title: A Hooke׳s law-based approach to protein folding rate.
abstract: 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׳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.
authors.affiliation: Unit of Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research (CAMBD-BIR Unit), Faculty of Chemistry-Pharmacy, Universidad Central "Marta Abreu" de Las Villas, Santa Clara 54830, Villa Clara, Cuba; Catalan Institute of Nanotechnology (CIN2-CSIC), Campus UAB, 08193 Bellaterra, Spain. Electronic address: yasserrb@uclv.edu.cu.
authors.forename: Yasser B
authors.initials: YB
authors.lastname: Ruiz-Blanco
authors.affiliation: Unit of Computer-Aided Molecular "Biosilico" Discovery and Bioinformatic Research (CAMBD-BIR Unit), Faculty of Chemistry-Pharmacy, Universidad Central "Marta Abreu" de Las Villas, Santa Clara 54830, Villa Clara, Cuba; Grupo de Investigación en Estudios Químicos y Biológicos, Facultad de Ciencias Básicas, Universidad Tecnológica de Bolívar, Cartagena de Indias, Bolívar, Colombia.
authors.forename: Yovani
authors.initials: Y
authors.lastname: Marrero-Ponce
authors.affiliation: Division de Postgrado. Instituto Tecnológico de Tijuana. Tijuana. Mexico.
authors.forename: Pablo J
authors.initials: PJ
authors.lastname: Prieto
authors.affiliation: Instituto de Ciencia Molecular (ICMol), Universitat de València. 46980 Paterna (Valencia), Spain.
authors.forename: Jesús
authors.initials: J
authors.lastname: Salgado
authors.affiliation: Catalan Institute of Nanotechnology (CIN2-CSIC), Campus UAB, 08193 Bellaterra, Spain.
authors.forename: Yamila
authors.initials: Y
authors.lastname: García
authors.affiliation: Catalan Institute of Nanotechnology (CIN2-CSIC), Campus UAB, 08193 Bellaterra, Spain; Instituciò Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
authors.forename: Clivia M
authors.initials: CM
authors.lastname: Sotomayor-Torres
mesh_terms: D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D008956:Models, Chemical; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D011506:Proteins; D004247:DNA
keywords: Elastic folding constant; Folding degree; Folding kinetics; PROTDCAL