Single molecule simulation of diffusion and enzyme kinetics
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Outros Autores: | , , , |
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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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 |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
institution |
RCAAP |
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 |
repository.mail.fl_str_mv |
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1799132716163137536 |