Efficient Monte Carlo trial moves for polypeptide simulations.
A new move set for the Monte Carlo simulations of polypeptide chains is introduced. It consists of a rigid rotation along the (C(alpha)) ends of an arbitrary long segment of the backbone in such a way that the atoms outside this segment remain fixed. This fixed end move, or FEM, alters only the backbone dihedral angles phi and psi and the C(alpha) bond angles of the segment ends. Rotations are restricted to those who keep the alpha bond angles within their maximum natural range of approximately +/-10 degrees. The equations for the angular intervals (tau) of the allowed rigid rotations and the equations required for satisfying the detailed balance condition are presented in detail. One appealing property of the FEM is that the required number of calculations is minimal, as it is evident from the simplicity of the equations. In addition, the moving backbone atoms undergo considerable but limited displacements of up to 3 A. These properties, combined with the small number of backbone angles changed, lead to high acceptance rates for the new conformations and make the algorithm very efficient for sampling the conformational space. The FEMs, combined with pivot moves, are used in a test to fold a group of coarse-grained proteins with lengths of up to 200 residues.
Betancourt
Marcos R
MR
Department of Physics, Indiana University Purdue University Indianapolis, Indianapolis, Indiana 46202, USA. mbetancourt@mailaps.org
D000465:Algorithms; D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry*; D011336:Probability; D017510:Protein Folding
D010455:Peptides