Utilize este identificador para referenciar este registo:
https://hdl.handle.net/1822/41658
Título: | Single molecule simulation of diffusion and enzyme kinetics |
Autor(es): | Pérez-Rodríguez, Gael Gameiro, Denise Pérez-Pérez, Martín Lourenço, Anália Azevedo, Nuno F. |
Data: | 2016 |
Editora: | American Chemical Society |
Revista: | Journal of Physical Chemistry B |
Citação: | Pérez-Rodríguez, Gael; Gameiro, Denise; Pérez-Pérez, Martín; Lourenço, Anália; Azevedo, Nuno F., Single molecule simulation of diffusion and enzyme kinetics. Journal of Physical Chemistry B, 120(16), 3809-3820, 2016 |
Resumo(s): | 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. |
Tipo: | Artigo |
URI: | https://hdl.handle.net/1822/41658 |
DOI: | 10.1021/acs.jpcb.5b12544 |
ISSN: | 1520-6106 |
Versão da editora: | http://pubs.acs.org/journal/jpcbfk |
Arbitragem científica: | yes |
Acesso: | Acesso aberto |
Aparece nas coleções: | CEB - Publicações em Revistas/Séries Internacionais / Publications in International Journals/Series |
Ficheiros deste registo:
Ficheiro | Descrição | Tamanho | Formato | |
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document_38978_1.pdf | 3,95 MB | Adobe PDF | Ver/Abrir |