, followed by a hyphen, followed by 9 characters resulting from a hash of the remaining layers of the InChI, followed by a single character indication the version of InChI used, another hyphen, followed by single checksum character
The posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
Assay of the posttranslational phosphopantetheinylation of peptidyl-serine to form peptidyl-O-phosphopantetheine-L-serine.
Databases that contain curated experimental interaction data and exchanging it with other IMEx databases.
Human and mouse experimentally verified interactions and pathways involved in innate immunity.
A fusion protein tag consisting of a portion of the constant region of IgG.
Used to study surface-associated interactions at the molecular level. In this method, the evanescent field from an internally reflected excitation source selectively excites fluorescent molecules on or near a surface.
total internal reflection fluorescence spectroscopy
Prevents export of experiment and associated interactions to IMEx
Author given name for a participant, not commonly found in source databases.
Catalysis of oxido-reductions. The substrate oxidized is regarded as the hydrogen or electron donor. The classification is based on 'donor:acceptor oxidoreductase'. The common name is 'dehydrogenase', wherever this is possible; as an alternative, 'acceptor reductase' can be used. 'Oxidase' is used only where O2 is an acceptor.
The protein is expressed as a hybrid protein fused to a tag containing an enzyme activity e.g. peroxidase. Subsequence observation or measurement of enzyme activity is used to identify the presence of the molecule in an interaction.
The protein is expressed as a hybrid protein fused to a tag containing a peroxidase activity. Subsequent observation or measurement of peroxidase activity is used to identify the presence of the molecule in an interaction.
tag visualisation by peroxidase activity
Any method which relies on the motion of particles relative to a matrix under the influence of an electrical field.
GEMMA is a method to study protein complexes in solution: a diluted protein sample is transmitted into the gas phase by a charged reduced electrospray process. The generated particles, each containing one protein molecule with a +1 charge, are separated according to size in a differential mobility analyzer and subsequently quantified by a particle counter. In contrast to mass spectrometry, this method is run at atmospheric pressure and measures the diameter of the particle rather than the mass.
The measurement of the removal of an amine group from a molecule.
The removal of an amine group from a molecule.
The lengthening of a strand of a nucleic acid by the systematic addition of bases by a polymerase.
The process by which an RNA strand is synthesized from template DNA by the action of polymerases, which add nucleotides to the 3' end of the nascent RNA strand.
Synthetic peptide consisting of 8 amino acids Trp-Ser-His-Pro-Gln-Phe-Glu-Lys (WSHPQFEK).
The measurement of the addition of an amine group to a molecule.
The cleavage of a biomolecule either into its component parts or sub-parts.
The cleavage of a lipid molecule from a larger biomolecule.
Measures the removal of S-farnesyl-L-cysteined, which is cleaved and returns a C residue.
Measures the removal of S-geranylgeranyl-L-cysteine, which is cleaved and returns a C residue.
measures the removal of N6-myristoyl-L-lysine, which is cleaved and returns a K residue.
Measures the removal of S-palmitoyl-L-cysteine, N6-palmitoyl-L-lysine, O-palmitoyl-L-threonine or O-palmitoyl-L-serine, which are cleaved and return C,K,T or S residues.
Measures the removal of N6-formyl-L-lysine, which is cleaved and returns a K residue.
Measures the reversible reaction that creates a covalent bond between a C-terminus G of ubiquitin and a K residue of the target.
Measures the cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins.
Measurement of the reaction that can affect K or G residues. Reside is functionalised with a formyl group.
Measurement of the irreversible introduction of a hydroxyl group that can affect K,P,Y or R residues.
The covalent binding of a lipid group to a peptide chain.
Measurement of the irreversible covalent addition of a myristoyl group via an amide bond to the alpha-amino group of an amino acid.
Measurement of the attachment of one or two 20-carbon lipophilic geranylgeranyl isoprene units from geranylgeranyl diphosphate to one or more cysteine residue(s).
Measurement of the covalent attachment of palmitic acid to a protein.
Measurement of the addition of one or more ADP-ribose moieties to molecules.
Measurement of the removal of a glycosyl residue to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
Measurement of the covalently attachment of glycosyl residues to one or more monomeric units in a polypeptide, polynucleotide, polysaccharide, or other biological polymer.
Measurement of the reversible reaction that creates a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
Measurement of the reaction that breaks a covalent bond between a C-terminus G of an ubiquitine like sumo protein and a K residue of the target.
Measurement of a reversible reaction that create a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
Measurement of the reaction that breaks a covalent bond between a Glycine residue of an ubiquitine like NEDD8 protein and a lysine residue of the target.
38 amino acid (MDEKTTGWRGGHWEGLAGELEQLRARLEHHPQGQREP) Streptavidin binding peptide.
Genome browser complementary to Ensembl which extends the search space across a broader taxonomic range. http://www.ensemblgenomes.org
STRING is a database and web resource dedicated to protein interactions, including both physical and functional interactions. It weights and integrates information from numerous sources, including experimental repositories, computational prediction methods and public text collections, thus acting as a meta-database that maps all interaction evidence onto a common set of genomes and proteins.
dictyBase (http://dictybase.org) is the model organism database for Dictyostelium discoideum. It houses the complete genome sequence, ESTs and the entire body of literature relevant to Dictyostelium. This information is curated to provide accurate gene models and functional annotations, with the goal of fully annotating the genome.
Slow rate of FRAP recovery when molecule is bound to another compared to inert, non-binding molecule taken as a measure of an interaction.
fluorescence recovery after photobleaching
Proteins are crosslinked to nucleic acids, for example by the addition of formaldehyde. RNA sequences that cross-link with a given protein are isolated by immunoprecipitation of the protein, and reversal of the cross-linking permits recovery and quantitative analysis of the immunoprecipitated RNA by reverse transcription PCR.
A database of protein post translational modifications. www.abrf.org/index.cfm/dm.home
Measures the catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate.
A carbonyl-reactive fluorescent labelling dye.
Nonfluorescent dye, act as a quencher in FRET assays.
A separation technique where a field is applied to a mixture perpendicular to the mixtures flow. The filed can be graviational, centrifugal, magnetic or a cross flow of fluids.
A nonfluorescent, biarsenical derivative of fluorescein. LumioGreen is supplied pre-complexed to EDT, is membrane-permeable, and readily enters the cell.
A type of electron microscope that images the sample surface by scanning it with a high-energy beam of electrons in a raster scan pattern. The electrons interact with the atoms that make up the sample producing signals that contain information about the sample's surface topography, composition and other properties such as electrical conductivity.
A database of protein modifications for mass spectrometry. www.unimod.org
Measurement of a modification that converts an L-histidine residue to diphthamide.
A modification that converts an L-histidine residue to diphthamide.
Chromatin-bound protein networks isolated using magnetic beads coated with antibodies.
Specific nucleic acid probes are fixed to solid supports (e.g. beads) and act as affinity probes. The molecules associated with the nucleic acid probes can then be isolated and identified.
proteomics of isolated chromatin segments
Excimer (excited-dimer) fluorescence is produced by complexes formed by two molecules, at least one of which is in an excited state. It is characterized by a lower energy (i.e. red shift) than fluorescence of a single, non-interacting molecule.
A change in the rate of protein folding/unfolding is taken as a measure of chaperone protein binding.
Fluorescent tag - maleimide couples to thiols.
Measures the cleavage of phosphodiesterase bonds between the nucleotide subunits of nucleic acids.
Measures the catalysis of the hydrolysis of phosphodiester bonds in chains of DNA.
Experiments monitoring interactions of nucleotide exchange factors with their cognate nucleotidases.
The N-terminal portion of synthetic renilla luciferase (hrluc) is attached to one protein through the linker peptide (GGGS)2 and C-terminal portion of synthetic renilla luciferase is connected to the second protein through the linker (GGGGS)2. Interaction of the 2 proteins recovers hrluc activity and produces light.
Split renilla luciferase complementation
Measures selective electrical response to molecules binding to the immobilised bait.
silicon nanowire field-effect transistor
The C-terminal region of a sequence, exact coordinates not available.
The N-terminal region of a sequence, exact coordinates not available.
Alternative name or descriptor for an entity.
PubMed Central is the US National Institute of Health free digital archive of biomedical and life science journals.
A repository for collecting, storing and and searching the annotation of gene or protein expression patterns in Drosophila melongaster. CPTI (Cambridge Protein Trap Identifier)
Indicates source, depth and standards by which an entry has been added to a database.
Defines an interaction by the type of binary molecule pairs it can generates.
Interaction between a protein or peptide and a corresponding protein or peptide.
Interaction between a small molecule and a corresponding protein or peptide.
Interaction between a nucleic acid and a corresponding protein or peptide.
Provides an indication of the level of post-processing of experimental data relating to specific binary pairs
Binary pair is defined by a single piece of experimental evidence.
Binary pair is defined by multiple pieces of experimental evidence which have been clustered together.
The source of the data entered into the database.
Data has been directly curated into the database from the paper describing the experimental evidence or by direct submission by the experimenter.
Data has been directly curated into this database from the paper describing the experimental evidence
The data has been entered into the database following extraction from the literature by a computational process.
The interaction has been predicted using a specific algorithm.
The data has been imported into the database form an external resource.
The method by which complex n-ary data is expanded into binary data. This may be performed manually on data input, or computationally on data export.
Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with a single designated molecule, usually the bait.
Complex n-ary data has been expanded to binary using the spoke model. This assumes that all molecules in the complex interact with each other.
Complex n-ary data has been expanded to binary using the bipartite model. This assumes that all molecules in the complex interact with a single externally designated entity.
ConsensusPathDB-human integrates functional interaction networks including complex protein-protein, metabolic, signaling and gene regulatory interaction networks in Homo sapiens. Data originate from currently 20 public resources for functional interactions (listed below), as well as interactions that we have curated from literature. Data are integrated in a complementary manner and redundancies are avoided.
A method used to derive a numerical or empirical measure of confidence in a particular interaction, or in the identification of the participants in an interaction.
Methods based on counting the number of replicates in which an interaction has been observed.
Confidence score based on similarity to interacting molecules of known structure, presence of known interacting domains etc.
Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO function terms.
Confidence in an interaction is based on shared functionality of interacting molecules e.g. co-occurrence of GO component terms or co-occurrence in the same tissues.
Network-based confidence scoring systems assign confidence based on multiple parameters, potentially shared by interacting proteins e.g. interaction partners, topological parameters, comparison with genetic interactions.
Confidence scoring system based on comparison to a 'gold standard' set of known interacting molecules.
Confidence in an interaction is based on co-occurrence of an interacting pair or molecules in the same article, or sentence within an article, usually identified by text-mining.
The confidence of an interaction is assessed on the number of different methods by which it is observed.
Confidence in an interaction is based on a measure of the probability of these molecules interacting.
The protein of interest is expressed as a fusion to a RGS(His)n tag.
The Beilstein database is in the field of organic chemistry, in which compounds are uniquely identified by their Beilstein Registry Number.
The EINECS database provides general information such as CAS number, EINECS number, Substance Name and Chemical Formula for 100,204 chemical substances. Where available each compound entry is linked to risk and safety phrases and IUCLID and OECD chemical data sheets.
European Inventory of Existing Commercial Chemical Substances
Comprehensive information on chemicals, drugs, and biologicals.
PlantGDB develops plant species-specific EST and GSS databases, to provide web-accessible tools and inter-species query capabilities, and to provide genome browsing and annotation capabilities.
The rat genome database RatMap (http://ratmap.org or http://ratmap.gen.gu.se) has been one of the main resources for rat genome information since 1994. The database is maintained by CMB Genetics at Gothenburg University in Sweden and provides information on rat genes, polymorphic rat DNA-markers and rat quantitative trait loci (QTLs), all curated at RatMap.
The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community.
The J. Craig Venter Institute was formed in October 2006 through the merger of several affiliated and legacy organizations including The Institute for Genomic Research (TIGR).
Extensive information on Danio rerio, including genomics databases, developmental stages, publications and molecular tools.
Clusters of Orthologous Groups of proteins (COGs) were delineated by comparing protein sequences encoded in complete genomes, representing major phylogenetic lineages. Each COG consists of individual proteins or groups of paralogs from at least 3 lineages and thus corresponds to an ancient conserved domain.
Any molecule that is able to transfer a photon to another chemical species.
Molecule to which a photon may be transferred from an photon donor.
Two chambers are separated by a dialysis membrane. The molecular weight cut off (MWCO) of this membrane is chosen such that it will retain the receptor component of the sample (the element which will bind the ligand). A known concentration and volume of ligand is placed into one of the chambers. The ligand is small enough to pass freely through the membrane. A known concentration of receptor is then placed in the remaining chamber in an equivalent volume to that placed in the first chamber. As the ligand diffuses across the membrane some of it will bind to the receptor and some will remain free in solution. The higher the affinity of the interaction, the higher the concentration of ligand that will be bound at any time.
Method to block a binding site on a molecule, such as a protein, using a monoclonal antibody to test that the binding site is involved in an interaction with another molecule.
Assays that are used to determine interactions by monitoring, for example activation of a certain pathway when screening for inhibitors of a given receptor.
Method to detect interaction by inducing nuclear localization of one participant, which would then pull an interacting participant along with it into the nucleus. As both participants are labeled, the difference in nuclear localization between the induced and non-induced states provides an indication of the interaction between the two molecules.
Bromobimanes are low molecular weight non-fluorescent alkyl halides which react with thiol groups to produce highly fluorescent derivatives. The bimane labels, monobromobimane, dibromobimane, and monobromotrimethylammoniobimane, are derivatives of syn-9,10-dioxabimane:1,5-diazabicyclo[3.3.0]octa-3,6-diene-2,8-dione.
Fluorescent dyes - spectral range 500 to 700 nm.
Databases which are the responsible for the maintenance and subsequent annotation of one or more genomic sequences.
HGNC is the nomenclature committee responsible for the naming of human genes.
Databases dedicated to the collection and annotation of protein sequences.
UniProt is a centralized repository of protein sequences with comprehensive coverage and a systematic approach to protein annotation, incorporating, interpreting, integrating and standardizing data from numerous sources and is the most comprehensive catalog of protein sequences and functional annotation.
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. UniProtKB/Swiss-Prot is manually curated which means that the information in each entry is annotated and reviewed by a curator. http://www.uniprot.org
UniProt (Universal Protein Resource) is the world's most comprehensive catalogue of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR. The records in UniProtKB/TrEMBL are automatically generated and are enriched with automatic annotation and classification. http://www.uniprot.org
Molecules showing activity in a living system but not encoded by a genomic sequence.
The Standard InChIKey has five distinct components, a 14-character hash of the basic (Mobile-H) InChI layer, an 8-character hash of the remaining layers (except for the /p segment, which accounts for added or removed protons: it is not hashed at all; the number of protons is encoded at the end of the standard InChIKey.) , a 1 flag character, a 1 version character and the last character is a [de]protonation indicator. The overall length of InChIKey is fixed at 27 characters, including separators (dashes).
