Small- and large-scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics.

ABSTRACT: Adenylate kinase, an enzyme that catalyzes the phosphoryl transfer between ATP and AMP, can interconvert between the open and catalytically potent (closed) forms even without binding ligands. Several aspects of the enzyme elasticity and internal dynamics are analyzed here by atomistic molecular dynamics simulations covering a total time span of 100 ns. This duration is sufficiently long to reveal a partial conversion of the enzyme that proceeds through jumps between structurally different substates. The intra- and intersubstates contributions to the enzyme's structural fluctuations are analyzed and compared both in magnitude and directionality. It is found that, despite the structural heterogeneity of the visited conformers, the generalized directions accounting for conformational fluctuat

SUBMITTER: Pontiggia F 

PROVIDER: S-EPMC2599863 | biostudies-literature | 2008 Dec

REPOSITORIES: biostudies-literature