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Author(s): Gael Pérez-Rodríguez
Denise Gameiro
Martín Pérez-Pérez
Anália Lourenço
Nuno F. Azevedo
Title: Single Molecule Simulation of Diffusion and Enzyme Kinetics
Issue Date: 2016
Abstract: 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, 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.
Related Information: info:eu-repo/grantAgreement/Autoriadade de Gestão do Programa Operacional Regional do Norte/Programas Integrados de IC&DT/NORTE-07-0124-FEDER-000025/(Bio) Chemical Engineering: Multi-Scale Approaches for Sustainable Environment and Health/LEPAE/CEFT - RL2
info:eu-repo/grantAgreement/FCT - Fundação para a Ciência e Tecnologia/Projetos Estratégicos/UID/EQU/00511/2013 - POCI-01-0145-FEDER-006939/Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia/LEPABE
Document Type: Artigo em Revista Científica Internacional
Rights: restrictedAccess
Appears in Collections:FEUP - Artigo em Revista Científica Internacional

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