Mechanochemical coupling in the myosin motor domain. II. Analysis of critical residues

Abstract

An important challenge in the analysis of mechanochemical coupling in molecular motors is to identify residues that dictate the tight coupling between the chemical site and distant structural rearrangements. In this work, a systematic attempt is made to tackle this issue for the conventional myosin. By judiciously combining a range of computational techniques with different approximations and strength, which include targeted molecular dynamics, normal mode analysis, and statistical coupling analysis, we are able to identify a set of important residues and propose their relevant function during the recovery stroke of myosin. These analyses also allowed us to make connections with previous experimental and computational studies in a critical manner. The behavior of the widely used reporter residue, Trp501, in the simulations confirms the concern that its fluorescence does not simply reflect the relay loop conformation or active-site open/close but depends subtly on its microenvironment. The findings in the targeted molecular dynamics and a previous minimum energy path analysis of the recovery stroke have been compared and analyzed, which emphasized the difference and complementarity of the two approaches. In conjunction with our previous studies, the current set of investigations suggest that the modulation of structural flexibility at both the local (e.g., active-site) and domain scales with strategically placed ''hotspot'' residues and phosphate chemistry is likely the general feature for mechanochemical coupling in many molecular motors. The fundamental strategies of examining both collective and local changes and combining physically motivated methods and informatics-driven techniques are expected to be valuable to the study of other molecular motors and allosteric systems in general.

The myosin start‐of‐power stroke state and how actin binding drives the power stroke

“…However, a comprehensive structural and dynamic understanding is still lacking on account of experimental difficulties in determining intermediate structures and the difficulty of finding specific signals that allow an unambiguous monitoring of the force generation pathway. A simple reversal of the processes suggested for the mechanism of the recovery stroke [Fischer et al, ; Koppole et al, ; Yu et al, ] is rather implausible. The recovery stroke drives the myosin protein from the postrigor state (state 2) to the prepower stroke state (state 3) at a time when myosin is dissociated from the actin filament (see Fig.…”

“…A tight communication exists between conformational changes in the actin‐binding region, the nucleotide‐binding site, and the position of the lever arm. Various crystallographic studies have provided high‐resolution insights into the structural features of the two actin‐detached myosin states [Rayment et al, ; Fisher et al, ; Dominguez et al, ; Houdusse et al, ; Gourinath et al, ; Coureux et al, ; Ménétrey et al, ; Fedorov et al, ], which have allowed supplementary computational approaches aimed at deciphering the mechanism of the recovery stroke [Fischer et al, ; Koppole et al, ; Yu et al, ]. Cryo‐electron microscopic analyses of myosin‐decorated actin filaments combined with the fitting of X‐ray crystallographic data to the obtained electron densities have dramatically improved our understanding of the actin–myosin interface and the rigor state conformation [Holmes et al, ; Lorenz and Holmes, ; Behrmann et al, ].…”

An intermediate along the recovery stroke of myosin VI revealed by X-ray crystallography and molecular dynamics

“…Based on various computational strategies (15)(16)(17)(18)(19)(20)(21)(22)(23)(24), several models were proposed (SI Appendix, Supplementary Text 1). A common feature of these models [with the notable exception of Cui and coworkers (17,18)] is that switch II closure is presented as the initiating event of the recovery stroke, which triggers the large-amplitude rotation of the converter. Although the details of the coupling between switch II closure and converter repriming are still under debate, the most accepted view [first proposed by Fischer et al (15)] is that closing of switch II exerts strain on the Relay helix that bends and kinks in response, driving the converter rotation.…”

Hysteresis-Based Mechanism for the Directed Motility of the Ncd Motor

“…However, as in the case of the conformational changes in Kinesin-1 (30), normal modes were not directly linked to the transition of the neck. MEP was not effective either, possibly because the Ncd neck moves diffusively, whereas MEP is a zero-temperature method (25,31). A comparison of these methods can be found in Section S3 in the Supporting Material.…”