Mesoscale modeling of molecular machines: cyclic dynamics and hydrodynamical fluctuations.
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.
Cressman
Andrew
A
Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario, Canada M5S 3H6. andrew.cressman@utoronto.ca
Togashi
Yuichi
Y
Mikhailov
Alexander S
AS
Kapral
Raymond
R
D003198:Computer Simulation; D004735:Energy Transfer; D008956:Models, Chemical; D008958:Models, Molecular; D020409:Molecular Motor Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D009038:Motion; D011487:Protein Conformation
D020409:Molecular Motor Proteins