Diffusive Dynamics of Contact Formation in Disordered Polypeptides

Zerze, Gül H.; Mittal, Jeetain; Best, Robert B.

doi:10.1103/PhysRevLett.116.068102

Title: Diffusive Dynamics of Contact Formation in Disordered Polypeptides

Authors:: Zerze, Gül H.; Mittal, Jeetain; Best, Robert B.

Publication Date:: Thu Feb 11 00:00:00 EST 2016

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1237783

Grant/Contract Number:: SC0013979

Resource Type:: Publisher's Accepted Manuscript

Journal Name:: Physical Review Letters

Additional Journal Information:: Journal Name: Physical Review Letters Journal Volume: 116 Journal Issue: 6; Journal ID: ISSN 0031-9007

Publisher:: American Physical Society

Country of Publication:: United States

Language:: English

Citation Formats


                    Zerze, Gül H., Mittal, Jeetain, and Best, Robert B. Diffusive Dynamics of Contact Formation in Disordered Polypeptides.  United States: N. p., 2016. 
Web.  doi:10.1103/PhysRevLett.116.068102.

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                    Zerze, Gül H., Mittal, Jeetain, & Best, Robert B. Diffusive Dynamics of Contact Formation in Disordered Polypeptides.  United States.  https://doi.org/10.1103/PhysRevLett.116.068102

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                    Zerze, Gül H., Mittal, Jeetain, and Best, Robert B. Thu .  
"Diffusive Dynamics of Contact Formation in Disordered Polypeptides".  United States.  https://doi.org/10.1103/PhysRevLett.116.068102.

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@article{osti_1237783,

  title        = {Diffusive Dynamics of Contact Formation in Disordered Polypeptides},

  author       = {Zerze, Gül H. and Mittal, Jeetain and Best, Robert B.},

  abstractNote = {},

  doi          = {10.1103/PhysRevLett.116.068102},

  journal      = {Physical Review Letters},

  number       = 6,

  volume       = 116,

  place        = {United States},

  year         = {Thu Feb 11 00:00:00 EST 2016},

  month        = {Thu Feb 11 00:00:00 EST 2016}

}

Copy to clipboard

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https://doi.org/10.1103/PhysRevLett.116.068102

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Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
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Effects of Denaturants on the Dynamics of Loop Formation in Polypeptides
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Title: Diffusive Dynamics of Contact Formation in Disordered Polypeptides

Citation Formats

First passage time approach to diffusion controlled reactions journal, April 1980

Dynamics of Intramolecular Contact Formation in Polypeptides: Distance Dependence of Quenching Rates in a Room-Temperature Glass journal, November 2001

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase journal, June 2013

Canonical sampling through velocity rescaling journal, January 2007

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse journal, November 2010

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems journal, June 1993

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids journal, July 2012

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation journal, February 2008

Enhanced Sampling in the Well-Tempered Ensemble journal, May 2010

Determination of Ultrafast Protein Folding Rates from Loop Formation Dynamics journal, April 2005

Diffusive Model of Protein Folding Dynamics with Kramers Turnover in Rate journal, June 2006

Universality in the Timescales of Internal Loop Formation in Unfolded Proteins and Single-Stranded Oligonucleotides journal, December 2010

Local conformational dynamics in α-helices measured by fast triplet transfer journal, January 2009

The protein folding ‘speed limit’ journal, February 2004

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations journal, February 2014

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides journal, July 2009

Kinetics of Contact Formation and End-to-End Distance Distributions of Swollen Disordered Peptides journal, February 2009

Ultrafast dynamics of protein collapse from single-molecule photon statistics journal, February 2007

Measuring Dynamic Flexibility of the Coil State of a Helix-forming Peptide journal, May 2002

Comparison of simple potential functions for simulating liquid water journal, July 1983

Diffusion models of protein folding journal, January 2011

Measuring the rate of intramolecular contact formation in polypeptides journal, June 2000

