The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization
- Autores
- Pohl, Gábor; Jákli, Imre; Csizmadia, Imre G.; Papp, Dóra; Garibotto, Francisco Matías; Perczel, András
- Año de publicación
- 2012
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- The initiation and progression of Alzheimer's disease is coupled to the oligo- and polymerization of amyloid peptides in the brain. Amyloid like aggregates of protein domains were found practically independent of their primary sequences. Thus, the driving force of the transformation from the original to a disordered amyloid fold is expected to lie in the protein backbone common to all proteins. In order to investigate the thermodynamics of oligomerization, full geometry optimizations and frequency calculations were performed both on parallel and antiparallel β-pleated sheet model structures of [HCO–(Ala)1–6–NH2]2 and (For–Ala1–2–NH2)1–6peptides, both at the B3LYP and M05-2X/6-311++G(d,p)//M05-2X/6-31G(d) levels of theory, both in vacuum and in water. Our results show that relative entropy and enthalpy both show a hyperbolic decrease with increasing residue number and with increasing number of strands as well. Thus, di- and oligomerization are always thermodynamically favored. Antiparallel arrangements were found to have greater stability than parallel arrangements of the polypeptide backbones. During our study the relative changes in thermodynamic functions are found to be constant for long enough peptides, indicating that stability and entropy terms are predictable. All thermodynamic functions of antiparallel di- and oligomers show a staggered nature along the increasing residue number. By identifying and analyzing the 6 newly emerging dimer vibrational modes of the 10- and 14-membered building units, the staggered nature of the entropy function can be rationalized. Thus, the vanishing rotational and translational modes with respect to single strands are converted into entropy terms “holding tight” the dimers and oligomers formed, rationalizing the intrinsic adherence of natural polypeptide backbones to aggregate.
Fil: Pohl, Gábor. Eötvös Loránd University; Hungría
Fil: Jákli, Imre. Eötvös Loránd University; Hungría
Fil: Csizmadia, Imre G.. Eötvös Loránd University; Hungría
Fil: Papp, Dóra. Eötvös Loránd University; Hungría
Fil: Garibotto, Francisco Matías. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia; Argentina
Fil: Perczel, András. Eötvös Loránd University; Hungría - Materia
-
Alzheimers Disease
Polymerization of Amyloid Peptides - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
- Repositorio
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/14506
Ver los metadatos del registro completo
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The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerizationPohl, GáborJákli, ImreCsizmadia, Imre G.Papp, DóraGaribotto, Francisco MatíasPerczel, AndrásAlzheimers DiseasePolymerization of Amyloid Peptideshttps://purl.org/becyt/ford/1.4https://purl.org/becyt/ford/1The initiation and progression of Alzheimer's disease is coupled to the oligo- and polymerization of amyloid peptides in the brain. Amyloid like aggregates of protein domains were found practically independent of their primary sequences. Thus, the driving force of the transformation from the original to a disordered amyloid fold is expected to lie in the protein backbone common to all proteins. In order to investigate the thermodynamics of oligomerization, full geometry optimizations and frequency calculations were performed both on parallel and antiparallel β-pleated sheet model structures of [HCO–(Ala)1–6–NH2]2 and (For–Ala1–2–NH2)1–6peptides, both at the B3LYP and M05-2X/6-311++G(d,p)//M05-2X/6-31G(d) levels of theory, both in vacuum and in water. Our results show that relative entropy and enthalpy both show a hyperbolic decrease with increasing residue number and with increasing number of strands as well. Thus, di- and oligomerization are always thermodynamically favored. Antiparallel arrangements were found to have greater stability than parallel arrangements of the polypeptide backbones. During our study the relative changes in thermodynamic functions are found to be constant for long enough peptides, indicating that stability and entropy terms are predictable. All thermodynamic functions of antiparallel di- and oligomers show a staggered nature along the increasing residue number. By identifying and analyzing the 6 newly emerging dimer vibrational modes of the 10- and 14-membered building units, the staggered nature of the entropy function can be rationalized. Thus, the vanishing rotational and translational modes with respect to single strands are converted into entropy terms “holding tight” the dimers and oligomers formed, rationalizing the intrinsic adherence of natural polypeptide backbones to aggregate.Fil: Pohl, Gábor. Eötvös Loránd University; HungríaFil: Jákli, Imre. Eötvös Loránd University; HungríaFil: Csizmadia, Imre G.. Eötvös Loránd University; HungríaFil: Papp, Dóra. Eötvös Loránd University; HungríaFil: Garibotto, Francisco Matías. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia; ArgentinaFil: Perczel, András. Eötvös Loránd University; HungríaRoyal Society of Chemistry2012-01-28info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/14506Pohl, Gábor; Jákli, Imre; Csizmadia, Imre G.; Papp, Dóra; Garibotto, Francisco Matías; et al.; The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization; Royal Society of Chemistry; Physical Chemistry Chemical Physics; 14; 4; 28-1-2012; 1507-15161463-9076enginfo:eu-repo/semantics/altIdentifier/url/http://pubs.rsc.org/en/Content/ArticleLanding/2012/CP/C2CP22821A#!divAbstractinfo:eu-repo/semantics/altIdentifier/doi/ 10.1039/c2cp22821ainfo:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by-nc-sa/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-09-29T09:44:32Zoai:ri.conicet.gov.ar:11336/14506instacron: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:34982025-09-29 09:44:33.289CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
dc.title.none.fl_str_mv |
The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization |
title |
The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization |
spellingShingle |
The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization Pohl, Gábor Alzheimers Disease Polymerization of Amyloid Peptides |
title_short |
The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization |
