Wedetermined and characterized the motion of the bacterial Hsp70 from E. coli (pdb2KHO) via canonical molecular dynamics simulations in simple systems modelingonly the ATP-bound and nucleotide-free chaperone. Our UNRES coarse-grained force field was used to model the whole chaperone; ATP-bound and free states wereimplicitly introduced by harmonic restraints in the nucleotide-binding domain (NBD).Coarse-graining enabled monitoring of time frames corresponding to up to 0.2 msof real time. 48 independent simulations revealed three  types of binding motion of the substrate-bindingdomain (SBD) towards the NBD. The frequency of any binding event was found tobe equally likely for all models of the NBD. Nonetheless, binding of the SBD inan open conformation was most strongly associated with the ATP-bound system,paralleling the experimental structure of the analogous Hsp 110 (pdb 3C7N). Anglesand distances were analyzed for all binding motions.

Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics

243rd National Meeting (2012)

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