A general purpose model for the condensed phases of water: TIP4P/2005 journal, December 2005

Effects of Chain Stiffness on the Dynamics of Loop Formation in Polypeptides. Appendix: Testing a 1-Dimensional Diffusion Model for Peptide Dynamics journal, November 2002

Peptide Loop-Closure Kinetics from Microsecond Molecular Dynamics Simulations in Explicit Solvent journal, May 2002

Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy journal, September 2012

The speed limit for protein folding measured by triplet-triplet energy transfer journal, August 1999

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association journal, October 2014

Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations journal, January 2005

Effects of Denaturants on the Dynamics of Loop Formation in Polypeptides journal, July 2006

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins journal, November 2009

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations journal, October 2003

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble journal, June 2012

Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments journal, March 2011

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins journal, April 2010

Layering and Position-Dependent Diffusive Dynamics of Confined Fluids journal, April 2008

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States journal, April 2015

First passage time approach to diffusion controlled reactions
journal, April 1980

Dynamics of Intramolecular Contact Formation in Polypeptides: Distance Dependence of Quenching Rates in a Room-Temperature Glass
journal, November 2001

Effects of oncogenic mutations on the conformational free-energy landscape of EGFR kinase
journal, June 2013

Canonical sampling through velocity rescaling
journal, January 2007

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse
journal, November 2010

Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems
journal, June 1993

Pair diffusion, hydrodynamic interactions, and available volume in dense fluids
journal, July 2012

GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
journal, February 2008

Enhanced Sampling in the Well-Tempered Ensemble
journal, May 2010

Determination of Ultrafast Protein Folding Rates from Loop Formation Dynamics
journal, April 2005

Diffusive Model of Protein Folding Dynamics with Kramers Turnover in Rate
journal, June 2006

Universality in the Timescales of Internal Loop Formation in Unfolded Proteins and Single-Stranded Oligonucleotides
journal, December 2010

Local conformational dynamics in α-helices measured by fast triplet transfer
journal, January 2009

The protein folding ‘speed limit’
journal, February 2004

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations
journal, February 2014

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides
journal, July 2009

Kinetics of Contact Formation and End-to-End Distance Distributions of Swollen Disordered Peptides
journal, February 2009

Ultrafast dynamics of protein collapse from single-molecule photon statistics
journal, February 2007

Measuring Dynamic Flexibility of the Coil State of a Helix-forming Peptide
journal, May 2002

Comparison of simple potential functions for simulating liquid water
journal, July 1983

Diffusion models of protein folding
journal, January 2011

Measuring the rate of intramolecular contact formation in polypeptides
journal, June 2000

A general purpose model for the condensed phases of water: TIP4P/2005
journal, December 2005

Effects of Chain Stiffness on the Dynamics of Loop Formation in Polypeptides. Appendix: Testing a 1-Dimensional Diffusion Model for Peptide Dynamics
journal, November 2002

Peptide Loop-Closure Kinetics from Microsecond Molecular Dynamics Simulations in Explicit Solvent
journal, May 2002

Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
journal, September 2012

The speed limit for protein folding measured by triplet-triplet energy transfer
journal, August 1999

Balanced Protein–Water Interactions Improve Properties of Disordered Proteins and Non-Specific Protein Association
journal, October 2014

Position-dependent diffusion coefficients and free energies from Bayesian analysis of equilibrium and replica molecular dynamics simulations
journal, January 2005

Effects of Denaturants on the Dynamics of Loop Formation in Polypeptides
journal, July 2006

Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins
journal, November 2009

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations
journal, October 2003

Efficient Simulation of Explicitly Solvated Proteins in the Well-Tempered Ensemble
journal, June 2012

Compaction and Tensile Forces Determine the Accuracy of Folding Landscape Parameters from Single Molecule Pulling Experiments
journal, March 2011

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journal, April 2010

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journal, April 2008

Water Dispersion Interactions Strongly Influence Simulated Structural Properties of Disordered Protein States
journal, April 2015