Solvent viscosity dependence of the folding rate of a small protein: distributed computing study.
By using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20-residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (gamma). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the low-viscosity regime (values below the viscosity of water). In accordance with Kramers' theory, we observe approximately linear dependence of the folding rate on 1/gamma for values from 1-10(-1)x that of water viscosity. However, for the regime between 10(-4)-10(-1)x that of water viscosity we observe power-law dependence of the form k approximately gamma(-1/5). These results suggest that estimating folding rates from molecular simulations run at low viscosity under the assumption of linear dependence of rate on inverse viscosity may lead to erroneous results.
Zagrovic
Bojan
B
Biophysics Program and Department of Chemistry, Stanford University, Stanford, CA 94305, USA.
Pande
Vijay
V
D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012997:Solvents; D013816:Thermodynamics; D014364:Tryptophan / Q000737:chemistry*; D014783:Viscosity
D011506:Proteins; D012997:Solvents; D014364:Tryptophan