Fine structure of conformational ensembles in adenylate kinase

Adenylate kinase (ADK) catalyzes the reversible Mg²⁺ -dependent phosphoryl transfer reaction Mg²⁺ +2ADP ↔Mg²⁺ +ATP + AMP in essential cellular systems. This reaction is a major player in cellular energy homeostasis and the isoform network of ADK plays an important role in AMP metabolic signaling circuits. ADK has 3 domains, the LID, NMP, and CORE domains, that undergo large conformational rearrangements during ADK's catalytic cycle. In spite of extensive experimental and computational studies, details of the conformational pathway from open to closed forms remain uncertain. In this paper we explore this pathway using coarse-grained molecular dynamics (MD) trajectories of ADK calculated by GROMACS using a SMOG model and classify the conformations within the resultant trajectories by K-means clustering. ADK conformations segregate naturally into open; intermediate; and closed forms with long-term residence in the intermediate state. Structural clustering divides the intermediate conformation into 3 sub-states that are distinguished from one another on the basis of differences in both structure and dynamics. These distinctions are defined on the basis of a number of different metrics including radius of gyration, dihedral angle fluctuation, and fluctuations of interatomic pair distances. Furthermore, differences in the sub-states appear to correspond to the distinct ways each sub-state contributes to the molecular mechanism of catalysis: One sub-state acts as a gate-way to the open conformation; one sub-state a gate-way to the closed conformation. A third intermediate sub-state appears to represent a metastable off-pathway structure that is nevertheless frequently visited during the passage from open to closed state.