OBO-Edit 2.3.1 15:04:2021 22:57 PSI-MI 1.2 pporras CVversion: 2.5.5 Each of the top level terms in this file is the root term of an independent controlled vocabulary Notes: 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 Pablo Porras Millán pporras@ebi.ac.uk 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. definition Label from MS DeltaMass Drugable Genome Project Alternate label curated by PSI-MI Unique short label curated by PSI-MI Subset of PSI-MI Alternate label curated by PSI-MOD Unique short label curated by PSI-MOD subset of protein modifications Agreed label from MS community Alternate name from RESID Misnomer label from RESID Name from RESID Systematic name from RESID Alternate name from UniMod Description (full_name) from UniMod Interim label from UniMod Label (title) from UniMod Protein feature description from UniProtKB subset_property synonym_type_property has_alternative_id has_broad_synonym database_cross_reference has_exact_synonym has_narrow_synonym has_obo_format_version has_obo_namespace has_related_synonym has_scope has_synonym_type in_subset Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions. mi PSI-MI MI:0000 molecular interaction Controlled vocabularies originally created for protein protein interactions, extended to other molecules interactions. PMID:14755292 mi Method to determine the interaction. interaction detect PSI-MI MI:0001 interaction detection method Method to determine the interaction. PMID:14755292 interaction detect Method to determine the molecules involved in the interaction. participant detection participant ident PSI-MI MI:0002 participant identification method Method to determine the molecules involved in the interaction. PMID:14755292 participant detection participant ident Method to determine the features of the proteins involved in the interaction. feature detection PSI-MI MI:0003 feature detection method Method to determine the features of the proteins involved in the interaction. PMID:14755292 feature detection 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. Affinity purification affinity chrom PSI-MI MI:0004 affinity chromatography technology 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. PMID:7708014 Affinity purification affinity chrom 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. PSI-MI MI:0005 alanine scanning 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. PMID:14755292 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. anti bait coip PSI-MI MI:0006 anti bait coimmunoprecipitation 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. PMID:7708014 anti bait coip 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. anti tag coip PSI-MI MI:0007 anti tag coimmunoprecipitation 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. PMID:7708014 anti tag coip 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. PSI-MI MI:0008 array technology 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. PMID:14755292 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. PSI-MI MI:0009 bacterial display 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. PMID:10436088 PMID:8248129 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. beta galactosidase PSI-MI MI:0010 beta galactosidase complementation 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. PMID:12042868 PMID:9237989 beta galactosidase 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. beta lactamase PSI-MI MI:0011 beta lactamase complementation 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. PMID:12042868 beta lactamase 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). BRET LRET bret PSI-MI MI:0012 bioluminescence resonance energy transfer 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). PMID:10725388 PMID:9874787 BRET LRET bret The application of physical principles and methods to biological experiments. PSI-MI MI:0013 biophysical The application of physical principles and methods to biological experiments. PMID:14755292 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. adenylate cyclase bacterial two-hybrid PSI-MI MI:0014 adenylate cyclase complementation 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. PMID:9576956 adenylate cyclase bacterial two-hybrid 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. CD cd PSI-MI MI:0016 circular dichroism 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. PMID:11578931 CD cd 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. fluorescence spectr PSI-MI MI:0017 classical fluorescence spectroscopy 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. PMID:7708014 fluorescence spectr 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. 2 hybrid 2-hybrid 2H 2h Gal4 transcription regeneration Y2H classical two hybrid two-hybrid yeast two hybrid PSI-MI Y-2H MI:0018 two hybrid 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. PMID:10967325 PMID:12634794 PMID:1946372 2 hybrid 2-hybrid 2H 2h Gal4 transcription regeneration classical two hybrid two-hybrid yeast two hybrid 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. Co-IP CoIp co-immunoprecipitation coip immunoprecipitation PSI-MI MI:0019 coimmunoprecipitation 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. PMID:7708014 Co-IP CoIp co-immunoprecipitation coip immunoprecipitation 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. tem PSI-MI MI:0020 transmission electron microscopy 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. PMID:14755292 tem 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. coloc fluoresc probe PSI-MI MI:0021 colocalization by fluorescent probes cloning true 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. PMID:14755292 coloc fluoresc probe 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. Immunofluorescence Staining Immunostaining coloc immunostaining PSI-MI MI:0022 colocalization by immunostaining true 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. PMID:14755292 Immunofluorescence Staining Immunostaining coloc immunostaining 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. coloc visual technol PSI-MI MI:0023 colocalization/visualisation technologies true 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. PMID:14755292 coloc visual technol Text mining is used to support interactions which have been determined by other methods. conformational tm PSI-MI MI:0024 confirmational text mining Text mining is used to support interactions which have been determined by other methods. PMID:14755292 conformational tm 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). PSI-MI MI:0025 copurification true 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). PMID:14755292 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. PSI-MI MI:0026 correlated mutations 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. PMID:11933068 Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact. PSI-MI MI:0027 cosedimentation Separation of a mixture of molecules under the influence of a force such as artificial gravity. Molecules sedimenting together are assumed to interact. PMID:14755292 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. solution sedimentati PSI-MI MI:0028 cosedimentation in solution 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. PMID:10410796 solution sedimentati 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. density sedimentation PSI-MI MI:0029 cosedimentation through density gradient 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. PMID:10410796 density sedimentation 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. crosslink PSI-MI MI:0030 cross-linking study 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. PMID:14755292 crosslink 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. Label transfer techniques Photoaffinity labelling bifunctional agent crosslink PSI-MI MI:0031 protein cross-linking with a bifunctional reagent 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. PMID:10679368 PMID:7708014 Label transfer techniques Photoaffinity labelling bifunctional agent crosslink 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 sequence PSI-MI MS/MS MI:0032 de novo protein sequencing by mass spectrometry 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. PMID:10984529 de novo protein sequence 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. PSI-MI MI:0033 deletion analysis 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. PMID:14755292 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. PSI-MI MI:0034 display technology 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. PMID:14755292 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. PSI-MI MI:0035 docking 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. PMID:11478868 PMID:9631301 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. Rosetta Stone PSI-MI MI:0036 domain fusion 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. PMID:10573422 Rosetta Stone 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. PSI-MI MI:0037 domain profile pairs 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. PMID:11473021 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. dls PSI-MI MI:0038 dynamic light scattering 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. PMID:9013660 dls 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. PSI-MI MI:0039 edman degradation 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. PMID:14755292 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. Electron cryomicroscopy Electron crystallography PSI-MI MI:0040 electron microscopy 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. PMID:11785754 Electron cryomicroscopy Electron crystallography 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. ENDOR endor PSI-MI MI:0041 electron nuclear double resonance 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. PMID:11817959 PMID:11988476 PMID:12186859 ENDOR endor 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. EPR ESR epr PSI-MI MI:0042 electron paramagnetic resonance 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. PMID:11817959 EPR ESR epr 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. PSI-MI MI:0043 electron resonance 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. PMID:14755292 Methods based on laboratory experiments to determine an interaction. experimental interac PSI-MI MI:0045 experimental interaction detection experimental interac Methods based on laboratory experiments to determine an interaction. PMID:14755292 Predictive algorithms that rely on the information obtained by experimental results. experimental info PSI-MI MI:0046 experimental knowledge based Predictive algorithms that rely on the information obtained by experimental results. PMID:14755292 experimental info 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. Affinity blotting PSI-MI MI:0047 far western blotting 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. PMID:7708014 Affinity blotting 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. filamentous phage PSI-MI MI:0048 filamentous phage display 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. PMID:7682645 filamentous phage 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. Filter overlay assay PSI-MI dot blot MI:0049 filter binding 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. PMID:7708014 Filter overlay assay 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). flag tag coip PSI-MI MI:0050 flag tag coimmunoprecipitation true 