Estudo computacional da eletroporação de membranas lipídicas
Autor(a) principal: | |
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Data de Publicação: | 2016 |
Tipo de documento: | Tese |
Idioma: | por |
Título da fonte: | Manancial - Repositório Digital da UFSM |
Texto Completo: | http://repositorio.ufsm.br/handle/1/12164 |
Resumo: | In this work we present a computational study of the electroporation process of lipid membranes in the presence of water. First, we developed an investigation of the formation of pores through simulations based on classical molecular dynamics using NAMD code. Subsequently we developed ab initio study using density functional theory, as implemented in the SIESTA code. This analysis showed the formation of pores within the lipid bilayer 1ns after the application of external electric field, 300 K. We found that set temperatures above 300 K may reduce the simulation time. We also observed a rearrangement of water molecules of a Okuno Tanioka cone due to the action of the electric field. Interestingly, this induced an increase of the number of hydrogen bonds, which was not observed using apolar molecules such as chloroform. After, we performed the analysis of structural and electronic properties of the structures of phospholipids,which were extracted from the molecular dynamics calculations. It is noteworthy that the action of the electric field changed the energy gap of both the structures of isolated phospholipid as for the lipid bilayer configuration. Through maps of electrostatic potential, we showed that the electric field leads to a polarization of phospholipid, which induced a torque in the electric dipole moments of the water molecule. The rotation of the electric dipole moments gave rise to stress in the lipid bilayer, which by itself was not enough to break it. In summary, the presence of water was critical since under the action of an electric field the molecules rearranged to form a cone. This fact, associated with the weakening of the lipid membrane due the stress from the realignment electric dipole, was the responsible for the poration process. |
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Estudo computacional da eletroporação de membranas lipídicasComputational study of electroporation of lipid membranesFosfolipídiosCampo elétricoPoroPhospholipidElectric fieldPoreCNPQ::CIENCIAS EXATAS E DA TERRA::FISICAIn this work we present a computational study of the electroporation process of lipid membranes in the presence of water. First, we developed an investigation of the formation of pores through simulations based on classical molecular dynamics using NAMD code. Subsequently we developed ab initio study using density functional theory, as implemented in the SIESTA code. This analysis showed the formation of pores within the lipid bilayer 1ns after the application of external electric field, 300 K. We found that set temperatures above 300 K may reduce the simulation time. We also observed a rearrangement of water molecules of a Okuno Tanioka cone due to the action of the electric field. Interestingly, this induced an increase of the number of hydrogen bonds, which was not observed using apolar molecules such as chloroform. After, we performed the analysis of structural and electronic properties of the structures of phospholipids,which were extracted from the molecular dynamics calculations. It is noteworthy that the action of the electric field changed the energy gap of both the structures of isolated phospholipid as for the lipid bilayer configuration. Through maps of electrostatic potential, we showed that the electric field leads to a polarization of phospholipid, which induced a torque in the electric dipole moments of the water molecule. The rotation of the electric dipole moments gave rise to stress in the lipid bilayer, which by itself was not enough to break it. In summary, the presence of water was critical since under the action of an electric field the molecules rearranged to form a cone. This fact, associated with the weakening of the lipid membrane due the stress from the realignment electric dipole, was the responsible for the poration process.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPESNeste trabalho, apresentamos um estudo computacional do processo de eletroporação de membranas lipídicas na presença de água. Na primeira etapa, realizamos a dinâmica da formação de poros através de simulações baseadas na dinâmica molecular clássica, utilizando o código NAMD. Posteriormente, desenvolvemos um estudo ab initio, empregando a teoria do funcional da densidade, conforme implementada no programa SIESTA. Os resultados da primeira análise mostraram a formação de poros no interior da bicamada após 1ns de aplicação de um campo elétrico externo, a uma temperatura de 300 K. Também verificamos que, para temperaturas acima de 300 K, esse tempo se reduz. Observamos um rearranjo das moléculas de água na forma de um cone de Okuno Tanioka devido à ação do campo elétrico. Isso ocasiona um aumento no número de ligações de hidrogênio das mesmas, o que não foi observado com o uso de moléculas apolares como o clorofórmio. Na segunda etapa, realizamos a análise das propriedades eletrônicas e estruturais, utilizando as estruturas dos fosfolipídios provindas dos cálculos de dinâmica molecular. Mostramos que a ação do campo elétrico modifica o gap de energia tanto da estrutura do fosfolipídio isolado quanto para a configuração de bicamada lipídica. Através dos mapas do potencial eletrostático, mostramos que a ação do campo elétrico leva a uma polarização do fosfolipídio ocasionando um torque no momentos de dipolo elétrico da molécula. A rotação dos momentos de dipolo elétrico causa um estresse na bicamada, que por si só não é capaz de rompe-la. Dessa forma, a presença da água é fundamental, pois diante a ação do campo elétrico