Intrinsic motions along an enzymatic reaction trajectory

The mechanisms by which enzymes achieve extraordinary rate acceleration and specificity have long been of key interest in biochem. It is generally recognized that substrate binding coupled to conformational changes of the substrate-​enzyme complex aligns the reactive groups in an optimal environment for efficient chem. Although chem. mechanisms have been elucidated for many enzymes, the question of how enzymes achieve the catalytically competent state has only recently become approachable by expt. and computation. Here, the authors show crystallog. evidence for conformational substates along the trajectory toward the catalytically competent 'closed' state in the ligand-​free form of adenylate kinase. Mol. dynamics simulations indicate that these partially closed conformations are sampled in nanoseconds, whereas NMR and single-​mol. fluorescence resonance energy transfer reveal rare sampling of a fully closed conformation occurring on the microsecond-​to-​millisecond timescale. Thus, the larger-​scale motions in substrate-​free adenylate kinase are not random, but preferentially follow the pathways that create the configuration capable of proficient chem. Such preferred directionality, encoded in the fold, may contribute to catalysis in many enzymes.