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

Adenylate kinase (Adk), an enzyme which 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 100ns. This duration is sufficiently long to reveal a partial conversion of the enzyme which proceeds through jumps between structurally-different substates. The intra- and inter-substates 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 fluctuations within and across the substates are consistent and can be described by a limited set of collective modes. The functional-oriented nature of the consensus modes is suggested by their good overlap with the deformation vector bridging the open and closed crystal structures. The consistency of Adk's internal dynamics over time-scales wide enough to capture intra-and inter-substates fluctuations adds elements in favor of the recent proposal that the free (apo) enzyme possesses an innate ability to sustain the open/close conformational changes.