Binding pocket dynamics along the recovery stroke of human β-cardiac myosin

Abstract

The druggability of small-molecule binding sites can be significantly affected by protein motions and conformational changes. Ligand binding, protein dynamics and protein function have been shown to be closely interconnected in myosins. The breakthrough discovery of omecamtiv mecarbil (OM) has led to an increased interest in small molecules that can target myosin and modulate its function for therapeutic purposes (myosin modulators). In this work, we use a combination of computational methods, including steered molecular dynamics, umbrella sampling and binding pocket tracking tools, to follow the evolution of the OM binding site during the recovery stroke transition of human β-cardiac myosin. We found that steering two internal coordinates of the motor domain can recapture the main features of the transition and in particular the rearrangements of the binding site, which shows significant changes in size, shape and composition. Possible intermediate conformations were also identified, in remarkable agreement with experimental findings. The differences in the binding site properties observed along the transition can be exploited for the future development of conformation-selective myosin modulators.

A weak coupling mechanism mediates the recovery stroke of myosin VI: a free energy simulation and string method analysis

“…The same is true for pathogenic mutations disrupting the converter-Relay interactions in Human -cardiac myosin, which would perturb the recovery stroke regardless of its mechanism, as supported by recent free energy calculations in Dd Myo2 [46] and -cardiac myosin [47]. In addition, recent free energy calculations on -cardiac myosin also identified a PTS-like intermediate [44]. Last, the ratchet-like mechanism is consistent with the structural intermediate of smooth muscle myosin II trapped off-actin by the CK-571 drug [43], which exhibits a partially re-primed converter, an “un-kinked” Relay helix and an open Switch II.…”

“…To advance on this question, detailed computational investigations of the recovery stroke mechanism in other myosin isoforms [48] are needed. As a bonus, these analyses would enable the characterization of cryptic binding pockets for the design of myosin's allosteric modulators [44,49,50].…”

“…In particular, we focused on the recovery stroke transition that couples the re-priming of the myosin lever arm to ATP hydrolysis. Our results shed light on the chemo-mechanical transduction mechanism and illuminate structural intermediates visited during this off-actin transition, which may be targeted by allosteric modulatory ligands [43, 44].…”

Omecamtiv mecarbil and Mavacamten target the same myosin pocket despite antagonistic effects in heart contraction

“…To decipher how small local differences near the binding site of these force modulators can translate into different energy landscapes and thus different control of actin-binding or Pi release from the motor, all atoms molecular dynamics simulations were performed. Such simulations provide indications for allosteric communication and subdomain reorganization when conformational sub-states are explored 30,35,36,37,38,39,40 . We made a comparative study between three simulations started from S1 bound to Mava, S1 bound to OM and S1 without compound (apo), all bound to Mg.ADP.Pi in the active site (Supplementary Movie 2, 3 and 4).…”