On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.

ABSTRACT: We characterized the conformational change of adenylate kinase (AK) between open and closed forms by conducting five all-atom molecular-dynamics simulations, each of 100 ns duration. Different initial structures and substrate binding configurations were used to probe the pathways of AK conformational change in explicit solvent, and no bias potential was applied. A complete closed-to-open and a partial open-to-closed transition were observed, demonstrating the direct impact of substrate-mediated interactions on shifting protein conformation. The sampled configurations suggest two possible pathways for connecting the open and closed structures of AK, affirming the prediction made based on available x-ray structures and earlier works of coarse-grained modeling. The trajectories of the all-ato

SUBMITTER: Brokaw JB 

PROVIDER: S-EPMC2980752 | biostudies-literature | 2010 Nov

REPOSITORIES: biostudies-literature