Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide

The Journal of Chemical Physics
Jed W PiteraWilliam C Swope

Abstract

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.

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Citations

May 1, 2012·Journal of the American Chemical Society·Robert M CulikFeng Gai
Feb 6, 2013·Proceedings of the National Academy of Sciences of the United States of America·Kevin C JonesAndrei Tokmakoff
Jul 8, 2009·International Journal of Molecular Sciences·Yi XiaoYi He
Feb 9, 2007·The Journal of Chemical Physics·Adam W Smith, Andrei Tokmakoff
Jul 5, 2011·The Journal of Chemical Physics·John D ChoderaVijay S Pande
Jan 19, 2007·The Journal of Chemical Physics·Philippe Derreumaux, Normand Mousseau
Nov 10, 2009·The Journal of Chemical Physics·Alexis J Lee, Steven W Rick
Jul 2, 2010·The Journal of Chemical Physics·Cheng Zhang, Jianpeng Ma
Feb 17, 2011·The Journal of Chemical Physics·Jason Gee, M Scott Shell
May 2, 2009·The Journal of Chemical Physics·Yuguang Mu
Dec 17, 2014·The Journal of Chemical Physics·Emanuel K PeterJoan-Emma Shea
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Nov 6, 2007·Biophysical Journal·Thomas la Cour Jansen, Jasper Knoester
May 18, 2016·The Journal of Physical Chemistry. B·Bei DingFeng Gai
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Dec 10, 2020·The Journal of Chemical Physics·Fahim FaiziEdina Rosta
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Aug 10, 2010·The Journal of Physical Chemistry. B·Adam W SmithJasper Knoester
Aug 17, 2010·The Journal of Physical Chemistry. B·Karin HauserTimothy A Keiderling

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