Inferring a weighted elastic network from partial unfolding with coarse-grained simulations
Contribuinte(s) |
Universidade Estadual Paulista (UNESP) |
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Data(s) |
03/12/2014
03/12/2014
01/01/2014
|
Resumo |
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 C coordinates, and they only take the pairs of C atoms within a given cutoff distance r(c) 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 C 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. Proteins 2014; 82:119-129. (c) 2013 Wiley Periodicals, Inc. |
Formato |
119-129 |
Identificador |
http://dx.doi.org/10.1002/prot.24381 Proteins-structure Function And Bioinformatics. Hoboken: Wiley-blackwell, v. 82, n. 1, p. 119-129, 2014. 0887-3585 http://hdl.handle.net/11449/112900 10.1002/prot.24381 WOS:000328090900011 |
Idioma(s) |
eng |
Publicador |
Wiley-Blackwell |
Relação |
Proteins: Structure, Function and Bioinformatics |
Direitos |
openAccess |
Palavras-Chave | #normal mode analysis #GNM #pfGNM #WCN #B-factor #vibrational dynamics |
Tipo |
info:eu-repo/semantics/article |