Overcoming entropic barrier with coupled sampling at dual resolutions.
An enhanced sampling method is proposed for ab initio protein folding simulations. The new method couples a high-resolution model for accuracy and a low-resolution model for efficiency. It aims to overcome the entropic barrier found in the exponentially large protein conformational space when a high-resolution model, such as an all-atom molecular mechanics force field, is used. The proposed method is designed to satisfy the detailed balance condition so that the Boltzmann distribution can be generated in all sampling trajectories in both high and low resolutions. The method was tested on model analytical energy functions and ab initio folding simulations of a beta-hairpin peptide. It was found to be more efficient than replica-exchange method that is used as its building block. Analysis with the analytical energy functions shows that the number of energy calculations required to find global minima and to converge mean potential energies is much fewer with the new method. Ergodic measure shows that the new method explores the conformational space more rapidly. We also studied imperfect low-resolution energy models and found that the introduction of errors in low-resolution models does decrease its sampling efficiency. However, a reasonable increase in efficiency is still observed when the global minima of the low-resolution models are in the vicinity of the global minimum basin of the high-resolution model. Finally, our ab initio folding simulation of the tested peptide shows that the new method is able to fold the peptide in a very short simulation time. The structural distribution generated by the new method at the equilibrium portion of the trajectory resembles that in the equilibrium simulation starting from the crystal structure.
Lwin
Thur Zar
TZ
Chemical and Material Physics Graduate Program, University of California, Irvine, CA 92697-3900, USA.
Luo
Ray
R
D000465:Algorithms; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D019277:Entropy; D008958:Models, Molecular; D015233:Models, Statistical; D008962:Models, Theoretical; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D015203:Reproducibility of Results; D012984:Software; D013816:Thermodynamics
D010455:Peptides