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

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.

Keywords:

• recombination
• RecA filament
• molecular plasticity
• conformational ensembles
• P-loop
• nucleotide binding

Acknowledgements

We thank Dr. J. Rajan Prabu for initiating the computational studies on RecA in our laboratory. Computations were carried out at the Interactive Graphics Facility, supported by the DBT and Supercomputer Education Research Centre (SERC), Indian Institute of Science. MV is the Albert Einstein Research Professor of the Indian National Science Academy.