{ "cells": [ { "cell_type": "markdown", "id": "5cbc8640", "metadata": {}, "source": [ "# **Enzyme Kinetics** : \n", "#### _Accurate numerical solution_ - compared to the **Michaelis-Menten** model approximation and to the alternative **Morrison** model.\n", "\n", "#### Two Coupled Reactions: `E + S <-> ES`, and `ES -> E + P` , using real-life kinetic parameters. \n", "#### Scenario with _small amount of Enzyme_, relative to the initial Substrate concentration.\n", "\n", "#### Unlike in experiment `enzyme_1_a`, we'll use data from a reaction that **VIOLATES the customary Michaelis-Menten assumption** that the rate constants satisfy `k1_reverse >> k2_forward`" ] }, { "cell_type": "markdown", "id": "604b150b-7812-4fd3-9403-69a06dd7e397", "metadata": {}, "source": [ "### THE REACTION: \n", "the enzyme `Aminopeptidase` with the substrate `Leu-Ala-DED`, \n", "and the initial concentration values choosen below, all satisfy the customary Michaelis-Menten assumptions that `[E] << [S]` BUT the reaction rate constants DON'T satisfy `k1_reverse >> k2_forward`\n", "\n", "For this reaction: k1_forward = 160 , k1_reverse = 0.089 , k2_forward = 0.58 \n", "\n", "Source of kinetic parameters: *page 16 of \"Analysis of Enzyme Reaction Kinetics, Vol. 1\", by F. Xavier Malcata, Wiley, 2023*" ] }, { "cell_type": "markdown", "id": "c123db4f-c802-47f0-a3d3-0b857314d8e5", "metadata": {}, "source": [ "### TAGS : \"uniform compartment\", \"chemistry\", \"numerical\", \"enzymes\"" ] }, { "cell_type": "code", "execution_count": 1, "id": "6e9d0902-6fc9-4692-ac39-0651d08902ca", "metadata": {}, "outputs": [], "source": [ "LAST_REVISED = \"Jan. 12, 2025\"\n", "LIFE123_VERSION = \"1.0.0rc2\" # Library version this experiment is based on" ] }, { "cell_type": "code", "execution_count": 2, "id": "1e0ae9a9-9d0c-4edf-a5f2-1c589419e6cf", "metadata": {}, "outputs": [], "source": [ "#import set_path # Using MyBinder? Uncomment this before running the next cell!" ] }, { "cell_type": "code", "execution_count": 3, "id": "a29db1c7", "metadata": { "tags": [] }, "outputs": [], "source": [ "#import sys\n", "#sys.path.append(\"C:/some_path/my_env_or_install\") # CHANGE to the folder containing your venv or libraries installation!\n", "# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try: import set_path \n", "\n", "import ipynbname\n", "import pandas as pd\n", "\n", "from life123 import check_version, ChemData, UniformCompartment, ReactionEnz, PlotlyHelper" ] }, { "cell_type": "code", "execution_count": 4, "id": "af15ecf0-e083-4fef-b68e-abe794dcc86e", "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "OK\n" ] } ], "source": [ "check_version(LIFE123_VERSION)" ] }, { "cell_type": "code", "execution_count": null, "id": "3713fa4d-e9bb-4e33-8734-c1d4d23cf177", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "code", "execution_count": null, "id": "34d1cefc-f644-410a-9fe4-5204964742ac", "metadata": {}, "outputs": [], "source": [] }, { "cell_type": "markdown", "id": "91a729ee-ad2f-4771-bc84-49ecb9d6a851", "metadata": {}, "source": [ "# 1. Accurate numerical solution" ] }, { "cell_type": "code", "execution_count": 5, "id": "959cf00a-47b3-455b-9923-9ec8741cc863", "metadata": {}, "outputs": [], "source": [ "chem_data = ChemData(names=[\"P\", \"ES\"], plot_colors=[\"green\", \"red\"])" ] }, { "cell_type": "code", "execution_count": 6, "id": "90f9ec41-6e1b-4558-9400-47e35ece6efc", "metadata": {}, "outputs": [ { "data": { "text/html": [ "