Sequence has been computationally remapped following removal or update of the original sequence in the underlying sequence database.
NMR solution state analysis provides useful data regarding the type, quantity and arrangement of different atoms in chemical systems, liquids and solids. Samples are dissolved in deuterated solvents and spectra consist of a series of very sharp transitions, due to averaging of anisotropic NMR interactions by rapid random tumbling. Solution-state NMR only requires that the molecule be soluble at sufficient concentration for data collection, but becomes increasingly difficult for biomolecules over 30 kDa so that a practical size limitation is placed on full structure determinations.
Solid-state NMR (ssNMR) does not require that the sample be soluble or form a crystal, and the approach can be used to study molecules larger than 100 kD. Solid-state NMR spectra are very broad, as the full effects of anisotropic or orientation-dependent interactions are observed in the spectrum.
BioCyc is a collection of Pathway/Genome Databases. Each database in the BioCyc collection describes the genome and metabolic pathways of a single organism. (http://biocyc.org/).
Databases which primarily exist to display biomolecular information in structured pathways. Interactions data can be inferred from the published pathways.
Curated collection of information about known biomolecular interactions and key cellular processes assembled into signaling pathways. It is a collaborative project between the US National Cancer Institute (NCI) and Nature Publishing Group (NPG), and is an open access online resource (http://pid.nci.nih.gov/).
BioCarta, whose core business is in assays and reagents, has also developed a collection of diagrams representing molecular and cellular signal transduction pathways.
Primarily nomenclature/cross-reference databases, used by curators to establish a link between a gene and protein ID. In some cases, database records do not contain actual sequence but point to loci on specific reference genomes.
Interaction has been predicted by either interologue mapping, by an algorithm or by a computational method.
Individual baits are mated against pools of preys, or pools of baits are mated against individual preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
two hybrid bait or prey pooling approach
Individual baits are mated against pools of preys. This approach required cloning baits and preys into both two-hybrid vectors, followed by pooling sets of transformants. The positive double hybrid clones are the interacting partners.
two hybrid bait and prey pooling approach
Signalling Pathways Integrated Knowledge Engine
GeneMANIA predicts interactions based on multiple evidences including physical and genetic interactions, pathways, co-localisation, co-expression and protein domain similarity.
TopFIND provides information on protein N- and C-termini. Information of proteases and their substrates is provided.
Termini-oriented protein function inferred database
A variation of yellow fluorescent protein derived from eGFP.
n-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
c-terminal fragment of yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
c-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
n-terminal fragment of enhanced yellow fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
BindingDB is a web-accessible public database of experimentally determined protein-ligand binding affinities for drug discovery. http://BindingDB.org
Allows the user to browse and search pathways across multiple public pathway databases. http://www.pathwaycommons.org
The defined region of protein which makes physical contact with the interacting partner.
Should normally be used with X-ray crystallography or NMR data.
Intra-molecular interaction between two or more regions of the same molecule.
The corresponding experimental role will be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.
Interaction between two or more regions of possibly the same molecule but it is also possible that the observation is due to an interaction between two identical molecules.
The corresponding experimental role should be self/putative self. Not to be used for autocatalysis, when the additional biological role self/putative self will supply this information.
Region of a molecule whose mutation or deletion totally disrupts an interaction strength.
mutation disrupting interaction strength
Region of a molecule whose mutation or deletion totally disrupts an interaction rate (in the case of interactions inferred from enzymatic reaction)..
Region of a molecule whose mutation or deletion decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
Region of a molecule whose mutation or deletion increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction).
Region of a molecule whose mutation or deletion increases significantly interaction strength.
mutation increasing interaction strength
Region of a molecule whose mutation or deletion decreases significantly interaction strength.
mutation decreasing interaction strength
mCherry is a red monomer which matures extremely rapidly, making it possible to see results very soon after activating transcription. It is highly photostable and resistant to photobleaching. Excitation maximum: 587 nm. Emission maximum: 610 nm.
Introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L), produced Venus. This mutation dramatically accelerates oxidation of the chromophore, the rate-limiting step in fluorescent protein maturation. Additional mutations were also introduced in order to increase the tolerance of Venus to acidic environments and to reduce the sensitivity to chloride. The absorption and emission spectral peaks are 515 and 528 nanometers, respectively.
Monomeric coral fluorescent reporter protein.
The measurement of a the introduction of a carboxylic acid group into a substrate.
Carboxylation is a posttranslational modification of glutamate residues, to gamma-carboxyglutamate, in proteins.
Decarboxylation is a chemical reaction that releases carbon dioxide (CO2). Usually, decarboxylation refers to a reaction of carboxylic acids, removing a carbon atom from a carbon chain. Enzymes that catalyze decarboxylations are called decarboxylases or, the more formal term, carboxy-lyases (EC number 4.1.1).
S-tag is the name of an oligopeptide derived from pancreatic ribonuclease A (RNase A). The amino acid sequence of the S-tag is: Lys-Glu-Thr-Ala-Ala-Ala-Lys-Phe-Glu-Arg-Gln-His-Met-Asp-Ser.
The measurement of the addition of an aminoacyl group to a compound.
Aminoacylation is the process of adding an aminoacyl group to a compound.
Protein A tag is visualized by interacting with IgG antibodies (or their derivatives) that are specifically recognized by protein A.
A phospholipase is an enzyme that hydrolyzes phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
Measurement of the hydrolysis of phospholipids into fatty acids and other lipophilic substances. There are four major classes, termed A, B, C and D, distinguished by the type of reaction which they catalyze.
Measurement of AMPylation, the formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
AMPylation, previously known as adenylylation, is formation of a phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
A set of molecular binding events that influence each other either positively or negatively through allostery or pre-assembly. In this context, covalent post-translational modifications are considered as binding events. CV terms that are part of this term allow the description of cooperative interactions using the current PSI-MI schema.
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates which subsequent interaction is affected. The affected interaction is identified by referring to its interaction id.
Referring to a previously described interaction as a participant allows the description of ordered assembly of molecular complexes in PSI-MI2.5. When one of the components of the preformed complex has a feature, the participant-ref term indicates on which component this feature is located. The component is identified by referring to its participant id in the previous interaction.
This value quantifies the cooperative effect of an interaction on a subsequent interaction. It is the fold change of the affinity or a catalytic parameter of a molecule for one ligand in the absence, versus presence, of a second ligand or a post-translational modification.
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates whether this effect is positive or negative, i.e. whether the subsequent interaction is augmented or diminished.
This term specifies that an interaction augments a subsequent interaction.
This term specifies that an interaction diminishes a subsequent interaction.
For an interaction that has a cooperative effect on a subsequent interaction, this term indicates the process that mediates this effect.
Reciprocal energetic coupling between two binding events at distinct sites on the same molecule. The first binding event alters the binding or catalytic properties of the molecule for the second binding event.
A non-allosteric mechanism where the strength of an interaction depends on whether or not a particular molecular complex already exists.
A molecule whose binding or catalytic properties at one site are altered by allosteric post-translational modification or binding of an allosteric effector at a distinct site. An allosteric molecule is identified by referring to its participant id.
A ligand that elicits an allosteric response upon binding to a target molecule.
This term describes the effect of an allosteric binding event. It specifies which properties of the allosteric molecule are altered, i.e. whether the interaction alters either (a) binding or (b) catalytic properties of the allosteric molecule at a site distinct from the allosteric site.
An allosteric response in which the affinity of a molecule is altered.
An allosteric response in which catalysis (kcat or Vmax) of an enzyme is altered.
The process that mediates the allosteric response of a molecule upon allosteric post-translational modification or binding of an allosteric effector.
The allosteric mechanism where changes in the local structure of an allosteric molecule result in altered binding or catalytic properties.
The allosteric mechanism where changes in the local dynamics of an allosteric molecule result in altered binding or catalytic properties.
This term indicates the chemical relationship between the two ligands whose binding is allosterically coupled.
The type of allostery that occurs when the two ligands whose binding is allosterically coupled are not chemically identical.
The type of allostery that occurs when the two ligands whose binding is allosterically coupled are chemically identical.
This term describes the way in which preformation of a molecular complex has a non-allosteric cooperative effect on subsequent interactions of its components.
The preformation of a complex results in the generation of a continuous binding site that spans more than one component of this complex. The functional binding site does not exist outside the context of the preformed complex.
The addition of a PTM to an interaction interface affects the physicochemical compatibility of the binding site with its binding partner. This can either induce or enhance an interaction, or result in inhibition or even abrogation of an interaction. Multisite modification can mediate rheostatic regulation of the interaction.
The occurrence of overlapping or adjacent, mutually exclusive binding sites promotes competitive binding. When there is a large difference in affinity of the different sites or in local abundance of competitors, binding at one site results in hiding of the second site, thereby precluding it from interacting when the hiding molecule is present.
Multivalent ligands form multiple discrete interactions with one or more binding partners. In some cases, An initial binding event can pre-organize other sites for binding. This reduces the degrees of freedom of these sites, thus reducing the entropic costs of their interactions. In addition, the combined strength of multiple interactions increases the enthalpic stability of each interaction (avidity effect). As a result of such effects, interactions of this kind can have a cooperative effect on subsequent interactions.
A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id.
allosteric post-translational modification
Sequence analysis of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur.
sequence based prediction of TG regulatory region binding sites for TF
sequence based prediction of gene regulatory region binding sites
Sequence analysis based on multiple homologous alignments of the regulatory region of a gene used to predict specific elements, transcription factor binding sites (TFBS), where binding of specific transcription factors can occur. These methods often also use transcription factor binding motif models.
phylogenetic profiling of predicted gene regulatory region binding sites
Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict a transcription factor using structural and sequence features of the protein, e.g., by evaluating if the potential transcription factor protein contains a DNA-binding domain that is known to bind to some regulatory elements, or prediction of transcription factor functional domains (DNA binding, transcription factor dimerization, etc.), all based on sequence or structural features of the transcription factor.
sequence based prediction of binding of TF to TG promoter
sequence based prediction of binding of transcription factor to transcribed gene regulatory elements
Identification of a part of a nucleotide sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clone.s
partial nucleotide sequence identification
Identification of a part of a DNA sequence, usually then related to the full length sequence by alignment. Depending on the experimental design, nucleotide sequence can be determined before the interaction detection while building a collection of clones or after the selection of randomly generated clones.
Paired-end tags (PET) are the short sequences at the 5 prime and 3 prime ends of the DNA fragment of interest, which can be a piece of genomic DNA or cDNA.
Sequencing occurs during the course of the experiment. To sequence RNA, the usual method is first to reverse transcribe the sample to generate cDNA fragments.
Binding of a molecule to a strand of nucleic acid protects that region of nucleic acid from the action of a nuclease. The protected region can subsequently be sequenced and the binding site identified.
DNA adenine methyltransferase identification is used to map the binding sites of DNA- and chromatin-binding proteins in eukaryotes. DamID identifies binding sites by expressing the proposed DNA-binding protein as a fusion protein with DNA methyltransferase. Binding of the protein of interest to DNA localizes the methyltransferase in the region of the binding site. Adenosine methylation does not occur naturally in eukaryotes and therefore adenine methylation in any region can be concluded to have been caused by the fusion protein, implying the region is located near a binding site.
dna adenine methyltransferase identification
Proteins of interest are tagged with Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites. The adenine-methylated DNA fragments are isolated by selective polymerase chain reaction amplification and can be identified by microarray hybridization.
tag visualisation by dna adenine methyltransferase
The protein of interest is fused to Escherichia coli DNA adenine methyltransferase (dam). Expression of this fusion protein in vivo leads to preferential methylation of adenines in DNA surrounding the native binding sites of the dam fusion partner. Because adenine methylation does not occur endogenously in most eukaryotes, it provides a unique tag to mark protein interaction sites.
A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA. Methylated DNA fragments are enriched with an antibody against N-6-methyladenine and used for further analysis.
A mutant form of DNA adenine methyltransferase (DamK9A) from E. coli is fused to the protein of interest and expressed. The fusion protein will bind to target binding sites and introduce N-6-adenine methylation in nearby sites in the genomic DNA.
tag visualisation by mutated dna adenine methyltransferase
In interference assays, the DNA will be methylated before the binding assay. Protein binding to DNA protects DNA from methylation by dimethylsulphate. If the contact points are methylated, the protein binding is prevented. After isolating the protein-DNA complex, the methylation sites are cleaved by chemical method. As a result, only those regions out of the binding sites will be cleaved. The protein binding region is not methylated; hence, this region is not cleaved. Although the pattern looks like a footprint, the blank region means "contact points".
Hydroxyl radicals are created from the Fenton reaction, which involves reducing Fe2+ with H2O2 to form free hydroxyl molecules. These hydroxyl molecules react with the DNA backbone, resulting in a break. Protein bound regions of the DNA are protected.
Ultraviolet irradiation excites nucleic acids and creates photoreactions, which results in damaged bases in the DNA strand. Protein bound regions of the DNA are protected. UV footprinting technique can detect sequence-specific protein-DNA interactions in vivo. Protein contacts can inhibit of enhance UV photoproduct formation by affecting the ability of DNA to adopt a geometry necessary for the formation of a UV photoproduct. Thus, differences in the strand-breakage patterns of protein-free and protein-bound DNA can be used to detect protein-DNA contacts.
This approach is based on the observation that a synthesized nucleic acid that is complementary to a specific mRNA can decrease the synthesis of its gene product either by increasing the degradation of the targeted mRNA or by interfering with its translation.
Identification of a part of a RNA sequence, usually then related to the full length sequence by alignment.
Reverse Transcription PCR (RT-PCR) is used for amplifying DNA from RNA. Reverse transcriptase reverse transcribes RNA into cDNA, which is then amplified by PCR.
Quantitative PCR (Q-PCR) is used to measure the quantity of a PCR product (commonly in real-time). It quantitatively measures starting amounts of DNA, cDNA, or RNA.
Technique used to measure the quantity of DNA amplified from RNA.
To perform a radioimmunoassay, a known quantity of an antigen is made radioactive, frequently by labeling it with gamma-radioactive isotopes of iodine attached to tyrosine. This radiolabeled antigen is then mixed with a known amount of antibody for that antigen, and as a result, the two chemically bind to one another. Then, a sample containing an unknown quantity of that same antigen is added. This causes the unlabeled (or "cold") antigen from the serum to compete with the radiolabeled antigen ("hot") for antibody binding sites. As the concentration of "cold" antigen is increased, more of it binds to the antibody, displacing the radiolabeled variant, and reducing the ratio of antibody-bound radiolabeled antigen to free radiolabeled antigen. The bound antigens are then separated from the unbound ones, and the radioactivity of the free antigen remaining in the supernatant is measured.
