Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study

Autores
Vila, Jorge Alberto; Baldoni, Héctor A.; Ripoll, Daniel R.; Ghosh, Avijit; Scheraga, Harold A.
Año de publicación
2004
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
Interest centers here on whether a polyproline II helix can propagate through adjacent non-proline residues, and on shedding light on recent experimental observations suggesting the presence of significant PPII structure in a short alaninebased peptide with no proline in the sequence. For this purpose, we explored the formation of polyproline II helices in prolinerich peptides with the sequences Ac-(Pro)3-X-(Pro)3-Gly-Tyr-NH2, with X ¼ Pro (PPP), Ala (PAP), Gln (PQP), Gly (PGP), and Val (PVP), and Ac-(Pro)3-Ala-Ala-(Pro)3-Gly-Tyr-NH2 (PAAP), by using a theoretical approach that includes a solvent effect as well as cis $ trans isomerization of the peptide groups and puckering conformations of the pyrrolidine ring of the proline residues. Since 13C chemical shifts have proven to be useful for identifying secondary-structure preferences in proteins and peptides, and because values of the dihedral angles (f,c) are the main determinants of their magnitudes, we have, therefore, computed the Boltzmann-averaged 13C chemical shifts for the guest residues in the PXP peptide (X ¼ Pro, Ala, Gln, Gly, and Val) with a combination of approaches, involving molecular mechanics, statistical mechanics, and quantum mechanics. In addition, an improved procedure was used to carry out the conformational searches and to compute the solvent polarization effects faster and more accurately than in previous work. The current theoretical work and additional experimental evidence show that, in short proline-rich peptides, alanine decreases the polyproline II helix content. In particular, the theoretical evidence accumulated in this work calls into question the proposal that alanine has a strong preference to adopt conformations in the polyproline II region of the Ramachandran map.
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina. Cornell University; Estados Unidos
Fil: Baldoni, Héctor A.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; Argentina
Fil: Ripoll, Daniel R.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; Argentina
Fil: Ghosh, Avijit. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; Argentina
Fil: Scheraga, Harold A.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; Argentina
Materia
POLIPROLINE
HELIX
PROLINE RICH ENVIRONMENT
Nivel de accesibilidad
acceso abierto
Condiciones de uso
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
Repositorio
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/273123
Acceder
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oai_identifier_str oai:ri.conicet.gov.ar:11336/273123
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repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical StudyVila, Jorge AlbertoBaldoni, Héctor A.Ripoll, Daniel R.Ghosh, AvijitScheraga, Harold A.POLIPROLINEHELIXPROLINE RICH ENVIRONMENThttps://purl.org/becyt/ford/1.3https://purl.org/becyt/ford/1Interest centers here on whether a polyproline II helix can propagate through adjacent non-proline residues, and on shedding light on recent experimental observations suggesting the presence of significant PPII structure in a short alaninebased peptide with no proline in the sequence. For this purpose, we explored the formation of polyproline II helices in prolinerich peptides with the sequences Ac-(Pro)3-X-(Pro)3-Gly-Tyr-NH2, with X ¼ Pro (PPP), Ala (PAP), Gln (PQP), Gly (PGP), and Val (PVP), and Ac-(Pro)3-Ala-Ala-(Pro)3-Gly-Tyr-NH2 (PAAP), by using a theoretical approach that includes a solvent effect as well as cis $ trans isomerization of the peptide groups and puckering conformations of the pyrrolidine ring of the proline residues. Since 13C chemical shifts have proven to be useful for identifying secondary-structure preferences in proteins and peptides, and because values of the dihedral angles (f,c) are the main determinants of their magnitudes, we have, therefore, computed the Boltzmann-averaged 13C chemical shifts for the guest residues in the PXP peptide (X ¼ Pro, Ala, Gln, Gly, and Val) with a combination of approaches, involving molecular mechanics, statistical mechanics, and quantum mechanics. In addition, an improved procedure was used to carry out the conformational searches and to compute the solvent polarization effects faster and more accurately than in previous work. The current theoretical work and additional experimental evidence show that, in short proline-rich peptides, alanine decreases the polyproline II helix content. In particular, the theoretical evidence accumulated in this work calls into question the proposal that alanine has a strong preference to adopt conformations in the polyproline II region of the Ramachandran map.Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina. Cornell University; Estados UnidosFil: Baldoni, Héctor A.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; ArgentinaFil: Ripoll, Daniel R.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; ArgentinaFil: Ghosh, Avijit. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; ArgentinaFil: Scheraga, Harold A.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; ArgentinaCell Press2004-02info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/273123Vila, Jorge Alberto; Baldoni, Héctor A.; Ripoll, Daniel R.; Ghosh, Avijit; Scheraga, Harold A.; Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study; Cell Press; Biophysical Journal; 86; 2; 2-2004; 731-7420006-3495CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S000634950474151Xinfo:eu-repo/semantics/altIdentifier/doi/10.1016/S0006-3495(04)74151-Xinfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-15T14:30:00Zoai:ri.conicet.gov.ar:11336/273123instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-15 14:30:01.132CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse
dc.title.none.fl_str_mv Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
title Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
spellingShingle Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
Vila, Jorge Alberto
POLIPROLINE
HELIX
PROLINE RICH ENVIRONMENT
title_short Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
title_full Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
title_fullStr Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
title_full_unstemmed Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
title_sort Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study
dc.creator.none.fl_str_mv Vila, Jorge Alberto
Baldoni, Héctor A.