| \n", " | name | \n", "label | \n", "plot_color | \n", "
|---|---|---|---|
| 0 | \n", "P | \n", "P | \n", "green | \n", "
| 1 | \n", "ES | \n", "ES | \n", "red | \n", "
| 2 | \n", "Aminopeptidase | \n", "E | \n", "violet | \n", "
| 3 | \n", "Leu-Ala-DED | \n", "S | \n", "darkturquoise | \n", "
| \n", " | SYSTEM TIME | \n", "P | \n", "ES | \n", "E | \n", "S | \n", "step | \n", "caption | \n", "
|---|---|---|---|---|---|---|---|
| 0 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "1.000000 | \n", "20.000000 | \n", "\n", " | Set concentration | \n", "
| 1 | \n", "0.000010 | \n", "0.000000e+00 | \n", "0.032000 | \n", "0.968000 | \n", "19.968000 | \n", "1 | \n", "1st reaction step | \n", "
| 2 | \n", "0.000021 | \n", "2.041600e-07 | \n", "0.066019 | \n", "0.933981 | \n", "19.933981 | \n", "2 | \n", "\n", " |
| 3 | \n", "0.000024 | \n", "3.305201e-07 | \n", "0.075849 | \n", "0.924151 | \n", "19.924151 | \n", "3 | \n", "\n", " |
| 4 | \n", "0.000025 | \n", "3.740726e-07 | \n", "0.078766 | \n", "0.921234 | \n", "19.921234 | \n", "4 | \n", "\n", " |
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 169 | \n", "0.001437 | \n", "6.495498e-04 | \n", "0.988861 | \n", "0.011139 | \n", "19.010489 | \n", "169 | \n", "\n", " |
| 170 | \n", "0.001454 | \n", "6.594576e-04 | \n", "0.989435 | \n", "0.010565 | \n", "19.009906 | \n", "170 | \n", "\n", " |
| 171 | \n", "0.001472 | \n", "6.693712e-04 | \n", "0.989979 | \n", "0.010021 | \n", "19.009352 | \n", "171 | \n", "\n", " |
| 172 | \n", "0.001489 | \n", "6.792902e-04 | \n", "0.990494 | \n", "0.009506 | \n", "19.008827 | \n", "172 | \n", "\n", " |
| 173 | \n", "0.001506 | \n", "6.892144e-04 | \n", "0.990982 | \n", "0.009018 | \n", "19.008329 | \n", "173 | \n", "last reaction step | \n", "
174 rows × 7 columns
\n", "| \n", " | SYSTEM TIME | \n", "rxn0_rate | \n", "rxn1_rate | \n", "step | \n", "
|---|---|---|---|---|
| 0 | \n", "0.000000 | \n", "3200.000000 | \n", "0.000000 | \n", "0 | \n", "
| 1 | \n", "0.000010 | \n", "3092.640992 | \n", "0.018560 | \n", "1 | \n", "
| 2 | \n", "0.000021 | \n", "2978.868127 | \n", "0.038291 | \n", "2 | \n", "
| 3 | \n", "0.000024 | \n", "2946.061101 | \n", "0.043992 | \n", "3 | \n", "
| 4 | \n", "0.000025 | \n", "2936.333355 | \n", "0.045684 | \n", "4 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 168 | \n", "0.001420 | \n", "35.636312 | \n", "0.573188 | \n", "168 | \n", "
| 169 | \n", "0.001437 | \n", "33.792720 | \n", "0.573539 | \n", "169 | \n", "
| 170 | \n", "0.001454 | \n", "32.046189 | \n", "0.573872 | \n", "170 | \n", "
| 171 | \n", "0.001472 | \n", "30.391600 | \n", "0.574188 | \n", "171 | \n", "
| 172 | \n", "0.001489 | \n", "28.824102 | \n", "0.574486 | \n", "172 | \n", "
173 rows × 4 columns
\n", "| \n", " | SYSTEM TIME | \n", "rxn0_rate | \n", "rxn1_rate | \n", "step | \n", "
|---|---|---|---|---|
| 0 | \n", "0.000000 | \n", "3200.000000 | \n", "0.000000 | \n", "0 | \n", "
