Single Molecule Simulation of Diffusion and Enzyme Kinetics

• Type: Article in International Scientific Journal
• Date: 2016

Authors

Gael Pérez-Rodríguez (Author) Other; Denise Gameiro (Author) Other; Martín Pérez-Pérez (Author) Other; Anália Lourenço (Author) Other; Nuno F. Azevedo (Author) FEUP

Journal

Title: Journal of Physical Chemistry B

Vol. 120 No. 16

Pages: 3809-3820

ISSN: 1520-6106

Publisher: American Chemical Society

Indexing

ISI Web of Knowledge

ISI Web of Science

Scopus

Associated Projects

LEPAE/CEFT - RL2 - (Bio) Chemical Engineering: Multi-Scale Approaches for Sustainable Environment and Health

LEPABE - Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia

Other information

DOI: 10.1021/acs.jpcb.5b12544

Abstract (EN): 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 12