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). PMID:14755292 flag tag coip 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. fluorescence PSI-MI MI:0051 fluorescence technology 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. PMID:14755292 fluorescence 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. FCS fcs PSI-MI fluctuation correlation specctrometry MI:0052 fluorescence correlation spectroscopy 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. PMID:10733953 FCS fcs 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. FPS Fluorescence anisotropy fps PSI-MI MI:0053 fluorescence polarization spectroscopy 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. PMID:12805227 PMID:7708014 FPS Fluorescence anisotropy fps 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. FACS Flow cytometry facs PSI-MI MI:0054 fluorescence-activated cell sorting 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. PMID:11988464 FACS Flow cytometry facs 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. FRET FRET analysis RET fret PSI-MI MI:0055 fluorescent resonance energy transfer 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. PMID:11558993 FRET FRET analysis RET fret 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. full dna sequence PSI-MI MI:0056 full identification by DNA sequencing 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. PMID:14755292 full dna sequence 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. PSI-MI MI:0057 gene neighbourhood 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. PMID:9787636 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. genome prediction PSI-MI MI:0058 genome based prediction 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. PMID:14755292 genome prediction 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). PSI-MI MI:0059 gst pull down true 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). PMID:14755292 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). ha tag coip PSI-MI MI:0060 ha tag coimmunoprecipitation true 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). PMID:14755292 ha tag coip 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). PSI-MI MI:0061 his pull down true 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). PMID:14755292 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). his tag coip PSI-MI MI:0062 his tag coimmunoprecipitation true 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). PMID:14755292 his tag coip Computational methods to predict an interaction. in silico methods predicted interac PSI-MI MI:0063 interaction prediction Computational methods to predict an interaction. PMID:14755292 in silico methods predicted interac Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties. Homology based interaction prediction PSI-MI MI:0064 interologs mapping Protein interactions, experimentally detected in an organism, are extended to a second organism assuming that homologue proteins, in different organisms, maintain their interaction properties. PMID:11731503 Homology based interaction prediction 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. ITC itc PSI-MI MI:0065 isothermal titration calorimetry 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. PMID:11785756 ITC itc 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. lambda phage PSI-MI MI:0066 lambda phage display 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. PMID:7682645 lambda phage 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. PSI-MI MI:0067 light scattering 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. PMID:9013660 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. modified residue ms PSI-MI MI:0068 mass detection of residue modification 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. PMID:11395414 PMID:11875433 modified residue ms 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. ms of complexes PSI-MI MI:0069 mass spectrometry studies of complexes 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. PMID:12057199 PMID:12504676 ms of complexes 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. PSI-MI MI:0070 mobility shift 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. PMID:14755292 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. Gel Filtration Size Exclusion Chromatography Sizing column PSI-MI MI:0071 molecular sieving 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. PMID:7708014 Gel Filtration Size Exclusion Chromatography Sizing column 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. monoclonal western PSI-MI MI:0072 monoclonal antibody western blot 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. PMID:14755292 monoclonal western 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. PSI-MI MI:0073 mrna display 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. PMID:11551470 Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding. PSI-MI MI:0074 mutation analysis Mutant molecules are produced by random or directed techniques and assayed for their ability to support binding. PMID:14755292 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). myc tag coip PSI-MI MI:0075 myc tag coimmunoprecipitation true 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). PMID:14755292 myc tag coip 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. interface predictor PSI-MI MI:0076 neural network on interface properties 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. PMID:11455607 PMID:11874449 interface predictor 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. NMR nmr PSI-MI MI:0077 nuclear magnetic resonance 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. PMID:12062432 PMID:12120505 NMR nmr 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. nucleotide sequence sequence cloning PSI-MI MI:0078 nucleotide sequence identification 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. PMID:14755292 nucleotide sequence sequence cloning Experimental methods that could not be assigned to the other large group of technologies. OBSOLETE use biochemical (MI:0401) instead. other biochemic tech PSI-MI MI:0079 other biochemical technologies true Experimental methods that could not be assigned to the other large group of technologies. OBSOLETE use biochemical (MI:0401) instead. PMID:14755292 other biochemic tech Genes are recognised by hybridization of a probe with a fragment of the gene sequence. partial dna sequence hybrid PSI-MI MI:0080 partial DNA sequence identification by hybridization Genes are recognised by hybridization of a probe with a fragment of the gene sequence. PMID:14755292 partial dna sequence hybrid 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. PSI-MI MI:0081 peptide array 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. PMID:11167074 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. fingerprinting PSI-MI MI:0082 peptide massfingerprinting 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. PMID:10967324 PMID:11752590 PMID:11805826 fingerprinting 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. PSI-MI MI:0083 peptide synthesis 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. PMID:14755292 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). PSI-MI MI:0084 phage display 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). PMID:10975452 PMID:7708014 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. PSI-MI MI:0085 phylogenetic profile 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. PMID:10200254 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. polyclonal western PSI-MI MI:0086 polyclonal antibody western blot 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. PMID:14755292 polyclonal western 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. predictive tm PSI-MI MI:0087 predictive text mining 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. PMID:11791231 predictive tm 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. PSI-MI MI:0088 primer specific pcr 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. PMID:14755292 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. PSI-MI MI:0089 protein array 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. PMID:10976071 PMID:12067604 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. PCA complementation PSI-MI MI:0090 protein complementation assay 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. PMID:11495741 PCA complementation 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). chromatography column chromatography PSI-MI MI:0091 chromatography technology 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). PMID:14755292 chromatography column chromatography 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. PISA pisa PSI-MI MI:0092 protein in situ array 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. PMID:11470888 PISA pisa Single amino acid identification along a protein sequence. protein sequence PSI-MI MI:0093 protein sequence identification Single amino acid identification along a protein sequence. PMID:14755292 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. PSI-MI MI:0094 protein staining 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. PMID:12015990 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. SELDI ProteinChip seldi chip PSI-MI MI:0095 proteinchip(r) on a surface-enhanced laser desorption/ionization 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. PMID:11827829 SELDI ProteinChip seldi chip 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. PSI-MI affinity capture pulldown MI:0096 pull down 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. PMID:14755292 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. reverse RRS reverse rrs PSI-MI MI:0097 reverse ras recruitment system 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. PMID:11160938 reverse RRS reverse rrs 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. PSI-MI MI:0098 ribosome display 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. PMID:11551470 PMID:12167034 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. RIA Radio Immuno Assay SPA spa PSI-MI MI:0099 scintillation proximity assay 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. PMID:3866247 RIA Radio Immuno Assay SPA spa 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. sequence phylogeny PSI-MI MI:0100 sequence based phylogenetic profile 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. PMID:11707606 sequence phylogeny Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs. predict from sequenc PSI-MI MI:0101 sequence based prediction Computational methods based on evolutionary hypothesis, used as criteria to browse sequences and predict interacting pairs. PMID:14755292 predict from sequenc 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. sequence tag PSI-MI MS/MS MI:0102 sequence tag identification 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. PMID:10967324 PMID:11752590 PMID:11805837 sequence tag 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. PSI-MI MI:0103 southern blot 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. PMID:14755292 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. sls PSI-MI MI:0104 static light scattering 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. PMID:9013660 sls Methods based on 3D structure information. predict from struct PSI-MI MI:0105 structure based prediction Methods based on 3D structure information. PMID:14755292 predict from struct 