A Hooke's law-based approach to protein folding rate

Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke[U+05F3]s law. A novel parameter called elastic-folding constant results from ou...

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Tipo de recurso:
Fecha de publicación:
2015
Institución:
Universidad Tecnológica de Bolívar
Repositorio:
Repositorio Institucional UTB
Idioma:
eng
OAI Identifier:
oai:repositorio.utb.edu.co:20.500.12585/9020
Acceso en línea:
https://hdl.handle.net/20.500.12585/9020
Palabra clave:
Elastic folding constant
Folding degree
Folding kinetics
PROTDCAL
Polypeptide
DNA
Protein
Energetics
Modeling
Peptide
Protein
Reaction kinetics
Amino acid sequence
Article
Elasticity
Protein folding
Protein structure
Structure analysis
Theoretical model
Chemical model
Chemistry
Computer simulation
Kinetics
Protein secondary structure
Thermodynamics
Computer simulation
DNA
Kinetics
Models, Chemical
Protein folding
Protein Structure, Secondary
Proteins
Thermodynamics
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restrictedAccess
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http://creativecommons.org/licenses/by-nc-nd/4.0/
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oai_identifier_str oai:repositorio.utb.edu.co:20.500.12585/9020
network_acronym_str UTB2
network_name_str Repositorio Institucional UTB
repository_id_str
dc.title.none.fl_str_mv A Hooke's law-based approach to protein folding rate
title A Hooke's law-based approach to protein folding rate
spellingShingle A Hooke's law-based approach to protein folding rate
Elastic folding constant
Folding degree
Folding kinetics
PROTDCAL
Polypeptide
DNA
Protein
Energetics
Modeling
Peptide
Protein
Reaction kinetics
Amino acid sequence
Article
Elasticity
Protein folding
Protein structure
Structure analysis
Theoretical model
Chemical model
Chemistry
Computer simulation
Kinetics
Protein secondary structure
Thermodynamics
Computer simulation
DNA
Kinetics
Models, Chemical
Protein folding
Protein Structure, Secondary
Proteins
Thermodynamics
title_short A Hooke's law-based approach to protein folding rate
title_full A Hooke's law-based approach to protein folding rate
title_fullStr A Hooke's law-based approach to protein folding rate
title_full_unstemmed A Hooke's law-based approach to protein folding rate
title_sort A Hooke's law-based approach to protein folding rate
dc.subject.keywords.none.fl_str_mv Elastic folding constant
Folding degree
Folding kinetics
PROTDCAL
Polypeptide
DNA
Protein
Energetics
Modeling
Peptide
Protein
Reaction kinetics
Amino acid sequence
Article
Elasticity
Protein folding
Protein structure
Structure analysis
Theoretical model
Chemical model
Chemistry
Computer simulation
Kinetics
Protein secondary structure
Thermodynamics
Computer simulation
DNA
Kinetics
Models, Chemical
Protein folding
Protein Structure, Secondary
Proteins
Thermodynamics
topic Elastic folding constant
Folding degree
Folding kinetics
PROTDCAL
Polypeptide
DNA
Protein
Energetics
Modeling
Peptide
Protein
Reaction kinetics
Amino acid sequence
Article
Elasticity
Protein folding
Protein structure
Structure analysis
Theoretical model
Chemical model
Chemistry
Computer simulation
Kinetics
Protein secondary structure
Thermodynamics
Computer simulation
DNA
Kinetics
Models, Chemical
Protein folding
Protein Structure, Secondary
Proteins
Thermodynamics
description Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke[U+05F3]s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons among structural classes and folding mechanisms were carried out showing the good performance of our model with proteins of different types. The present model constitutes a simple rationale for the structural and energetic factors involved in protein folding kinetics. © 2014 Elsevier Ltd.
publishDate 2015
dc.date.issued.none.fl_str_mv 2015
dc.date.accessioned.none.fl_str_mv 2020-03-26T16:32:47Z
dc.date.available.none.fl_str_mv 2020-03-26T16:32:47Z
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dc.type.driver.none.fl_str_mv info:eu-repo/semantics/article
dc.type.hasVersion.none.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.spa.none.fl_str_mv Artículo
status_str publishedVersion
dc.identifier.citation.none.fl_str_mv Journal of Theoretical Biology; Vol. 364, pp. 407-417
dc.identifier.issn.none.fl_str_mv 00225193
dc.identifier.uri.none.fl_str_mv https://hdl.handle.net/20.500.12585/9020
dc.identifier.doi.none.fl_str_mv 10.1016/j.jtbi.2014.09.002
dc.identifier.instname.none.fl_str_mv Universidad Tecnológica de Bolívar
dc.identifier.reponame.none.fl_str_mv Repositorio UTB
dc.identifier.orcid.none.fl_str_mv 36933887400
55665599200
53878266200
7102811634
36945042600
35403074800
identifier_str_mv Journal of Theoretical Biology; Vol. 364, pp. 407-417
