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Title: Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY

Abstract

The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.

Authors:
 [1];  [2];  [1];  [3];  [4];  [4];  [5];  [1]
+ Show Author Affiliations
  1. Stanford Univ., CA (United States). Dept. of Chemistry
  2. Adimab LLC., Lebanon, NH (United States)
  3. Sanofi Genzyme, Cambridge, MA (United States)
  4. Univ. of Massachusetts, Worcester, MA (United States). Dept. of Biochemistry and Molecular Pharmacology
  5. SLAC National Accelerator Lab., Menlo Park, CA (United States)
Publication Date:
Research Org.:
SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)
OSTI Identifier:
1352641
Grant/Contract Number:  
AC02-76SF00515; AC02-06CH11357; MCB1121945; MCB1517888; IDBR1353945
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 60 APPLIED LIFE SCIENCES; protein folding; statistics

Citation Formats

Shi, Jade, Nobrega, R. Paul, Schwantes, Christian, Kathuria, Sagar V., Bilsel, Osman, Matthews, C. Robert, Lane, T. J., and Pande, Vijay S. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY. United States: N. p., 2017. Web. doi:10.1038/srep44116.
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Shi, Jade, Nobrega, R. Paul, Schwantes, Christian, Kathuria, Sagar V., Bilsel, Osman, Matthews, C. Robert, Lane, T. J., & Pande, Vijay S. Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY. United States. https://doi.org/10.1038/srep44116
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Shi, Jade, Nobrega, R. Paul, Schwantes, Christian, Kathuria, Sagar V., Bilsel, Osman, Matthews, C. Robert, Lane, T. J., and Pande, Vijay S. Wed . "Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY". United States. https://doi.org/10.1038/srep44116. https://www.osti.gov/servlets/purl/1352641.
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@article{osti_1352641,
title = {Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY},
author = {Shi, Jade and Nobrega, R. Paul and Schwantes, Christian and Kathuria, Sagar V. and Bilsel, Osman and Matthews, C. Robert and Lane, T. J. and Pande, Vijay S.},
abstractNote = {The dynamics of globular proteins can be described in terms of transitions between a folded native state and less-populated intermediates, or excited states, which can play critical roles in both protein folding and function. Excited states are by definition transient species, and therefore are difficult to characterize using current experimental techniques. We report an atomistic model of the excited state ensemble of a stabilized mutant of an extensively studied flavodoxin fold protein CheY. We employed a hybrid simulation and experimental approach in which an aggregate 42 milliseconds of all-atom molecular dynamics were used as an informative prior for the structure of the excited state ensemble. The resulting prior was then refined against small-angle X-ray scattering (SAXS) data employing an established method (EROS). The most striking feature of the resulting excited state ensemble was an unstructured N-terminus stabilized by non-native contacts in a conformation that is topologically simpler than the native state. We then predict incisive single molecule FRET experiments, using these results, as a means of model validation. Our study demonstrates the paradigm of uniting simulation and experiment in a statistical model to study the structure of protein excited states and rationally design validating experiments.},
doi = {10.1038/srep44116},
journal = {Scientific Reports},
number = ,
volume = 7,
place = {United States},
year = {Wed Mar 08 00:00:00 EST 2017},
month = {Wed Mar 08 00:00:00 EST 2017}
}
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