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. PSI-MI MI:0106 surface patches 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. PMID:9299343 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. BIAcore(r) Optical biosensor spr PSI-MI MI:0107 surface plasmon resonance 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. PMID:11896282 PMID:12120258 PMID:16338355 BIAcore(r) Optical biosensor spr 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. t7 phage PSI-MI MI:0108 Reference not index in medline: Rosenberg, A, Griffin, K, Studier, WS, McCormick, M, Berg, J, Novy, R, Mierendorf, R inNovations, 1996, 6, 1. t7 phage display 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. PMID:14755292 t7 phage 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). tap tag coip PSI-MI MI:0109 tap tag coimmunoprecipitation true 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). PMID:10504710 tap tag coip 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. PSI-MI MI:0110 text mining 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. PMID:14755292 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. dhfr reconstruction PSI-MI MI:0111 dihydrofolate reductase reconstruction 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. PMID:10318894 dhfr reconstruction 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. ub reconstruction PSI-MI membrane yeast two-hybrid myth split-ubiquitin MI:0112 ubiquitin reconstruction 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. PMID:9560251 ub reconstruction 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. Immuno blot PSI-MI MI:0113 western blot 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. PMID:14755292 Immuno blot 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. X-ray x-ray diffraction PSI-MI co-crystallization co-crystallography MI:0114 x-ray crystallography 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. PMID:14755292 X-ray x-ray diffraction 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. PSI-MI MI:0115 yeast display 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. PMID:9181578 Property of a subsequence that may interfere with the binding of a molecule. PSI-MI MI:0116 feature type Property of a subsequence that may interfere with the binding of a molecule. PMID:14755292 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. binding site binding region PSI-MI binding component MI:0117 binding-associated region 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. PMID:14755292 binding region A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event. PSI-MI MI:0118 mutation A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event. PMID:14755292 Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction). hotspot mutation decreasing PSI-MI MI:0119 mutation decreasing interaction Region of a molecule whose mutation or deletion decreases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction). PMID:14755292 hotspot mutation decreasing Residue covalent modifications occurring in the specific protein form involved in an interaction. OBSOLETE remap to MOD:00000. ptm PSI-MI MI:0120 post translation modification true Residue covalent modifications occurring in the specific protein form involved in an interaction. OBSOLETE remap to MOD:00000. PMID:14755292 ptm Residue modification. OBSOLETE remap to MOD:00394. PSI-MI MI:0121 acetylated residue true Residue modification. OBSOLETE remap to MOD:00394. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00050. (S)-2-(acetylamino)propanoic acid AAC N-acetyl-L-alanine [A:ac] acetylalanine PSI-MI MI:0122 n-acetyl-alanine true Residue modification. OBSOLETE remap to MOD:00050. PMID:11125103 RESID:AA0041 (S)-2-(acetylamino)propanoic acid AAC N-acetyl-L-alanine [A:ac] acetylalanine acetylalanine Residue modification. OBSOLETE remap to MOD:00359. N2-acetyl-L-arginine RAC [R:ac] acetylarginine alpha-acetylamino-delta-guanidinovaleric acid PSI-MI MI:0123 n2-acetyl-arginine true Residue modification. OBSOLETE remap to MOD:00359. PMID:11125103 RESID:AA0354 N2-acetyl-L-arginine RAC [R:ac] acetylarginine acetylarginine alpha-acetylamino-delta-guanidinovaleric acid Residue modification. OBSOLETE remap to MOD:00780. N-acetyl-L-asparagine NAC [N:ac] acetylasparagine PSI-MI MI:0124 n-acetyl-asparagine true Residue modification. OBSOLETE remap to MOD:00780. PMID:11125103 N-acetyl-L-asparagine NAC [N:ac] acetylasparagine Residue modification. OBSOLETE remap to MOD:00051. (S)-2-(acetylamino)butanedioic acid DAC N-acetyl-L-aspartic acid [D:ac] acetylaspartate acetylaspartic acid PSI-MI MI:0125 n-acetyl-aspartic acid true Residue modification. OBSOLETE remap to MOD:00051. PMID:11125103 RESID:AA0042 (S)-2-(acetylamino)butanedioic acid DAC N-acetyl-L-aspartic acid [D:ac] acetylaspartate acetylaspartic acid Residue modification. OBSOLETE remap to MOD:00052. (R)-2-acetylamino-3-sulfanylpropanoic acid 2-acetylamino-3-mercaptopropanoic acid CAC N-acetyl-L-cysteine N-acetylcysteine [C:ac] acetylcysteine PSI-MI MI:0126 n-acetyl-cysteine true Residue modification. OBSOLETE remap to MOD:00052. PMID:11125103 RESID:AA0043 (R)-2-acetylamino-3-sulfanylpropanoic acid 2-acetylamino-3-mercaptopropanoic acid CAC N-acetyl-L-cysteine N-acetylcysteine [C:ac] acetylcysteine Residue modification. OBSOLETE remap to MOD:00054. (S)-2-acetylamino-5-pentanediamic acid N-acetyl-L-glutamine QAC [Q:ac] acetylglutamine PSI-MI MI:0127 n-acetyl-glutamine true Residue modification. OBSOLETE remap to MOD:00054. PMID:11125103 RESID:AA0045 (S)-2-acetylamino-5-pentanediamic acid N-acetyl-L-glutamine QAC [Q:ac] acetylglutamine acetylglutamine Residue modification. OBSOLETE remap to MOD:00053. (S)-2-(acetylamino)pentanedioic acid EAC N-acetyl-L-glutamic acid [E:ac] acetylglutamate acetylglutamic acid PSI-MI MI:0128 n-acetyl-glutamic acid true Residue modification. OBSOLETE remap to MOD:00053. PMID:11125103 RESID:AA0044 (S)-2-(acetylamino)pentanedioic acid EAC N-acetyl-L-glutamic acid [E:ac] acetylglutamate acetylglutamic acid Residue modification. OBSOLETE remap to MOD:00055. 2-(acetylamino)ethanoic acid GAC N-acetylglycine [G:ac] aceturic acid acetylglycine PSI-MI MI:0129 n-acetylglycine true Residue modification. OBSOLETE remap to MOD:00055. PMID:11125103 RESID:AA0046 2-(acetylamino)ethanoic acid GAC N-acetylglycine [G:ac] aceturic acid acetylglycine Residue modification. OBSOLETE remap to MOD:00781. HAC N-acetyl-L-histidine [H:ac] acetylhistidine PSI-MI MI:0130 n-acetyl-histidine true Residue modification. OBSOLETE remap to MOD:00781. PMID:11125103 HAC N-acetyl-L-histidine [H:ac] acetylhistidine Residue modification. OBSOLETE remap to MOD:00056. (2S,3S)-2-acetylamino-3-methylpentanoic acid IAC N-acetyl-L-isoleucine [I:ac] acetylisoleucine PSI-MI MI:0131 n-acetyl-isoleucine true Residue modification. OBSOLETE remap to MOD:00056. PMID:11125103 RESID:AA0047 (2S,3S)-2-acetylamino-3-methylpentanoic acid IAC N-acetyl-L-isoleucine [I:ac] acetylisoleucine acetylisoleucine Residue modification. OBSOLETE remap to MOD:00782. LAC N-acetyl-L-leucine [L:ac] acetylleucine PSI-MI MI:0132 n-acetyl-leucine true Residue modification. OBSOLETE remap to MOD:00782. PMID:11125103 LAC N-acetyl-L-leucine [L:ac] acetylleucine Residue modification. OBSOLETE remap to MOD:00057. (S)-2-acetylamino-6-aminohexanoic acid KAC N2-acetyl-L-lysine N2-acetyllysine [K:ac] n2-acetyllysine PSI-MI MI:0133 n2-acetyl-lysine true Residue modification. OBSOLETE remap to MOD:00057. PMID:11125103 RESID:AA0048 (S)-2-acetylamino-6-aminohexanoic acid KAC N2-acetyl-L-lysine N2-acetyllysine [K:ac] n2-acetyllysine Residue modification. OBSOLETE remap to MOD:00064. (S)-2-amino-6-(acetylamino)hexanoic acid KA6 N(zeta)-acetyllysine N6-acetyl-L-lysine [K:N6ac] epsilon-acetyllysine n6-acetyllysine PSI-MI MI:0134 n6-acetyl-lysine true Residue modification. OBSOLETE remap to MOD:00064. PMID:11125103 RESID:AA0055 (S)-2-amino-6-(acetylamino)hexanoic acid KA6 N(zeta)-acetyllysine N6-acetyl-L-lysine [K:N6ac] epsilon-acetyllysine n6-acetyllysine Residue modification. OBSOLETE remap to MOD:00058. (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid 2-acetylamino-4-(methylthio)butanoic acid MAC N-acetyl-L-methionine [M:ac] acetylmethionine methionamine PSI-MI MI:0135 n-acetyl-methionine true Residue modification. OBSOLETE remap to MOD:00058. PMID:11125103 RESID:AA0049 (S)-2-acetylamino-4-(methylsulfanyl)butanoic acid 2-acetylamino-4-(methylthio)butanoic acid MAC N-acetyl-L-methionine [M:ac] acetylmethionine acetylmethionine methionamine Residue modification. OBSOLETE remap to MOD:00784. FAC N-acetyl-L-phenylalanine [F:ac] acetylphenylalanine PSI-MI MI:0136 n-acetyl-phenylalanine true Residue modification. OBSOLETE remap to MOD:00784. PMID:11125103 FAC N-acetyl-L-phenylalanine [F:ac] acetylphenylalanine Residue modification. OBSOLETE remap to MOD:00059. (2S)-1-acetyl-2-pyrrolidinecarboxylic acid N-acetyl-L-proline PAC [P:ac] acetylproline PSI-MI MI:0137 n-acetyl-proline true Residue modification. OBSOLETE remap to MOD:00059. PMID:11125103 RESID:AA0050 (2S)-1-acetyl-2-pyrrolidinecarboxylic acid N-acetyl-L-proline PAC [P:ac] acetylproline acetylproline Residue modification. OBSOLETE remap to MOD:00060. (S)-2-acetylamino-3-hydroxypropanoic acid N-acetyl-L-serine N-acetylserine SAC [S:ac] acetylserine PSI-MI MI:0138 n-acetyl-serine true Residue modification. OBSOLETE remap to MOD:00060. PMID:11125103 RESID:AA0051 (S)-2-acetylamino-3-hydroxypropanoic acid N-acetyl-L-serine N-acetylserine SAC [S:ac] acetylserine Residue modification. OBSOLETE remap to MOD:00061. (2S,3R)-2-acetylamino-3-hydroxybutanoic acid N-acetyl-L-threonine N-acetylthreonine TAC [T:ac] acetylthreonine PSI-MI MI:0139 n-acetyl-threonine true Residue modification. OBSOLETE remap to MOD:00061. PMID:11125103 RESID:AA0052 (2S,3R)-2-acetylamino-3-hydroxybutanoic acid N-acetyl-L-threonine N-acetylthreonine TAC [T:ac] acetylthreonine Residue modification. OBSOLETE remap to MOD:00785. N-acetyl-L-tryptophan WAC [W:ac] acetyltryptophan PSI-MI MI:0140 n-acetyl-tryptophan true Residue modification. OBSOLETE remap to MOD:00785. PMID:11125103 N-acetyl-L-tryptophan WAC [W:ac] acetyltryptophan Residue modification. OBSOLETE remap to MOD:00062. (S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid N-acetyl-L-tyrosine N-acetyltyrosine YAC [Y:ac] acetyltyrosine PSI-MI MI:0141 n-acetyl-tyrosine true Residue modification. OBSOLETE remap to MOD:00062. PMID:11125103 RESID:AA0053 (S)-2-acetylamino-3-(4-hydoxyphenyl)propanoic acid N-acetyl-L-tyrosine N-acetyltyrosine YAC [Y:ac] acetyltyrosine Residue modification. OBSOLETE remap to MOD:00063. (S)-2-acetylamino-3-methylbutanoic acid N-acetyl-L-valine N-acetylvaline VAC [V:ac] acetylvaline PSI-MI MI:0142 n-acetyl-valine true Residue modification. OBSOLETE remap to MOD:00063. PMID:11125103 RESID:AA0054 (S)-2-acetylamino-3-methylbutanoic acid N-acetyl-L-valine N-acetylvaline VAC [V:ac] acetylvaline Residue modification. OBSOLETE remap to MOD:00674. PSI-MI MI:0143 amidated residue true Residue modification. OBSOLETE remap to MOD:00674. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00091. (S)-2-amino-5-guanidinopentanamide L-arginine amide RAM [R:am] argininamide arginineamide PSI-MI MI:0145 arginine amide true Residue modification. OBSOLETE remap to MOD:00091. PMID:11125103 RESID:AA0082 (S)-2-amino-5-guanidinopentanamide L-arginine amide RAM [R:am] argininamide arginineamide Residue modification. OBSOLETE remap to MOD:00493. PSI-MI MI:0146 formylated residue true Residue modification. OBSOLETE remap to MOD:00493. