Single Molecule Simulation of Diffusion and Enzyme Kinetics
Authored by Gael Perez-Rodriguez, Martin Perez-Perez, Nuno F Azevedo, Analia Lourenco, Denise Gameiro
Date Published: 2016
DOI: 10.1021/acs.jpcb.5b12544
Sponsors:
European Union
Platforms:
Java
MASON
Model Documentation:
Other Narrative
Flow charts
Mathematical description
Model Code URLs:
Model code not found
Abstract
This work presents a molecular-scale agent-based model for the
simulation of enzymatic reactions at experimentally measured
concentrations. The model incorporates stochasticity and spatial
dependence, using diffusing and reacting particles with physical
dimensions. We developed strategies to adjust and validate the enzymatic
rates and diffusion coefficients to the information required by the
computational agents, i.e., collision efficiency, interaction logic
between agents, the time scale associated with interactions (e.g., kinetics), and agent velocity. Also, we tested the impact of molecular
location (a source of biological noise) in the speed at which the
reactions take place. Simulations were conducted for experimental data
on the 2-hydroxymuconate tautomerase (EC 5.3.2.6, UniProt ID Q01468) and
the Steroid Delta-isomerase (EC 5.3.3.1, UniProt ID P07445). Obtained
results demonstrate that our approach is in accordance to existing
experimental data and long-term biophysical and biochemical assumptions.
Tags
noise
Origins
Gene-expression
Escherichia-coli
Identification
Michaelis-menten equation
Active-site
Isomerase
Pathways