Alexandre G. de Brevern's publications

Year 2013

  1. Craveur P.#, Joseph A.P., Rebehmed J., de Brevern A.G.#
    ▀-bulges: Extensive structural analyses of ▀-sheets irregularities
    Protein Science (2013) 22(10):1366-78.

    ▀-Sheets are quite frequent in protein structures and are stabilized by regular main-chain hydrogen bond patterns. Irregularities in ▀-sheets, named ▀-bulges, are distorted regions between two consecutive hydrogen bonds. They disrupt the classical alternation of side chain direction and can alter the directionality of ▀-strands. They are implicated in protein-protein interactions and are introduced to avoid ▀-strand aggregation. Five different types of ▀-bulges are defined. Previous studies on ▀-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 ▀-bulge distribution and conservation in terms of local backbone conformations and amino acid composition. Our dataset consists of 66 times more ▀-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 ▀-bulges are preferably localized at the N- and C-termini of ▀-strands, but contrary to the earlier studies, no significant conservation of ▀-bulges was observed among structural homologues. Displacement of ▀-bulges along the sequence was also investigated by Molecular Dynamics simulations.
    preprint paper .
    Table I Table I Table II Table II Table III Table III Table IV Table IV Table V Table V Table VI Table VI Supplementary_Material Supplementary_Material

    collaboration with Dr. Agnel Praveen Joseph of National Centre for Biological Sciences (Tata Institute, Bangalore, India).


    Funding:
    • The Ministry of Research (France)
    • The University Paris Diderot, Sorbonne Paris Cite (France)
    • The National Institute of Blood Transfusion (INTS, France)
    • The National Institute of Health and Medical Research (INSERM, France)
    • The Laboratories of Excellence, GR-Ex (France)
    • ANR Naturadyre [Projet ANR- 10-CD2I-014] - RÚactions dĺoxydation biocatalysÚes pour la synthŔse de composÚs naturels ou Únantiopurs (France)
    • HFSP (India)
    • NCBS (India)



Alexandre G. de Brevern
Last Modification : January 2014
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