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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

Prediction of kinetics of protein folding with non-redundant contact information

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Author(s):
Censoni, Luciano [1, 2] ; Martinez, Leandro
Total Authors: 2
Affiliation:
[1] Univ Estadual Campinas, Inst Chem, Campinas, SP - Brazil
[2] Univ Estadual Campinas, Ctr Computat Engn & Sci, Campinas, SP - Brazil
Total Affiliations: 2
Document type: Journal article
Source: Bioinformatics; v. 34, n. 23, p. 4034-4038, DEC 1 2018.
Web of Science Citations: 1
Abstract

Motivation: The majority of the inter-residue distances in a protein structure are correlated given a fixed topology. Here, we investigate whether we are able to predict a structure's folding rate, which is known to depend on the complexity of its fold, while considering only a small, uncorrelated fraction of its contacts. Results: We define an expression for the probabilistic information content associated to the relative position of a pair of amino acid residues in a protein structure. By means of fitting the protein chain to a self-avoiding random walk model, we derive a probability distribution for the distance between residues as a function of their separation along the sequence. We then show that the average information content for all residue pairs in a structure, considered as an estimate of its fold's complexity, is well correlated to the logarithm of its folding rate. Moreover, the same information content measure may be exploited to rank contacts and identify redundancies, allowing the prediction the structure's folding rate with similar accuracy while taking into account less than 5% of its contacts. (AU)

FAPESP's process: 13/05475-7 - Computational methods in optimization
Grantee:Sandra Augusta Santos
Support type: Research Projects - Thematic Grants
FAPESP's process: 10/16947-9 - Correlations between dynamics, structure and function in protein: computer simulations and algorithms
Grantee:Leandro Martinez
Support type: Regular Research Grants
FAPESP's process: 13/08293-7 - CCES - Center for Computational Engineering and Sciences
Grantee:Munir Salomao Skaf
Support type: Research Grants - Research, Innovation and Dissemination Centers - RIDC