as moléculas se reordenam arranjando-se de maneira a formar um cone. Este fato, associado ao enfraquecimento da membrana lipídica, devido ao estresse causado pelo realinhamento nos momentos de dipolo elétrico, são a origem do processo de poração.Universidade Federal de Santa MariaBrasilFísicaUFSMPrograma de Pós-Graduação em FísicaCentro de Ciências Naturais e ExatasSilva, Leandro Barros dahttp://lattes.cnpq.br/2500664315353832Figueiredo, Jacieli Evangelho de2017-12-18T12:59:21Z2017-12-18T12:59:21Z2016-08-03info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/doctoralThesisapplication/pdfhttp://repositorio.ufsm.br/handle/1/12164porAttribution-NonCommercial-NoDerivatives 4.0 Internationalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccessreponame:Manancial - Repositório Digital da UFSMinstname:Universidade Federal de Santa Maria (UFSM)instacron:UFSM2017-12-18T12:59:21Zoai:repositorio.ufsm.br:1/12164Biblioteca Digital de Teses e Dissertaçõeshttps://repositorio.ufsm.br/ONGhttps://repositorio.ufsm.br/oai/requestatendimento.sib@ufsm.br||tedebc@gmail.comopendoar:2017-12-18T12:59:21Manancial - Repositório Digital da UFSM - Universidade Federal de Santa Maria (UFSM)false |
dc.title.none.fl_str_mv |
Estudo computacional da eletroporação de membranas lipídicas Computational study of electroporation of lipid membranes |
title |
Estudo computacional da eletroporação de membranas lipídicas |
spellingShingle |
Estudo computacional da eletroporação de membranas lipídicas Figueiredo, Jacieli Evangelho de Fosfolipídios Campo elétrico Poro Phospholipid Electric field Pore CNPQ::CIENCIAS EXATAS E DA TERRA::FISICA |
title_short |
Estudo computacional da eletroporação de membranas lipídicas |
title_full |
Estudo computacional da eletroporação de membranas lipídicas |
title_fullStr |
Estudo computacional da eletroporação de membranas lipídicas |
title_full_unstemmed |
Estudo computacional da eletroporação de membranas lipídicas |
title_sort |
Estudo computacional da eletroporação de membranas lipídicas |
author |
Figueiredo, Jacieli Evangelho de |
author_facet |
Figueiredo, Jacieli Evangelho de |
author_role |
author |
dc.contributor.none.fl_str_mv |
Silva, Leandro Barros da http://lattes.cnpq.br/2500664315353832 |
dc.contributor.author.fl_str_mv |
Figueiredo, Jacieli Evangelho de |
dc.subject.por.fl_str_mv |
Fosfolipídios Campo elétrico Poro Phospholipid Electric field Pore CNPQ::CIENCIAS EXATAS E DA TERRA::FISICA |
topic |
Fosfolipídios Campo elétrico Poro Phospholipid Electric field Pore CNPQ::CIENCIAS EXATAS E DA TERRA::FISICA |
description |
In this work we present a computational study of the electroporation process of lipid membranes in the presence of water. First, we developed an investigation of the formation of pores through simulations based on classical molecular dynamics using NAMD code. Subsequently we developed ab initio study using density functional theory, as implemented in the SIESTA code. This analysis showed the formation of pores within the lipid bilayer 1ns after the application of external electric field, 300 K. We found that set temperatures above 300 K may reduce the simulation time. We also observed a rearrangement of water molecules of a Okuno Tanioka cone due to the action of the electric field. Interestingly, this induced an increase of the number of hydrogen bonds, which was not observed using apolar molecules such as chloroform. After, we performed the analysis of structural and electronic properties of the structures of phospholipids,which were extracted from the molecular dynamics calculations. It is noteworthy that the action of the electric field changed the energy gap of both the structures of isolated phospholipid as for the lipid bilayer configuration. Through maps of electrostatic potential, we showed that the electric field leads to a polarization of phospholipid, which induced a torque in the electric dipole moments of the water molecule. The rotation of the electric dipole moments gave rise to stress in the lipid bilayer, which by itself was not enough to break it. In summary, the presence of water was critical since under the action of an electric field the molecules rearranged to form a cone. This fact, associated with the weakening of the lipid membrane due the stress from the realignment electric dipole, was the responsible for the poration process. |
publishDate |
2016 |
dc.date.none.fl_str_mv |
2016-08-03 2017-12-18T12:59:21Z 2017-12-18T12:59:21Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/doctoralThesis |
format |
doctoralThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://repositorio.ufsm.br/handle/1/12164 |
url |
http://repositorio.ufsm.br/handle/1/12164 |
dc.language.iso.fl_str_mv |
por |
language |
por |
dc.rights.driver.fl_str_mv |
Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
Attribution-NonCommercial-NoDerivatives 4.0 International http://creativecommons.org/licenses/by-nc-nd/4.0/ |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Universidade Federal de Santa Maria Brasil Física UFSM Programa de Pós-Graduação em Física Centro de Ciências Naturais e Exatas |
publisher.none.fl_str_mv |
Universidade Federal de Santa Maria Brasil Física UFSM Programa de Pós-Graduação em Física Centro de Ciências Naturais e Exatas |
dc.source.none.fl_str_mv |
reponame:Manancial - Repositório Digital da UFSM instname:Universidade Federal de Santa Maria (UFSM) instacron:UFSM |
instname_str |
Universidade Federal de Santa Maria (UFSM) |
instacron_str |
UFSM |
institution |
UFSM |
reponame_str |
Manancial - Repositório Digital da UFSM |
collection |
Manancial - Repositório Digital da UFSM |
repository.name.fl_str_mv |
Manancial - Repositório Digital da UFSM - Universidade Federal de Santa Maria (UFSM) |
repository.mail.fl_str_mv |
atendimento.sib@ufsm.br||tedebc@gmail.com |
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