Global optimization and folding pathways of selected alpha-helical proteins.
The results of basin-hopping global optimization simulations are presented for four small, alpha-helical proteins described by a coarse-grained potential. A step-taking scheme that incorporates the local conformational preferences extracted from a large number of high-resolution protein structures is compared with an unbiased scheme. In addition, the discrete path sampling method is used to investigate the folding of one of the proteins, namely, the villin headpiece subdomain. Folding times from kinetic Monte Carlo simulations and iterative calculations based on a Markovian first-step analysis for the resulting stationary-point database are in good mutual agreement, but differ significantly from the experimental values, probably because the native state is not the global free energy minimum for the potential employed.
Carr
Joanne M
JM
University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
Wales
David J
DJ
D000465:Algorithms; D002627:Chemistry, Physical / Q000379:methods*; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008390:Markov Chains; D008840:Microfilament Proteins / Q000737:chemistry; D008968:Molecular Conformation; D009010:Monte Carlo Method; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012984:Software; D013696:Temperature
D008840:Microfilament Proteins; D011506:Proteins; C026615:villin