Solvent viscosity dependence of the protein folding dynamics

Area of Science:

• Computational biophysics
• Protein dynamics

Background:

• Solvent viscosity is a parameter adjusted in computational studies, particularly for protein folding simulations using implicit solvent models.
• Low viscosities are commonly employed to accelerate simulations, based on Kramers' theory relating viscosity to folding kinetics.

Purpose of the Study:

• To investigate the impact of solvent viscosity on the detailed dynamics and mechanism of protein folding.
• To assess the validity of using unphysically low viscosities in computational simulations.

Main Methods:

• Development of a simple mathematical model to analyze viscosity effects on protein folding dynamics.
• Application of the mathematical model to simulate the folding process of a small protein.

Main Results:

• The study demonstrates that viscosity can influence protein folding dynamics in complex ways.
• Unphysically low viscosities were shown to pronouncedly affect the detailed folding dynamics, challenging their use in simulations.

Conclusions:

• Using unphysically low solvent viscosities in protein folding simulations may lead to inaccurate mechanistic insights.
• The developed model can serve as a diagnostic tool for validating low-viscosity simulations and potentially yield further information on protein folding mechanisms.