Solvent viscosity dependence of the protein folding dynamics.
Solvent viscosity has been frequently adopted as an adjustable parameter in various computational studies (e.g., protein folding simulations) with implicit solvent models. A common approach is to use low viscosities to expedite simulations. While using viscosities lower than that of aqueous is unphysical, such treatment is based on observations that the viscosity affects the kinetics (rates) in a well-defined manner as described by Kramers' theory. Here, we investigate the effect of viscosity on the detailed dynamics (mechanism) of protein folding. On the basis of a simple mathematical model, we first show that viscosity may indeed affect the dynamics in a complex way. By applying the model to the folding of a small protein, we demonstrate that the detailed dynamics is affected rather pronouncedly especially at unphysically low viscosities, cautioning against using such viscosities. In this regard, our model may also serve as a diagnostic tool for validating low-viscosity simulations. It is also suggested that the viscosity dependence can be further exploited to gain information about the protein folding mechanism.
Rhee
Young Min
YM
Department of Chemistry, Stanford University, Stanford, California 94305, USA. pande@stanford.edu
Pande
Vijay S
VS
D004058:Diffusion; D011336:Probability; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012680:Sensitivity and Specificity; D012997:Solvents / Q000737:chemistry*; D014783:Viscosity
D011506:Proteins; D012997:Solvents