00225193
10.1016/j.jtbi.2014.09.002
Universidad Tecnológica de Bolívar
Repositorio UTB
36933887400
55665599200
53878266200
7102811634
36945042600
35403074800
url https://hdl.handle.net/20.500.12585/9020
dc.language.iso.none.fl_str_mv eng
language eng
dc.rights.coar.fl_str_mv http://purl.org/coar/access_right/c_16ec
dc.rights.uri.none.fl_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
dc.rights.accessRights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
dc.rights.cc.none.fl_str_mv Atribución-NoComercial 4.0 Internacional
rights_invalid_str_mv http://creativecommons.org/licenses/by-nc-nd/4.0/
Atribución-NoComercial 4.0 Internacional
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eu_rights_str_mv restrictedAccess
dc.format.medium.none.fl_str_mv Recurso electrónico
dc.format.mimetype.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Academic Press
publisher.none.fl_str_mv Academic Press
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institution Universidad Tecnológica de Bolívar
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spelling 2020-03-26T16:32:47Z2020-03-26T16:32:47Z2015Journal of Theoretical Biology; Vol. 364, pp. 407-41700225193https://hdl.handle.net/20.500.12585/902010.1016/j.jtbi.2014.09.002Universidad Tecnológica de BolívarRepositorio UTB36933887400556655992005387826620071028116343694504260035403074800Kinetics is a key aspect of the renowned protein folding problem. Here, we propose a comprehensive approach to folding kinetics where a polypeptide chain is assumed to behave as an elastic material described by the Hooke[U+05F3]s law. A novel parameter called elastic-folding constant results from our model and is suggested to distinguish between protein with two-state and multi-state folding pathways. A contact-free descriptor, named folding degree, is introduced as a suitable structural feature to study protein-folding kinetics. This approach generalizes the observed correlations between varieties of structural descriptors with the folding rate constant. Additionally several comparisons among structural classes and folding mechanisms were carried out showing the good performance of our model with proteins of different types. The present model constitutes a simple rationale for the structural and energetic factors involved in protein folding kinetics. © 2014 Elsevier Ltd.DNA, 9007-49-2; protein, 67254-75-5; DNA; ProteinsRecurso electrónicoapplication/pdfengAcademic Presshttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/restrictedAccessAtribución-NoComercial 4.0 Internacionalhttp://purl.org/coar/access_right/c_16echttps://www.scopus.com/inward/record.uri?eid=2-s2.0-84910086539&doi=10.1016%2fj.jtbi.2014.09.002&partnerID=40&md5=d32479becf63730a4252ec30e659e982A Hooke's law-based approach to protein folding rateinfo:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionArtículohttp://purl.org/coar/version/c_970fb48d4fbd8a85http://purl.org/coar/resource_type/c_2df8fbb1Elastic folding constantFolding degreeFolding kineticsPROTDCALPolypeptideDNAProteinEnergeticsModelingPeptideProteinReaction kineticsAmino acid sequenceArticleElasticityProtein foldingProtein structureStructure analysisTheoretical modelChemical modelChemistryComputer simulationKineticsProtein secondary structureThermodynamicsComputer simulationDNAKineticsModels, ChemicalProtein foldingProtein Structure, SecondaryProteinsThermodynamicsRuiz-Blanco Y.B.Marrero-Ponce Y.Prieto P.J.Salgado J.García Y.Sotomayor-Torres C.M.Baker, D., A surprising simplicity to protein folding (2000) Nature, 405, pp. 39-42Basilevsky, A., (1994) Statistical Factor Analysis and Related Methods, , Wiley, New YorkBergasa-Caceres, F., Rabitz, H.A., Two-state folding kinetics of small proteins in the sequential collapse model: dependence of the folding rate on contact order and temperature (2003) J. 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Bull., 1, pp. 80-83Zagrovic, B., Snow, C.D., Shirts, M.R., Pande, V.S., Simulation of folding of a small alpha-helical protein in atomistic detail using worldwidedistributed computing (2002) J. Mol. Biol., 323, pp. 927-937Zhou, H., Zhou, Y., Folding rate prediction using total contact distance (2002) Biophys. J., 82, pp. 458-463Zimmermann, O., Hansmann, U.H.E., Understanding protein folding: small proteins in silico (2008) Biochim. Biophys. Acta, 1784, pp. 252-258http://purl.org/coar/resource_type/c_6501THUMBNAILMiniProdInv.pngMiniProdInv.pngimage/png23941https://repositorio.utb.edu.co/bitstream/20.500.12585/9020/1/MiniProdInv.png0cb0f101a8d16897fb46fc914d3d7043MD5120.500.12585/9020oai:repositorio.utb.edu.co:20.500.12585/90202021-02-02 14:14:19.399Repositorio Institucional UTBrepositorioutb@utb.edu.co

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