Peptide folding using multiscale coarse-grained models.
The multiscale coarse-graining (MS-CG) method has been previously used to describe the equilibrium properties of peptides. The present study reveals that MS-CG models of alpha-helical polyalanine and the beta-hairpin V 5PGV 5 possess the capacity to efficiently refold in simulations initiated from unfolded configurations. The MS-CG peptides exhibit free energy landscapes that are funneled toward folded configurations and two-state folding behavior, consistent with the known characteristics of small, rapidly folding peptides. Moreover, the models demonstrate enhanced sampling capabilities when compared to systems with full atomic detail. The significance of these observations with respect to the theoretical basis of the MS-CG approach is discussed. The MS-CG peptides were used to reconstruct atomically detailed configurations in order to evaluate the extent to which MS-CG ensembles embody all-atom peptide free energy landscapes. Ensembles obtained from these reconstructed configurations display good agreement with the all-atom simulation data used to generate the MS-CG models and also corroborate the presence of features observed in the MS-CG peptide free energy landscapes. These findings suggest that MS-CG models may be of significant utility in the study of peptide folding.
Thorpe
Ian F
IF
Center for Biophysical Modeling and Simulation, Department of Chemistry, University of Utah, Salt Lake City, UT 84112-0850, USA.
Zhou
Jian
J
Voth
Gregory A
GA
D003198:Computer Simulation; D006860:Hydrogen Bonding; D008956:Models, Chemical; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry*; D020673:Protein Renaturation; D013816:Thermodynamics
D010455:Peptides; C019529:polyalanine