Variations in the fast folding rates of the lambda-repressor: a hybrid molecular dynamics study

Biophysical Journal
Taras V Pogorelov, Zaida Luthey-Schulten

Abstract

The ability to predict the effects of mutations on protein folding rates and mechanisms would greatly facilitate folding studies. Using a realistic full atom potential coupled with a Gō-like potential biased to the native state structure, we have investigated the effects of point mutations on the folding rates of a small single domain protein. The hybrid potential provides a detailed level of description of the folding mechanism that we correlate to features of the folding energy landscapes of fast and slow mutants of an 80-residue-long fragment of the lambda-repressor. Our computational reconstruction of the folding events is compared to the recent experimental results of W. Y. Yang and M. Gruebele (see companion article) and T. G. Oas and co-workers on the lambda-repressor, and helps to clarify the differences observed in the folding mechanisms of the various mutants.

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Citations

Mar 31, 2012·The Journal of Physical Chemistry. B·Ke ChenZaida Luthey-Schulten
Sep 7, 2007·Proceedings of the National Academy of Sciences of the United States of America·Jorge ChahineJin Wang
Feb 9, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hairong Ma, Martin Gruebele
Mar 20, 2014·Quarterly Reviews of Biophysics·Hannah Gelman, Martin Gruebele
Apr 15, 2016·Proceedings of the National Academy of Sciences of the United States of America·Wookyung YuTobin R Sosnick
Jul 8, 2009·Biophysical Journal·Seung Joong KimMartin Gruebele
Jun 28, 2012·The Journal of Physical Chemistry Letters·Yanxin LiuKlaus Schulten
Mar 30, 2017·Journal of Chemical Theory and Computation·Hamed Meshkin, Fangqiang Zhu
Nov 26, 2009·FEBS Letters·Rebecca W AlexanderZaida Luthey-Schulten
Nov 23, 2005·Journal of Computational Chemistry·Hairong Ma, Martin Gruebele
Dec 24, 2018·The Journal of Chemical Physics·Ronaldo Junio de Oliveira
Dec 21, 2011·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Yann von HansenRoland R Netz
Nov 12, 2009·The Journal of Physical Chemistry. B·Amandeep K Sangha, T Keyes
Dec 13, 2011·Journal of Chemical Theory and Computation·Ludovico SuttoFrancesco Luigi Gervasio
Aug 25, 2018·The Journal of Physical Chemistry. B·Yong WangKresten Lindorff-Larsen

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