β-Bulges: extensive structural analyses of β-sheets irregularities.Report as inadecuate




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* Corresponding author 1 GR-Ex, Laboratoire d-Excellence 2 DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques 3 NCBS - National Centre for Biological Sciences 4 DSIMB GR-Ex, Laboratoire d-Excellence, DSIMB - Dynamique des Structures et Interactions des Macromolécules Biologiques

Abstract : β-Sheets are quite frequent in protein structures and are stabilized by regular main-chain hydrogen bond patterns. Irregularities in β-sheets, named β-bulges, are distorted regions between two consecutive hydrogen bonds. They disrupt the classical alternation of side chain direction and can alter the directionality of β-strands. They are implicated in protein-protein interactions and are introduced to avoid β-strand aggregation. Five different types of β-bulges are defined. Previous studies on β-bulges were performed on a limited number of protein structures or one specific family. These studies evoked a potential conservation during evolution. In this work, we analyze the β-bulge distribution and conservation in terms of local backbone conformations and amino acid composition. Our dataset consists of 66 times more β-bulges than the last systematic study Chan et al. Protein Science 1993, 2:1574-1590. Novel amino acid preferences are underlined and local structure conformations are highlighted by the use of a structural alphabet. We observed that β-bulges are preferably localized at the N- and C-termini of β-strands, but contrary to the earlier studies, no significant conservation of β-bulges was observed among structural homologues. Displacement of β-bulges along the sequence was also investigated by Molecular Dynamics simulations.

Keywords : sequence structure relationship protein structure protein aggregation bioinformatics





Author: Pierrick Craveur - Agnel Praveen Joseph - Joseph Rebehmed - Alexandre De Brevern -

Source: https://hal.archives-ouvertes.fr/



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