title: Single Molecule Simulation of Diffusion and Enzyme Kinetics.
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.
authors.affiliation: ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico , Campus Universitario As Lagoas s/n, 32004 Ourense, Spain.
authors.forename: Gael
authors.initials: G
authors.lastname: Pérez-Rodríguez
authors.affiliation: LEPABE - Department of Chemical Engineering, Faculty of Engineering, University of Porto , Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
authors.forename: Denise
authors.initials: D
authors.lastname: Gameiro
authors.affiliation: ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico , Campus Universitario As Lagoas s/n, 32004 Ourense, Spain.
authors.forename: Martín
authors.initials: M
authors.lastname: Pérez-Pérez
authors.affiliation: ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico , Campus Universitario As Lagoas s/n, 32004 Ourense, Spain.|CEB - Centre of Biological Engineering, University of Minho , Campus de Gualtar, 4710-057 Braga, Portugal.
authors.forename: Anália
authors.initials: A
authors.lastname: Lourenço
authors.affiliation: LEPABE - Department of Chemical Engineering, Faculty of Engineering, University of Porto , Rua Dr. Roberto Frias, 4200-465 Porto, Portugal.
authors.forename: Nuno F
authors.initials: NF
authors.lastname: Azevedo
mesh_terms: D004058:Diffusion; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D013251:Steroid Isomerases / Q000737:chemistry* / Q000378:metabolism*
chemical_list: D013251:Steroid Isomerases; C022660:steroid delta-isomerase