Method using an antibody coupled with some colouring agent to detect a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
Method using an antibody coupled with some colouring agent to detect a tag fused to a specific protein within a tissue sample. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
Method using an antibody coupled with some colouring agent to detect a specific protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
Method using an antibody coupled with some colouring agent to detect a specific tag fused to a protein within a cell. In some cases the primary antibody is directly linked to a colouring agent, more often the primary antibody is targeted by a secondary antibody, targeting the primary antibody.
Synthetic peptide tag (SAWSHPQFEK-(GGGS)2-SAWSHPQFEK)
Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
Two proteins of interest, a bait and prey, which are genetically fused to amino- and carboxy-terminal fragments of firefly (Photinus pyralis) luciferase, are transiently expressed. Physical interactions of these bait and prey proteins reconstitute some of the luciferase activity and result in light emission in the presence of the luciferase substrate.
split firefly luciferase complementation
Luciferase is a generic term for the class of oxidative enzymes used in bioluminescence and is distinct from a photoprotein. Luciferase catalyzes a bioluminescent reaction which requires the substrate luciferin as well as Mg2+ and ATP, produces green light with a wavelength of 562 nm.
The n-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
N-terminal fragment of renilla luciferase
The c-terminus of the renilla luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
C-terminal fragment of renilla luciferase
Firefly luciferase, is an enzyme from beetles (Photinus pyralis) catalyzing the oxidation of the lucifering pigment (reaction with ATP or oxygen) that produces light. Firefly luciferase produces a greenish yellow light in the 550-570nm range.
The c-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
C-terminal fragment of firefly luciferase
The n-terminus of the firefly luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
N-terminal fragment of firefly luciferase
Lipid binding proteins incubated with liposomes of known lipid content. Mixture is then centrifuged and proteins bound to liposomes separated out.
A fixed-size datum calculated (by using a hash function) for a molecular sequence or structure, typically for purposes of error detection or indexing.
N-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
C-terminal region of the Venus fusion protein, created by the introduction of a point mutation into Aequorea-derived YFP, the substitution of leucine for phenylalanine at position 46 (F46L). This tag is used for split flurescence complementation assays.
Fusion protein which consists of either the N- or C-terminal sequence of a fluorescent or luciferase protein. Binding of the proteins of interest enable the reassembly of the molecule, indicating that an interaction has occured.
c-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
n-terminal fragment of green fluorescent protein used as a tag in bimolecular fluorescence complementation (BiFC).
Chromosome conformation capture,[1] or 3C, is a high-throughput molecular biology technique used to analyze the organization of chromosomes in a cell's natural state. The basic 3C technique consists of cross-linking by addition of formaldehyde followed by addition of a restriction enzyme in excess to the cross-linked DNA, separating the non-cross-linked DNA from the cross-linked chromatin. A intramolecular ligation step using very low concentrations of DNA favors the ligation of relevant DNA fragments with the corresponding junctions instead of the ligation of random fragments. There are two major types of ligation junctions that are over-represented. One is the junction that forms between neighboring DNA fragments due to incomplete digestion, which represents about 20-30% of all junctions. This number is decreased by reducing the cross-linking stringency in the first step. The other type of junctions over-represented in this technique is the junction that forms when one end of the fragment ligates with the other end of the same fragment, and contributes up to 30% of all junctions formed. High temperature then results in the reversal of the previously formed cross-links. The resulting linear DNA fragment has specific restriction ends as well as a central restriction site corresponding to the site of ligation. The pool of these fragments is collectively referred to as the 3C library.
Enzyme-mediated activation of radical sources is used to identify partners of a given molecule on the cell surface in living cells Activation of the cross-linking reagent arylazide-biotin tag is accomplished by an enzyme, horseradish peroxidase is featured by radical formation of the labelling reagent by horseradish peroxidase (HRP).
enzyme-mediated activation of radical sources
The protein is expressed as a hybrid protein fused to a tag containing a luciferase activity. Subsequence observation or measurement of luciferase activity is used to identify the presence of the molecule in an interaction.
A score generated by an author, usually only relevant for that particular dataset.
MBInfo is a wiki based, multimedia, educational resource providing up to date reviews on topics relating to mechanobiology (http://www.mechanobio.info/).
Post translational modification on a protein observed to decrease the strength or rate of an interaction.
Post translational modification on a protein observed to increase the strength or rate of an interaction.
Post translational modification on a protein observed to disrupt the strength or rate of an interaction.
Formation of phosphodiester or phosphoramide ester of AMP on Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids
Tag encoding green fluorescent protein (GFP) , a TEV cleavage site, and a second purification tag such as S peptide or 6xHis. The tag can therefore be used for both localisation and affinity purification.
A polyoma virus-derived (Pyo) epitope tag (amino acids MEYMPME).
Measures the formation of a phosphodiester or phosphoramide ester of UMP and an amino acid (MOD:01166).
The formation of a phosphodiester or phosphoramide ester of UMP and amino acid (MOD:01166).
AMC (aminomethylcoumarin ) is a blue fluorescent tag with reactive derivatives that are used as contrasting probes for double- and triple-labeling in immunofluorescence microscopy, arrays and in situ hybridization and can be attached to proteins or small molecules for reaction monitoring.
An interaction between two proteins is inferred from monitoring the effect of the presence of one of them on the aggregation state of the second.
The cleavage which results due to the action of a proteolytic enzyme on its substrate.
Any feature range given should span the cleavage region e.g. 102-103 if the peptide bond between residues 102 and 103 is cut.
SILAC (Stable Isotope Labeling by Amino acids in Cell culture) can be used to detect features (typically PTMs) required for a given interaction.
Ligand binding to a target protein can stabilize a protein's native state, as shown in the increase of the bound protein's melting temperature. The midpoint of the melting curve of a protein will increase in the presence of ligands that bind more tightly to the native state than the unfolded state.
Measurment of the conversion between cis- and trans- peptide bonds formed by the amine group of a proline. Peptide bonds to proline, and to other N-substituted amino acids (such as sarcosine), are able to populate both the cis and trans isomers the cis and trans isomers of the X-Pro peptide bond (where X represents any amino acid) both experience steric clashes with the neighboring substitution and are nearly equal energetically. Hence, the fraction of X-Pro peptide bonds in the cis isomer under unstrained conditions ranges from 10-40%; the fraction depends slightly on the preceding amino acid, with aromatic residues favoring the cis isomer slightly.
The conversion between cis- and trans- peptide bonds formed by the amine group of a proline.
Heavy/light isotope-labelled subunits are prepared and allowed to form their respective mature oligomeric structure. Oligomers are then mixed and subunit exchange is monitored, usually by electrospray ionisation-ion mobility spectrometry-mass spectrometry.
mass spectrometry studies of subunit exchange
A naturally-occuring amino-acid variation to the reference sequence, including polymorphisms, variations between strains, isolates or cultivars, disease-associated mutations and RNA editing events.
A naturally-occuring amino-acid variation to the reference sequence which results in the organism developing, or becoming susceptible to a particular disease condition.
A natural change in a sequence or structure in comparison to a reference entity.
A fusion protein tag consisting of a portion of the constant region of IgG1.
A fusion protein tag consisting of a portion of the constant region of IgG2.
Monomeric far-red fluorescent protein generated from the wild-type RFP from sea anemone Entacmaea quadricolor. It possesses bright fluorescence with excitation/emission maxima at 588 and 635 nm, respectively.
IM-MS analysis is performed by first ionizing the protein complex of interest followed by ion mobility separation according to their cross-section-to-charge (Q/z) ratio. After separation, ions are sampled by a mass spectrometer and analyzed according to their mass-to-charge (m/z) ratio. Combined knowledge of both Q/z and m/z can be used to infer the size and shape of the complex.
ion mobility mass spectrometry of complexes
Measurement of the directed movement of particles in a microscopic temperature gradient. Any change of the hydration shell of biomolecules due to changes in their structure/conformation results in a relative change of movement along the temperature gradient and is used to determine binding affinities, binding kinetics and activity kinetics. Events such as the phosphorylation of a protein or the binding of small molecules to a target can be monitored.
Composed of dipyrromethene complexed with a disubstituted boron atom, typically a BF2 unit. Notable for their uniquely small Stokes shift, high, environment-independent fluorescence quantum yields.
Measurement of the catalysis of the structural rearrangement of isomers.
The catalysis of the structural rearrangement of isomers.
The catalysis of the conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2.
The catalysis othe conversion of methylmalonyl-CoA to succinyl-CoA by transfer of the carbonyl group. It requires a cobamide coenzyme. EC 5.4.99.2
Luminescent dyes such as cyanines,commonly used for DNA labelling.
Rhodamines are supplements to fluoresceins, as they offer longer wavelength emission maxima and provide opportunities for multicolor labeling or staining.
Tetramethyl rhodamine - a derivative of rhodamine.
The thiol reactive acrylodan (6-acryloyl-2-dimethylaminonaphthalene) generally reacts with thiols more slowly than iodoacetamides or maleimides, but does form very strong thioether bonds that are expected to remain stable under conditions required for complete amino acid analysis. The fluorescence emission peak and intensity of these adducts are particularly sensitive to conformational changes or ligand binding.
Pyrene is a polycyclic aromatic hydrocarbon (PAH) consisting of four fused benzene rings, resulting in a flat aromatic system. The chemical formula is C16H10. Its derivatives are valuable molecular probes via fluorescence spectroscopy, having a high quantum yield and lifetime.
Oregon Green 488 and Oregon Green 514 dyes are fluorinated analogs of fluoresceins
Interologous Interaction Database is an on-line database of known and predicted mammalian and eukaryotic protein-protein interactions.
Molecular Connections Private Limited is an in silico discovery Services Company with expertise in drug-discovery, informatics and information technology. They perform pro bono work for the IMEx Consortium. http://www.molecularconnections.com
Norwegian University of Science and Technology. www.ntnu.no/home.
In the split-ubiquitin system, two integral membrane proteins to be studied are fused to two different ubiquitin moieties: a C-terminal ubiquitin moiety (residues 35-76) and an N-terminal ubiquitin moiety (residues 1-34). These fused proteins are called the bait and prey, respectively. In addition to being fused to an integral membrane protein, the Cub moiety is also fused to a transcription factor that can be cleaved off by ubiquitin specific proteases.
A C-terminal ubiquitin moiety (cub, residues 35-76) plus a transcription factor that can be cleaved off by ubiquitin specific proteases. Regarded as attached to the bait molecules in ubiquitin reconstruction assays.
N-terminal ubiquitin moiety (nub, residues 1-34).
N-terminal ubiquitin moiety (residues 1-34) containing a Ile13Gly mutation.
An identical protein sequence is coded for by the multiple genes within the same organism. These proteins may previously be merged into a single entry by UniProt and subsequently demerged.
Contains a polyhistidine sequence, the Xpress epitope (part of bacteriophage T7 gene 10 protein) and an enterokinase cleavage site. Anti-Xpress antibodies recognise the Xpress epitope sequence found in this leader peptide. Asp-Leu-Tyr-Asp-Asp-Asp-Asp-Lys.
An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation to a severity/penetrance beyond (further from wild type) that expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < E < wt OR wt < E < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in the same direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ((a* < b < wt) OR (wt < b < a*)) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a* < b < wt OR wt < b < a* = ab where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic masking genetic interaction
An effect in which individual perturbations of two different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination is equal in severity/penetrance to the least severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab = b < wt OR wt < b = ab < a* where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic semi-suppressing converging genetic interaction
cisphenotypic semi-suppressing genetic interaction
OBSOLETE: An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are EITHER traits measured on the same quantitative scale but each significantly deviating, in opposite directions, from wild type, OR completely (qualitatively) different phenotypes), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) OR (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value, and 'a != b' indicates qualitatively different phenotypes.
An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
transphenotypic masking genetic interaction
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits that cannot be measured on the same scale and, hence, qualitatively different), and the resulting phenotype of their combination is equal to that of only one of the perturbations. This may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotypes of the individual perturbations, 'ab' is the observed phenotype of the double perturbation, 'wt' is the wild type phenotype and 'a != b' indicates qualitatively different phenotypes.
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is more severe/penetrant (further from wild type) than expected by the superimposition or addition of effects of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a* <= b < wt [E = a*] OR wt < b <= a* < ab [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic enhancing diverging genetic interaction
mutual genetic enhancement (sensu unexpected)
An effect in which the phenotype of one genetic perturbation is enhanced by a second perturbation (which, on its own, has no effect on the phenotype in question) to a severity/penetrance beyond (further from wild type) that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < a < b = wt [E = a] OR wt = b < a < ab [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
monophenotypic enhancing diverging genetic interaction
monophenotypic enhancing genetic interaction
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab <= wt) [E = a*] OR (wt < b <= a*) AND (wt <= ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic suppressing converging genetic interaction
cisphenotypic suppressing genetic interaction
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting combination is wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < ab = wt OR wt = ab < b <= a* OR a < wt = ab < b where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is less severe/penetrant than expected, but not wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (a* < ab < wt) [E = a*] OR (wt < b <= a*) AND (wt < ab < a*) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic sub-suppressing converging genetic interaction
cisphenotypic sub-suppressing genetic interaction
cisphenotypic genetic suppression (partial)
An effect in which individual perturbations of different genes result in the same mutant phenotype to varying degrees of severity/penetrance and the resulting phenotype of their combination has a phenotype more severe/penetrant than the least severe/penetrant and less severe/penetrant than the most severe/penetrant of the individual perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < b < wt [E = a*] OR wt < b < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic inter-suppressing converging genetic interaction
cisphenotypic inter-suppressing genetic interaction
An effect in which individual perturbations of two different genes result in different mutant phenotypes (which are traits measured on the same quantitative scale but each significantly deviating, in any direction, from wild type), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a != wt AND b != wt AND a != b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'wt' is the wild type phenotype value and 'a != b' indicates quantitatively different phenotypes.
