Why do protein folding rates correlate with metrics of native topology?

PloS One
Patrícia F N FaíscaAntonio Rey

Abstract

For almost 15 years, the experimental correlation between protein folding rates and the contact order parameter has been under scrutiny. Here, we use a simple simulation model combined with a native-centric interaction potential to investigate the physical roots of this empirical observation. We simulate a large set of circular permutants, thus eliminating dependencies of the folding rate on other protein properties (e.g. stability). We show that the rate-contact order correlation is a consequence of the fact that, in high contact order structures, the contact order of the transition state ensemble closely mirrors the contact order of the native state. This happens because, in these structures, the native topology is represented in the transition state through the formation of a network of tertiary interactions that are distinctively long-ranged.

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Citations

Jul 17, 2014·The Journal of Chemical Physics·Miguel A SolerPatrícia F N Faísca
Sep 12, 2013·PloS One·Miguel A Soler, Patrícia F N Faísca
Sep 19, 2015·Computational and Structural Biotechnology Journal·Patrícia F N Faísca
Nov 26, 2014·Protein Science : a Publication of the Protein Society·Aron BroomElizabeth M Meiering
Mar 24, 2016·Chemical Communications : Chem Comm·A LjubetičR Jerala
Aug 16, 2014·Structure·Alireza MashaghiSander J Tans
Dec 24, 2014·Physical Chemistry Chemical Physics : PCCP·Heinrich KrobathPatrícia F N Faísca
Oct 11, 2016·Physical Chemistry Chemical Physics : PCCP·Miguel A SolerPatrícia F N Faísca
May 24, 2018·Proteins·Susan Khor
Jan 4, 2013·Physical Biology·Heinrich Krobath, Patrícia F N Faísca
Sep 18, 2014·Physical Chemistry Chemical Physics : PCCP·Andrew MuglerAlireza Mashaghi
Aug 14, 2019·Frontiers in Microbiology·Maria S LoosAnastassios Economou
May 23, 2019·Physical Chemistry Chemical Physics : PCCP·João EspecialPatrícia Fn Faísca
Feb 18, 2020·Biophysical Journal·Daniel Trotter, Stefan Wallin
Jun 9, 2021·The Journal of Physical Chemistry. B·Beatriz Fernández Del Río, Antonio Rey

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Methods Mentioned

BETA
protein folding

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