Using free energy perturbation to predict effects of changing force field parameters on computed conformational equilibriums of peptides.
We propose a method that may allow data about the conformational equilibriums of peptides to enter the parameter calibration phase in force field developments. The method combines free energy perturbation with techniques for extensive sampling in the conformational space. It predicts shifts in computed conformational equilibriums in response to separate or combined perturbations of force field parameters. As an example we considered a force field associated with an implicit solvent model. We considered two different approaches to define conformational states of four peptides. One is based on reaction coordinates and two-dimensional free energy surfaces. The other is based on the clustering analysis of sampled conformations. Effects of perturbing various model parameters on the equilibriums between nativelike states with other conformational states were considered. For one type of perturbation predicted to have consistent effects on different peptides, the predictions have been verified by actual simulations using a perturbed model.
Cao
Zanxia
Z
School of Life Sciences and Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China (USTC), Hefei, Anhui 230027, People's Republic of China.
Liu
Haiyan
H
D003198:Computer Simulation; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D013816:Thermodynamics
D010455:Peptides