Simulation of the Opening and Closing of Hsp70 Chaperones by Coarse-Grained Molecular Dynamics

Heat-shock proteins 70 (Hsp70s) are key molecular chaperones, which assist in the folding and refolding/disaggregation of proteins. Hsp70s, which consist of a nucleotide-binding domain (NBD, consisting of NBD-I and NBD-II subdomains) and a substrate-binding domain [SBD, further split into the beta-sheet (SBD-beta) and alpha-helical (SBD-alpha) subdomains], occur in two major conformations having (a) a closed SBD, in which the SBD and NBD domains do not interact, and (b) an open SBD, in which SBD-alpha interacts with NBD-I and SBD-beta interacts with the top parts of NBD-I and NBD-II. In the SBD-closed conformation, SBD is bound to a substrate protein, with release occurring after transition to the open conformation. While the transition from the closed to the open conformation is triggered efficiently by binding of adenosine triphosphate (ATP) to the NBD, it also occurs, although less frequently, in the absence of ATP. The reverse transition occurs after ATP hydrolysis. Here, we report canonical and multiplexed replica exchange simulations of the conformational dynamics of Hsp70s using a coarse-grained molecular dynamics approach with the UNRES force field. The simulations were run in the following three modes: (i) with the two halves of the NBD unrestrained relative to each other, (ii) with the two halves of the NBD restrained in an open geometry as in the SBD-closed form of DnaK (2KHO), and (iii) with the two halves of NBD restrained in a closed geometry as in known experimental structures of ATP-bound NBD forms of Hsp70. Open conformations, in which the SBD interacted strongly with the NBD, formed spontaneously during all simulations; the number of transitions was largest in simulations carried out with the closed NBD domain, and smallest in those carried out with the open NBD domain; this observation is in agreement with the experimentally observed influence of ATP-binding on the transition of Hsp70s from the SBD-closed to the SBD-open form. Two kinds of open conformations were observed: one in which SBD-alpha interacts with NBD-I and SBD-beta interacts with the top parts of NBD-I and NBD-II (as observed in the structures of nucleotide exchange factors), and another one in which this interaction pattern is swapped. A third type of motion, in which SBD-alpha binds to NBD without dissociating from SBD-beta, was also observed. It was found that the first stage of interdomain communication (approach of SBD-beta, to NBD) is coupled with the rotation of the long axes of NBD-I and NBD-II toward each other. To the best of our knowledge, this is the first successful simulation of the full transition of an Hsp70 from the SBD-closed to the SBD-open conformation.