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

Shi, Jade; Nobrega, R. Paul; Schwantes, Christian; Kathuria, Sagar V.; Bilsel, Osman; Matthews, C. Robert; Lane, T. J.; Pande, Vijay S.

doi:10.1038/srep44116

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

Journal Article · Wed Mar 08 00:00:00 EST 2017 · Scientific Reports

DOI:https://doi.org/10.1038/srep44116· OSTI ID:1352641

Shi, Jade ^[1]; Nobrega, R. Paul ^[2]; Schwantes, Christian ^[1]; Kathuria, Sagar V. ^[3]; Bilsel, Osman ^[4]; Matthews, C. Robert ^[4]; Lane, T. J. ^[5]; Pande, Vijay S. ^[1]

Stanford Univ., CA (United States). Dept. of Chemistry
Adimab LLC., Lebanon, NH (United States)
Sanofi Genzyme, Cambridge, MA (United States)
Univ. of Massachusetts, Worcester, MA (United States). Dept. of Biochemistry and Molecular Pharmacology
SLAC National Accelerator Lab., Menlo Park, CA (United States)

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.

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Research Organization:: SLAC National Accelerator Laboratory (SLAC), Menlo Park, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC); National Institutes of Health (NIH); National Science Foundation (NSF)

Grant/Contract Number:: AC02-76SF00515; AC02-06CH11357; MCB1121945; MCB1517888; IDBR1353945

OSTI ID:: 1352641

Journal Information:: Scientific Reports, Vol. 7; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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Cited by: 7 works

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