| 1 | \n", "0.000010 | \n", "3092.640992 | \n", "0.018560 | \n", "1 | \n", "
| 2 | \n", "0.000021 | \n", "2978.868127 | \n", "0.038291 | \n", "2 | \n", "
| 3 | \n", "0.000024 | \n", "2946.061101 | \n", "0.043992 | \n", "3 | \n", "
| 4 | \n", "0.000025 | \n", "2936.333355 | \n", "0.045684 | \n", "4 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 11262 | \n", "39.665419 | \n", "-0.000790 | \n", "0.010425 | \n", "110889 | \n", "
| 11263 | \n", "39.670501 | \n", "-0.000339 | \n", "0.010393 | \n", "110899 | \n", "
| 11264 | \n", "39.683681 | \n", "-0.000027 | \n", "0.010313 | \n", "110909 | \n", "
| 11265 | \n", "39.717866 | \n", "0.000006 | \n", "0.010110 | \n", "110919 | \n", "
| 11266 | \n", "39.806534 | \n", "0.000006 | \n", "0.009602 | \n", "110929 | \n", "
11267 rows × 4 columns
\n", "| \n", " | SYSTEM TIME | \n", "P | \n", "ES | \n", "E | \n", "S | \n", "step | \n", "caption | \n", "P_rate | \n", "
|---|---|---|---|---|---|---|---|---|
| 0 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "1.000000 | \n", "20.000000 | \n", "\n", " | Set concentration | \n", "0.000000 | \n", "
| 1 | \n", "0.000010 | \n", "0.000000e+00 | \n", "0.032000 | \n", "0.968000 | \n", "19.968000 | \n", "1 | \n", "1st reaction step | \n", "0.018560 | \n", "
| 2 | \n", "0.000021 | \n", "2.041600e-07 | \n", "0.066019 | \n", "0.933981 | \n", "19.933981 | \n", "2 | \n", "\n", " | 0.038291 | \n", "
| 3 | \n", "0.000024 | \n", "3.305201e-07 | \n", "0.075849 | \n", "0.924151 | \n", "19.924151 | \n", "3 | \n", "\n", " | 0.043992 | \n", "
| 4 | \n", "0.000025 | \n", "3.740726e-07 | \n", "0.078766 | \n", "0.921234 | \n", "19.921234 | \n", "4 | \n", "\n", " | 0.045684 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 11262 | \n", "39.665419 | \n", "1.998202e+01 | \n", "0.017975 | \n", "0.982025 | \n", "0.000005 | \n", "110889 | \n", "\n", " | 0.010425 | \n", "
| 11263 | \n", "39.670501 | \n", "1.998207e+01 | \n", "0.017919 | \n", "0.982081 | \n", "0.000008 | \n", "110899 | \n", "\n", " | 0.010393 | \n", "
| 11264 | \n", "39.683681 | \n", "1.998221e+01 | \n", "0.017781 | \n", "0.982219 | \n", "0.000010 | \n", "110909 | \n", "\n", " | 0.010313 | \n", "
| 11265 | \n", "39.717866 | \n", "1.998256e+01 | \n", "0.017431 | \n", "0.982569 | \n", "0.000010 | \n", "110919 | \n", "\n", " | 0.010110 | \n", "
| 11266 | \n", "39.806534 | \n", "1.998344e+01 | \n", "0.016556 | \n", "0.983444 | \n", "0.000009 | \n", "110929 | \n", "\n", " | 0.009602 | \n", "
11267 rows × 8 columns
\n", "| \n", " | SYSTEM TIME | \n", "P | \n", "ES | \n", "E | \n", "S | \n", "step | \n", "caption | \n", "P_rate | \n", "Michaelis_rate | \n", "
|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "1.000000 | \n", "20.000000 | \n", "\n", " | Set concentration | \n", "0.000000 | \n", "0.579879 | \n", "
| 1 | \n", "0.000010 | \n", "0.000000e+00 | \n", "0.032000 | \n", "0.968000 | \n", "19.968000 | \n", "1 | \n", "1st reaction step | \n", "0.018560 | \n", "0.579879 | \n", "
| 2 | \n", "0.000021 | \n", "2.041600e-07 | \n", "0.066019 | \n", "0.933981 | \n", "19.933981 | \n", "2 | \n", "\n", " | 0.038291 | \n", "0.579878 | \n", "
| 3 | \n", "0.000024 | \n", "3.305201e-07 | \n", "0.075849 | \n", "0.924151 | \n", "19.924151 | \n", "3 | \n", "\n", " | 0.043992 | \n", "0.579878 | \n", "