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00030. (S)-2-formylamino-4-(methylsulfanyl)butanoic acid 2-formylamino-4-(methylthio)butanoic acid MFM N-formyl-L-methionine [M:form] formylmethionine PSI-MI MI:0147 n-formyl-methionine true Residue modification. OBSOLETE remap to MOD:00030. PMID:11125103 RESID:AA0021 (S)-2-formylamino-4-(methylsulfanyl)butanoic acid 2-formylamino-4-(methylthio)butanoic acid MFM N-formyl-L-methionine [M:form] formylmethionine Residue modification. OBSOLETE remap to MOD:00428. PSI-MI MI:0148 hydroxylated residue true Residue modification. OBSOLETE remap to MOD:00428. PMID:11125103 Residue modification. OBSOLETE remap to MOD:01155. PSI-MI MI:0150 lipid modification true Residue modification. OBSOLETE remap to MOD:01155. PMID:11125103 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 CFN S-farnesyl-L-cysteine [C:farn] farnesylcysteine PSI-MI MI:0151 s-farnesyl-cysteine true Residue modification. OBSOLETE remap to MOD:00111. PMID:11125103 RESID:AA0102 (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 CFN S-farnesyl-L-cysteine [C:farn] farnesylcysteine 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 CGR S-geranylgeranyl-L-cysteine [C:ger] geranylgeranylcys PSI-MI MI:0152 s-geranylgeranyl-cysteine true Residue modification. OBSOLETE remap to MOD:00113. PMID:11125103 RESID:AA0104 (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 CGR S-geranylgeranyl-L-cysteine [C:ger] geranylgeranylcys Residue modification. OBSOLETE remap to MOD:00069. (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid 2-hexadecanoylamino-3-mercaptopropanoic acid CPN N-(1-oxahexadecyl)-L-cysteine N-palmitoyl-L-cysteine [C:palm_n] n-palmitoylcysteine PSI-MI MI:0153 n-palmitoyl-cysteine true Residue modification. OBSOLETE remap to MOD:00069. PMID:11125103 RESID:AA0060 (R)-2-hexadecanoylamino-3-sulfanylpropanoic acid 2-hexadecanoylamino-3-mercaptopropanoic acid CPN N-(1-oxahexadecyl)-L-cysteine N-palmitoyl-L-cysteine [C:palm_n] n-palmitoylcysteine Residue modification. OBSOLETE remap to MOD:00115. (R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid 2-amino-3-(hexadecanoylthio)propanoic acid CPS S-palmitoyl-L-cysteine [C:palm_s] cysteine hexadecanoate thioester cysteine palmitate thioester s-palmitoylcysteine PSI-MI MI:0154 s-palmitoyl-cysteine true Residue modification. OBSOLETE remap to MOD:00115. PMID:11125103 RESID:AA0106 (R)-2-amino-3-(hexadecanoylsulfanyl)propanoic acid 2-amino-3-(hexadecanoylthio)propanoic acid CPS S-palmitoyl-L-cysteine [C:palm_s] cysteine hexadecanoate thioester cysteine palmitate thioester s-palmitoylcysteine Residue modification. OBSOLETE remap to MOD:00068. GMY N-myristoyl-glycine [G:myr] myristoylglycine PSI-MI MI:0155 n-myristoyl-glycine true Residue modification. OBSOLETE remap to MOD:00068. PMID:11125103 RESID:AA0059 GMY N-myristoyl-glycine [G:myr] myristoylglycine Residue modification. OBSOLETE remap to MOD:00087. (S)-2-amino-6-(tetradecanoylamino)hexanoic acid KMY N(zeta)-myristoyllysine N6-(1-oxotetradecyl)-L-lysine N6-myristoyl-L-lysine [K:myr] epsilon-myristoyllysine myristoyllysine PSI-MI MI:0156 n6-myristoyl-lysine true Residue modification. OBSOLETE remap to MOD:00087. PMID:11125103 RESID:AA0078 (S)-2-amino-6-(tetradecanoylamino)hexanoic acid KMY N(zeta)-myristoyllysine N6-(1-oxotetradecyl)-L-lysine N6-myristoyl-L-lysine [K:myr] epsilon-myristoyllysine myristoyllysine Residue modification. OBSOLETE remap to MOD:00427. PSI-MI MI:0157 methylated residue true Residue modification. OBSOLETE remap to MOD:00427. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00070. (S)-2-methylaminopropanoic acid AMT N-methyl-L-alanine N-methylalanine [A:meth_n] methylalanine PSI-MI MI:0158 n-methyl-alanine true Residue modification. OBSOLETE remap to MOD:00070. PMID:11125103 RESID:AA0061 (S)-2-methylaminopropanoic acid AMT N-methyl-L-alanine N-methylalanine [A:meth_n] methylalanine Residue modification. OBSOLETE remap to MOD:00071. (S)-1-carboxy-N,N,N-trimethylethanaminium (S)-2-(trimethylammonio)propanoic acid AM3 N,N,N-trimethyl-L-alanine [A:meth_n3] trimethylalanine PSI-MI MI:0159 n,n,n-trimethyl-alanine true Residue modification. OBSOLETE remap to MOD:00071. PMID:11125103 RESID:AA0062 (S)-1-carboxy-N,N,N-trimethylethanaminium (S)-2-(trimethylammonio)propanoic acid AM3 N,N,N-trimethyl-L-alanine [A:meth_n3] trimethylalanine Residue modification. OBSOLETE remap to MOD:00077. (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid NG,NG-dimethylarginine RM2 [R:meth_n7] asymmetric dimethylarginine dimethylarginine omega-N,omega-N-dimethyl-L-arginine PSI-MI MI:0160 omega-n,omega-n-dimethyl-arginine true Residue modification. OBSOLETE remap to MOD:00077. PMID:11125103 RESID:AA0068 (S)-2-amino-5-[((dimethylamino)iminomethyl)amino]pentanoic acid NG,NG-dimethylarginine RM2 [R:meth_n7] asymmetric dimethylarginine dimethylarginine omega-N,omega-N-dimethyl-L-arginine Residue modification. OBSOLETE remap to MOD:00237. (2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid 3-carboxy-S-methyl-cysteine 3-methylthio-aspartic acid DM2 L-beta-methylthioaspartic acid [D:meth_b] beta-methylthio-aspartic acid methylthioaspartate PSI-MI MI:0161 beta-methylthioaspartic acid true Residue modification. OBSOLETE remap to MOD:00237. PMID:11125103 RESID:AA0232 (2R,3Xi)-2-amino-3-methylsulfanylbutanedioic acid 3-carboxy-S-methyl-cysteine 3-methylthio-aspartic acid DM2 L-beta-methylthioaspartic acid [D:meth_b] beta-methylthio-aspartic acid methylthioaspartate Residue modification. OBSOLETE remap to MOD:00080. (S)-2-amino-N5-methylpentanediamic acid N(delta)-methylglutamine N-methylglutamine N5-methyl-L-glutamine QM5 [Q:meth_n5] gamma-methylglutamine methylglutamine PSI-MI MI:0162 n5-methyl-glutamine true Residue modification. OBSOLETE remap to MOD:00080. PMID:11125103 RESID:AA0071 (S)-2-amino-N5-methylpentanediamic acid N(delta)-methylglutamine N-methylglutamine N5-methyl-L-glutamine QM5 [Q:meth_n5] gamma-methylglutamine methylglutamine Residue modification. OBSOLETE remap to MOD:00081. (S)-2-aminopentanedioic acid 5-methyl ester 5-methyl-L-glutamate EM5 L-glutamic acid 5-methyl ester [E:meth_o5] glutamatemethylester glutamic acid gamma-methyl ester PSI-MI MI:0163 glutamic acid 5-methyl ester true Residue modification. OBSOLETE remap to MOD:00081. PMID:11125103 RESID:AA0072 (S)-2-aminopentanedioic acid 5-methyl ester 5-methyl-L-glutamate EM5 L-glutamic acid 5-methyl ester [E:meth_o5] glutamatemethylester glutamic acid gamma-methyl ester Residue modification. OBSOLETE remap to MOD:00085. (S)-2-amino-6-methylaminohexanoic acid MLZ N(zeta)-methyllysine N6-methyl-L-lysine [K:meth_1] epsilon-methyllysine methyllysine PSI-MI MI:0165 n6-methyl-lysine true Residue modification. OBSOLETE remap to MOD:00085. PMID:11125103 (S)-2-amino-6-methylaminohexanoic acid MLZ N(zeta)-methyllysine N6-methyl-L-lysine [K:meth_1] epsilon-methyllysine methyllysine Residue modification. OBSOLETE remap to MOD:00084. (S)-2-amino-6-dimethylaminohexanoic acid MLY N(zeta)-dimethyllysine N6,N6-dimethyl-L-lysine [K:meth_2] dimethyllysine epsilon-dimethyllysine lysine derivative Lys(y) PSI-MI MI:0166 n6,n6-dimethyl-lysine true Residue modification. OBSOLETE remap to MOD:00084. PMID:11125103 RESID:AA0075 (S)-2-amino-6-dimethylaminohexanoic acid MLY N(zeta)-dimethyllysine N6,N6-dimethyl-L-lysine [K:meth_2] dimethyllysine epsilon-dimethyllysine lysine derivative Lys(y) Residue modification. OBSOLETE remap to MOD:00083. (S)-2-amino-6-(trimethylammonio)hexanoic acid (S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium M3L N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine [K:meth_3] epsilon-trimethyllysine trimethyllysine PSI-MI MI:0167 n6,n6,n6-trimethyl-lysine true Residue modification. OBSOLETE remap to MOD:00083. PMID:11125103 RESID:AA0074 (S)-2-amino-6-(trimethylammonio)hexanoic acid (S)-5-amino-5-carboxy-N,N,N-trimethylpentanaminium M3L N(zeta)-trimethyllysine N6,N6,N6-trimethyl-L-lysine [K:meth_3] epsilon-trimethyllysine trimethyllysine Residue modification. OBSOLETE remap to MOD:00073. (S)-2-methylamino-4-(methylsulfanyl)butanoic acid 2-methylamino-4-(methylthio)butanoic acid MMT N-methyl-L-methionine N-methylmethionine [M:meth] methylmethionine PSI-MI MI:0168 n-methyl-methionine true Residue modification. OBSOLETE remap to MOD:00073. PMID:11125103 RESID:AA0064 (S)-2-methylamino-4-(methylsulfanyl)butanoic acid 2-methylamino-4-(methylthio)butanoic acid MMT N-methyl-L-methionine N-methylmethionine [M:meth] methylmethionine Residue modification. OBSOLETE remap to MOD:00074. (S)-2-methylamino-3-phenylpropanoic acid FMT N-methyl-L-phenylalanine N-methylphenylalanine [F:meth] methylphenylalanine PSI-MI MI:0169 n-methyl-phenylalanine true Residue modification. OBSOLETE remap to MOD:00074. PMID:14755292 (S)-2-methylamino-3-phenylpropanoic acid FMT N-methyl-L-phenylalanine N-methylphenylalanine [F:meth] methylphenylalanine Residue modification. OBSOLETE remap to MOD:00696. phosphorylated PSI-MI MI:0170 phosphorylated residue true Residue modification. OBSOLETE remap to MOD:00696. PMID:11125103 phosphorylated Residue modification. OBSOLETE remap to MOD:00227. (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid N5-[imino(phosphonoamino)methyl]-L-ornithine RPO [R:po] alpha-amino-delta-phosphonoguanidinovaleric acid omega-N-phospho-L-arginine phosphoarginine PSI-MI MI:0171 omega-n-phospho-arginine true Residue modification. OBSOLETE remap to MOD:00227. PMID:11125103 RESID:AA0222 (S)-2-amino-5-[imino(phosphonoamino)methyl]aminopentanoic acid N5-[imino(phosphonoamino)methyl]-L-ornithine RPO [R:po] alpha-amino-delta-phosphonoguanidinovaleric acid omega-N-phospho-L-arginine phosphoarginine Residue modification. OBSOLETE remap to MOD:00042. (S)-2-aminobutanedioic 4-phosphoric anhydride DPO L-aspartic 4-phosphoric anhydride [D:po] beta-aspartyl phosphate phosphoaspartic acid PSI-MI MI:0172 aspartic 4-phosphoric anhydride true Residue modification. OBSOLETE remap to MOD:00042. PMID:11125103 RESID:AA0033 (S)-2-aminobutanedioic 4-phosphoric anhydride DPO L-aspartic 4-phosphoric anhydride [D:po] beta-aspartyl phosphate phosphoaspartic acid phosphoaspartic acid Residue modification. OBSOLETE remap to MOD:00043. (R)-2-amino-3-(phosphonosulfanyl)propanoic acid CPO S-phospho-L-cysteine S-phosphonocysteine S3-phosphocysteine [C:po] cysteine phosphate thioester phosphocysteine PSI-MI MI:0173 s-phospho-cysteine true Residue modification. OBSOLETE remap to MOD:00043. PMID:11125103 RESID:AA0034 (R)-2-amino-3-(phosphonosulfanyl)propanoic acid CPO S-phospho-L-cysteine S-phosphonocysteine S3-phosphocysteine [C:po] cysteine phosphate thioester phosphocysteine 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 O-phospho-L-serine O-phosphonoserine O3-phosphoserine SPO [S:po] phosphoserine serine phosphate ester PSI-MI MI:0176 o-phospho-serine true Residue modification. OBSOLETE remap to MOD:00046. PMID:11125103 RESID:AA0037 (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 O-phospho-L-serine O-phosphonoserine O3-phosphoserine SPO [S:po] phosphoserine serine phosphate ester Residue modification. OBSOLETE remap to MOD:00047. (2S,3R)-2-amino-3-phosphonooxybutanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate O-phospho-L-threonine O3-phosphothreonine TPO [T:po] phosphothreonine threonine phosphate ester PSI-MI MI:0177 o-phospho-threonine true Residue modification. OBSOLETE remap to MOD:00047. PMID:11125103 RESID:AA0038 (2S,3R)-2-amino-3-phosphonooxybutanoic acid 2-amino-3-hydroxybutanoic acid 3-phosphate O-phospho-L-threonine O3-phosphothreonine TPO [T:po] phosphothreonine threonine phosphate ester Residue modification. OBSOLETE remap to MOD:00048. (S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4-phosphotyrosine YPO [Y:po] phosphotyrosine tyrosine phosphate PSI-MI MI:0178 o4'-phospho-tyrosine true Residue modification. OBSOLETE remap to MOD:00048. PMID:11125103 RESID:AA0039 (S)-2-amino-3-(4-phosphonooxyphenyl)propanoic acid 2-amino-3-(4-hydroxyphenyl)propanoic acid 4'-phosphate O4'-phospho-L-tyrosine O4-phosphotyrosine YPO [Y:po] phosphotyrosine tyrosine phosphate Residue modification. OBSOLETE remap to MOD:00032. PSI-MI MI:0179 other modification true Residue modification. OBSOLETE remap to MOD:00032. PMID:11125103 Residue modification. OBSOLETE remap to MOD:00031. 