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• W2016367231 abstract "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." @default.
• W2016367231 created "2016-06-24" @default.
• W2016367231 creator A5024552074 @default.
• W2016367231 creator A5032418986 @default.
• W2016367231 date "2008-01-30" @default.
• W2016367231 modified "2023-09-23" @default.
• W2016367231 title "Solvent Viscosity Dependence of the Protein Folding Dynamics" @default.
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• W2016367231 doi "https://doi.org/10.1021/jp076301d" @default.
• W2016367231 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/18229911" @default.
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