Many local motions cooperate to produce the adenylate kinase conformational transition.

ABSTRACT: Conformational transitions are functionally important in many proteins. In the enzyme adenylate kinase (AK), two small domains (LID and NMP) close over the larger CORE domain; the reverse (opening) motion limits the rate of catalytic turnover. Here, using double-well Gō simulations of Escherichia coli AK, we elaborate on previous investigations of the AK transition mechanism by characterizing the contributions of rigid-body (Cartesian), backbone dihedral, and contact motions to transition-state (TS) properties. In addition, we compare an apo simulation to a pseudo-ligand-bound simulation to reveal insights into allostery. In Cartesian space, LID closure precedes NMP closure in the bound simulation, consistent with prior coarse-grained models of the AK transition. However, NMP-first closure

SUBMITTER: Daily MD 

PROVIDER: S-EPMC2902635 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature