Native contacts determine protein folding mechanisms in atomistic simulations
The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key interactions driving folding. We find that the collective fraction of native amino acid contacts, Q , captures remarkably well the transition states...
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Published in | Proceedings of the National Academy of Sciences - PNAS Vol. 110; no. 44; pp. 17874 - 17879 |
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Main Authors | , , |
Format | Journal Article |
Language | English |
Published |
United States
National Academy of Sciences
29.10.2013
NATIONAL ACADEMY OF SCIENCES National Acad Sciences |
Subjects | |
Online Access | Get full text |
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Summary: | The recent availability of long equilibrium simulations of protein folding in atomistic detail for more than 10 proteins allows us to identify the key interactions driving folding. We find that the collective fraction of native amino acid contacts, Q , captures remarkably well the transition states for all the proteins with a folding free energy barrier. Going beyond this global picture, we devise two different measures to quantify the importance of individual interresidue contacts in the folding mechanism: (i) the log-ratio of lifetimes of contacts during folding transition paths and in the unfolded state and (ii) a Bayesian measure of how predictive the formation of each contact is for being on a transition path. Both of these measures indicate that native, or near-native, contacts are important for determining mechanism, as might be expected. More remarkably, however, we found that for almost all the proteins, with the designed protein α ₃D being a notable exception, nonnative contacts play no significant part in determining folding mechanisms. |
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Bibliography: | http://dx.doi.org/10.1073/pnas.1311599110 ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Edited by Michael Levitt, Stanford University School of Medicine, Stanford, CA, and approved September 10, 2013 (received for review June 18, 2013) Author contributions: R.B.B., G.H., and W.A.E. designed research; R.B.B. performed research; R.B.B. analyzed data; and R.B.B., G.H., and W.A.E. wrote the paper. 2Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany. |
ISSN: | 0027-8424 1091-6490 |
DOI: | 10.1073/pnas.1311599110 |