Multiscale enhanced sampling of glucokinase: Regulation of the enzymatic reaction via a large scale domain motion

Enhanced sampling yields a comprehensive structural ensemble or a free energy landscape. We have recently developed “multiscale enhanced sampling (MSES)”, which employs a coarse-grained model coupled with the target physical system for the efficient acceleration of the dynamics. MSES has demonstrated applicability to large protein systems in solution, such as intrinsically disordered proteins, and protein-protein and protein-ligand interactions. Here, we applied MSES to an important drug discovery target, glucokinase (GCK), to elucidate the structural basis of the positive cooperativity of the enzymatic reaction at an atomistic resolution. MSES enabled us to compare two sets of the free energy landscapes of GCK, for the glucose-bound and glucose-unbound forms, and thus demonstrated the drastic change of the free energy surface depending on the glucose concentration. The energy landscapes, together with the weighted ensemble simulations, revealed the kinetics of the structural changes in GCK with the rate constant 1.1 ms-1, which is comparable to the experimental catalytic rate, kcat = 0.22 ms-1, and indicates the origin of the cooperativity. The present study demonstrated the capability of the enhanced sampling and associated kinetic calculations to understand the atomistic structural dynamics of biological and pharmacological protein systems.