Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations

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Abstract
Although the major structural transitions in molecular motors are often argued to couple to the binding of Adenosine triphosphate (ATP), the recovery stroke in the conventional myosin has been shown to be dependent on the hydrolysis of ATP. To obtain a clearer mechanistic picture for such “mechanochemical coupling” in myosin, equilibrium active-site simulations with explicit solvent have been carried out to probe the behavior of the motor domain as functions of the nucleotide chemical state and conformation of the converter/relay helix. In conjunction with previous studies of ATP hydrolysis with different active-site conformations and normal mode analysis of structural flexibility, the results help establish an energetics-based framework for understanding the mechanochemical coupling. It is proposed that the activation of hydrolysis does not require the rotation of the lever arm per se, but the two processes are tightly coordinated because both strongly couple to the open/close transition of the active site. The underlying picture involves shifts in the dominant population of different structural motifs as a consequence of changes elsewhere in the motor domain. The contribution of this work and the accompanying paper [36] is to propose the actual mechanism behind these “population shifts” and residues that play important roles in the process. It is suggested that structural flexibilities at both the small and large scales inherent to the motor domain make it possible to implement tight couplings between different structural motifs while maintaining small free-energy drops for processes that occur in the detached states, which is likely a feature shared among many molecular motors. The significantly different flexibility of the active site in different X-ray structures with variable level arm orientations supports the notation that external force sensed by the lever arm may transmit into the active site and influence the chemical steps (nucleotide hydrolysis and/or binding). The hydrolysis of Adenosine triphosphate (ATP) provides the energy for most life processes, including the motility of molecular motors. How the chemical energy of hydrolysis is converted into mechanical work in these fascinating “nanomachines” is a central question that has only been answered in an outline form for almost all molecular motors. The fundamental challenge is that the working cycle of molecular motors involves processes of different physicochemical natures and scales, including ATP chemistry and protein structural transitions of diverse magnitudes (from a few Angstroms to a few nanometers), which makes mechanistic analysis using experiments alone difficult. Combined with previous computational studies from this lab, molecular dynamics simulations help identify energetic and structural properties of myosin, a prototypical molecular motor, that are essential to its energy conversion function. In addition to the role of flexibilities at the domain scale, which has been emphasized in previous studies of similar systems, the current results highlight the comparable significance of local flexibilities and how these flexibilities at different scales are modulated by ATP chemistry.