Ripoll, Daniel R.
Ghosh, Avijit
Scheraga, Harold A.
author Vila, Jorge Alberto
author_facet Vila, Jorge Alberto
Baldoni, Héctor A.
Ripoll, Daniel R.
Ghosh, Avijit
Scheraga, Harold A.
author_role author
author2 Baldoni, Héctor A.
Ripoll, Daniel R.
Ghosh, Avijit
Scheraga, Harold A.
author2_role author
author
author
author
dc.subject.none.fl_str_mv POLIPROLINE
HELIX
PROLINE RICH ENVIRONMENT
topic POLIPROLINE
HELIX
PROLINE RICH ENVIRONMENT
purl_subject.fl_str_mv https://purl.org/becyt/ford/1.3
https://purl.org/becyt/ford/1
dc.description.none.fl_txt_mv Interest centers here on whether a polyproline II helix can propagate through adjacent non-proline residues, and on shedding light on recent experimental observations suggesting the presence of significant PPII structure in a short alaninebased peptide with no proline in the sequence. For this purpose, we explored the formation of polyproline II helices in prolinerich peptides with the sequences Ac-(Pro)3-X-(Pro)3-Gly-Tyr-NH2, with X ¼ Pro (PPP), Ala (PAP), Gln (PQP), Gly (PGP), and Val (PVP), and Ac-(Pro)3-Ala-Ala-(Pro)3-Gly-Tyr-NH2 (PAAP), by using a theoretical approach that includes a solvent effect as well as cis $ trans isomerization of the peptide groups and puckering conformations of the pyrrolidine ring of the proline residues. Since 13C chemical shifts have proven to be useful for identifying secondary-structure preferences in proteins and peptides, and because values of the dihedral angles (f,c) are the main determinants of their magnitudes, we have, therefore, computed the Boltzmann-averaged 13C chemical shifts for the guest residues in the PXP peptide (X ¼ Pro, Ala, Gln, Gly, and Val) with a combination of approaches, involving molecular mechanics, statistical mechanics, and quantum mechanics. In addition, an improved procedure was used to carry out the conformational searches and to compute the solvent polarization effects faster and more accurately than in previous work. The current theoretical work and additional experimental evidence show that, in short proline-rich peptides, alanine decreases the polyproline II helix content. In particular, the theoretical evidence accumulated in this work calls into question the proposal that alanine has a strong preference to adopt conformations in the polyproline II region of the Ramachandran map.
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina. Cornell University; Estados Unidos
Fil: Baldoni, Héctor A.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; Argentina
Fil: Ripoll, Daniel R.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; Argentina
Fil: Ghosh, Avijit. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; Argentina
Fil: Scheraga, Harold A.. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia. Departamento de Química; Argentina
description Interest centers here on whether a polyproline II helix can propagate through adjacent non-proline residues, and on shedding light on recent experimental observations suggesting the presence of significant PPII structure in a short alaninebased peptide with no proline in the sequence. For this purpose, we explored the formation of polyproline II helices in prolinerich peptides with the sequences Ac-(Pro)3-X-(Pro)3-Gly-Tyr-NH2, with X ¼ Pro (PPP), Ala (PAP), Gln (PQP), Gly (PGP), and Val (PVP), and Ac-(Pro)3-Ala-Ala-(Pro)3-Gly-Tyr-NH2 (PAAP), by using a theoretical approach that includes a solvent effect as well as cis $ trans isomerization of the peptide groups and puckering conformations of the pyrrolidine ring of the proline residues. Since 13C chemical shifts have proven to be useful for identifying secondary-structure preferences in proteins and peptides, and because values of the dihedral angles (f,c) are the main determinants of their magnitudes, we have, therefore, computed the Boltzmann-averaged 13C chemical shifts for the guest residues in the PXP peptide (X ¼ Pro, Ala, Gln, Gly, and Val) with a combination of approaches, involving molecular mechanics, statistical mechanics, and quantum mechanics. In addition, an improved procedure was used to carry out the conformational searches and to compute the solvent polarization effects faster and more accurately than in previous work. The current theoretical work and additional experimental evidence show that, in short proline-rich peptides, alanine decreases the polyproline II helix content. In particular, the theoretical evidence accumulated in this work calls into question the proposal that alanine has a strong preference to adopt conformations in the polyproline II region of the Ramachandran map.
publishDate 2004
dc.date.none.fl_str_mv 2004-02
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/11336/273123
Vila, Jorge Alberto; Baldoni, Héctor A.; Ripoll, Daniel R.; Ghosh, Avijit; Scheraga, Harold A.; Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study; Cell Press; Biophysical Journal; 86; 2; 2-2004; 731-742
0006-3495
CONICET Digital
CONICET
url http://hdl.handle.net/11336/273123
identifier_str_mv Vila, Jorge Alberto; Baldoni, Héctor A.; Ripoll, Daniel R.; Ghosh, Avijit; Scheraga, Harold A.; Polyproline II Helix Conformation in a Proline-Rich Environment: A Theoretical Study; Cell Press; Biophysical Journal; 86; 2; 2-2004; 731-742
0006-3495
CONICET Digital
CONICET
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://www.sciencedirect.com/science/article/pii/S000634950474151X
info:eu-repo/semantics/altIdentifier/doi/10.1016/S0006-3495(04)74151-X
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Cell Press
publisher.none.fl_str_mv Cell Press
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
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score 12.891075

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