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Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15975-80. doi: 10.1073/pnas.1404213111. Epub 2014 Oct 27.

Benchmarking all-atom simulations using hydrogen exchange.

Author information

1
Departments of Biochemistry and Molecular Biology and.
2
Departments of Biochemistry and Molecular Biology and Center for Proteome Biophysics, Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology, Daegu 711-873, Korea.
3
Departments of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637; and.
4
Chemistry.
5
Chemistry, James Franck Institute, Computation Institute, and freed@uchicago.edu trsosnic@uchicago.edu.
6
Departments of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637; and Computation Institute, and freed@uchicago.edu trsosnic@uchicago.edu.

Abstract

Long-time molecular dynamics (MD) simulations are now able to fold small proteins reversibly to their native structures [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520]. These results indicate that modern force fields can reproduce the energy surface near the native structure. To test how well the force fields recapitulate the other regions of the energy surface, MD trajectories for a variant of protein G are compared with data from site-resolved hydrogen exchange (HX) and other biophysical measurements. Because HX monitors the breaking of individual H-bonds, this experimental technique identifies the stability and H-bond content of excited states, thus enabling quantitative comparison with the simulations. Contrary to experimental findings of a cooperative, all-or-none unfolding process, the simulated denatured state ensemble, on average, is highly collapsed with some transient or persistent native 2° structure. The MD trajectories of this protein G variant and other small proteins exhibit excessive intramolecular H-bonding even for the most expanded conformations, suggesting that the force fields require improvements in describing H-bonding and backbone hydration. Moreover, these comparisons provide a general protocol for validating the ability of simulations to accurately capture rare structural fluctuations.

KEYWORDS:

HX; denatured states; molecular dynamics; protein folding; unfolded state

PMID:
25349413
PMCID:
PMC4234613
DOI:
10.1073/pnas.1404213111
[Indexed for MEDLINE]
Free PMC Article

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