3-selenylalanine CSE L-selenocysteine [C:sel] selenium cysteine PSI-MI MI:0180 selenocysteine true Residue modification. OBSOLETE remap to MOD:00031. PMID:11125103 RESID:AA0022 3-selenylalanine CSE L-selenocysteine [C:sel] selenium cysteine Residue modification. OBSOLETE remap to MOD:00530. L-selenomethionine MSE [M:sel] PSI-MI MI:0181 selenomethionine true Residue modification. OBSOLETE remap to MOD:00530. PMID:11125103 L-selenomethionine MSE [M:sel] Residue modification. OBSOLETE remap to MOD:01169. (S)-2-amino-3-oxopropanoic acid 2-amino-3-oxopropionic acid L-3-oxoalanine L-alpha-formylglycine L-amino-malonic acid semialdehyde L-aminomalonaldehydic acid L-serinesemialdehyde [misnomer] SOX [S:oxal] oxoalanine PSI-MI MI:0182 3-oxoalanine true Residue modification. OBSOLETE remap to MOD:01169. PMID:11125103 RESID:AA0185 (S)-2-amino-3-oxopropanoic acid 2-amino-3-oxopropionic acid L-3-oxoalanine L-alpha-formylglycine L-amino-malonic acid semialdehyde L-aminomalonaldehydic acid L-serinesemialdehyde [misnomer] SOX [S:oxal] oxoalanine Residue modification. OBSOLETE remap to MOD:00179. (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid EGE L-glutamyl 5-glycerophosphoethanolamine L-glutamyl 5-glycerophosphorylethanolamine L-glutamyl 5-glycerylphosphorylethanolamine [E:gpe] glycerylpo4etohamine PSI-MI MI:0184 glutamyl 5-glycerylphosphorylethanolamine true Residue modification. OBSOLETE remap to MOD:00179. PMID:11125103 RESID:AA0170 (S)-2-amino-5-[2-([([2,3-dihydroxypropyl]oxy)(hydroxy)phosphoryl]oxy)ethyl]amino-5-oxopentanoic acid EGE L-glutamyl 5-glycerophosphoethanolamine L-glutamyl 5-glycerophosphorylethanolamine L-glutamyl 5-glycerylphosphorylethanolamine [E:gpe] glycerylpo4etohamine Residue modification. OBSOLETE remap to MOD:00126. (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine (S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid KBT N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine N6-biotinyl-L-lysine N6-biotinyllysine [K:biotin] biocytin biotinyllysine epsilon-N-biotinyllysine PSI-MI MI:0186 n6-biotinyl-lysine true Residue modification. OBSOLETE remap to MOD:00126. PMID:11125103 RESID:AA0117 (3aS-(3aalpha,4beta,6aalpha))-N6-(5-(hexahydro-2-oxo-1H-thieno(3,4-d)imidazol-4-yl)-1-oxopentyl)-L-lysine (S)-2-amino-6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]aminohexanoic acid KBT N6-[5-((3aS,4S,6aR)-hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-4-yl)-1-oxopentyl]-L-lysine N6-biotinyl-L-lysine N6-biotinyllysine [K:biotin] biocytin biotinyllysine epsilon-N-biotinyllysine Residue modification. OBSOLETE remap to MOD:00125. (S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid KHY N6-(4-amino-2-hydroxybutyl)-L-lysine [K:hypu] hypusine PSI-MI MI:0187 n6-(4-amino-2-hydroxybutyl)-lysine true Residue modification. OBSOLETE remap to MOD:00125. PMID:11125103 RESID:AA0116 (S,R)-2-amino-6-(4-amino-2-hydroxybutylamino)hexanoic acid KHY N6-(4-amino-2-hydroxybutyl)-L-lysine [K:hypu] hypusine hypusine 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 KRT N6-retinal-L-lysine N6-retinyl-lysine N6-retinylidene-L-lysine [K:retin] retinallysine PSI-MI MI:0188 n6-retinal-lysine true Residue modification. OBSOLETE remap to MOD:00129. PMID:11125103 RESID:AA0120 (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 KRT N6-retinal-L-lysine N6-retinyl-lysine N6-retinylidene-L-lysine [K:retin] retinallysine Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein. OBSOLETE remap to MOD:00134. KUB N6-glycyl-L-lysine N6-glycyllysine [K:ub] PSI-MI MI:0189 ubiquitinated lysine true Residue modification due to a cross-link between a lysine and a glycine from the ubiquitine protein. OBSOLETE remap to MOD:00134. PMID:11125103 RESID:AA0125 KUB N6-glycyl-L-lysine N6-glycyllysine [K:ub] Connection between molecule. PSI-MI MI:0190 interaction type Connection between molecule. PMID:14755292 Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead. PSI-MI MI:0191 aggregation true Physical association among molecules. OBSOLETE since too non-specific. Consider using physical interaction (MI:0218) instead. PMID:14755292 Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. acetylation PSI-MI MI:0192 acetylation reaction Reaction, that can affect K,C,A,D,E,Q,G,I,K,M,P,S,T,Y,V residues. GO:0006473 PMID:14755292 RESID:AA0041 RESID:AA0042 RESID:AA0043 RESID:AA0044 RESID:AA0045 RESID:AA0046 RESID:AA0047 RESID:AA0048 RESID:AA0049 RESID:AA0050 RESID:AA0051 RESID:AA0052 RESID:AA0053 RESID:AA0054 RESID:AA0055 RESID:AA0056 acetylation 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. amidation PSI-MI MI:0193 amidation reaction 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. GO:0001519 PMID:14755292 RESID:AA0081 RESID:AA0082 RESID:AA0083 RESID:AA0084 RESID:AA0085 RESID:AA0086 RESID:AA0087 RESID:AA0088 RESID:AA0089 RESID:AA0090 RESID:AA0091 RESID:AA0092 RESID:AA0093 RESID:AA0094 RESID:AA0095 RESID:AA0096 RESID:AA0097 RESID:AA0098 RESID:AA0099 RESID:AA0100 amidation Covalent bond breakage in a molecule leading to the formation of smaller molecules. cleavage PSI-MI MI:0194 cleavage reaction Covalent bond breakage in a molecule leading to the formation of smaller molecules. PMID:14755292 cleavage Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners. PSI-MI MI:0195 covalent binding Interaction leading to the formation of covalent bond within an autocatalytic molecule or between partners. PMID:14755292 Physical interaction mediated by covalent bond rearrangement. OBSOLETE use covalent binding (MI:0195) instead. PSI-MI MI:0196 covalent interaction true Physical interaction mediated by covalent bond rearrangement. OBSOLETE use covalent binding (MI:0195) instead. PMID:14755292 N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. deacetylation PSI-MI MI:0197 deacetylation reaction N6-acetyl-L-lysine or S-acetyl-L-cysteine are cleaved and return K or C residues. GO:0006476 PMID:14755292 RESID:AA0055 RESID:AA0056 deacetylation S-farnesyl-L-cysteined is cleaved and returns a C residue. defarnesylation PSI-MI MI:0198 defarnesylation reaction S-farnesyl-L-cysteined is cleaved and returns a C residue. PMID:14755292 RESID:AA0102 defarnesylation N6-formyl-L-lysine is cleaved and returns a K residue. deformylation PSI-MI MI:0199 deformylation reaction N6-formyl-L-lysine is cleaved and returns a K residue. PMID:14755292 RESID:AA0211 deformylation S-geranylgeranyl-L-cysteine is cleaved and returns a C residue. degeranylation PSI-MI MI:0200 degeranylation reaction S-geranylgeranyl-L-cysteine is cleaved and returns a C residue. PMID:14755292 RESID:AA0104 degeranylation N6-myristoyl-L-lysine is cleaved and returns a K residue. demyristoylation PSI-MI MI:0201 demyristoylation reaction N6-myristoyl-L-lysine is cleaved and returns a K residue. PMID:14755292 RESID:AA0078 demyristoylation 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. depalmitoylation PSI-MI MI:0202 depalmitoylation reaction 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. PMID:14755292 RESID:AA0060 RESID:AA0077 RESID:AA0106 depalmitoylation Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues. dephosphorylation PSI-MI MI:0203 dephosphorylation reaction Phosphoresidues are cleaved and return D,C,H,S,T,Y or R residues. GO:0016311 PMID:14755292 RESID:AA0033 RESID:AA0034 RESID:AA0035 RESID:AA0036 RESID:AA0037 RESID:AA0038 RESID:AA0039 RESID:AA0222 dephosphorylation Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. deubiquitination PSI-MI MI:0204 deubiquitination reaction Cleavage of the G-K bond and release of ubiquitin or ubiquitin like proteins. GO:0016579 PMID:11583613 RESID:AA0125 deubiquitination Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading. PSI-MI MI:0205 disaggregation true Dissociation of partners interacting via non-covalent bond. OBSOLETE because considered misleading. PMID:14755292 Reversible reaction that can affect C residue. farnesylation PSI-MI MI:0206 farnesylation reaction Reversible reaction that can affect C residue. GO:0018347 PMID:14755292 RESID:AA0102 farnesylation Reaction that can affect K or G residues. Reside is functionalised with a formyl group. formylation PSI-MI MI:0207 formylation reaction Reaction that can affect K or G residues. Reside is functionalised with a formyl group. GO:0018256 PMID:14755292 RESID:AA0057 RESID:AA0211 formylation 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. Fisher epistasis PSI-MI MI:0208 genetic interaction (sensu unexpected) 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 PMID:16527956 Fisher epistasis PMID:17510664 https://doi.org/10.1017/S0080456800012163 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. geranylgeranylation PSI-MI MI:0209 geranylgeranylation reaction 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. GO:0018348 PMID:14755292 RESID:AA0104 geranylgeranylation 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. hydroxylation PSI-MI MI:0210 hydroxylation reaction 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. GO:0018126 PMID:14755292 RESID:AA0028 RESID:AA0029 RESID:AA0030 RESID:AA0146 RESID:AA0215 hydroxylation Covalent or non covalent binding of lipid group on a protein residue. PSI-MI MI:0211 lipid addition Covalent or non covalent binding of lipid group on a protein residue. GO:0006497 PMID:14755292 Cleavage of a lipid group covalently bound to a protein residue. lipid cleavage PSI-MI MI:0212 lipoprotein cleavage reaction Cleavage of a lipid group covalently bound to a protein residue. PMID:14755292 lipid cleavage 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. methylation PSI-MI MI:0213 methylation reaction 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. GO:0043414 PMID:14755292 RESID:AA0061 RESID:AA0062 RESID:AA0063 RESID:AA0064 RESID:AA0065 RESID:AA0066 RESID:AA0067 RESID:AA0068 RESID:AA0069 RESID:AA0070 RESID:AA0071 RESID:AA0072 RESID:AA0073 RESID:AA0074 RESID:AA0075 RESID:AA0076 RESID:AA0234 RESID:AA0272 methylation 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. myristoylation PSI-MI MI:0214 myristoylation reaction 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. GO:0018319 PMID:14755292 RESID:AA0059 RESID:AA0078 myristoylation Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead. non covalent inter PSI-MI MI:0215 non covalent interaction true Interaction mediated by non-covalent, weak forces rearrangement. OBSOLETE use physical interaction (MI:0218) instead. PMID:14755292 non covalent inter Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues. palmitoylation PSI-MI MI:0216 palmitoylation reaction Covalent attachment of palmitic acid to the cysteine residues of membrane proteins. Reversible reaction that can affect C,K,T or S residues. GO:0018318 