Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide.
We have carried out extensive all atom explicit solvent simulations of the high-temperature folding and unfolding of the trpzip2 beta-hairpin peptide and examined the resulting trajectories for evidence of folding via a reptation mechanism. Over 300 microcanonical simulations of 10 ns each were initiated from a Boltzmann ensemble of conformations at 425 K. Though we observed numerous folding and unfolding events, no evidence of reptation was found. The diffusional dynamics of the peptide are orders of magnitude faster than any observed reptation-like motion. Our data suggest that the dominant mechanisms for beta-hairpin folding under these conditions are hydrophobic collapse and turn formation, and that rearrangements occur via significant expansion of the polypeptide chain.
Pitera
Jed W
JW
IBM Almaden Research Center, San Jose, California 95120, USA. pitera@us.ibm.com
Haque
Imran
I
Swope
William C
WC
D002627:Chemistry, Physical / Q000379:methods*; D003198:Computer Simulation; D004058:Diffusion; D006860:Hydrogen Bonding; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D012997:Solvents / Q000737:chemistry; D013696:Temperature
D010455:Peptides; D012997:Solvents