OBSOLETE: An effect in which individual perturbations of two different genes result in opposite mutant phenotypes (traits measured on the same scale but each on opposing sides relative to the wild type phenotype), and the resulting phenotype of their combination is equal to that of only one of the perturbations. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (ab = a OR ab = b) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
Term replaced by http://purl.obolibrary.org/obo/MI_1276
An effect in which the observed phenotype of a double perturbation is opposite (relative to the wild type phenotype) to that which is expected upon the double perturbation. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab < wt < E OR E < wt < ab where 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is opposite (relative to wild type) to that expected from the original phenotypes. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* <= b < wt < ab [E = a*] OR ab < wt < b <= a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic super-suppressing genetic interaction
An effect in which two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is more severe than the phenotype observed with the same directionality. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < wt < b < ab OR ab < a < wt < b where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
transphenotypic enhancing genetic interaction
OBSOLETE: An effect when two individual perturbations result in opposite mutant phenotypes (relative to wild type) and their combination results in a phenotype that is intermediate to the individual mutant phenotypes, but greater or less than wild type. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a < wt < b) AND (a < ab < b) AND (ab != wt) where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
An effect in which the perturbation of one gene results in complete suppression (to wild type) of the mutant phenotype caused by perturbation of another gene. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = ab != a = E where 'a' is the observed phenotype values of an individual perturbation, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
An effect in which the perturbation of one gene results in the amelioration or lessening of the severity/penetrance of a mutant phenotype caused by perturbation of another gene, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. The phenotype of the suppressing perturbation may or may not be known. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < ab < wt [E = a*] OR wt < ab < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab <= b = wt [E = a] OR wt = b <= ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
monophenotypic suppressing converging genetic interaction
monophenotypic suppressing genetic interaction
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the complete suppression (to wild type) of the mutant phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab = b = wt [E = a] OR wt = b = ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
monophenotypic all-suppressing converging genetic interaction
monophenotypic all-suppressing genetic interaction
unilateral genetic suppression (complete)
monophenotypic genetic suppression (complete)
An effect in which the perturbation of one gene, which has no effect on the phenotype in question, is combined with the perturbation of another gene, which causes the mutant phenotype in question, and results in the amelioration or lessening of the severity/penetrance of the mutant phenotype, in effect making the organism more, but not completely, "wild type" in character with regards to the phenotype in question. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a < ab < b = wt [E = a] OR wt = b < ab < a [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
monophenotypic sub-suppressing converging genetic interaction
monophenotypic sub-suppressing genetic interaction
unilateral genetic suppression (partial)
monophenotypic genetic suppression (partial)
An effect in which the perturbation of one gene (which has no individual effect on the phenotype in question), when combined with a perturbation of another gene (which causes the phenotype in question), results in a mutant phenotype opposite (relative to wild type) to that of the original phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: E = a < b = wt < ab OR ab < wt = b < a = E where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
monophenotypic super-suppressing genetic interaction
The presence of particular residues,for example those altered through post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
The presence of amino acid residues phosphorylated as a result of post-translational modification, can be identified by amino acid analysis. Popular techniques for this include mass spectrometry or residue-specific antibodies.
A classification of the structural characteristics of a macromolecular complex.
A description of the molecule types of which a macromolecular complex is composed.
The protein chains present in the complex are not found as independent stable structures in vivo.
Protein chains present in the complex may also be found as independent stable proteins in vivo.
A stable set (2 or more) of interacting molecules which can be co-purified and have been shown to exist as a functional unit in vivo.
A macromolecular complex of which the participants associate and dissociate in vivo. Weak transient complexes feature a dynamic oligomeric equilibrium in solution where the interaction is broken and formed continuously. Strong transient associations that require a molecular trigger to shift the oligomeric equilibrium.
A group of molecules linked by a high degree of similarity of sequence and/or function and not easily separated by participant identification methods.
A group of interactors hypothesized to perform a specified function. Example: Two splice variants of Raptor mRNA encode closely related proteins. One (member) has been shown to participate in formation of active mTORC complex; the other (candidate) is thought to do so.
A group of interactors that can be counted in principle but not in practice, such as mRNA or long-chain fatty acid. Examples - ceruloplasmin mRNA, palmitic acid.
Two or more interactors, grouped to denote interchangeable function. Thus the addition of a single nucleotide residue during RNA transcription could be annotated with the definedSet NTP (members ATP, CTP, GTP, and UTP).
Used to specify the identity of the residue (or residues) introduced by mutation or variant (of child terms). The attribute would be used concurrently with the description provided in the feature name.
Hydrolytic reactions that release ADP-ribose.
Measure of hydrolytic reactions that release ADP-ribose.
Differential scanning calorimetry (DSC) is a thermoanalytical technique in which the difference in the amount of heat required to increase the temperature of a sample and reference in solution is measured as a function of temperature. By measuring the temperature dependence of this partial heat capacity, a basic thermodynamic property, DSC gives immediate access to the thermodynamic mechanism that governs a conformational equilibrium, for example between a protein complex and its individual participants.
Method allowing the detection of interactions between two or more molecules by their very close proximity or the overlap of their respective bands in a SDS gel containing urea as an additional denaturing agent.
Methods depend on a modification that only takes place with the close proximity of two molecules - a protein fused to the bait can then modify any neighbouring prey proteins, for example. The resulting tag can be used for isolation and/or identification.
A promiscuous biotin protein ligase is fused to the bait protein, neighbouring prey are then biotinylated. The biotin tag may be used for isolation and/or identification.
proximity-dependent biotin identification
The most accepted name in the literature for this complex.
A name for a complex built of the component parts of that complex.
The ELM resource provides a database of curated short linear motif classes and instances, as well as a sequence analysis tool to detect putative short linear motif instances in query sequences. http://elm.eu.org/
Any molecule that is able to transfer a sulphate group to another chemical species.
Molecule to which a sulphate group may be transferred from a sulphate donor.
Traditional yeast two hybrid assays are not suitable for the analysis of membrane proteins, as they require the interactions to occur in the nucleus. Methods have been specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners.
Upon interaction of N-terminal generated Ire1p-fusions, the Ire1p kinase domains oligomerize, transphosphorylate and activate their C-terminal RNAseL domains, which specifically splice the mRNA of a transcriptional activator, Hac1. The expression of the mature form of Hac1p leads to the interaction-specific expression of a reporter. Specifically designed to identify interactors of proteins found in the endoplasmic reticulum.
endoplasmic reticulum membrane yeast-two hybrid
The protein is expressed as a hybrid protein fused to a tag containing an alkaline phosphatase activity. Subsequent observation or measurement of alkaline phosphatase activity is used to identify the presence of the molecule in an interaction.
tag visualisation by alkaline phosphatase activity
Molecule present in media harvested from cultured cells.
Measures the rate of a sulphate molecule transfer between two molecules.
Reaction where a sulfate group is transferred between two proteins
A class of labels derived from the benzopyrone coumarin.
The thiol-reactive coumarin, CPM is very weakly fluorescent until reacted with thiols producing a conjugate with excitation/emission maxima of ~384/470 nm.
7-diethylamino-3-(4' maleimidylphenyl)-4-methylcoumarin
Fluorescent dye. Also acts as an uncoupler of oxidative phosphorylation in the mitochondria.
The Evidence Ontology (ECO) describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means.
The Cardiovascular Gene Annotation Initiative represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by the British Heart Foundation. This annotation group is a member of the IMEx Consortium.
Cardiovascular Gene Annotation Initiative
SEGUID's are SHA-1 keys written in canonical base64 form with trailing = characters removed. ROG identifiers concatenate a SEGUID with a numerical taxonomy identifier. Therefore, the allowable characters in a SEGUID or ROG identifier are (in ascending ASCII or Unicode value): +/0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz Lists of SEGUID or ROG identifiers were sorted in ascending ASCII-based lexicographical order.
A global unique identifier to identify interactions that are identical. A RIG identifier (RIGID) is constructed by concatenating ROGID MI:1335 (after sorting them in ascending lexicographical order ), applying the SHA-1 algorithm to the resulting string, converting the digest to its base64 representation and removing all trailing "=" characters used for padding.
Host-pathogen database. HPIDB integrates experimental PPIs from several public databases into a single, non-redundant web accessible resource. Manual curation is performed via the IntAct (ww.ebi.ac.uk/intact) curation interface. http://www.agbase.msstate.edu/hpi/main.html
Databases that contain information used to add additional information to experiments (meta-data).
The Experimental Factor Ontology provides a systematic description of many experimental variables, combining parts of several biological ontologies to additional new terms.
Glu-Glu-Phe epitope tag, allowing its detection with rat monoclonal antibody YL1/2
Mutated green fluorescent protein with altered net charge and thus altered intermolecular properties, such as resistence to aggregation.
A central resource of single-colony, fully-sequenced cloned human ORFs which can be readily transferred to Gateway compatible destination vectors for various functional proteomics studies. This set of ORFs ranges in size from 75 to more than 10,000 base pairs, and contains over 1,000 ORFs from genes with multiple splice variants.
Indicates that this protein is a member of a set of proteins with similar sequence and/or function.
The quartz crystal microbalance is a physical technique that detects changes in the resonance frequency of an electrically driven quartz crystal with changes in mass. It provides qualitative and quantitative information about biomolecular interactions by translating changes in mass at the probe-immobilized surface of the crystal sensor into measurable changes in the resonant frequency of the quartz crystal. QCM-D enables real-time, label free measurements of molecular adsorption and/or interactions on various surfaces and is able to monitor conformational changes upon interactions.
Quartz Crystal Microbalance with Dissipation monitoring
Regulatory subunits of enzyme complexes can determine the activity level or specificity of catalytic subunits.
A 9-amino acid peptide representing C terminus of bovine rhodopsin widely used as an epitope tag. A number of anti-rhodopsin antibodies recognize this epitope.
Database for NMR spectroscopy information on biomolecules hosted at the University of Wisconsin, Madison, US.
PRO provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities, including specific modified forms, orthologous isoforms, and protein complexes.
Orphanet is a reference portal for information on rare diseases and orphan drugs. Its aim is to help improve the diagnosis, care and treatment of patients with rare diseases.
Refers to the original experimentally verified object from which the described object has been derived.
In uracil interference assays, the DNA will be amplified by PCR in the presence of a mixture of TTP and dUTP to randomly replace thymine by deoxyuracil residues before the binding assay. If T nucleotides involved in protein-DNA interactions are replaced by deoxyuracil, protein binding is prevented. After isolating the protein-DNA complex, DNA is cleaved with uracil-N-glycosylase, which specifically targets uracil bases, and the products are electrophoresed on a denaturing polyacrylamide gel. As a result, DNA in which a thymine involved in binding is replaced by uracil will be depleted. Hence, although the pattern looks like a footprint, the blank region means "contact points".
Epitope tag engineered onto the N- or C- terminus of a protein of interest so that the tagged protein can be analyzed and visualized by immunochemical methods. The recognized AU5 epitope represents the amino acid sequence TDFYLK.
Cleavage (hydrolysis) of a lipid molecule.
Reaction monitoring the cleavage (hydrolysis) or a lipid molecule.
The protein pairs, often initially identified by a separate 2-hybrid screening methodology, are subjected to a rigorous re-analysis which may include independent re-screening of the entire search space, retesting the assay in different strain backgrounds, and multiple retesting of identified protein pairs reversing bait-prey orientations. Orthogonal data from other experimental and bioinformatic approaches may also be used to support the identification of the final high-confidence protein pairs but the primary means of selection must be experimentally based. This method would be expected to identify protein pairs with a higher degree of confidence than any single protein complementation technique.
Provides unified access to the ncRNA sequence data supplied by the expert databases.
DrugBank Accession number consisting of the 4 letter prefix and a 5 number suffix. Each Accession number is unique to the drug's generic name. The 4 letter suffix (APRD, EXPT, BIOD, NUTR) indicates the type of drug (APRD=approved small molecule drug, EXPT=experimental drug, BIOD=biotech drug, NUTR=nutraceutical or natural product). Biotech drugs consist of FDA approved peptide, protein or nucleic acid drugs, approved small molecule drugs are FDA approved non-biotech drugs, nutraceuticals are natural products (amino acids, vitamins, other metabolites) and experimental drugs include drugs under trial, pre-clinical drugs, unapproved drugs, well known inhibitors and possible toxins.
Standard name of drug or any reagent as provided by its manufacturer.
Alternate names of the drug, brand names from different manufacturers.
Brand names and composition of mixtures that include the drug described in this DrugCard file.
Description of the drug (for biotech drugs) describing its composition and/or preparation.
IUPAC or standard chemical name for a drug, or a chemical.
Chemical formula describing atomic or elemental composition
Image of the drug structure (if small molecule) or its sequence (if biotech drug)
IUPAC International Chemical Identifier (InChI) - a machine-readable character string describing a chemical structure, developed by IUPAC and the InChI Trust as a standard to allow interoperability and linking between chemical resources. The standard InChI differs from the non-standard InChI in that it is generated with a fixed set of parameters, ensuring consistency between different resources. The current version of the standard InChI software is 1.03.
Chemical Abstract Service identification number
Kyoto Encyclopedia of Genes and Genomes compound identification number (if molecule is in KEGG)
NCBI's PubChem database identification number (if molecule is in PubChem). OBSOLETE as redudant with MI:0730
Pharmacogenomics Knowledge Base identification number (if molecule is in PharmGKB)
BIND database Small Molecule Identification number (if molecule is in BIND)
May not be publicly available any more since now owned by Thompson Scientific.
The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied. Groups are considered HET if they are: - not one of the standard amino acids, and - not one of the nucleic acids (C, G, A, T, U, and I), and - not one of the modified versions of nucleic acids (+C, +G, +A, +T, +U, and +I), and - not an unknown amino acid or nucleic acid where UNK is used to indicate the unknown residue name. Het records also describe heterogens for which the chemical identity is unknown, in which case the group is assigned the hetID UNK.
Drug Identification Number (Canadian Drug ID system)
Hyperlink to RxList entry for the given drug (if it exists)
Material Safety Data Sheet (if it exists). A Material Safety Data Sheet (MSDS) is designed to provide both workers and emergency personnel with the proper procedures for handling or working with a particular substance. MSDS's include information such as physical data (melting point, boiling point, flash point etc.), toxicity, health effects, first aid, reactivity, storage, disposal, protective equipment, andspill/leak procedures. These are of particular use if a spill or other accident occurs.
number of the patent describing a drug's synthesis or use.
Molecular weight in g/mol, determined from molecular formula or sequence.
The melting point of a solid is the temperature range at which it changes state from solid to liquid.
Water/octanol partition coefficient of a small molecule.
The isoelectric point (pI) is the pH at which a particular molecule or surface carries no net electrical charge. For an amino acid with only one amine and one carboxyl group, the pI can be calculated from the pKas of this molecule.
Physical property of a molecule (known as a hydrophobe) that is repelled from a mass of water. Gravy score.
The boiling point of a liquid is the temperature at which the vapor pressure of the liquid equals the environmental pressure surrounding the liquid. A liquid in a vacuum environment has a lower boiling point than when the liquid is at atmospheric pressure. A liquid in a high pressure environment has a higher boiling point than when the liquid is at atmospheric pressure. In other words, the boiling point of liquids varies with and depends upon the surrounding environmental pressure.
SMILES string corresponding to drug structure
Type of drug (approved, experimental, biotech, nutraceutical)
Therapeutic category or general category of drug (anti-convulsant, antibacterial, etc.).
Description or common names of diseases that the drug is used to treat.
Source of further terms could be MeSH term or SNOWMAN.
Text description of how the drug works at a clinical or physiological level.
Description of how the drug works or what it binds to at a molecular level.
Determination of how quickly and how much of a drug reaches its intended target (site) of action.