PMID:14755292 RESID:AA0060 RESID:AA0077 RESID:AA0079 RESID:AA0080 RESID:AA0106 palmitoylation Reversible reaction that can affect D,C,H,S,T,Y,R residues. phosphorylation PSI-MI MI:0217 phosphorylation reaction Reversible reaction that can affect D,C,H,S,T,Y,R residues. GO:0016310 PMID:14755292 RESID:AA0033 RESID:AA0034 RESID:AA0035 RESID:AA0036 RESID:AA0037 RESID:AA0038 RESID:AA0039 RESID:AA0222 phosphorylation 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. PSI-MI MI:0218 physical interaction true 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. PMID:14755292 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) PSI-MI MI:0219 synthetic lethal true 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) PMID:15608217 Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. ubiquitination PSI-MI MI:0220 ubiquitination reaction Reversible reaction that create a covalent bond between a C-terminus G of ubiquitin and a K residue of the target. GO:0016567 PMID:11583613 RESID:AA0125 ubiquitination Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell. PSI-MI MI:0221 expression level Synthesis rate of a molecule under investigation described in comparison with its naturally occurring expression level in a cell. PMID:14755292 A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate. endogenous endogenous level PSI-MI MI:0222 physiological level A molecule whose synthesis is under control of its natural gene promoter or estimated to be expressed at a similar rate. PMID:14755292 endogenous endogenous level A molecule is estimated to be expressed at lower levels than in physiological condition. under-expressed PSI-MI MI:0223 under expressed level A molecule is estimated to be expressed at lower levels than in physiological condition. PMID:14755292 under-expressed 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. chip-chip PSI-MI MI:0225 chromatin immunoprecipitation array 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. PMID:11125145 PMID:11206552 chip-chip 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. IEC ion exchange chrom PSI-MI MI:0226 ion exchange chromatography 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. PMID:14755292 IEC ion exchange chrom 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. reverse phase chrom PSI-MI MI:0227 reverse phase chromatography 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. PMID:14755292 reverse phase chrom 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 cytoplasmic compl PSI-MI MI:0228 cytoplasmic complementation assay true 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 PMID:14755292 cytoplasmic compl true OBSOLETE remap to MI:0090 protein complementation assay. membrane compl PSI-MI MI:0230 membrane bound complementation assay true OBSOLETE remap to MI:0090 protein complementation assay. PMID:14755292 membrane compl 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. mappit PSI-MI MI:0231 mammalian protein protein interaction trap 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. PMID:12853652 mappit 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. transcription compl PSI-MI MI:0232 transcriptional complementation assay 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. PMID:14755292 transcription compl A stable set of interacting protein and DNA that can be copurified and operate as a functional unit. PSI-MI MI:0233 protein dna complex A stable set of interacting protein and DNA that can be copurified and operate as a functional unit. PMID:14755292 Molecule labelled with 131 radio isotope of iodine atoms. 131I I131 PSI-MI MI:0234 131i radiolabel Molecule labelled with 131 radio isotope of iodine atoms. PMID:14755292 131I I131 Molecule labelled with the radio isotope 14 of carbon atoms. 14C C14 PSI-MI MI:0235 14c radiolabel Molecule labelled with the radio isotope 14 of carbon atoms. PMID:14755292 14C C14 Molecule labelled with the radio isotope 32 of phosphorus atoms. 32P P32 PSI-MI MI:0236 32p radiolabel Molecule labelled with the radio isotope 32 of phosphorus atoms. PMID:14755292 32P P32 Molecule labelled with the radio isotope 33 of phosphorus atoms. 33P P33 PSI-MI MI:0237 33p radiolabel Molecule labelled with the radio isotope 33 of phosphorus atoms. PMID:14755292 33P P33 Molecules labelled with isotope 3 of hydrogen atoms. 3H H3 tritium PSI-MI MI:0238 3h radiolabel Molecules labelled with isotope 3 of hydrogen atoms. PMID:14755292 3H H3 tritium 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. PSI-MI MI:0239 biotin tag 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. PMID:14755292 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. PSI-MI MI:0240 fusion protein 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. PMID:14755292 Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein. hrp tag PSI-MI MI:0241 horseradish peroxidase tag Protein is fused to horseradish peroxidase, and the measure of this enzyme activity can be taken as indicative of presence of protein. PMID:14755292 hrp tag This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference. go-definition-ref PSI-MI MI:0242 gene ontology definition reference This qualifier is used when the crossreference is imported from the Gene Ontology tag definition_reference. PMID:14755292 go-definition-ref Reference to the master sequence from which this isoform has been derived. isoform-parent PSI-MI MI:0243 isoform parent sequence reference Reference to the master sequence from which this isoform has been derived. PMID:14755292 isoform-parent Collection of functional complexes within Reactome - a knowledgebase of biological processes. http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome. id-validation-regexp: search-url: PSI-MI MI:0244 reactome complex true Collection of functional complexes within Reactome - a knowledgebase of biological processes. http://www.reactome.org/. OSOLETE - this concept no longer exists within Reactome. PMID:21067998 id-validation-regexp: REACT_[0-9]{1,5}\.[0-9]{1,3}|[0-9]+ search-url: http://www.reactome.org/cgi-bin/eventbrowser?ID=${ac} Collection of protein within the Reactome database - a knowledgebase of biological processes. http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome. id-validation-regexp: search-url: PSI-MI MI:0245 reactome protein true Collection of protein within the Reactome database - a knowledgebase of biological processes. http://www.reactome.org/. OBSOLETE - this concept no longer exists within Reactome. PMID:21067998 id-validation-regexp: REACT_[0-9]{1,4}\.[0-9]{1,3}|[OPQ][0-9][A-Z0-9]{3}[0-9]|[OPQ][0-9][A-Z0-9]{3}[0-9]-[0-9]+|[A-Z]{3}[0-9]{5}|[OPQ][0-9][A-Z0-9]{3}[0-9]-PRO_[0-9]{10} search-url: http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=${ac} CABRI cell lines catalogue available at. http://www.cabri.org/ id-validation-regexp: search-url: PSI-MI MI:0246 cabri CABRI cell lines catalogue available at. http://www.cabri.org/ PMID:14755292 id-validation-regexp: [0-9]+|ACC\s[A-Z0-9]+|ECACC\s[A-Z0-9]+|LMBP\s[A-Z0-9]+|ICLC\s[A-Z0-9]+|CIP-[0-9]+|DSMZ_MUTZ\:ACC\s[0-9]+ search-url: http://www.cabri.org/CABRI/srs-bin/wgetz?-e+-page+EntryPage+[$id] New EBI Web Taxonomy. http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942 id-validation-regexp: search-url: PSI-MI MI:0247 newt true New EBI Web Taxonomy. http://www.ebi.ac.uk/newt OBSOLETE: Consider remapping to uniprot taxonomy MI:0942 PMID:14755292 id-validation-regexp: [0-9]+ search-url: http://www.ebi.ac.uk/newt/display?search=${ac} 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 id-validation-regexp: search-url: PSI-MI MI:0248 resid 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 PMID:14755292 id-validation-regexp: AA[0-9]{4} search-url: http://srs.ebi.ac.uk/cgi-bin/wgetz?[resid-id:${ac}]+-e A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/ id-validation-regexp: search-url: PSI-MI MI:0249 huge A Database of Human Unidentified Gene-Encoded Large Proteins Analyzed by Kazusa Human cDNA Project. http://www.kazusa.or.jp/huge/ PMID:14755292 id-validation-regexp: KIAA[0-9]{4}[A-Z]{0,1} search-url: http://www.kazusa.or.jp/huge/gfpage/${ac} 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. PSI-MI MI:0250 gene 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. PMID:14755292 SO:0000704 Reference of a protein object pointing to its genomic or nucleic acid sequence. PSI-MI MI:0251 gene product Reference of a protein object pointing to its genomic or nucleic acid sequence. PMID:14755292 Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences. PSI-MI MI:0252 biological feature Property of a subsequence that may be involved with or interfere with the binding of a molecule and are supported by experimental evidences. PMID:14755292 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. PSI-MI MI:0253 isotope label 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. PMID:14755292 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. PSI-MI MI:0254 genetic interference 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. PMID:14755292 This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself. expression interfer PSI-MI MI:0255 post transcriptional interference This term refers to methods designed to interfere with gene expression at post-transcriptional level rather than with the gene itself. PMID:14755292 expression interfer 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. rnai PSI-MI MI:0256 rna interference 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. PMID:12110901 PMID:12408823 rnai 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. PSI-MI MI:0257 antisense rna 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. PMID:1340158 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). PSI-MI MI:0258 inhibitor antibodies true 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). PMID:10189716 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). perturbagens pep PSI-MI MI:0259 perturbagens peptides true 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). PMID:11731788 PMID:8606778 perturbagens pep 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). inhibitor small mol PSI-MI MI:0260 inhibitor small molecules true 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). PMID:10542155 PMID:10780927 inhibitor small mol 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. PSI-MI MI:0261 obsolete suppression true 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. PMID:15608217 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. PSI-MI MI:0262 suppression mutation true 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. PMID:15608217 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. suppress knockout PSI-MI MI:0263 suppression knockout true 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. PMID:15608217 suppress knockout 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. suppression partial PSI-MI MI:0264 suppression partial alteration true 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. PMID:15608217 suppression partial 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. suppress expression PSI-MI MI:0265 suppression expression alteration true 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. PMID:15608217 suppress expression 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. suppress overexpress PSI-MI MI:0266 suppression overexpression true 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. PMID:15608217 suppress overexpress 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. PSI-MI