Home > Research > Publications & Outputs > Why do protein folding rates correlate with met...

Links

Text available via DOI:

View graph of relations

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

Research output: Contribution to journalJournal articlepeer-review

Published

Standard

Why do protein folding rates correlate with metrics of native topology? / Faísca, Patrícia F N; Travasso, Rui D M; Parisi, Andrea; Rey, Antonio.

In: PLoS ONE, Vol. 7, No. 4, e35599, 27.04.2012.

Research output: Contribution to journalJournal articlepeer-review

Harvard

Faísca, PFN, Travasso, RDM, Parisi, A & Rey, A 2012, 'Why do protein folding rates correlate with metrics of native topology?', PLoS ONE, vol. 7, no. 4, e35599. https://doi.org/10.1371/journal.pone.0035599

APA

Faísca, P. F. N., Travasso, R. D. M., Parisi, A., & Rey, A. (2012). Why do protein folding rates correlate with metrics of native topology? PLoS ONE, 7(4), [e35599]. https://doi.org/10.1371/journal.pone.0035599

Vancouver

Faísca PFN, Travasso RDM, Parisi A, Rey A. Why do protein folding rates correlate with metrics of native topology? PLoS ONE. 2012 Apr 27;7(4). e35599. https://doi.org/10.1371/journal.pone.0035599

Author

Faísca, Patrícia F N ; Travasso, Rui D M ; Parisi, Andrea ; Rey, Antonio. / Why do protein folding rates correlate with metrics of native topology?. In: PLoS ONE. 2012 ; Vol. 7, No. 4.

Bibtex

@article{e10f5b8c5721416b890aec7289e9565b,
title = "Why do protein folding rates correlate with metrics of native topology?",
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.",
keywords = "Computer Simulation, Kinetics, Models, Molecular, Protein Folding, Protein Structure, Tertiary, Proteins, Thermodynamics, Journal Article, Research Support, Non-U.S. Gov't",
author = "Fa{\'i}sca, {Patr{\'i}cia F N} and Travasso, {Rui D M} and Andrea Parisi and Antonio Rey",
year = "2012",
month = apr,
day = "27",
doi = "10.1371/journal.pone.0035599",
language = "English",
volume = "7",
journal = "PLoS ONE",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "4",

}

RIS

TY - JOUR

T1 - Why do protein folding rates correlate with metrics of native topology?

AU - Faísca, Patrícia F N

AU - Travasso, Rui D M

AU - Parisi, Andrea

AU - Rey, Antonio

PY - 2012/4/27

Y1 - 2012/4/27

N2 - 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.

AB - 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.

KW - Computer Simulation

KW - Kinetics

KW - Models, Molecular

KW - Protein Folding

KW - Protein Structure, Tertiary

KW - Proteins

KW - Thermodynamics

KW - Journal Article

KW - Research Support, Non-U.S. Gov't

U2 - 10.1371/journal.pone.0035599

DO - 10.1371/journal.pone.0035599

M3 - Journal article

C2 - 22558173

VL - 7

JO - PLoS ONE

JF - PLoS ONE

SN - 1932-6203

IS - 4

M1 - e35599

ER -