title: Inferring a weighted elastic network from partial unfolding with coarse-grained simulations.
abstract: A number of studies have demonstrated that simple elastic network models can reproduce experimental B-factors, providing insights into the structure-function properties of proteins. Here, we report a study on how to improve an elastic network model and explore its performance by predicting the experimental B-factors. Elastic network models are built on the experimental Cα coordinates, and they only take the pairs of Cα atoms within a given cutoff distance rc into account. These models describe the interactions by elastic springs with the same force constant. We have developed a method based on numerical simulations with a simple coarse-grained force field, to attribute weights to these spring constants. This method considers the time that two Cα atoms remain connected in the network during partial unfolding, establishing a means of measuring the strength of each link. We examined two different coarse-grained force fields and explored the computation of these weights by unfolding the native structures.
authors.affiliation: Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, 14040-901, SP, Brazil.
authors.forename: Matheus R
authors.initials: MR
authors.lastname: de Mendonça
authors.forename: Leandro G
authors.initials: LG
authors.lastname: Rizzi
authors.forename: Vinicius
authors.initials: V
authors.lastname: Contessoto
authors.forename: Vitor B P
authors.initials: VB
authors.lastname: Leite
authors.forename: Nelson A
authors.initials: NA
authors.lastname: Alves
mesh_terms: D000465:Algorithms; D001400:Azurin / Q000737:chemistry; D021984:Cyclophilin A / Q000737:chemistry; D045304:Cytochromes c / Q000737:chemistry; D008956:Models, Chemical; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry; D010940:Plant Proteins / Q000737:chemistry; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012260:Ribonucleases / Q000737:chemistry; D013696:Temperature; D025801:Ubiquitin / Q000737:chemistry
chemical_list: D009842:Oligopeptides; D010940:Plant Proteins; D011506:Proteins; D025801:Ubiquitin; D001400:Azurin; C047473:N-(3-N-(benzyloxycarbonyl)amino-1-carboxypropyl)leucyl-O-methyltyrosine N-methylamide; C024934:crambin protein, Crambe abyssinica; D045304:Cytochromes c; D012260:Ribonucleases; C077002:ribonuclease Sa3; D021984:Cyclophilin A
keywords: B-factor; GNM; WCN; normal mode analysis; pfGNM; vibrational dynamics