A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis

• Published in: PLoS computational biology 2024-04, Vol.20 (4), p.e1012005
• Main Authors: Blanc, Florian E C, Houdusse, Anne, Cecchini, Marco
• Format: Article
• Language: English
• Subjects: Actin; Adenosine triphosphate; Adenosine Triphosphate - chemistry; Adenosine Triphosphate - metabolism; Analysis; Arm; ATP; Binding Sites; Biochemistry; Biochemistry, Molecular Biology; Closures; Computational Biology - methods; Coupling; Energy; Free energy; Hydrolysis; Levers; Life Sciences; Models, Molecular; Molecular Dynamics Simulation; Myosin; Myosin Heavy Chains - chemistry; Myosin Heavy Chains - metabolism; Nucleotides; Priming; Protein Conformation; Recovery; Relay; Simulation; Strings; Structural Biology; Thermodynamics
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1012005

Myosin motors use the energy of ATP to produce force and directed movement on actin by a swing of the lever-arm. ATP is hydrolysed during the off-actin re-priming transition termed recovery stroke. To provide an understanding of chemo-mechanical transduction by myosin, it is critical to determine how the reverse swing of the lever-arm and ATP hydrolysis are coupled. Previous studies concluded that the recovery stroke of myosin II is initiated by closure of the Switch II loop in the nucleotide-binding site. Recently, we proposed that the recovery stroke of myosin VI starts with the spontaneous re-priming of the converter domain to a putative pre-transition state (PTS) intermediate that precedes Switch II closing and ATPase activation. Here, we investigate the transition from the pre-recovery, post-rigor (PR) state to PTS in myosin VI using geometric free energy simulations and the string method. First, our calculations rediscover the PTS state agnostically and show that it is accessible from PR via a low free energy transition path. Second, separate path calculations using the string method illuminate the mechanism of the PR to PTS transition with atomic resolution. In this mechanism, the initiating event is a large movement of the converter/lever-arm region that triggers rearrangements in the Relay-SH1 region and the formation of the kink in the Relay helix with no coupling to the active site. Analysis of the free-energy barriers along the path suggests that the converter-initiated mechanism is much faster than the one initiated by Switch II closure, which supports the biological relevance of PTS as a major on-pathway intermediate of the recovery stroke in myosin VI. Our analysis suggests that lever-arm re-priming and ATP hydrolysis are only weakly coupled, so that the myosin recovery stroke is initiated by thermal fluctuations and stabilised by nucleotide consumption via a ratchet-like mechanism.