MI:0267 suppression scalable true 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. PMID:15608217 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. suppress underexpres PSI-MI MI:0268 suppression underexpression true 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. PMID:15608217 suppress underexpres 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. PSI-MI MI:0269 synthetic phenotype true 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. PMID:15608217 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) cond syntetic lethal PSI-MI MI:0270 conditional synthetic lethal true 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) PMID:15608217 cond syntetic lethal 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') temprtr synt lethal PSI-MI MI:0271 conditional synthetic lethal temperature-sensitivity true 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') PMID:15608217 temprtr synt lethal 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') synt growth effect PSI-MI MI:0273 synthetic growth effect true 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') PMID:15608217 synt growth effect 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') synt growth defect PSI-MI MI:0274 synthetic growth defect true 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') PMID:15608217 synt growth defect 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') synt growth increase PSI-MI MI:0275 synthetic growth increase true 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') PMID:15608217 synt growth increase 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. bn-page PSI-MI MI:0276 blue native page 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. PMID:14665681 bn-page Descriptor of type of nomenclature used to describe interactor. CvAliasType PSI-MI MI:0300 alias type Descriptor of type of nomenclature used to describe interactor. PMID:14755292 CvAliasType Gene name. gene PSI-MI MI:0301 gene name Gene name. PMID:14755292 gene Gene name synonym. PSI-MI MI:0302 gene name synonym Gene name synonym. PMID:14755292 Synonym as used in Gene Ontology. go synonym PSI-MI MI:0303 gene ontology synonym Synonym as used in Gene Ontology. PMID:14755292 go synonym Isoform synonym. PSI-MI MI:0304 isoform synonym Isoform synonym. PMID:14755292 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. CDS number ONL ORF number Ordered locus name locus name systematic gene number PSI-MI MI:0305 For instance HI0934, Rv3245c, At5g34500, YER456W. ordered locus name 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. PMID:14755292 CDS number ONL ORF number Ordered locus name locus name systematic gene number A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system. orf name PSI-MI MI:0306 For instance MtCY277-28c, SYGP-ORF50, SpBC2F12-04, C06E1, CG10954. Also called Sequencing names or Contig names or Temporary ORFNames. open reading frame name A name temporarily attributed by a sequencing project to an open reading frame. This name is generally based on a cosmid numbering system. PMID:14755292 orf name Method by which molecule is delivered or engineered into a cell. PSI-MI MI:0307 delivery method Method by which molecule is delivered or engineered into a cell. PMID:14755292 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. PSI-MI MI:0308 electroporation 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. PMID:6329708 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). genetic tag insertion PSI-MI MI:0309 genomic tagging true 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). PMID:14755292 genetic tag insertion Molecule introduced into a cell via an external organism, usually a virus or bacteria. PSI-MI MI:0310 infection Molecule introduced into a cell via an external organism, usually a virus or bacteria. PMID:14755292 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. micro-injection PSI-MI MI:0311 microinjection 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. PMID:3016916 micro-injection 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. nucl transfection PSI-MI MI:0312 nucleic acid transfection 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. PMID:14755292 nucl transfection Molecular species involved in the interaction. participant type PSI-MI MI:0313 interactor type Molecular species involved in the interaction. PMID:14755292 participant type Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level. PSI-MI MI:0314 complex Set of interacting molecules that can be copurified. This term and its children should be use only at PARTICIPANT level. PMID:14755292 A stable set of interacting proteins that can be copurified and operate as a functional unit. PSI-MI MI:0315 protein complex A stable set of interacting proteins that can be copurified and operate as a functional unit. PMID:14755292 A macromolecular complex containing both protein and RNA molecules. protein rna complex ribonucleoprot compl PSI-MI MI:0316 ribonucleoprotein complex A macromolecular complex containing both protein and RNA molecules. GO:0030529 PMID:14755292 protein rna complex ribonucleoprot compl Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes. PSI-MI MI:0317 interaction Previously described interaction now being used as an interactor to describe hierarchical build-up of complexes. PMID:14755292 Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages. PSI-MI MI:0318 nucleic acid Linear polymers of nucleotides, linked by 3',5' phosphodiester linkages. PMID:14755292 SO:0000348 Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine. DNA deoxyribonucleic acid dna PSI-MI MI:0319 deoxyribonucleic acid Polymer formed by the deoxyribose sugar group, and the nucleotides bases adenine, guanine, thymine and cytosine. PMID:14755292 SO:0000352 DNA deoxyribonucleic acid dna Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine. RNA rna PSI-MI MI:0320 ribonucleic acid Polymer formed by ribose sugar group, and the bases of the nucleotides adenine, guanine, uracil and cytosine. PMID:14755292 SO:0000356 RNA rna Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link. catalytic RNA catalytic ribonucleic acid crna PSI-MI MI:0321 catalytic rna Species of RNA that catalyses cleavage or trans-esterification of the phosphodiester link. PMID:14755292 catalytic RNA catalytic ribonucleic acid crna Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing. grna guide RNA PSI-MI MI:0322 guide rna Small RNA molecules that hybridize to specific mRNAs and direct their RNA editing. PMID:14755292 grna guide RNA 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. heterogeneous nuclear RNA heterogeneous nuclear ribonucleic acid hnrna PSI-MI MI:0323 heterogeneous nuclear rna 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. PMID:14755292 heterogeneous nuclear RNA heterogeneous nuclear ribonucleic acid hnrna Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains. mRNA mrna PSI-MI MI:0324 messenger rna Single-stranded RNA molecule that specifies the amino acid sequence of one or more polypeptide chains. PMID:14755292 mRNA mrna 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. tRNA transfer RNA transfer ribonucleic acid trna PSI-MI MI:0325 transfer rna 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. PMID:14755292 tRNA transfer RNA transfer ribonucleic acid trna A linear polymer of amino acids joined by peptide bonds in a specific sequence. PSI-MI MI:0326 protein A linear polymer of amino acids joined by peptide bonds in a specific sequence. PMID:14755292 SO:0000358 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. oligopeptide polypeptide PSI-MI MI:0327 peptide 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. PMID:14755292 oligopeptide polypeptide 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. PSI-MI MI:0328 small molecule 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. PMID:14755292 Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level. PSI-MI MI:0329 unknown participant Any type of molecule, including complexes, that may be observed but not identified. This term should be use only at PARTICIPANT level. PMID:14755292 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. PSI-MI MI:0330 molecular source 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. PMID:14755272 Molecule has been added into system from an external source or altered within the cell. PSI-MI MI:0331 engineered Molecule has been added into system from an external source or altered within the cell. PMID:14755292 Unaltered endogenous molecule in its naturally occurring state. endogenous PSI-MI MI:0332 naturally occurring Unaltered endogenous molecule in its naturally occurring state. PMID:14755292 endogenous 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. CvFuzzyType endStatus startStatus PSI-MI MI:0333 feature range status 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. PMID:14755292 CvFuzzyType endStatus startStatus Term describing the last amino acid of a peptide chain. c-term c-terminal c-terminus carboxy-terminus PSI-MI MI:0334 Displayed as 'c'. c-terminal position Term describing the last amino acid of a peptide chain. PMID:14755292 c-term c-terminal c-terminus carboxy-terminus Position within the sequence clearly defined. certain PSI-MI MI:0335 certain sequence position Position within the sequence clearly defined. PMID:14755292 certain Partially determined sequence position known to be in a location higher than a given position. PSI-MI MI:0336 Displayed as '>'. greater-than Partially determined sequence position known to be in a location higher than a given position. PMID:14755292 Partially determined sequence position known to be in a position lower than a given position. PSI-MI MI:0337 Displayed as '<'. less-than Partially determined sequence position known to be in a position lower than a given position. PMID:14755292 Describes a sequence position known to be in a certain range, where the exact position is unclear. PSI-MI MI:0338 For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'. range Describes a sequence position known to be in a certain range, where the exact position is unclear. PMID:14755292 Term describing a completely unknown or unspecified sequence position. undetermined PSI-MI MI:0339 Displayed as '?'