The folding pathway of spectrin R17 from experiment and simulation: using experimentally validated MD simulations to characterize States hinted at by experiment

Journal of Molecular Biology
Kathryn A ScottJ Clarke

Abstract

We present an experimental and computational analysis of the folding pathway of the 17th domain of chicken brain alpha-spectrin, R17. Wild-type R17 folds in a two-state manner and the chevron plot (plot of the logarithm of the observed rate constant against concentration of urea) shows essentially linear folding and unfolding arms. A number of mutant proteins, however, show a change in slope of the unfolding arm at high concentration of denaturant, hinting at complexity in the folding landscape. Through a combination of mutational studies and high temperature molecular dynamics simulations we show that the folding of R17 can be described by a model with two sequential transition states separated by an intermediate species. The rate limiting transition state for folding in water has been characterized both through experimental Phi-value analysis and by simulation. In contrast, a detailed analysis of the transition state predicted to dominate under highly denaturing conditions is only possible by simulation.

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Citations

Feb 17, 2007·Journal of the American Chemical Society·Hai-Feng Chen, Ray Luo
Jun 20, 2012·Proceedings of the National Academy of Sciences of the United States of America·Beth G WensleyJane Clarke
Feb 21, 2014·International Journal of Molecular Sciences·Guodong HuJihua Wang
Feb 19, 2008·Current Opinion in Structural Biology·Wilfred F van GunsterenAlan E Mark
May 24, 2008·Proteins·Bengt Nölting, David A Agard
Nov 7, 2006·Biophysical Journal·Lucy G RandlesJane Clarke
Sep 25, 2007·Biophysical Journal·Lucy G RandlesJane Clarke
Dec 26, 2012·Current Opinion in Structural Biology·Adrian A NicksonJane Clarke
Aug 25, 2012·Journal of Molecular Biology·Beth G WensleyJane Clarke
Jan 24, 2007·Current Opinion in Structural Biology·David J Brockwell, Sheena E Radford
Nov 21, 2007·Journal of Molecular Biology·Ilkka LappalainenJane Clarke
Mar 13, 2012·Biophysical Journal·Whasil LeePiotr E Marszalek
Jul 7, 2017·Angewandte Chemie·Wilfred F van GunsterenLorna J Smith
Apr 20, 2018·Proceedings of the National Academy of Sciences of the United States of America·Daniela BauerGabriel Žoldák
Mar 23, 2019·Annual Review of Biophysics·Ashok Sekhar, Lewis E Kay
Aug 1, 2008·Journal of Chemical Theory and Computation·Hai-Feng Chen
Aug 21, 2013·The Journal of Physical Chemistry. B·Robert B Best
Nov 9, 2018·The Journal of Physical Chemistry. B·Fernando Bruno da SilvaVitor B P Leite
Oct 3, 2018·The Journal of Physical Chemistry. B·Fernando Miguel YrazuCecilia Clementi

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