Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61989592%3A15310%2F12%3A33142576" target="_blank" >RIV/61989592:15310/12:33142576 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1016/j.bpj.2012.03.024" target="_blank" >http://dx.doi.org/10.1016/j.bpj.2012.03.024</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.bpj.2012.03.024" target="_blank" >10.1016/j.bpj.2012.03.024</a>

Result language

angličtina

Original language name

Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign

Original language description

We study the folding of the designed hairpin chignolin, using simulations with four different force fields. Interestingly, we find a misfolded, out-of-register, structure comprising 20-50% of the ordered structures with three force fields, but not with afourth. A defining feature of the misfold is that Gly-7 adopts a beta(PR) conformation rather than alpha(L). By reweighting, we show that differences between the force fields can mostly be attributed to differences in glycine properties. Benchmarking against NMR data suggests that the preference for beta(PR) is not a force-field artifact. For chignolin, we show that including the misfold in the ensemble results in back-recalculated NMR observables in slightly better agreement with experiment than parameters calculated from a folded ensemble only. For comparison, we show by NMR and circular dichroism spectroscopy that the G7K mutant of chignolin, in which formation of this misfold is impossible, is well folded with stability similar to

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CF - Physical chemistry and theoretical chemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Publication year

2012

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Biophysical Journal

ISSN

0006-3495

e-ISSN

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Volume of the periodical

102

Issue of the periodical within the volume

8

Country of publishing house

US - UNITED STATES

Number of pages

10

Pages from-to

1897-1906

UT code for WoS article

000303003300024

EID of the result in the Scopus database

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