. undetermined sequence position Term describing a completely unknown or unspecified sequence position. PMID:14755292 undetermined Term describing the first amino acid of a peptide chain. amino-terminus n-term n-terminal n-terminus PSI-MI MI:0340 Displayed as 'n'. n-terminal position Term describing the first amino acid of a peptide chain. PMID:14755292 amino-terminus n-term n-terminal n-terminus Mixture of protein forms where N-terminus has been progressively truncated. PSI-MI MI:0341 ragged n-terminus Mixture of protein forms where N-terminus has been progressively truncated. PMID:14755292 Indicates the sample context in which each interacting molecule is presented to its partner. PSI-MI MI:0342 sample process Indicates the sample context in which each interacting molecule is presented to its partner. PMID:14755292 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. PSI-MI MI:0343 cdna library 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. PMID:6110205 Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components. PSI-MI MI:0344 cell lysate Cell has been physically or chemically broken open and molecule present in resulting mixture of cellular components. PMID:14755292 Name assigned to a molecule by the authors within a paper that may differ from the reference database. PSI-MI MI:0345 author assigned name Name assigned to a molecule by the authors within a paper that may differ from the reference database. PMID:14755292 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. experimental prep PSI-MI MI:0346 experimental preparation 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. PMID:14755292 experimental prep Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis. PSI-MI MI:0348 fixed cell Cells has been fixed by treatment with organic solvent, staining and inclusion in a resin for microscopic analysis. PMID:14755292 Molecule is observed within in a living cell. PSI-MI MI:0349 living cell Molecule is observed within in a living cell. PMID:14755292 Molecule has undergone one or more purification steps to isolate it from the cellular environment. PSI-MI MI:0350 purified Molecule has undergone one or more purification steps to isolate it from the cellular environment. PMID:14755292 The author states a molecule is completely pure, i.e. no other molecular species are present. pure PSI-MI MI:0351 homogeneous The author states a molecule is completely pure, i.e. no other molecular species are present. PMID:14755292 pure The author states a molecule is only partially purified, i.e. other molecular species also known to be present. PSI-MI MI:0352 partially purified The author states a molecule is only partially purified, i.e. other molecular species also known to be present. PMID:14755292 Qualifier to describe the type of information a cross-reference is pointing to. CvXrefQualifier refType xref type PSI-MI MI:0353 cross-reference type Qualifier to describe the type of information a cross-reference is pointing to. PMID:14755292 CvXrefQualifier refType xref type Cross reference pointing to a Gene Ontology -'cellular component' term. search-url: component go component term PSI-MI MI:0354 cellular component Cross reference pointing to a Gene Ontology -'cellular component' term. PMID:14681407 search-url: https://www.ebi.ac.uk/QuickGO/term/${ac} component go component term Cross reference pointing to a Gene Ontology -'molecular function' term. search-url: function go function term PSI-MI MI:0355 molecular function Cross reference pointing to a Gene Ontology -'molecular function' term. PMID:14681407 search-url: https://www.ebi.ac.uk/QuickGO/term/${ac} function go function term Reference to the corresponding object in another database. Correspondence may be complete or partial. identity PSI-MI MI:0356 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 the corresponding object in another database. Correspondence may be complete or partial. PMID:14755292 identity Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment. PSI-MI MI:0357 method reference Reference to a related paper which more fully describes either the experimental method or one or more of the interactors used within the experiment. PMID:14755292 Used to indicate the PMID from which the experimental data is extracted. PSI-MI MI:0358 primary-reference Used to indicate the PMID from which the experimental data is extracted. PMID:14755292 Cross reference pointing to a Gene Ontology -'cellular process' term. search-url: go process term process PSI-MI MI:0359 biological process Cross reference pointing to a Gene Ontology -'cellular process' term. PMID:14681407 search-url: https://www.ebi.ac.uk/QuickGO/term/${ac} go process term process 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. secondary-ac PSI-MI MI:0360 secondary accession number 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. PMID:14755292 secondary-ac Related object within the same database or pointing to an external database. see-also PSI-MI MI:0361 additional information Related object within the same database or pointing to an external database. PMID:14755292 see-also 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. modeled modelled PSI-MI MI:0362 inference 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. PMID:14755292 modeled modelled 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. modeled by author modelled by author PSI-MI MI:0363 inferred by author 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. PMID:14755292 modeled by author modelled by author 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. modeled by curator modelled by curator PSI-MI MI:0364 inferred by curator 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. PMID:14755292 modeled by curator modelled by curator 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. PSI-MI MI:0365 enzyme tag 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. PMID:10935637 Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein. alk phosphatase tag PSI-MI MI:0366 alkaline phosphatase tag Protein is fused to alkaline phosphatase, and the measure of this enzyme activity can be taken as indicative of presence of protein. PMID:10935637 alk phosphatase tag 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. GFP gfp tag green fluorescent protein PSI-MI MI:0367 green fluorescent protein tag 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. PMID:7491768 GFP gfp tag green fluorescent protein 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. YFP yellow fluorescent protein yfp tag PSI-MI MI:0368 yellow fluorescent protein tag 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. PMID:10929120 YFP yellow fluorescent protein yfp tag 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. gallex PSI-MI MI:0369 lex-a dimerization assay 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. PMID:12446730 gallex gallex 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. toxcat PSI-MI MI:0370 tox-r dimerization assay 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. PMID:9927659 toxcat toxcat Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium. 35S S35 s35 radiolabelled PSI-MI MI:0371 35s radiolabel Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium. PMID:14755292 35S S35 s35 radiolabelled Cell lysates are partially fractionated to isolate a specific subcellular fraction. subcellular prep PSI-MI MI:0372 subcellular preparation Cell lysates are partially fractionated to isolate a specific subcellular fraction. PMID:14755292 subcellular prep Dye coupled to a molecule allowing its identification isolation and monitoring. dye labelled PSI-MI MI:0373 dye label Dye coupled to a molecule allowing its identification isolation and monitoring. PMID:14577292 dye labelled 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. PSI-MI MI:0374 cyanine label 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. PMID:14577292 The organic cyanine Cy3 emits maximally at 570 nm. PSI-MI MI:0375 cy3 label The organic cyanine Cy3 emits maximally at 570 nm. PMID:14577292 The organic cyanine Cy5 emits maximally at 670 nm. PSI-MI MI:0376 cy5 label The organic cyanine Cy5 emits maximally at 670 nm. PMID:14577292 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. FITC labelled fitc labelled fluorescein isothiocyanate labbeled PSI-MI MI:0377 fluorescein isothiocyanate label 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. PMID:14577292 FITC labelled fitc labelled fluorescein isothiocyanate labbeled Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. rare isotope label PSI-MI MI:0378 rare isotope label Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule. PMID:14577292 rare isotope label Molecules labelled with isotope 13 of carbon atoms. 13C C13 PSI-MI MI:0379 13c label Molecules labelled with isotope 13 of carbon atoms. PMID:14577292 13C C13 Molecules labelled with isotope 15 of nytrogen atoms. 15N N15 PSI-MI MI:0380 15n label Molecules labelled with isotope 15 of nytrogen atoms. PMID:14577292 15N N15 Molecules labelled with isotope 2 of hydrogen atoms. 2H2 D2 deuterium PSI-MI MI:0381 2h label Molecules labelled with isotope 2 of hydrogen atoms. PMID:14577292 2H2 D2 deuterium Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction). mutation increasing PSI-MI MI:0382 mutation increasing interaction Region of a molecule whose mutation or deletion increases significantly interaction strength or rate (in the case of interactions inferred from enzymatic reaction). PMID:14577292 mutation increasing Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds. PSI-MI MI:0383 biopolymer Molecule consisting of a specific sequence of amino acidic or nucleotidic monomers strung together through chemical bonds. PMID:14577292 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). PSI-MI MI:0384 alexa label 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). PMID:10449539 Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm. PSI-MI MI:0385 alexa 350 label Alexa fluorescent dye analogue to AMCA (7-amino-4-methylcoumarin-3-acetic acid) with an approximate excitation wavelength maximum of 350 nm. PMID:10449539 Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm. PSI-MI MI:0386 alexa 430 label Alexa fluorescent dye analogue to Lucifer Yellow with an approximate excitation wavelength maximum of 430 nm. PMID:10449539 Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm. PSI-MI MI:0387 alexa 488 label Alexa fluorescent dye analogue to Oregon Green 488 with an approximate excitation wavelength maximum of 488 nm. PMID:10449539 Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm. PSI-MI MI:0388 alexa 532 label Alexa fluorescent dye analogue to Rhodamine 6G with an approximate excitation wavelength maximum of 532nm. PMID:10449539 Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm. PSI-MI MI:0389 alexa 546 label Alexa fluorescent dye analogue to Cy3 with an approximate excitation wavelength maximum of 546nm. PMID:10449539 Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm. PSI-MI MI:0390 alexa 568 label Alexa fluorescent dye analogue to Rhodamine Red-X with an approximate excitation wavelength maximum of 568nm. PMID:10449539 Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm. PSI-MI MI:0391 alexa 594 label Alexa fluorescent dye analogue to Texas Red-X with an approximate excitation wavelength maximum of 594nm. PMID:10449539 Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s). predetermined PSI-MI MI:0396 predetermined participant Molecule whose sequence identity is not checked and has been assumed from external or previous experimental evidence(s). PMID:14755292 predetermined 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. PSI-MI MI:0397 two hybrid array 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. PMID:10688190 PMID:11827624 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. two hybrid pooling PSI-MI MI:0398 two hybrid pooling approach 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. PMID:11283351 PMID:20946815 two hybrid pooling 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. 2h fragment pooling PSI-MI MI:0399 two hybrid fragment pooling approach 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. PMID:12634794 2h fragment pooling Techniques which depend upon the strength of the interaction between two entities. affinity techniques PSI-MI MI:0400 affinity technology Techniques which depend upon the strength of the interaction between two entities. PMID:14755292 affinity techniques The application of chemical principles and methods to biological experiments to demonstrate an interaction. PSI-MI MI:0401 biochemical The application of chemical principles and methods to biological experiments to demonstrate an interaction.