Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament

Abstract

Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of Cdomain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering

“…Based on the existing RecA::ssDNA crystal structure [3] we built RecA::ssDNA presynaptic complex models for a short filament containing 42 dT nucleotides and a longer filament containing 102‐base oligonucleotide. Unlike RecA homopolimer [37], neither of the modeled filaments has shown any substantial changes in its structure during 100 ns molecular dynamics simulation, except for some minor motions of the C‐terminal domain and in L1 and L2 loops regions that have contacts with ssDNA.…”

Modeling the Homologous Recombination Process: Methods, Successes and Challenges

“…To a lesser extent, flexibility was also found in the terminal loop of the LexA-binding hairpin (226-245). (Figure 3A) [50,87,[98][99][100][101]. In the filament, the N-terminal helix is bound to the adjacent monomer so its movements, accompanied by the reorganization of its long flexible linker akin to a welcoming handshake, reflect the inter-monomer movements [102] (Figure 3B).…”