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

Authors:
; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)
Sponsoring Org.:
National Institutes of Health (NIH)
OSTI Identifier:
1352209
Resource Type:
Journal Article
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 7; Journal Issue: 03, 2017; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
ENGLISH

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.
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. doi:10.1038/srep44116.
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. doi:10.1038/srep44116.
@article{osti_1352209,
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 = {},
doi = {10.1038/srep44116},
journal = {Scientific Reports},
issn = {2045-2322},
number = 03, 2017,
volume = 7,
place = {United States},
year = {2017},
month = {3}
}

Works referenced in this record:

Hidden alternative structures of proline isomerase essential for catalysis
journal, December 2009

  • Fraser, James S.; Clarkson, Michael W.; Degnan, Sheena C.
  • Nature, Vol. 462, Issue 7273
  • DOI: 10.1038/nature08615

Unfolded-State Dynamics and Structure of Protein L Characterized by Simulation and Experiment
journal, April 2010

  • Voelz, Vincent A.; Singh, Vijay R.; Wedemeyer, William J.
  • Journal of the American Chemical Society, Vol. 132, Issue 13
  • DOI: 10.1021/ja908369h

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
journal, December 1995

  • Svergun, D.; Barberato, C.; Koch, M. H. J.
  • Journal of Applied Crystallography, Vol. 28, Issue 6
  • DOI: 10.1107/S0021889895007047

Integrative, dynamic structural biology at atomic resolution—it's about time
journal, March 2015

  • van den Bedem, Henry; Fraser, James S.
  • Nature Methods, Vol. 12, Issue 4
  • DOI: 10.1038/nmeth.3324

Contact order, transition state placement and the refolding rates of single domain proteins 1 1Edited by P. E. Wright
journal, April 1998

  • Plaxco, Kevin W.; Simons, Kim T.; Baker, David
  • Journal of Molecular Biology, Vol. 277, Issue 4
  • DOI: 10.1006/jmbi.1998.1645

WAXSiS: a web server for the calculation of SAXS/WAXS curves based on explicit-solvent molecular dynamics
journal, April 2015

  • Knight, Christopher J.; Hub, Jochen S.
  • Nucleic Acids Research, Vol. 43, Issue W1
  • DOI: 10.1093/nar/gkv309

GROMACS: Fast, flexible, and free
journal, January 2005

  • Van Der Spoel, David; Lindahl, Erik; Hess, Berk
  • Journal of Computational Chemistry, Vol. 26, Issue 16
  • DOI: 10.1002/jcc.20291

Improved Fitting of Solution X-ray Scattering Data to Macromolecular Structures and Structural Ensembles by Explicit Water Modeling
journal, November 2010

  • Grishaev, Alexander; Guo, Liang; Irving, Thomas
  • Journal of the American Chemical Society, Vol. 132, Issue 44
  • DOI: 10.1021/ja106173n

Subdomain Competition, Cooperativity, and Topological Frustration in the Folding of CheY
journal, October 2008


Intrinsic dynamics of an enzyme underlies catalysis
journal, November 2005

  • Eisenmesser, Elan Z.; Millet, Oscar; Labeikovsky, Wladimir
  • Nature, Vol. 438, Issue 7064
  • DOI: 10.1038/nature04105

Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment
journal, July 2012

  • Voelz, Vincent A.; Jäger, Marcus; Yao, Shuhuai
  • Journal of the American Chemical Society, Vol. 134, Issue 30
  • DOI: 10.1021/ja302528z

Exploring protein native states and large-scale conformational changes with a modified generalized born model
journal, March 2004

  • Onufriev, Alexey; Bashford, Donald; Case, David A.
  • Proteins: Structure, Function, and Bioinformatics, Vol. 55, Issue 2
  • DOI: 10.1002/prot.20033

Enzyme Dynamics During Catalysis
journal, February 2002


SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions
journal, January 2011


A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation
journal, June 2008

  • Shell, M. Scott; Ritterson, Ryan; Dill, Ken A.
  • The Journal of Physical Chemistry B, Vol. 112, Issue 22
  • DOI: 10.1021/jp800282x

Molecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
journal, February 2010

