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Mesoscale modeling of molecular machines: cyclic dynamics and hydrodynamical fluctuations
Andrew Cressman1, Yuichi Togashi, Alexander S Mikhailov
1Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6. andrew.cressman@utoronto.ca
Abstract:
Proteins acting as molecular machines can undergo cyclic internal conformational motions that are coupled to ligand binding and dissociation events. In contrast to their macroscopic counterparts, nanomachines operate in a highly fluctuating environment, which influences their operation. To bridge the gap between detailed microscopic and simple phenomenological descriptions, a mesoscale approach, which combines an elastic network model of a machine with a particle-based mesoscale description of the solvent, is employed. The time scale of the cyclic hinge motions of the machine prototype is strongly affected by hydrodynamical coupling to the solvent.
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