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Structure and interactions of RecA: plasticity revealed by molecular dynamics simulations

Chandran, Anu V and Jayanthi, S and Vijayan, M (2018) Structure and interactions of RecA: plasticity revealed by molecular dynamics simulations. In: JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 36 (1). pp. 98-111.

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Official URL: http://dx.doi.org/10.1080/07391102.2016.1268975

Abstract

Eleven independent simulations, each involving three consecutive molecules in the RecA filament, carried out on the protein from Mycobacterium tuberculosis, Mycobacterium smegmatis and Escherichia coli and their Adenosine triphosphate (ATP) complexes, provide valuable information which is complementary to that obtained from crystal structures, in addition to confirming the robust common structural framework within which RecA molecules from different eubacteria function. Functionally important loops, which are largely disordered in crystal structures, appear to adopt in each simulation subsets of conformations from larger ensembles. The simulations indicate the possibility of additional interactions involving the P-loop which remains largely invariant. The phosphate tail of the ATP is firmly anchored on the loop while the nucleoside moiety exhibits substantial structural variability. The most important consequence of ATP binding is the movement of the `switch' residue. The relevant simulations indicate the feasibility of a second nucleotide binding site, but the pathway between adjacent molecules in the filament involving the two nucleotide binding sites appears to be possible only in the mycobacterial proteins.

Item Type: Journal Article
Additional Information: Copy right for this article belongs to the TAYLOR & FRANCIS INC, 530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA
Department/Centre: Division of Biological Sciences > Molecular Biophysics Unit
Depositing User: Id for Latest eprints
Date Deposited: 02 Mar 2018 15:07
Last Modified: 02 Mar 2018 15:07
URI: http://eprints.iisc.ac.in/id/eprint/58884

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