Folding of small proteins using a single continuous potential.
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single continuous potential (united-residue force field). In all cases, collapse occurs at a very early stage, and proteins fold into their nativelike conformations at appropriate temperatures. We also observe that glassy transitions occur at low temperatures. The simulation results demonstrate that the folding mechanism is controlled not only by thermodynamic factors but also by kinetic factors: The way a protein folds into its native structure is also determined by the convergence point of early folding trajectories, which cannot be obtained by the free energy surface.
Kim
Seung-Yeon
SY
School of Computational Sciences, Korea Institute for Advanced Study, 207-43 Cheongryangri-dong, Dongdaemun-gu, Seoul 130-722, Korea.
Lee
Julian
J
Lee
Jooyoung
J
D001703:Biophysics / Q000379:methods*; D002627:Chemistry, Physical / Q000379:methods; D008958:Models, Molecular; D015233:Models, Statistical; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D011336:Probability; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D013696:Temperature; D013816:Thermodynamics
D010455:Peptides