| 4 | \n", "0.000025 | \n", "3.740726e-07 | \n", "0.078766 | \n", "0.921234 | \n", "19.921234 | \n", "4 | \n", "\n", " | 0.045684 | \n", "0.579878 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 11262 | \n", "39.665419 | \n", "1.998202e+01 | \n", "0.017975 | \n", "0.982025 | \n", "0.000005 | \n", "110889 | \n", "\n", " | 0.010425 | \n", "0.000714 | \n", "
| 11263 | \n", "39.670501 | \n", "1.998207e+01 | \n", "0.017919 | \n", "0.982081 | \n", "0.000008 | \n", "110899 | \n", "\n", " | 0.010393 | \n", "0.001106 | \n", "
| 11264 | \n", "39.683681 | \n", "1.998221e+01 | \n", "0.017781 | \n", "0.982219 | \n", "0.000010 | \n", "110909 | \n", "\n", " | 0.010313 | \n", "0.001370 | \n", "
| 11265 | \n", "39.717866 | \n", "1.998256e+01 | \n", "0.017431 | \n", "0.982569 | \n", "0.000010 | \n", "110919 | \n", "\n", " | 0.010110 | \n", "0.001371 | \n", "
| 11266 | \n", "39.806534 | \n", "1.998344e+01 | \n", "0.016556 | \n", "0.983444 | \n", "0.000009 | \n", "110929 | \n", "\n", " | 0.009602 | \n", "0.001301 | \n", "
11267 rows × 9 columns
\n", "| \n", " | SYSTEM TIME | \n", "P | \n", "ES | \n", "E | \n", "S | \n", "step | \n", "caption | \n", "P_rate | \n", "Michaelis_rate | \n", "Morrison_rate | \n", "
|---|---|---|---|---|---|---|---|---|---|---|
| 0 | \n", "0.000000 | \n", "0.000000e+00 | \n", "0.000000 | \n", "1.000000 | \n", "20.000000 | \n", "\n", " | Set concentration | \n", "0.000000 | \n", "0.579879 | \n", "0.579872 | \n", "
| 1 | \n", "0.000010 | \n", "0.000000e+00 | \n", "0.032000 | \n", "0.968000 | \n", "19.968000 | \n", "1 | \n", "1st reaction step | \n", "0.018560 | \n", "0.579879 | \n", "0.579872 | \n", "
| 2 | \n", "0.000021 | \n", "2.041600e-07 | \n", "0.066019 | \n", "0.933981 | \n", "19.933981 | \n", "2 | \n", "\n", " | 0.038291 | \n", "0.579878 | \n", "0.579872 | \n", "
| 3 | \n", "0.000024 | \n", "3.305201e-07 | \n", "0.075849 | \n", "0.924151 | \n", "19.924151 | \n", "3 | \n", "\n", " | 0.043992 | \n", "0.579878 | \n", "0.579872 | \n", "
| 4 | \n", "0.000025 | \n", "3.740726e-07 | \n", "0.078766 | \n", "0.921234 | \n", "19.921234 | \n", "4 | \n", "\n", " | 0.045684 | \n", "0.579878 | \n", "0.579872 | \n", "
| ... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "... | \n", "
| 11262 | \n", "39.665419 | \n", "1.998202e+01 | \n", "0.017975 | \n", "0.982025 | \n", "0.000005 | \n", "110889 | \n", "\n", " | 0.010425 | \n", "0.000714 | \n", "0.010384 | \n", "
| 11263 | \n", "39.670501 | \n", "1.998207e+01 | \n", "0.017919 | \n", "0.982081 | \n", "0.000008 | \n", "110899 | \n", "\n", " | 0.010393 | \n", "0.001106 | \n", "0.010354 | \n", "
| 11264 | \n", "39.683681 | \n", "1.998221e+01 | \n", "0.017781 | \n", "0.982219 | \n", "0.000010 | \n", "110909 | \n", "\n", " | 0.010313 | \n", "0.001370 | \n", "0.010275 | \n", "
| 11265 | \n", "39.717866 | \n", "1.998256e+01 | \n", "0.017431 | \n", "0.982569 | \n", "0.000010 | \n", "110919 | \n", "\n", " | 0.010110 | \n", "0.001371 | \n", "0.010073 | \n", "
| 11266 | \n", "39.806534 | \n", "1.998344e+01 | \n", "0.016556 | \n", "0.983444 | \n", "0.000009 | \n", "110929 | \n", "\n", " | 0.009602 | \n", "0.001301 | \n", "0.009567 | \n", "
11267 rows × 10 columns
\n", "