  • Voelz, Vincent A.; Bowman, Gregory R.; Beauchamp, Kyle
  • Journal of the American Chemical Society, Vol. 132, Issue 5
  • DOI: 10.1021/ja9090353

Flexible Fitting of Atomic Structures into Electron Microscopy Maps Using Molecular Dynamics
journal, May 2008


Everything you wanted to know about Markov State Models but were afraid to ask
journal, September 2010


Progress and challenges in the automated construction of Markov state models for full protein systems
journal, September 2009

  • Bowman, Gregory R.; Beauchamp, Kyle A.; Boxer, George
  • The Journal of Chemical Physics, Vol. 131, Issue 12
  • DOI: 10.1063/1.3216567

The Dynamic Energy Landscape of Dihydrofolate Reductase Catalysis
journal, September 2006

  • Boehr, D. D.; McElheny, D.; Dyson, H. J.
  • Science, Vol. 313, Issue 5793, p. 1638-1642
  • DOI: 10.1126/science.1130258

Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9
journal, March 2013

  • Schwantes, Christian R.; Pande, Vijay S.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 4
  • DOI: 10.1021/ct300878a

Comparison of super-secondary structures in proteins
journal, May 1973


Visualization of transient encounter complexes in protein–protein association
journal, October 2006

  • Tang, Chun; Iwahara, Junji; Clore, G. Marius
  • Nature, Vol. 444, Issue 7117
  • DOI: 10.1038/nature05201

Markov models of molecular kinetics: Generation and validation
journal, May 2011

  • Prinz, Jan-Hendrik; Wu, Hao; Sarich, Marco
  • The Journal of Chemical Physics, Vol. 134, Issue 17
  • DOI: 10.1063/1.3565032

The TIM-barrel fold: a versatile framework for efficient enzymes
journal, March 2001


Kinetic Traps in the Folding of βα-Repeat Proteins: CheY Initially Misfolds before Accessing the Native Conformation
journal, October 2008

  • Kathuria, Sagar V.; Day, Iain J.; Wallace, Louise A.
  • Journal of Molecular Biology, Vol. 382, Issue 2
  • DOI: 10.1016/j.jmb.2008.06.054

Multidomain assembled states of Hck tyrosine kinase in solution
journal, August 2010

  • Yang, S.; Blachowicz, L.; Makowski, L.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 36
  • DOI: 10.1073/pnas.1004569107

The energy landscape of adenylate kinase during catalysis
journal, January 2015

  • Kerns, S. Jordan; Agafonov, Roman V.; Cho, Young-Jin
  • Nature Structural & Molecular Biology, Vol. 22, Issue 2
  • DOI: 10.1038/nsmb.2941

FoXS: a web server for rapid computation and fitting of SAXS profiles
journal, May 2010

  • Schneidman-Duhovny, D.; Hammel, M.; Sali, A.
  • Nucleic Acids Research, Vol. 38, Issue Web Server
  • DOI: 10.1093/nar/gkq461

Molecular dynamics and protein function
journal, May 2005

  • Karplus, M.; Kuriyan, J.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 19
  • DOI: 10.1073/pnas.0408930102

Simultaneous determination of protein structure and dynamics
journal, January 2005

  • Lindorff-Larsen, Kresten; Best, Robert B.; DePristo, Mark A.
  • Nature, Vol. 433, Issue 7022
  • DOI: 10.1038/nature03199

Structure and flexibility within proteins as identified through small angle X-ray scattering
journal, January 2009

  • Pelikan, M.; Hura, G.; Hammel, M.
  • General Physiology and Biophysics, Vol. 28, Issue 2
  • DOI: 10.4149/gpb_2009_02_174

On the Use of Experimental Observations to Bias Simulated Ensembles
journal, March 2012

  • Pitera, Jed W.; Chodera, John D.
  • Journal of Chemical Theory and Computation, Vol. 8, Issue 10
  • DOI: 10.1021/ct300112v

A toolkit and benchmark study for FRET-restrained high-precision structural modeling
journal, November 2012

  • Kalinin, Stanislav; Peulen, Thomas; Sindbert, Simon
  • Nature Methods, Vol. 9, Issue 12
  • DOI: 10.1038/nmeth.2222