title_full |
The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization |
title_fullStr |
The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization |
title_full_unstemmed |
The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization |
title_sort |
The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization |
dc.creator.none.fl_str_mv |
Pohl, Gábor Jákli, Imre Csizmadia, Imre G. Papp, Dóra Garibotto, Francisco Matías Perczel, András |
author |
Pohl, Gábor |
author_facet |
Pohl, Gábor Jákli, Imre Csizmadia, Imre G. Papp, Dóra Garibotto, Francisco Matías Perczel, András |
author_role |
author |
author2 |
Jákli, Imre Csizmadia, Imre G. Papp, Dóra Garibotto, Francisco Matías Perczel, András |
author2_role |
author author author author author |
dc.subject.none.fl_str_mv |
Alzheimers Disease Polymerization of Amyloid Peptides |
topic |
Alzheimers Disease Polymerization of Amyloid Peptides |
purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.4 https://purl.org/becyt/ford/1 |
dc.description.none.fl_txt_mv |
The initiation and progression of Alzheimer's disease is coupled to the oligo- and polymerization of amyloid peptides in the brain. Amyloid like aggregates of protein domains were found practically independent of their primary sequences. Thus, the driving force of the transformation from the original to a disordered amyloid fold is expected to lie in the protein backbone common to all proteins. In order to investigate the thermodynamics of oligomerization, full geometry optimizations and frequency calculations were performed both on parallel and antiparallel β-pleated sheet model structures of [HCO–(Ala)1–6–NH2]2 and (For–Ala1–2–NH2)1–6peptides, both at the B3LYP and M05-2X/6-311++G(d,p)//M05-2X/6-31G(d) levels of theory, both in vacuum and in water. Our results show that relative entropy and enthalpy both show a hyperbolic decrease with increasing residue number and with increasing number of strands as well. Thus, di- and oligomerization are always thermodynamically favored. Antiparallel arrangements were found to have greater stability than parallel arrangements of the polypeptide backbones. During our study the relative changes in thermodynamic functions are found to be constant for long enough peptides, indicating that stability and entropy terms are predictable. All thermodynamic functions of antiparallel di- and oligomers show a staggered nature along the increasing residue number. By identifying and analyzing the 6 newly emerging dimer vibrational modes of the 10- and 14-membered building units, the staggered nature of the entropy function can be rationalized. Thus, the vanishing rotational and translational modes with respect to single strands are converted into entropy terms “holding tight” the dimers and oligomers formed, rationalizing the intrinsic adherence of natural polypeptide backbones to aggregate. Fil: Pohl, Gábor. Eötvös Loránd University; Hungría Fil: Jákli, Imre. Eötvös Loránd University; Hungría Fil: Csizmadia, Imre G.. Eötvös Loránd University; Hungría Fil: Papp, Dóra. Eötvös Loránd University; Hungría Fil: Garibotto, Francisco Matías. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Universidad Nacional de San Luis. Facultad de Química, Bioquímica y Farmacia; Argentina Fil: Perczel, András. Eötvös Loránd University; Hungría |
description |
The initiation and progression of Alzheimer's disease is coupled to the oligo- and polymerization of amyloid peptides in the brain. Amyloid like aggregates of protein domains were found practically independent of their primary sequences. Thus, the driving force of the transformation from the original to a disordered amyloid fold is expected to lie in the protein backbone common to all proteins. In order to investigate the thermodynamics of oligomerization, full geometry optimizations and frequency calculations were performed both on parallel and antiparallel β-pleated sheet model structures of [HCO–(Ala)1–6–NH2]2 and (For–Ala1–2–NH2)1–6peptides, both at the B3LYP and M05-2X/6-311++G(d,p)//M05-2X/6-31G(d) levels of theory, both in vacuum and in water. Our results show that relative entropy and enthalpy both show a hyperbolic decrease with increasing residue number and with increasing number of strands as well. Thus, di- and oligomerization are always thermodynamically favored. Antiparallel arrangements were found to have greater stability than parallel arrangements of the polypeptide backbones. During our study the relative changes in thermodynamic functions are found to be constant for long enough peptides, indicating that stability and entropy terms are predictable. All thermodynamic functions of antiparallel di- and oligomers show a staggered nature along the increasing residue number. By identifying and analyzing the 6 newly emerging dimer vibrational modes of the 10- and 14-membered building units, the staggered nature of the entropy function can be rationalized. Thus, the vanishing rotational and translational modes with respect to single strands are converted into entropy terms “holding tight” the dimers and oligomers formed, rationalizing the intrinsic adherence of natural polypeptide backbones to aggregate. |
publishDate |
2012 |
dc.date.none.fl_str_mv |
2012-01-28 |
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/11336/14506 Pohl, Gábor; Jákli, Imre; Csizmadia, Imre G.; Papp, Dóra; Garibotto, Francisco Matías; et al.; The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization; Royal Society of Chemistry; Physical Chemistry Chemical Physics; 14; 4; 28-1-2012; 1507-1516 1463-9076 |
url |
http://hdl.handle.net/11336/14506 |
identifier_str_mv |
Pohl, Gábor; Jákli, Imre; Csizmadia, Imre G.; Papp, Dóra; Garibotto, Francisco Matías; et al.; The role of entropy in initializing the aggregation of peptides: a first principle study on oligopeptide oligomerization; Royal Society of Chemistry; Physical Chemistry Chemical Physics; 14; 4; 28-1-2012; 1507-1516 1463-9076 |
dc.language.none.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
info:eu-repo/semantics/altIdentifier/url/http://pubs.rsc.org/en/Content/ArticleLanding/2012/CP/C2CP22821A#!divAbstract info:eu-repo/semantics/altIdentifier/doi/ 10.1039/c2cp22821a |
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 |
Royal Society of Chemistry |
publisher.none.fl_str_mv |
Royal Society of Chemistry |
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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1844613402429751296 |
score |
13.070432 |