The LD50 is the dose that kills half (50%) of the animals tested
Percentage of the drug that is bound in plasma proteins
The chemical conversion of drugs to other compounds in the body, excluding degradation due to any inherent chemical instability of drugs in biological media.
Rate The time it takes for the body to eliminate or breakdown half of a dose of a pharmacologic agent, in practice the time taken for plasma concentration to reduce by 50%.
How the drug is dispensed (tablets, capsules, solutions), packing material.
Information on the disease indications and treatment regime for the drug. May also include contra-indications.
Cautions or conditions indicating why or when the drug should not be taken or prescribed.
General on-line reference to other details about a drug or other bioactive entity.
chemical stability occurs when a substance is in a (dynamic) chemical equilibrium with its environment. In this well-defined state, the substance is expected to persist indefinitely (assuming that the environment does not change). A substance which is not chemically stable (yet exists) is metastable or kinetically persistent.
Potential ability of a substance to dissolve in a liquid.
Names of organisms which are affected, positively or negatively, by the drug.
Chemical and physical properties of a molecule.
Properties of a chemical tested or used as a drug, herbicide, insecticide etc.
Human artefact to describe and report the structure of a molecule.
Therapeutic category or general category of drug -anti-convulsant
Therapeutic category or general category of drug -anti-bacterial
A drug licensed for sale in the USA by the FDA.
A drug which has yet to be formally approved for the indication which it is currently being used to treat.
A natural product, such as a protein or peptide, which is produced used biotechnology as a drug.
A drug which may also be regarded as a foodstuff.
Negative decimal logarithm of Ka, acid dissociation equilibrium constant for the dissociation of a weak acid.
Quantitative prediction of this parameter is possible.
The degree of ionization refers to the proportion of neutral particles such as those in a gas or aqueous solution, that are ionized into charged particles. A low degree of ionization is sometimes called partially ionized, and a very high degree of ionization as fully ionized. This measurment is performed at pH 7.4
The LogD is the ratio of the equilibrium concentrations of all species (unionized and ionized) of a molecule in octanol to same species in the water phase at a given temperature, normally 25 C. It differs from LogP in that ionized species are considered as well as the neutral form of the molecule.pH 7.4
Diffusion coefficient D is proportional to the velocity of the diffusing particles, which depends on the temperature, viscosity of the fluid and the size of the particles according to the Stokes-Einstein relation. In dilute aqueous solutions the diffusion coefficients of most ions are similar and have values that at room temperature are in the range of 0.6x10-9 to 2x10-9 m2/s. For biological molecules the diffusion coefficients normally range from 10-11 to 10-10 m2/s.
Qualitative prediction of this parameter is possible.
The rate of dissolution is a key target for controlling the duration of a drug's effect, and as such, several dosage forms that contain the same active ingredient may be available, differing only in the rate of dissolution. If a drug is supplied in a form that is not readily dissolved, the drug may be released more gradually over time with a longer duration of action. Having a longer duration of action may improve compliance since the medication will not have to be taken as often. Additionally, slow-release dosage forms may maintain concentrations within an acceptable therapeutic range over a long period of time, as opposed to quick-release dosage forms which may result in sharper peaks and troughs in serum concentrations.
The prediction of the value for this paramter is currently not possible.
Determination of the fate of substances administered externally to a living organism i.e. the study of what the body does to a drug.
The permitting or activating of the passage of substances into, out of, or through cells.
The Volume of Distribution is the amount of drug in the body divided by the concentration in the blood. Drugs that are highly lipid soluble have a very high volume of distribution (500 litres). Drugs which are lipid insoluble remain in the blood, and have a low Vd.
Accumulation of a drug or chemical substance in various organs (including those not relevant to its pharmacologic or therapeutic action). This distribution depends on the blood flow or perfusion rate of the organ, the ability of the drug to penetrate organ membranes, tissue specificity, protein binding. The distribution is usually expressed as tissue to plasma ratios.
Algorithms have been published to predict the value of this parameter but the quality of the prediction is unknown.
Substrate of a carrier system allowing the intake of an agent into an organ or part of body.
The prediction of the value for this parameter is currently not possible.
The ratio of excretion is or measure of the speed at which a constituent is lost from the body.
The renal clearance ratio or fractional excretion is a measure of the speed at which a constituent of urine passes through the kidneys, in this context the rate at which a pharmacological agent is lost from the body via urine.
The clearance of a drug is the volume of plasma from which the drug is completely removed per unit time. The amount eliminated is proportional to the concentration of the drug in the blood.
The Maximum Absorbable Dose (MAD) represents the amount of drug that can permeate across a barrier.
Water soluble compounds are absorbed in the small intestine mainly via two pathways, the transcellular and the paracellular pathways. The paracellular absorption involves movement of solutes through a restrictive aqueous channel in the tight junctions of adjoining cells by diffusion.
Ratio between the time value at Cmax (maximum concentration) in a dose response curve, and the Cmax value itself.
Substrate for the representitive member of the ABC transprorter family ABCB1 (MDR1, pgy1, P08183). ABC transporters preventing uptake or facilitating clearance of toxic substances, playing an important role in drug excretion through the bile.
Substrate of the bile acid carrier system in both the intestinal tract and the liver. System catalyses of the transfer of bile acid from one side of the membrane to the other. Bile acids are any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
The prediction of the value for this paramater is currently not possible.
Inhibitor of one or more of the family of cytochrome p450 enzymes, probably the most important elements of oxidative metabolism of exogenous compounds.
Identification of the breakdown products of a substance, either through chemical instability or the actions of enzymes within the body
Derivative molecule which has formed from a reaction with glutathione.
Neutralization of a compound occuring via its glucuronidation or sulfatation.
neutralization by glucuronidation or sulfatation
The mechanism by which a substance can harm humans or animals.
Binds to the hERG (human Ether-a-go-go Related Gene) (Q12809) which encodes the Kv11.1 potassium ion channel responsible for the repolarizing IKr current in the cardiac action potential.
Tendency of a bioactive entity to induce damage at the level of the gene.
Tendency of a bioactive entity to induce genetic mutations at the nucleotide level e.g. substitution of nucleotide base-pairs and insertions and deletions of one or more nucleotides in DNA sequences.
Tendency of a bioactive entity to induce a cancer.
Tendency of a bioactive entity to induce damage at the level of the chromosome e.g. induce a change in chromosome structure and number.
Tendency of a bioactive entity to affect liver function.
Causes excess phospholipids to accumulate within cells.
A drug currently under clinical development.
A drug for which the licencing for prescriptive use has been withdrawn.
A drug which has not been approved for sale, a drug taken for recreational purposes or a licensed drug sold without a prescription.
Effect of additional drug treatments on a given drug action.
Effect of food ingestion on a given drug treatment.
Hyperlink to PDRhealth entry for the given drug (if it exists)
Hyperlink to wikipedia entry for the given drug (if it exists)
Solubility of a molecule in a given solvant.
Experimental derived value for the solubility of a molecule in a given solvant.
Experimentally derived value for ability of a compound to cross epithelial and endothelial cell barriers Using the CaCo2 cell line derived from a human colorectal adenocarcinoma. Used as an in vitro permeability models to predict human intestinal absorption
Reference assigned to a molecule by sequence homology with another similar sequence.
The Membrane-based Interactome Network Database (MIND) holds a network of over 25,000 putative PPI (PPPI) obtained by screening of over 3,000 unique Arabidopsis ORFs for pair-wise interactions using the yeast mating-based split-ubiquitin system (mbSUS). http://cas-biodb.cas.unt.edu/project/mind/index.php
The Arabidopsis Interactions Viewer of BAR (the Bio-Array Resource for plant biology) queries a database of 70944 predicted and 28556 confirmed Arabidopsis interacting proteins. The predicted interactions (interologs) were generated by Drs Matt Geisler and Jane Geisler-Lee at the Southern Illinois University. Their current version is Interactome 2.0. The confirmed Arabidopsis interacting proteins come from BIND, the Biomolecular Interaction Network Database, from high-density Arabidopsis protein microarrays, from Braun et al.'s Arabidopsis Interactome 2011 , from Wolf Frommer's Membrane protein INteractome Database MIND, from Etsuko Moryiama's Arabidopsis G-signaling Interactome Database, and over 1190 other literature sources. The interactions in BIND were identified using several different methods, such as yeast two hybrid screens, but also via traditional biochemical methods. http://bar.utoronto.ca/interactions/cgi-bin/arabidopsis_interactions_viewer.cgi" [PMID:15960624]
The Arabidopsis Interactome network map is a proteome-wide binary protein-protein interaction map for the interactome network of the plant Arabidopsis thaliana containing ~6,200 highly reliable interactions between ~2,700 proteins. http://interactome.dfci.harvard.edu/A_thaliana/index.php
In the kinetic exclusion assay one of the interaction components (bait) is immobilized to a solid phase (beads) and is used to capture the prey from a solution containing free molecules of both the prey and the bait that has reached kinetic equilibrium. This mixture of free components is only allowed to contact the immobilized bait for a very short time, so bait-prey complexes do not dissociate. The immobilized bait captures a small percentage of the prey, which is proportional to the free prey concentration, and the captured prey is detected usually via a fluorescent tag.
The interaction is detected through labelling of a specific site -which can be an active site- that is only accessible once the participants are interacting. This conditional site is then marked with a chemical label for detection.
Techniques based upon the measurement of the emission of one or more photons in a bioluminescent reaction. Such reactions are typically catalyzed by two groups of enzymes: photoproteins and luciferases. Photoproteins emit light in proportion to the concentration of the protein itself, while in a luciferin-luciferase reaction, photon emission is directly proportional to the amount of luciferin.
The bimolecular luminescence complementation (BiLC) is an assay for determination of protein interactions and/or their location in living cells. This approach is based on complementation between two fragments of a bioluminescent enzyme such as luciferin or aequorin. Interactions between proteins fused to each fragment bring the fragments together resulting in the reconstitution of a fully functional bioluminescent enzyme that can be identified through microscopy or luminescence detection.
bimolecular luminiscence complementation
This technology is based on quantifying the BRET between a pair of participants bearing complementation tags and a participant tagged with a bioluminescent enzyme or a fluorescent tag. The tags held by the pair of participants are complementary halves of either a fluorescent tag (N- and C- fragments of the Venus fluorescent protein, for example) or a bioluminescent enzyme (N- and C- fragments of Renilla luciferase, for example). Interaction between the pair of participants leads to reconstruction of the bioluminescent enzyme/fluorescent protein, which can then emit/accept photons that are accepted/emitted by the tag in the third participant, generating the signal used to detect the interaction. The signals emitted by the bioluminescent enzyme and the fluorescent tag have different wavelengths, so they can be distinguished.
complemented donor-acceptor resonance energy transfer
AspGD is an organized collection of genetic and molecular biological information about the filamentous fungi of the genus Aspergillus. Among its many species, the genus contains an excellent model organism (A. nidulans, or its teleomorph Emericella nidulans), an important pathogen of the immunocompromised (A. fumigatus), an agriculturally important toxin producer (A. flavus), and two species used in industrial processes (A. niger and A. oryzae). AspGD contains information about genes and proteins of multiple Aspergillus species; descriptions and classifications of their biological roles, molecular functions, and subcellular localizations; gene, protein, and chromosome sequence information; tools for analysis and comparison of sequences; and links to literature information; as well as a multispecies comparative genomics browser tool (Sybil) for exploration of orthology and synteny across multiple sequenced Aspergillus species. www.aspergillusgenome.org/
Candida Genome Database is a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database and is funded by the National Institute of Dental & Craniofacial Research at the US National Institutes of Health. www.candidagenome.org/
Community annotation portal associated with PortEco (formerly EcoliHub, http://porteco.org/). It aims to generate community-based pages about everything related to non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements. http://ecoliwiki.net/colipedia/
The GeneDB project is a core part of the Sanger Institute's Pathogen Genomics activities. Its primary goals are: -to provide reliable access to the latest sequence data and annotation/curation for the whole range of organisms sequenced by the Pathogen group. -to develop the website and other tools to aid the community in accessing and obtaining the maximum value from these data. GeneDB currently provides access to more than 40 genomes, at various stages of completion, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. www.genedb.org
Gramene is a curated, open-source, integrated data resource for comparative functional genomics in crops and model plant species. Gramene currently hosts annotated whole genomes in over two dozen plant species and partial assemblies for almost a dozen wild rice species in the Ensembl browser, genetic and physical maps with genes, ESTs and QTLs locations, genetic diversity data sets, structure-function analysis of proteins, plant pathways databases (BioCyc and Plant Reactome platforms), and descriptions of phenotypic traits and mutations. http://www.gramene.org
PomBase is a comprehensive database for the fission yeast Schizosaccharomyces pombe, providing structural and functional annotation, literature curation and access to large-scale data sets. www.pombase.org
The Arabidopsis Genome Initiative comprises TAIR, TIGR and MIPS.
Reference to the corresponding object in another database. It implies the object is part of a cross-referenced entity (usually a complex).
AgBase is a curated, open-source, Web-accessible resource for functional analysis of agricultural plant and animal gene products. Their long-term goal is to serve the needs of the agricultural research communities by facilitating post-genome biology for agriculture researchers and for those researchers primarily using agricultural species as biomedical models. They use the Gene Ontology for functional annotation. http://www.agbase.msstate.edu/
The Community Assessment of Community Annotation with Ontologies (CACAO) is a project to do large-scale manual community annotation of gene function using the Gene Ontology as a multi-institution student competition. http://gowiki.tamu.edu/wiki/index.php/Category:CACAO
Community Assessment of Community Annotation with Ontologies
Database dedicated to annotating gene function related to human fetal development using the Gene Ontology for functional annotation. http://bcb.cs.tufts.edu/dflat/
Developmental FunctionaL Annotation at Tufts
The GO Consortium coordinated an effort to maximize and optimize GO annotations for a large and representative set of key genomes, known as 'reference genomes'. The Reference Genome Annotation Project aimed to completely annotate twelve reference genomes, producing a resource that may effectively seed automatic annotation efforts of other genomes. This resource represents manual annotation from PAINT curators into the UniProt Protein2GO curation tool. http://www.geneontology.org/GO.refgenome.shtml
Collection and Refinement of Physiological Data on Mycobacterium tuberculosis in the form of GO annitations. MTBBASE data has also been rendered as pathway information in Reactome. http://www.ark.in-berlin.de/Site/MTBbase.html http://www.reactome.org/cgi-bin/eventbrowser_st_id?ST_ID=REACT_121237.1
The Parkinson's UK Gene Ontology Project represents a collaboration between University College London and the European Bioinformatics Institute (EBI), funded by Parkinson's UK. This annotation group is a member of the IMEx Consortium. http://www.ucl.ac.uk/functional-gene-annotation/neurological
Parkinsons Disease Gene Ontology Initiative
The Alzheimers-University of Toronto project adds functional annotation to Alzheimer's related gene products using the Gene Ontology. http://www.ims.utoronto.ca/
Alzheimers Project at University of Toronto
The Roslin Institute uses the Gene Ontology to add functional annotation to different gene products. http://www.roslin.ac.uk/
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) is a biochemical method used for identifying the binding sites of cellular RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs). The method relies on the incorporation of photoreactive ribonucleoside analogs, such as 4-thiouridine (4-SU) and 6-thioguanosine (6-SG) into nascent RNA transcripts by living cells. Irradiation of the cells by UV light of 365 nm induces efficient crosslinking of photoreactive nucleoside-labeled cellular RNAs to interacting RBPs. Immunoprecipitation of the RBP of interest is followed by isolation of the crosslinked and coimmunoprecipitated RNA. The isolated RNA is converted into a cDNA library and deep sequenced using next-generation sequencing technology. http://en.wikipedia.org/wiki/PAR-CLIP
Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation
Low-affinity interaction detection method designed specifically to detect interactions between extracellular proteins. Recombinant soluble fragments of these proteins are produced in a (generally) mammalian expression cell line and secreted into the medium and produced in two forms: a biotinylated bait which can be captured on a streptavidin-coated solid phase suitable for screening, and a pentamerised enzyme-tagged (beta-lactamase) prey. The bait and prey proteins are presented to each other in a binary fashion to detect direct interactions between them, similar to a conventional ELISA. The pentamerisation of the proteins in the prey is achieved through a peptide sequence from the cartilage oligomeric matrix protein (COMP) and increases the local concentration of the ectodomains thereby providing significant avidity gains to enable even very transient interactions to be detected. By normalising the activities of both the bait and prey to predetermined levels prior to screening, interactions having monomeric half-lives of 0.1 sec can be detected with low false positive rates.
