Mesoscale modeling of molecular machines: Cyclic dynamics and hydrodynamical fluctuations

Publication Type:

Journal Article

Authors:

Cressman, A.; Togashi, Y.; Mikhailov, A.S.; Kapral, R.

Source:

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics, Volume 77, Number 5 (2008)

URL:

https://www.scopus.com/inward/record.uri?eid=2-s2.0-43449104714&doi=10.1103%2fPhysRevE.77.050901&partnerID=40&md5=1a804e8f25cf1d60bd6929b631bb46a6

Keywords:

Cyclic dynamics, Dissociation, Hydrodynamical fluctuations, Hydrodynamics, Ligands, Mesoscale modeling, Molecular dynamics, Molecular machines, Proteins, Solvents

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. © 2008 The American Physical Society.

File Attachment:

PDF