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

doi:10.1038/srep44116

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

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

Publication Date:: 2017-03-08

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.

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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.  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., 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.

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@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}

}

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DOI: 10.1038/srep44116

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

Citation Formats

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

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

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

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

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

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

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

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

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

Intrinsic dynamics of an enzyme underlies catalysis journal, November 2005

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

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

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

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

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

Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules journal, January 1996

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

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

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

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

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

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

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

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Molecular dynamics and protein function journal, May 2005

Simultaneous determination of protein structure and dynamics journal, January 2005

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

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

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

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

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

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

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

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

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

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

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

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

Intrinsic dynamics of an enzyme underlies catalysis
journal, November 2005

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

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

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

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

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

Advances and Continuing Challenges in Achieving Realistic and Predictive Simulations of the Properties of Organic and Biological Molecules
journal, January 1996

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

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

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

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

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

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

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

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

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

Molecular dynamics and protein function
journal, May 2005

Simultaneous determination of protein structure and dynamics
journal, January 2005

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

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

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