Effects of long-range electrostatic forces on simulated protein folding kinetics.
Molecular dynamics simulations are a useful tool for characterizing protein folding pathways. There are several methods of treating electrostatic forces in these simulations with varying degrees of physical fidelity and computational efficiency. In this article, we compare the reaction field (RF) algorithm, particle-mesh Ewald (PME), and tapered cutoffs with increasing cutoff radii to address the impact of the electrostatics method employed on the folding kinetics. We quantitatively compare different methods by a correlation of quantitative measures of protein folding kinetics. The results of these comparisons show that for protein folding kinetics, the RF algorithm can quantitatively reproduce the kinetics of the more costly PME algorithm. These results not only assist the selection of appropriate algorithms for future simulations, but also give insight on the role that long-range electrostatic forces have in protein folding.
Robertson
Alex
A
Department of Chemistry, Stanford University, Stanford, California 94305, USA.
Luttmann
Edgar
E
Pande
Vijay S
VS
D000465:Algorithms; D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D055672:Static Electricity
D011506:Proteins