The Trp cage: folding kinetics and unfolded state topology via molecular dynamics simulations.

摘要: Using over 75 μs of molecular dynamics simulation, we have generated several thousand folding simulations the 20-residue Trp cage at experimental temperature and solvent viscosity. A total 116 independent reach RMSDcα values below 3 RMSDcα, some as close 1.4 RMSDcα. We estimate a time 5.5±3.5 μs, rate that is in reasonable agreement with kinetics. Finally, characterize both folded unfolded ensemble under native conditions note average topology very similar to state.