AVidity-based EXtracellular Interaction Screen
Non-protein coding transcripts longer than 200 nucleotides and that can be involved in a number of functions, like transcription, post-translational and epigenetic regulation. Most lncRNAs do not have a known function so far.
Combination of cross-linking and co-immunoprecipitation aimed to find protein-RNA interactions. The canonical method uses first a cross-linking procedure over a tissue sample or lysate, and the immunoprecipitated with specific antibodies for the protein of interest. Unspecific proteins are digested via proteinase K treatment. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA. https://en.wikipedia.org/wiki/CLIP
This method combines UV cross-linking and immunoprecipitation with high-throughput sequencing to identify binding sites of RNA-binding proteins. https://en.wikipedia.org/wiki/HITS-CLIP
UV cross-linking immunoprecipitation combined with high-throughput sequencing
iCLIP allows for the stringent purification of UV cross-linked protein-RNA complexes, using immunoprecipitation followed by SDS-PAGE and membrane transfer. The radiolabelled protein-RNA complexes are then excised from the membrane, and treated with proteinase to release the RNA. This leaves one or two amino acids at the RNA cross-link site. The RNA is then reverse transcribed using barcoded primers. Because reverse transcription stops prematurely at the cross-link site, iCLIP allows RNA-protein interaction sites to be identified at high resolution. https://en.wikipedia.org/wiki/ICLIP
individual-nucleotide resolution cross-linking and immunoprecipitation
Combination of UV cross-linking and affinity purification where the protein of interest bears a tag used for pull-down or immunoprecipitation. As in CLIP, unspecific proteins are digested via proteinase K treatment and RNAs are tagged with oligonucleotide linkers. RNA can be then identified via Northern blotting or using RT-PCR and then sequencing of the generated cDNA.
This method is a variation of CRAC where after combined cross-linking and affinity purification of protein-RNA complexes, RNA-RNA interactions are specifically detected. Base-paired RNA molecules can be linked together while tagging RNA with oligonucleotides, generating chimeric RNAs that allow identification of RNA-RNA pairs.
cross-linking, ligation, and sequencing of hybrids
A method that monitors ligand binding by measuring the change in frequency of a quartz crystal resonator resulting from the addition or removal of a small mass of a ligand specifically binding at the surface of the resonator.
An assay that uses molecular probes, such as ions, small molecules or antibodies to monitor interactions between biomolecules under study.
The interaction is inferred from the effect it exerts on specific chemical labelling of one of the interacting partners.
The interaction is detected through selective, chemical blockage of a specific site -which can be an active site- that becomes inaccessible once the participants are interacting. The interaction is detected through loss of signal of the chemical label
PRIMESDB is a systems biology platform that is developed to enable the collection, integration and analysis of state-of-the-art genomics, proteomics and mathematical modelling data being generated by the PRIMES project. PRIMES iinvestigates the role of protein interaction machines in oncogenic signalling with a particular focus on the EGFR network. PRIMESDB provides a centralised knowledgebase and analysis platform for cancer protein interaction networks. http://primesdb.eu/
Chemical alterations occurring at the nucleotide level in the specific DNA molecule involved in an interaction. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification.
Chemical alterations occurring at the nucleotide level in the specific RNA molecule involved in an interaction. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation).
Primer extension can be used to determine the 3' end of a given sequence of RNA. This technique requires a radiolabelled primer which is complementary to a region near the 3' end of the RNA. The primer is allowed to anneal to the RNA and reverse transcriptase is used to synthesize a strand of DNA from the RNA until it reaches the 5' end of the RNA. By denaturing the hybrid and using the extended primer DNA strand as a marker on an electrophoretic gel, it is possible to determine the transcriptional start site.
A micro RNA (abbreviated miRNA) is a small non-coding RNA molecule (containing about 22 nucleotides) found in plants, animals, and some viruses, which functions in RNA silencing and post-transcriptional regulation of gene expression.
The PIR-International Protein Sequence Database (PIR-PSD) was the world's first database of classified and functionally annotated protein sequences that grew out of the Atlas of Protein Sequence and Structure (1965-1978) edited by Margaret Dayhoff. Produced and distributed by the Protein Information Resource in collaboration with MIPS (Munich Information Center for Protein Sequences) and JIPID (Japan International Protein Information Database), PIR-PSD has been the most comprehensive and expertly-curated protein sequence database in the public domain for over 20 years. In 2002, PIR joined EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics) to form the UniProt consortium. PIR-PSD sequences and annotations have been integrated into UniProt Knowledgebase. Bi-directional cross-references between UniProt (UniProt Knowledgebase and/or UniParc) and PIR-PSD are established to allow easy tracking of former PIR-PSD entries. PIR-PSD unique sequences, reference citations, and experimentally-verified data can now be found in the relevant UniProt records. Legacy data can be found at http://pir.georgetown.edu/pirwww/dbinfo/pir_psd.shtml
Chemical modification observed on a nucleic acid molecule in the context of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
observed nucleic acid chemical modification
Chemical modification observed on an RNA molecule resulting subsequently of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
resulting nucleic acid chemical modification
Chemical modification observed on a nucleic acid molecule required for an interaction to occur. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
prerequisite-nucleic acid chemical modification
Chemical modification observed on a nucleic acid molecule observed to decrease the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
nucleic acid chemical modification decreasing an interaction
Chemical modification observed on a nucleic acid molecule observed to disrupt an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
nucleic acid chemical modification disrupting an interaction
Chemical modification observed on a nucleic acid molecule observed to increase the strength or rate of an interaction. Modifications involving full nucleotide substitutions/deletions are excluded from this definition.
nucleic acid chemical modification increasing an interaction
The ProteomeXchange consortium was set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. The data is actually hosted by consortium member databases like PeptideAtlas or PRIDE. http://www.proteomexchange.org
Super-resolution microscopy is a form of light microscopy that allows images to be taken with a higher resolution than the diffraction limit. Several different methods can be used to achieve beyond-diffraction limit resolution and these can be broadly divided in two categories: "true" super-resolution techniques, which capture information contained in evanescent waves, and "functional" super-resolution techniques, which use clever experimental techniques and known limitations on the matter being imaged to reconstruct a super-resolution image.
SIGNOR, the SIGnaling Network Open Resource, organizes and stores in a structured format signaling information published in the scientific literature. The captured information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. The signaling information is mapped to the human proteome even if the experimental evidence is based on experiments on mammalian model organisms.
This method allows screening of a full matrix of protein pairs in a single multiplexed strain pool. A doubly engineered clone pool is prepared so that each clone bears two distinct DNA barcodes flanked by site specific recombination sequences. Positive bait-prey combinations allow activation of reporter genes and their respective barcodes undergo recombination, creating unique barcode combinations. Recombined barcode tags are then fused, extracted and sequenced for identification of interacting pairs.
Measurement of de-AMPylation, the removal of a phosphodiester or phosphoramide ester of AMP from Tyr (RESID:AA0203), Lys (RESID:AA0227), Thr (RESID:AA0267), His (RESID:AA0371) and other amino acids.
The c-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
The n-terminus of a luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
Gaussia luciferase, is an enzyme from the crustacean Gaussia princeps catalyzing the oxidation of coelenterazine to coelenteramide that produces light. Gaussia luciferase produces a blue light around the 480 nm range.
The c-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
The n-terminus of the gaussia luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
Socio-affinity index provides a single measure of the association between each pair of proteins based on an entire AP-MS dataset, considering both the spoke (when one protein retrieves another when tagged) and the matrix (when two proteins are retrieved by another) evidence, and the overall frequency of each protein in the data set.
This method measures co-purification of proteins through several orthogonal purification steps, deriving a set of correlation measures that are then computationally weighted and combined to infer interacting pairs.
inference by quantitative co-purification
quantitative tagless co - purification
In this method predicted RNA-RNA pairings are tested by knocking down one of the two interacting RNAs and then experimentally determine if its presence is required for the other to be chemically modified.
chemical rna modification plus base pairing prediction
ZINC is a database of commercially available compounds for virtual screening. It uses publicly available bioactivity data to allow investigators to access chemical tools for biology. http://zinc15.docking.org/
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that does not have any effect over an interaction when compared with the wild-type.
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that enables an interaction when compared with the wild-type, which does not interact.
Interactions and complexes curated by scientists at the Central European Institute of Technology (CEITEC).
Central European Institute of Technology
Interaction between a nucleic acid and a gene region.
Interaction between a nucleic acid and a corresponding nucleic acid.
This approach infers interacting pairs of proteins looking at expression data coming from transcript expression datasets. Co-expressed pairs of genes are ranked and predicted to be interacting proteins as well.
A particular way two or more molecules influence one another.
Binary causative relationships between biological entities. CV terms belonging to this term allow the description of causal interactions using the current PSI-MI schema.
The effect of modulator entity A on a modulated entity B.
The effect of a modulator entity A on a modulated entity B that increases the concentration and/or frequency and/or rate and/or extent of the molecular function of B.
The effect of a modulator entity A on a modulated entity B that increases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B.
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B, by promoting its gene expression.
The effect of a modulator entity A on a modulated entity B that increases the concentration of the modulated entity B by preventing its degradation.
The effect of a modulator entity A on a modulated entity B that decreases the concentration and/or frequency and/or ate and/or extent of molecular function of B.
The effect of a modulator entity A on a modulated entity B that decreases the frequency, rate or extent of the molecular function of B, an elemental biological activity occurring at the molecular level, such as catalysis or binding (GO:0044093).
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B.
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B, by preventing its gene expression.
The effect of a modulator entity A on a modulated entity B that decreases the concentration of the modulated entity B by promoting its degradation.
down-regulates quantity by destabilization
Type of relationship between entities involved in a causal interaction. This term is to be used only to describe the effect of a modulator entity A on a modulated entity B when A is not immediately upstream of B.
The effect of a modulator entity A on a modulated entity B that occurs when A is not immediately upstream of B.
Any process that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA.
Any process that control gene expression at the RNA level, between the transcription and the translation of the gene.
The effect of a modulator entity A on a modulated entity B that occurs when A is immediately upstream of B.
Direct binding of a DbTF to a DNA regulatory sequence that modulates the frequency, rate or extent of the chemical reactions resulting in the transcription of DNA to RNA and gene activity regulation.
transcriptional regulation by direct binding of dbTF to DNA regulatory element
The process mediated by guanine nucleotide exchange factors (GEFs) that catalyze the exchange of bound GDP with cytosolic GTP.
guanine nucleotide exchange factor reaction
A family of cellular proteins able to increases the activity of a GTPase.
The effect of a chemical compound that results in the activation or in an increased activation of a target molecule.
The effect of a chemical compound that stops, prevents, or reduces the activity of a target molecule.
Any process that modulates the frequency, rate or extent of any process in which a cell, a substance, or a cellular entity is transported to, or maintained in, a specific location.
The chemical reactions and pathways resulting in the formation, breakdown, modification of small molecules.
Molecule that encompasses any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity, which is not physiologically part of a cell, tissue, organ, or organism.
Entity involved in a causative relationship. These terms have to be used as interactor types only if associated with causal statements.
Any detectable change in the internal or external environment of a cell, tissue, organ, or organism.
Cellular phenotype is the conglomerate of multiple cellular processes involving gene and protein expression that result in the elaboration of a cell's particular morphology and function.
The modification of a subsequence that regulates the concentration and/or frequency and/or rate and/or extent of the molecular function of an entity.
CAUTION: This is a temporary branch. These terms will be soon added in the PSI-MOD ontology and this branch will became obsolete.
Reaction that create a covalent bond between a nitrogen monoxide group and the thiol group of cysteine.
A protein modification that effectively add a tyrosine residues to the c-terminal end of alpha-tubulin.
A protein modification that effectively remove an acyl group from a protein.
A protein modification that effectively remove a phosphate group from a protein by hydrolysis.
A protein modification that effectively cleaves the G-K bond and releases SUMO proteins.
A protein modification that effectively removes one or more methyl groups from a protein.
A protein modification that effectively cleaves the G-K bond and releases ubiquitin or ubiquitin like proteins.
SignaLink 2.0 is a signaling pathway resource with multi-layered regulatory networks. http://signalink.org
EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. http://edamontology.org/
Reversible reaction that add a tyrosine residue to an amino-acid.
Reversible reaction that add a tyrosine residues to the c-terminal end of alpha-tubulin.
Entity whose activity exerts an effect on the concentration, frequency, rate or extent of the target entity.
Entity whose concentration, frequency, rate or extent are regulated by the regulator entity.
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification.
This method uses Cre recombinase as a two-hybrid protein-protein interaction reporter that functions intracellularly to covalently and unidirectionally link interacting bait and prey plasmids via specialized loxP sites that flank the protein-coding sequences. The linked protein-coding sequences serve as interaction-identifying DNA molecules that enable massively multiplexed screening coupled with next-generation DNA sequencing to detect protein-protein interactions.
Length of a repetitive polymer chain. Applicable to carbohydrates and other non-protein, non-nucleic acid polymers.
