Single Molecule Simulation of Diffusion and Enzyme Kinetics

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.