Single Molecule Simulation of Diffusion and Enzyme Kinetics

This work presents a molecular-scale agent-based model for the simulationof enzymatic reactions at experimentally measured concentrations. The modelincorporates stochasticity and spatial dependence, using diffusing and reacting particleswith physical dimensions. We developed strategies to adjust and validate the enzymaticrates and diffusion coefficients to the information required by the computational agents,i.e., collision efficiency, interaction logic between agents, the time scale associated withinteractions (e.g., kinetics), and agent velocity. Also, we tested the impact of molecularlocation (a source of biological noise) in the speed at which the reactions take place.Simulations were conducted for experimental data on the 2-hydroxymuconatetautomerase (EC 5.3.2.6, UniProt ID Q01468) and the Steroid Delta-isomerase (EC5.3.3.1, UniProt ID P07445). Obtained results demonstrate that our approach is inaccordance to existing experimental data and long-term biophysical and biochemicalassumptions