The Complex Portal is a manually curated, encyclopaedic resource of macromolecular complexes from a number of key model organisms, entered into the IntAct molecular interaction database . Data includes protein-only complexes as well as protein-small molecule and protein-nucleic acid complexes. All complexes are derived from physical molecular interaction evidences extracted from the literature and cross-referenced in the entry, or by curator inference from information on homologs in closely related species or by inference from scientific background. All complexes are tagged with Evidence and Conclusion Ontology codes to indicate the type of evidence available for each entry.
Reaction in which an amide functional group in the side chain of the amino acids asparagine or glutamine is removed or converted to another functional group. Typically, asparagine is converted to aspartic acid or isoaspartic acid and glutamine is converted to glutamic acid or pyroglutamic acid (5-oxoproline).
Assay to measure the catalysis of the reaction: a monocarboxylic acid amide + H2O = a monocarboxylate + NH3.
Complex object unique primary identifier that is assigned to a complex in the Complex Portal.
Southwestern blotting, is a lab technique which involves identifying and characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes, generally radioactively labeled. The proteins are separated by gel electrophoresis and are subsequently transferred to nitrocellulose membranes similar to other types of blotting.
Indicates that the cross-referenced molecule is a component of a containing complex.
The method is based on the functional effect of the binding of the microRNA on the target (mRNA or LncRNA), which is the repression of the expression of the target. To validate a sequence as a direct target of a microRNA, a luciferase reporter gene carrying the wt candidate sequence or its mutated form is used, and the expression of the target is evaluated with a luciferase assay. If the wt is significantly less expressed than the mutant, the binding occurs.
miRNA interference luciferase reporter assay
Binary relationship between biological entities when one of them modulates the other in terms of function, expression, degradation or stability of the other and the relationship between the partners cannot be ascertained as direct, so intermediate steps are implicitly present. This relation specifically does not imply a physical interaction between the entities involved.
Identity of the participant was established (or confirmed) by fitting its molecular model to the experimentally determined electron density.
identification by structure determination
DAP-seq is an in vitro TF-DNA binding assay in which a DAP-seq gDNA library is prepared by attaching a short DNA sequencing adaptor onto purified and fragmented gDNA. In a separate reaction, an affinity-purified TF is prepared by in vitro expression, bound to ligand-coupled beads, and washed to remove non-specific cellular components. The gDNA library is added to the affinity-bound TF and the unbound DNA is washed away. The bound fraction is eluted, amplified with PCR primers to introduce an indexed adaptor, and the DNA is sequenced.
The bait fused to a viral protein (e.g. HIV-1 GAG protein) allows the trapping of interaction partners (preys) within virus-like particles (VLPs) that bud from mammalian cells. Once the VLPs are enriched and purified, this technique allows the isolation of multimeric complexes as well as binary interactions and their subsequent identification by methods such as MS and western blots.
Optical tweezers are instruments that use a focused laser beam to apply force to particles suspended in a liquid medium. This allows to measure forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
Molecules adsorbed on a solid surface are picked up by a microscopic tip (nanometers wide) that is located at the end of an elastic cantilever. Piezoelectric controller is used to measure forces generated by single molecules or molecular complexes stretched between the substrate and the cantilever tip.
Magnetic tweezers are instruments that use a set of magnets to apply forces to physically hold and move individual molecules attached to ferromagnetic beads. Such instruments allow to measure the forces generated between interacting molecules - either at the level of just single interacting pair of molecules or at the level of larger molecular assemblies.
Term describing the upstream end of a nucleotide sequence.
Term describing the upstream region of a nucleotide sequence, exact coordinates not available.
Term describing the downstream end of a nucleotide sequence.
Term describing the downstream region of a nucleotide sequence, exact coordinates not available.
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that enables an interaction when compared with the unaltered carbohydrate, which does not interact.
carbohydrate chemical modification causing
carbohydrate chemical modification causing an interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that does not have any effect over an interaction when compared with the unaltered form.
carbohydrate chemical modification not affecting interaction
carbohydrate chemical modification with no effect
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
carbohydrate chemical modification decreasing
carbohydrate chemical modification decreasing interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
carbohydrate chemical modification decreasing rate
carbohydrate chemical modification decreasing interaction rate
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that decreases significantly interaction strength when compared with the unaltered carbohydrate.
carbohydrate chemical modification decreasing strength
carbohydrate chemical modification decreasing interaction strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
carbohydrate chemical modification disrupting
carbohydrate chemical modification disrupting interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction strength when compared with the unaltered carbohydrate.
carbohydrate chemical modification disrupting strength
carbohydrate chemical modification disrupting interaction strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
carbohydrate chemical modification disrupting rate
carbohydrate chemical modification disrupting interaction rate
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
carbohydrate chemical modification increasing
carbohydrate chemical modification increasing interaction
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction strength when compared with the unaltered carbohydrate.
carbohydrate chemical modification increasing strength
carbohydrate chemical modification increasing interaction strength
Chemical alterations occurring in the specific carbohydrate molecule involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the unaltered carbohydrate.
carbohydrate chemical modification increasing rate
carbohydrate chemical modification increasing interaction rate
Carbohydrate species chemically attached to proteins, or other organic molecules.
Specific carbohydrate species can be represented through the MOD ontology and their representation escapes the scope of this CV.
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that enables an interaction when compared with the non-glycosylated molecule, which does not interact.
attached carbohydrate causing an interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that has no effect over an interaction when compared with the non-glycosylated molecule, which does not interact.
attached carbohydrate not affecting interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
attached carbohydrate decreasing interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
attached carbohydrate increasing interaction
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction strength when compared with the non-glycosylated molecule.
attached carbohydrate increasing strength
attached carbohydrate increasing interaction strength
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that increases significantly interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
attached carbohydrate increasing interaction rate
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
attached carbohydrate disrupting interaction rate
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength when compared with the non-glycosylated molecule.
attached carbohydrate disrupting strength
attached carbohydrate disrupting interaction strength
Carbohydrate species chemically attached to proteins, or other organic molecules involved in an interaction that disrupts interaction strength or rate (in the case of interactions inferred from enzymatic reaction) when compared with the non-glycosylated molecule.
attached carbohydrate disrupting interaction
A technique that measures forces generated by interactions between molecules.
A technique that measures interaction force between two surfaces as they are brought together and retracted.
The Alzheimer's Research UK Gene Ontology Project represents a collaboration between University College London, the European Bioinformatics Institute (EBI) and the University of Manchester, funded by Alzheimer's Research UK. This annotation group is a member of the IMEx Consortium. www.ucl.ac.uk/functional-gene-annotation/neurological
Alzheimer's Research UK Gene Ontology Project
High-throughput (a.k.a. "next-generation") sequencing applies to methods that allow for sequencing of genome-scale number of bases.
This method generates several billion bases of accurate nucleotide sequence per experiment at low cost. Single molecules of DNA are attached to a flat surface, amplified in situ and used as templates for synthetic sequencing with fluorescent reversible terminator deoxyribonucleotides. Images of the surface are analysed to generate high-quality sequence.
KISS (KInase Substrate Sensor) is a protein complementation technology that allows in situ analysis of protein-protein interactions in intact mammalian cells. In this method, which is derived from MAPPIT (mammalian protein-protein interaction trap), the bait protein is coupled to the kinase domain of TYK2, while the prey protein is fused to a fragment of the gp130 cytokine receptor chain. Bait and prey interaction leads to phosphorylation of the gp130 anchor by TYK2, followed by recruitment and activation of STAT3, resulting in transcription of a STAT3-dependent reporter system. This approach enables the identification of interactions between proteins, including transmembrane and cytosolic proteins, and their modulation in response to physiological or pharmacological challenges.
dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations and clinical mutations.
NanoLuc luciferase (Nluc) is a small (19 kDa), highly stable, ATP independent, bioluminescent protein derived from the luciferase complex of the deep-sea shrimp O. gracilirostris.
The n-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
N-terminal fragment of nanoluc luciferase
The c-terminus of the nanoluc luciferase protein, fused to a protein of interest for use in the split luciferase complementation assay.
C-terminal fragment of nanoluc luciferase
The SNAP-tag protein is an engineered version of the ubiquitous mammalian enzyme AGT, encoded in humans by the O-6-methylguanine-DNA methyltransferase (MGMT) gene. The tag is a 182 residues polypeptide with self-labeling activity that accepts O6-benzylguanine derivatives.
Hydrophobic interaction chromatography (HIC) separates proteins according to differences in their surface hydrophobicity by utilizing a reversible interaction between these proteins and the hydrophobic surface of a HIC matrix.
Covalent attachment of the small ubiquitin-like modifier (SUMO) protein as a fusion protein.
A bacteriophage library of genes encoding proteins or peptides fused to a phage coat protein that are expressed on the surface of the phage virion.
Paramagnetic molecule formed by a gadolinium complex based on 4-mercaptomethyl-dipicolinic acid (4MMDPA) attached to a cysteine side chain.
A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event that has a complex effect over the interaction when compared with the wild-type. A complex effect is such that cannot be described in increasing, decreasing, causing, disrupting or no effect terms.
Fluorophore or luminiscence source which emits electromagnetic radiation of given wavelength.
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor, then re-emit its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore it self.
Pair of luminescence donor-fluorophore or fluorophores attached to the same molecule used in a bret or fret experiment to observe the details of conformational changes.
Luminiscence source which emits electromagnetic radiation of given wavelength through a chemical process.
Three-dimensional (3D) reconstruction of single, transparent objects from a series of projection images from a tilt series recorded with a transmission electron microscope.
Three-dimensional (3D) reconstruction of single, transparent objects from a collection of images of randomly oriented particles recorded with a transmission electron microscope.
electron microscopy 3D single particle reconstruction
Three-dimensional (3D) reconstruction of helical objects from a collection of fiber images recorded with a transmission electron microscope.
electron microscopy 3D helical reconstruction
Fluorophore able to absorb the electromagnetic radiation at given wavelength from a specific luminescence donor and then act as a donor via re-emission of its own characteristic fluorescence. The luminescence donor may or may not be a fluorophore itself.
Reference to the corresponding object in another database. Correspondence is partial, so the objects are similar but explicitly not identical.
Coordinates of a reference DNA sequence in the genome, providing information about the chromosome name, start and end of the sequence, optionally including the strand as well if it applies.
Rhea is an expert curated resource of biochemical reactions designed for the annotation of enzymes and genome-scale metabolic networks and models. Rhea uses the ChEBI (Chemical Entities of Biological Interest) ontology of small molecules to precisely describe reactions participants and their chemical structures. All reactions are balanced for mass and charge and are linked to source literature, metabolic resources and other functional vocabularies such as the enzyme classification of the NC-IUBMB.
The protein is fused to a 12-residue peptide segment (GVAMPGAEDDVV) derived from human podoplanin PLAG domain for which antibodies are available.
Protein is fused to a 21 amino acid residues-long peptide (YPGQYPGQYPGQYPGQYPGQV) derived from human PAR-4 N-terminal peptide. The final sequence of the peptide resulted from optimization involving mutagenesis and repetition of the original reference sequence in order to maximize affinity with the P20.1 antibody.
tandemly-arranged recognition motif combined with gentle elution technology tag
bioRxiv is a free online archive and distribution service for unpublished preprints in the life sciences, operated by Cold Spring Harbor Laboratory. Articles are not peer-reviewed, edited, or typeset before being posted online. http://biorxiv.org/
In sequential BRET-FRET (BRET combined with FRET) bioluminiscence generated by a luciferase triggers acceptor excitation by BRET and subsequent energy transfer to a FRET acceptor. This technique can identify multimolecular complexes through detection of the resulting fluoresecence.
ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. https://www.ncbi.nlm.nih.gov/clinvar
EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images. The purpose of EMPIAR is to provide easy access to state-of-the-art raw data to facilitate methods development and validation, which will lead to better 3D structures. It complements the Electron Microscopy Data Bank (EMDB), where 3D volumes are stored, and uses the fault-tolerant Aspera platform for data transfers. https://www.ebi.ac.uk/empiar
Electron Microscopy Public Image Archive
A gene whose genetic perturbation enhances the phenotype resulting from a different genetic perturbation.
A gene whose genetic perturbation phenotype is enhanced by a different genetic perturbation.
A gene whose genetic perturbation masks the phenotype resulting from a different genetic perturbation.
A gene whose genetic perturbation phenotype is masked by a different genetic perturbation.
Measurement of the substraction of one or more ADP-ribose moieties to molecules.
Involves the substraction of one or more ADP-ribose moieties to proteins. Reaction that can affect Arg, Cys, Glu, Arg and Asn residues.
This parameter represents the rate of the reaction at negligible substrate concentration, indicating how the velocity varies according to how often enzyme and substrate combine.
A searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. Homepage: http://www.mirbase.org/
RNA that consists of two base pairing strands. The 2 nucleotide chains are held together by hydrogen bonds between base pairs of nucleotides.
Protein is fused to beta-galactosidase, and the measure of this enzyme activity can be taken as indicative of presence of protein.
Bait protein is fused to a standard protein fusion tag and an intein fragment, prey a with a different protein fusion tag and the complementary intein fragment. The bait and prey are co-expressed in a cell line where the association of bait and prey brings the intein fragments into close proximity, allowing them to reconstitute a fully functional intein, which then catalyzes its own excision and the concurrent ligation of the bait and the prey peptides (as well as the standard protein fusion tags). The resulting spliced protein can be resolved by regular western blot analysis due to its altered mobility, while the presence of the standard protein fusion tags allows visualization or purification of protein using regular biochemical techniques.
Intein C-terminal fragment tag, commonly used in SIMPL and related methods.
Intein N-terminal fragment tag, commonly used in SIMPL and related methods.
Coincident occurrence of molecules within very close proximity (in the nanometer range), detected through molecule-level resolution methodology, but from which a physical interaction among those molecules cannot be inferred.
FluoPPI system (Fluorescent Protein-Protein Interaction-visualization):-FLUOPPI utilises the formation of fluorescence foci whereby the interacting proteins of interest are genetically fused with either a tetramerizing fluorescent protein (FP-tag) or an assembly helper tag (Ash-tag). The incorporation of these tags onto a pair of interacting proteins enables the formation of intensely bright foci when co-expressed in mammalian cells. In these foci the FP-tag induces the fused protein to form a tetramer that can now interact with up to 4 copies of the Ash-tagged partner protein. The cognate interacting protein also forms an oligomer through the Ash tag, which in turn can interact with multiple copies of the FP-fused partner protein. The potential of both constructs to interact with multiple copies of each other enable large foci incorporating the fluorescent protein to form, which can be clearly observed when imaging the cell.
fluorescent protein-protein interaction-visualization
The phenotype outcome resulting from two or more genetic perturbations to an organism, individually and in combination.
A multigenic phenotype result in which the phenotype of a single genetic perturbation has been modified by the introduction of one or more additional genetic perturbations.
genetic interaction (sensu phenotype modification)
Genetic perturbation of multiple genes in combination that results in a more severe phenotype (except lethality or growth defect) than individual genetic perturbations.
