Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation

Detalhes bibliográficos
Autor(a) principal: Pascutti, Pedro Geraldo
Data de Publicação: 1999
Outros Autores: Mundim, Kleber Carlos, Ito, Amando Siuiti, Bisch, Paulo Mascarello
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Institucional da UFBA
Texto Completo: http://www.repositorio.ufba.br/ri/handle/ri/13243
Resumo: Texto completo. Acesso restrito. p. 971-982
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spelling Pascutti, Pedro GeraldoMundim, Kleber CarlosIto, Amando SiuitiBisch, Paulo MascarelloPascutti, Pedro GeraldoMundim, Kleber CarlosIto, Amando SiuitiBisch, Paulo Mascarello2013-10-15T15:23:35Z2013-10-15T15:23:35Z19990192-8651http://www.repositorio.ufba.br/ri/handle/ri/13243v. 20, n. 9Texto completo. Acesso restrito. p. 971-982The electrostatic image method was applied to investigate the conformation of peptides characterized by different hydrophobicities in a water]membrane interface model. The interface was represented by a surface of discontinuity between two media with different dielectric constants, taking into account the difference between the polarizabilities of the aqueous medium and the hydrocarbon one. The method consists of a substitution of the real problem, which involves the charges and the induced polarization at the surface of discontinuity, by a simpler problem formed with charges and their images. The electric field due to the polarization induced at the surface by charge q was calculated using a hypothetical charge q9 image of q., symmetrically located on the opposite side of the surface. The value of q9 was determined using the appropriate electrostatic boundary conditions at the surface. By means of this procedure, the effect of the interface can be introduced easily in the usual force field. We included this extension in the computational package that we are developing for molecular dynamics simulations THOR.. The peptides studied included hydrophilic tetraaspartic acid Asp]Asp]Asp]Asp., tetralysine Lys]Lys]Lys]Lys., hydrophobic tetrapeptide His]Phe]Arg]Trp., an amphiphilic fragment of b-endorphin, and the signal sequence of the E. coli l-receptor. The simulation results are in agreement with known experimental data regarding the behavior of peptides at the water]membrane interface. An analysis of the conformational dynamics of the signal sequence peptide at the interface was performed over the course of a few nanoseconds.Submitted by Santiago Fabio (fabio.ssantiago@hotmail.com) on 2013-08-06T19:20:24Z No. of bitstreams: 1 66666666666666666.pdf: 355834 bytes, checksum: d9b0720f37da2a21090d9277004d0a0e (MD5)Approved for entry into archive by Rodrigo Meirelles(rodrigomei@ufba.br) on 2013-10-15T15:23:35Z (GMT) No. of bitstreams: 1 66666666666666666.pdf: 355834 bytes, checksum: d9b0720f37da2a21090d9277004d0a0e (MD5)Made available in DSpace on 2013-10-15T15:23:35Z (GMT). No. of bitstreams: 1 66666666666666666.pdf: 355834 bytes, checksum: d9b0720f37da2a21090d9277004d0a0e (MD5) Previous issue date: 1999SalvadorJournal of Computational Chemistryhttp://onlinelibrary-wiley-com.ez10.periodicos.capes.gov.br/doi/10.1002/(SICI)1096-987X(19990715)20:9%3C971reponame:Repositório Institucional da UFBAinstname:Universidade Federal da Bahia (UFBA)instacron:UFBAhydrophobic effectmolecular dynamics simulationselectrostatic image methodwater]membrane modelb-endorphin and signal sequence conformationsPolarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics SimulationJournal of Computational Chemistryinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleenginfo:eu-repo/semantics/openAccessORIGINAL66666666666666666.pdf66666666666666666.pdfapplication/pdf355834https://repositorio.ufba.br/bitstream/ri/13243/1/66666666666666666.pdfd9b0720f37da2a21090d9277004d0a0eMD51LICENSElicense.txtlicense.txttext/plain1762https://repositorio.ufba.br/bitstream/ri/13243/2/license.txt1b89a9a0548218172d7c829f87a0eab9MD52TEXT66666666666666666.pdf.txt66666666666666666.pdf.txtExtracted texttext/plain42449https://repositorio.ufba.br/bitstream/ri/13243/3/66666666666666666.pdf.txt159f2ce63063841ddcb1510f0d8241e6MD53ri/132432022-07-05 14:03:09.385oai:repositorio.ufba.br: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Repositório InstitucionalPUBhttp://192.188.11.11:8080/oai/requestopendoar:19322022-07-05T17:03:09Repositório Institucional da UFBA - Universidade Federal da Bahia (UFBA)false
dc.title.pt_BR.fl_str_mv Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation
dc.title.alternative.pt_BR.fl_str_mv Journal of Computational Chemistry
title Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation
spellingShingle Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation
Pascutti, Pedro Geraldo
hydrophobic effect
molecular dynamics simulations
electrostatic image method
water]membrane model
b-endorphin and signal sequence conformations
title_short Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation
title_full Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation
title_fullStr Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation
title_full_unstemmed Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation
title_sort Polarization Effects on Peptide Conformations at Water]Membrane Interface by Molecular Dynamics Simulation
author Pascutti, Pedro Geraldo
author_facet Pascutti, Pedro Geraldo
Mundim, Kleber Carlos
Ito, Amando Siuiti
Bisch, Paulo Mascarello
author_role author
author2 Mundim, Kleber Carlos
Ito, Amando Siuiti
Bisch, Paulo Mascarello
author2_role author
author
author
dc.contributor.author.fl_str_mv Pascutti, Pedro Geraldo
Mundim, Kleber Carlos
Ito, Amando Siuiti
Bisch, Paulo Mascarello
Pascutti, Pedro Geraldo
Mundim, Kleber Carlos
Ito, Amando Siuiti
Bisch, Paulo Mascarello
dc.subject.por.fl_str_mv hydrophobic effect
molecular dynamics simulations
electrostatic image method
water]membrane model
b-endorphin and signal sequence conformations
topic hydrophobic effect
molecular dynamics simulations
electrostatic image method
water]membrane model
b-endorphin and signal sequence conformations
description Texto completo. Acesso restrito. p. 971-982
publishDate 1999
dc.date.issued.fl_str_mv 1999
dc.date.accessioned.fl_str_mv 2013-10-15T15:23:35Z
dc.date.available.fl_str_mv 2013-10-15T15:23:35Z
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://www.repositorio.ufba.br/ri/handle/ri/13243
dc.identifier.issn.none.fl_str_mv 0192-8651
dc.identifier.number.pt_BR.fl_str_mv v. 20, n. 9
identifier_str_mv 0192-8651
v. 20, n. 9
url http://www.repositorio.ufba.br/ri/handle/ri/13243
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Journal of Computational Chemistry
publisher.none.fl_str_mv Journal of Computational Chemistry
dc.source.pt_BR.fl_str_mv http://onlinelibrary-wiley-com.ez10.periodicos.capes.gov.br/doi/10.1002/(SICI)1096-987X(19990715)20:9%3C971
dc.source.none.fl_str_mv reponame:Repositório Institucional da UFBA
instname:Universidade Federal da Bahia (UFBA)
instacron:UFBA
instname_str Universidade Federal da Bahia (UFBA)
instacron_str UFBA
institution UFBA
reponame_str Repositório Institucional da UFBA
collection Repositório Institucional da UFBA
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