Single molecule simulation of diffusion and enzyme kinetics

Detalhes bibliográficos
Autor(a) principal: Pérez-Rodríguez, Gael
Data de Publicação: 2016
Outros Autores: Gameiro, Denise, Pérez-Pérez, Martín, Lourenço, Anália, Azevedo, Nuno F.
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/1822/41658
Resumo: 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.
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spelling Single molecule simulation of diffusion and enzyme kineticsScience & TechnologyThis 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.This work was financially supported by Project UID/EQU/ 00511/2013-LEPABE, by the FCT/MEC with national funds and when applicable cofunded by FEDER in the scope of the P2020 Partnership Agreement; Project NORTE-07-0124FEDER-000025 - RL2 Environment&Health, by FEDER funds through Programa Operacional Factores de Competitividade - COMPETE, by the Programa Operacional do Norte (ON2) program and by national funds through FCT Fundação para a Ciência e a Tecnologia. This work was also partially funded by the [14VI05] Contract-Programme from the University of Vigo and the Agrupamento INBIOMED from DXPCTSUG-FEDER unha maneira de facer Europa (2012/ 273). The research leading to these results has received funding from the European Union’s Seventh Framework Programme FP7/REGPOT-2012-2013.1 under Grant Agreement No. 316265, BIOCAPS. This document reflects only the author’s views and the European Union is not liable for any use that may be made of the information contained herein.American Chemical SocietyUniversidade do MinhoPérez-Rodríguez, GaelGameiro, DenisePérez-Pérez, MartínLourenço, AnáliaAzevedo, Nuno F.20162016-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/41658engPérez-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, 20161520-610610.1021/acs.jpcb.5b1254427049044http://pubs.acs.org/journal/jpcbfkinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-21T12:29:01Zoai:repositorium.sdum.uminho.pt:1822/41658Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:23:55.650693Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Single molecule simulation of diffusion and enzyme kinetics
title Single molecule simulation of diffusion and enzyme kinetics
spellingShingle Single molecule simulation of diffusion and enzyme kinetics
Pérez-Rodríguez, Gael
Science & Technology
title_short Single molecule simulation of diffusion and enzyme kinetics
title_full Single molecule simulation of diffusion and enzyme kinetics
title_fullStr Single molecule simulation of diffusion and enzyme kinetics
title_full_unstemmed Single molecule simulation of diffusion and enzyme kinetics
title_sort Single molecule simulation of diffusion and enzyme kinetics
author Pérez-Rodríguez, Gael
author_facet Pérez-Rodríguez, Gael
Gameiro, Denise
Pérez-Pérez, Martín
Lourenço, Anália
Azevedo, Nuno F.
author_role author
author2 Gameiro, Denise
Pérez-Pérez, Martín
Lourenço, Anália
Azevedo, Nuno F.
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Universidade do Minho
dc.contributor.author.fl_str_mv Pérez-Rodríguez, Gael
Gameiro, Denise
Pérez-Pérez, Martín
Lourenço, Anália
Azevedo, Nuno F.
dc.subject.por.fl_str_mv Science & Technology
topic Science & Technology
description 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.
publishDate 2016
dc.date.none.fl_str_mv 2016
2016-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/1822/41658
url http://hdl.handle.net/1822/41658
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv 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
1520-6106
10.1021/acs.jpcb.5b12544
27049044
http://pubs.acs.org/journal/jpcbfk
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv American Chemical Society
publisher.none.fl_str_mv American Chemical Society
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
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reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
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