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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.)

Extended secondary structures in proteins

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Author(s):
Degreve, Leo [1] ; Fuzo, Carlos A. [1] ; Caliri, Antonio [2]
Total Authors: 3
Affiliation:
[1] Univ Sao Paulo, Fac Filosofia Ciencias & Letras Ribeirao Preto, Dept Quim, BR-14040901 Ribeirao Preto - Brazil
[2] Univ Sao Paulo, Fac Ciencias Farmaceut Ribeirao Preto, Dept Quim & Fis, BR-14040903 Ribeirao Preto - Brazil
Total Affiliations: 2
Document type: Journal article
Source: BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS; v. 1844, n. 2, p. 384-388, FEB 2014.
Web of Science Citations: 0
Abstract

Supersecondary structures of proteins have been systematically searched and classified, but not enough attention has been devoted to such large edifices beyond the basic identification of secondary structures. The objective of the present study is to show that the association of secondary structures that share some of their backbone residues is a commonplace in globular proteins, and that such deeper fusion of secondary structures, namely extended secondary structures (ESSs), helps stabilize the original secondary structures and the resulting tertiary structures. For statistical purposes, a set of 163 proteins from the protein databank was randomly selected and a few specific cases are structurally analyzed and characterized in more detail. The results point that about 30% of the residues from each protein, on average, participate in ESS. Alternatively, for the specific cases considered, our results were based on the secondary structures produced after extensive Molecular Dynamics simulation of a protein-aqueous solvent system. Based on the very small width of the time distribution of the root mean squared deviations, between the ESS taken along the simulation and the ESS from the mean structure of the protein, for each ESS, we conclude that the ESSs significantly increase the conformational stability by forming very stable aggregates. The ubiquity and specificity of the ESS suggest that the role they play in the structure of proteins, including the domains formation, deserves to be thoroughly investigated. (C) 2013 Elsevier B.V. All rights reserved. (AU)

FAPESP's process: 08/11706-3 - Investigation of the molecular mechanisms of the infection processes of human cells by dengue virus
Grantee:Leo Degreve
Support Opportunities: Research Projects - Thematic Grants