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Journal Article

Mesoscale modeling of molecular machines: Cyclic dynamics and hydrodynamical fluctuations


Mikhailov,  Alexander S.
Physical Chemistry, Fritz Haber Institute, Max Planck Society;

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Cressman, A., Togashi, Y., Mikhailov, A. S., & Kapral, R. (2008). Mesoscale modeling of molecular machines: Cyclic dynamics and hydrodynamical fluctuations. Physical Review E, 77(5): 050901(R). doi:10.1103/PhysRevE.77.050901.

Cite as: https://hdl.handle.net/11858/00-001M-0000-0010-FCF2-8
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.