Folding pathways and rates for the three-stranded beta-sheet peptide Beta3s using discrete path sampling.
The discrete path sampling method was used to investigate the folding of a three-stranded antiparallel beta-sheet peptide, Beta3s, described by an empirical potential and implicit solvent model. After application of a coarse-graining scheme that groups together sets of minima in local equilibrium, the calculated folding time was in reasonable agreement with other simulations and consistent with the experimental upper bound. The folding mechanism exhibited by the most significant discrete paths involves early formation of the C-terminal hairpin followed by docking of the N-terminal strand.
Carr
Joanne M
JM
University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.
Wales
David J
DJ
D000465:Algorithms; D003198:Computer Simulation; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
D010455:Peptides; D012997:Solvents