Mutation of multiple genes in combination that results in a more severe growth defect than from individual mutation.
Mutation of multiple genes in combination that results in lethality when individual single mutations are viable.
Genetic perturbation of multiple genes in combination that results in a less severe phenotype than from individual perturbations. This term is reserved for high throughput studies with scores.
positive genetic interaction (sensu BioGRID)
Genetic perturbations of multiple genes in combination that results in a more severe growth defect than each individual perturbation, when one mutation is hemizygous.
synthetic haploinsufficiency (sensu BioGRID)
Genetic perturbation of multiple genes in combination that results in a more severe phenotypic defect (or lethality) than from individual viable perturbations. This term is reserved for high throughput studies with scores.
negative genetic interaction (sensu BioGRID)
Genetic perturbation of one gene suppresses a phenotype (other than lethality or growth defect) associated with perturbation of another gene.
Mutation of one gene rescues lethality or a growth defect associated with perturbation of another gene.
Increased dosage of one gene rescues lethality or a growth defect associated with perturbation of another gene.
Increased dosage of one gene causes lethality in combination with another viable genetic perturbation.
Increased dosage of one gene causes a growth defect in (or enhances an existing growth defect of) a strain with perturbation of another gene.
A genetic phenotype modification whereby one genetic perturbation suppresses, or alleviates, the phenotype of another genetic perturbation. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result.
A genetic phenotype modification whereby one genetic perturbation enhances, or exacerbates, the phenotype of another genetic perturbation. Note that this may be an expected result.
A phenotype result in which each of multiple perturbations results in no (or only a minimal) phenotype for the phenotype in question.
A phenotype result in which only one of multiple perturbations results in the phenotype in question.
The expression of a phenotype in an organism or a population of organisms resulting from one or more organismal perturbations, including genetic perturbations and environmental (including chemical/drug exposure) perturbations.
A phenotype result in which multiple perturbations affect an organism individually and in combination.
A phenotype result in which both of two perturbations result in the phenotype in question and do so in the same manner compared to wild type. For example, both perturbations result in an increased quality phenotype, or both perturbations result in a decreased quality phenotype.
A cisphenotypic phenotype result in which both of two perturbations result in the same phenotype, both in manner and degree, compared to wild type.
A phenotype result in which two perturbations result in the opposite phenotype compared to wild type. For example, one perturbation results in an increased quality phenotype and the second perturbation results in a decreased quality phenotype.
A genetic phenotype modification whereby introduction of one genetic perturbation to another genetic perturbation results in the opposite phenotype compared to the phenotype of the starting individual genetic perturbation. For example, one perturbation results in an increased quality phenotype and introduction of the second perturbation results in a decreased quality phenotype. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result.
A genetic phenotype modification whereby each of two genetic perturbations suppress, or alleviate, the phenotype of the other genetic perturbation. Note that if the individual genetic perturbations have opposite phenotypes, this may be an expected result.
A genetic mutual suppression in which each genetic perturbation results in opposite phenotypes (for example, one genetic perturbation results in an increased quality phenotype and the second genetic perturbation results in a decreased quality phenotype), and their combination (the double genetic perturbation) results in an intermediate phenotype that is at least closer to wild type than the most severe phenotype of the individual genetic perturbations. Note that the double genetic perturbation phenotype may be expected according to some chosen neutrality function.
transphenotypic suppressing genetic interaction
A transphenotypic suppression in which the double genetic perturbation phenotype is equivalent to the wild type (or control) phenotype.
transphenotypic all-suppressing genetic interaction
transphenotypic genetic suppression (complete)
A genetic enhancement in which the double genetic perturbation phenotype is equivalent to the expected phenotype, according to some chosen neutrality function.
cisphenotypic enhancing neutral genetic interaction
A transphenotypic suppression in which the double genetic perturbation phenotype is expected, according to some chosen neutrality function.
transphenotypic suppressing neutral genetic interaction
transphenotypic genetic suppression (expected)
An effect in which two genetic perturbations, when combined, result in a fitness that is less than expected given the fitness resulting from the individual perturbations.
Negative genetic interactions describe double mutants whose phenotype is stronger than expected (66, 77) (Figure 1b).
Negative interactions (also called aggravating or synergistic interactions) describe double mutants exhibiting a more severe phenotype than expected, such as synthetic sickness or synthetic lethality (35, 49) (Figure 2a).
An effect in which two genetic perturbations, when combined, result in a fitness that is greater than expected given the fitness resulting from the individual perturbations.
Positive genetic interactions define double mutants whose phenotype is less severe than expected based on single-mutant phenotypes (30, 66, 87) (Figure 1c,d).
Positive interactions describe double mutants exhibiting a less severe phenotype than expected from the multiplicative model. Positive interactions have also been referred to as alleviating or epistatic interactions.
An effect in which individual perturbations of different genes result in the same mutant phenotype (but, perhaps, to varying degrees of severity/penetrance) and the resulting phenotype of their combination is equivalent to the wild type phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: (a* <= b < wt) AND (ab = wt) [E = a*] OR (wt < b <= a*) AND (ab = wt) [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic all-suppressing converging genetic interaction
cisphenotypic all-suppressing genetic interaction
cisphenotypic genetic suppression (complete)
An effect in which individual perturbations of different genes result in the same mutant phenotype but to varying degrees of severity/penetrance and the resulting phenotype of their combination is less severe/penetrant than both of the phenotypes resulting from the individual perturabtions. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: a* < b < ab < wt [E = a*] OR wt < ab < b < a* [E = a*] where 'a' and 'b' are the observed phenotype values of the individual perturbations ('a*' being the most severe of the two), 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
cisphenotypic co-suppressing genetic interaction
A genetic aphenotypic phenotype result (both genetic perturbations result in a wild type (or control) phenotype) in which case the double genetic perturbation also results in the wild type (or control) phenotype, thus resulting in the expected phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: wt = a = b = ab [E = wt] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
aphenotypic neutral multigenic phenotype result
A phenotype modification whereby introduction of a genetic perturbation in an organism with another genetic perturbation results in, or enhances, a phenotype in that organism.
A phenotype result in which only one of two perturbations results in the phenotype in question and the phenotype of the combined perturbations a and b result in the expected phenotype, namely the same phenotype as the single perturbation that exhibits that phenotype. The interpretation is that no interaction was observed between the two genes, for the indicated phenotype. With respect to any single quantifiable phenotype, this may be expressed as an inequality as: ab = a ≠ wt = b [E = a] where 'a' and 'b' are the observed phenotype values of the individual perturbations, 'ab' is the observed phenotype value of the double perturbation, 'E' is the expected phenotype value of the double perturbation, and 'wt' is the wild type phenotype value.
monophenotypic neutral multigenic phenotype result
A phenotype result in which both of two genetic perturbations result in the phenotype in question and do so in the same manner compared to wild type (for example, both genetic perturbations result in an increased quality phenotype, or both genetic perturbations result in a decreased quality phenotype) and the resulting double genetic perturbation results in a phenotype that is more severe than the most severe single genetic perturbation phenotype. Note that this may be an expected result.
cisphenotypic enhancing genetic interaction
A multigenic phenotype result in which (1) the phenotype of a single genetic perturbation has been modified by the introduction of one or more additional genetic perturbations AND/OR (2) an effect in which two genetic perturbations, when combined, result in a phenotype that does not appear to be merely explained by the superimposition or addition of effects of the original perturbations. ab (not=) E
E. coli BirA* biotin ligase tag used in BioID experiments. This generally refers to a promiscuous mutant version of the biotin ligase with an R118H mutation.
Enzymatic oxido-reductions where only O2 is an acceptor of hydrogen or electrons
Circular RNAs are stable circular transcripts generated when a pre-mRNA undergoes “backsplicing” to join a splice donor to an upstream splice acceptor. They can originate from exons, introns or lncRNAs.
Ribozymes (ribonucleic acid enzymes) are folded catalytic RNA molecules that perform important biological functions.
Uberon is an integrated cross-species anatomy ontology representing a variety of entities classified according to traditional anatomical criteria such as structure, function and developmental lineage. https://www.ebi.ac.uk/ols/ontologies/uberon
The COVID-19 Vocabulary (COVoc) is an ontology containing terms related to the research of the COVID-19 pandemic. This includes host organisms, pathogenicity, gene and gene products, barrier gestures, treatments and more. https://www.ebi.ac.uk/ols/ontologies/COVOC
The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. https://www.ebi.ac.uk/ols/ontologies/po
A semi-automatically constructed ontology that merges in multiple disease resources to yield a coherent merged ontology. https://www.ebi.ac.uk/ols/ontologies/mondo
The protein of interest is expressed as a fusion to a MAC-tag, which contains a twin-strep affinity tag and BirA* in one construct, requires generation of only one isogenic cell line and allows one-step protein purification by Strep-Tactin matrix for both AP–MS and BioID pipelines.
Protein complementation methods specifically developed to assay for interactions of membrane proteins with both cytosolic or membrane-bound partners.
A membrane bait protein is tagged with the C-terminal half of ubiquitin (Cub) and a chimeric transcription factor, and a cytosolic or membrane-bound prey is tagged with the N-terminal half of ubiquitin (Nub). Upon interaction of bait and prey, the split halves form pseudoubiquitin, which is recognized by cytosolic deubiquitinating enzymes, resulting in cleavage of the transcription factor and expression of a reporter gene.
The Cellosaurus is a knowledge resource on cell lines. It aims to describe all cell lines used in biomedical research.
The Cell Line Ontology (CLO) is a community-based ontology of cell lines. The CLO is developed to unify publicly available cell line entry data from multiple sources to a standardized logically defined format based on consensus design patterns.
Ensembl Bacteria is a browser for bacterial and archaeal genomes. https://bacteria.ensembl.org/
Ensembl Fungi is a browser for fungal genomes. https://fungi.ensembl.org/
Ensembl Metazoa is a is a browser for genomes of metazoan species of scientific interest. https://metazoa.ensembl.org/
Ensembl Plants is a browser for plant genomes. https://plants.ensembl.org/
Ensembl Protists is a browser for protist genomes. https://protists.ensembl.org/
SubtiList is the reference database dedicated to the genome of Bacillus subtilis, the paradigm of Gram-positive endospore-forming bacteria. http://genolist.pasteur.fr/SubtiList/
Mass photometry measures mass at the single molecule level in solution and enables the quantification of protein–protein interactions in solution with sufficient sensitivity to accurately determine stoichiometry and rate of reactions.
Reference to the gene encoding for the observed nucleic acid or protein
HuMap is a machine learning framework to identify protein complexes from mass spectrometry and other large-scale interaction experiments. HuMap 3.0 is presented as a searchable web resource (https://humap3.proteincomplexes.org/) using data from >25,000 mass spectrometry experiments to identify nearly >15,000 human protein complexes.
A web-resource (https://www.proteomehd.net/index) that provides a co-regulation map of the human proteome built from ProteomeHD data (5,288 individual mass spectrometry experiments) and datasets from the Proteomics Identifications dataset using the machine learning algorithm treeClust to identify functional associations between co-regulated human proteins. https://www.proteomehd.net/proteomehd
Reference to an orthology database group. Gathers orthologous entities across species in a single identifier for their group
Used to link large ML assemblies to smaller curated complexes which are a subset of this. Added as qualifier to all entries linked by a common cross reference to an entry which represents a superset.
A unit of mass used to express molecular mass, especially for large molecules, such as proteins and polysaccharides. It is equal to 1000 daltons. A dalton is equal to one twelfth of the mass of an atom of carbon-12, or 1.660 33 × 10−27 kg.
Relative or absolute number of molecules in a sample. Used in the context of quantatative proteomics
MuSIC (multi-scale integrated cell ) is a machine learning framework to identify protein complexes from mass spectrometry and other large-scale interaction experiments
Biotin ligase tags that can be used as label as they confer some property that facilitates identification purification and monitoring to the labeled molecule.
An engineered biotin ligase that uses ATP to convert biotin into biotin–AMP, a reactive intermediate that covalently labels proximal proteins. BioID2, derived from Aquifex aeolicus biotin ligase, is ~30% smaller than BirA
An engineered biotin ligase that uses ATP to convert biotin into biotin–AMP, a reactive intermediate that covalently labels proximal proteins. TurboID has faster labeling kinetics than \bir\a and will operate at lower temperatures.
The location on a molecule where the molecule is broken down by enzymatic or chemical activity.
The location on a polypeptide chain where peptide bonds are broken down by hydrolysis.
A method for high-throughput measurement of protein-ligand binding affinities. A resin is saturated at high concentration with either a control or a bait molecule. The loaded resins are incubated with a prey solution containing either individual purified proteins/domains or complex mixtures. The bait is present in substantial molar excess relative to all potential preys, ensuring non-saturating binding conditions. Each significantly interacting prey is depleted from the solution by the resin, in a proportion related to its own affinity constant for the bait. After incubation, the liquid phases containing the unbound fractions are recovered, without any washing step to maintain thermodynamic equilibrium. For each prey, its amount in the unbound fraction of the bait sample is quantified relatively to its amount in the unbound fraction of the control sample. This relative quantification enables calculation of dissociation constants (Kd), with rigorously validated accuracy and precision. Prey that are well-quantified but not significantly depleted (their affinity for the bait is lower than the assay’s known detection threshold) may be regarded as a negative interaction.
The Immune Epitope Database (IEDB) catalogs experimental data on antibody and T cell epitopes studied in humans and other animal species in the context of infectious disease, allergy, autoimmunity and transplantation. https://www.iedb.org
The ABCD (AntiBodies Chemically Defined) database is a manually curated depository of sequenced antibodies(https://web.expasy.org/abcd/), developed by the Geneva Antibody Facility at the University of Geneva, in collaboration with the CALIPHO and Swiss-Prot groups at SIB Swiss Institute of Bioinformatics.
An immunoglobulin molecule having a specific amino acid sequence that gives each antibody the ability to adhere to and interact with the antigen that induced its synthesis and with molecules containing structures similar to that antigen. http://purl.obolibrary.org/obo/XCO_0000194
The term “lipid” is broadly defined as a substance of biological origin that is soluble in nonpolar solvents. Lipids include saponifiable classes such as glycerides (fats and oils) and phospholipids, as well as nonsaponifiable classes such as steroids.
A structural arrangement consisting predominantly of lipid molecules organized into one or more continuous layers.
QSProteome is a centralized, community-driven structural biology resource that hosts over 35,000 predicted oligomeric protein complex models, covering more than 42,000 genes across multiple species. It prevents redundant modeling by allowing researchers to track existing predictions and provides clear quality metrics (pLDDT, ipTM, PAE) to assess model reliability. Each entry includes interactive 3D visualization, functional annotations, and links to databases such as BioCyc, ComplexPortal, PDB, and UniProt, integrating computational predictions with experimental data. The platform also supports community curation, enabling users to refine models and contribute to the expanding structural proteome. https://qsproteome.org/