Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations.
The folding of a 15-residue beta-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5 micros-long for a total of 37.5 micros, are performed of the peptide in explicit solvent, at room temperature, and without the use of enhanced sampling techniques. The computed folding time of 1-1.5 micros obtained from the simulations is in good agreement with experiment [Xu, Y.; et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. A common folding mechanism is observed, in which the turn is always found to be the major determinant in initiating the folding process, followed by cooperative formation of the interstrand hydrogen bonds and the side-chain packing. Furthermore, direct transition to the folded state from fully unstructured conformations does not take place. Instead, the peptide is always observed to form partially structured conformations involving a non-native (ESYI) turn from which the native (NPDG) turn forms, triggering the folding to the beta-hairpin.
Thukral
Lipi
L
Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
Smith
Jeremy C
JC
Daidone
Isabella
I
D007700:Kinetics; D056004:Molecular Dynamics Simulation; D019906:Nuclear Magnetic Resonance, Biomolecular; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D012996:Solutions
D010446:Peptide Fragments; D012996:Solutions