Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase

Yang, Shuo; Cui, Qiang

doi:10.1016/j.bpj.2011.05.004

Title: Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase

Authors:: Yang, Shuo; Cui, Qiang

Publication Date:: Fri Jul 01 00:00:00 EDT 2011

Sponsoring Org.:: USDOE

OSTI Identifier:: 1198358

Grant/Contract Number:: FG02-04ER25627

Resource Type:: Published Article

Journal Name:: Biophysical Journal

Additional Journal Information:: Journal Name: Biophysical Journal Journal Volume: 101 Journal Issue: 1; Journal ID: ISSN 0006-3495

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

Citation Formats


                    Yang, Shuo, and Cui, Qiang. Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase.  United States: N. p., 2011. 
Web.  doi:10.1016/j.bpj.2011.05.004.

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                    Yang, Shuo, & Cui, Qiang. Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase.  United States.  https://doi.org/10.1016/j.bpj.2011.05.004

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                    Yang, Shuo, and Cui, Qiang. Fri .  
"Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase".  United States.  https://doi.org/10.1016/j.bpj.2011.05.004.

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@article{osti_1198358,

  title        = {Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase},

  author       = {Yang, Shuo and Cui, Qiang},

  abstractNote = {},

  doi          = {10.1016/j.bpj.2011.05.004},

  journal      = {Biophysical Journal},

  number       = 1,

  volume       = 101,

  place        = {United States},

  year         = {Fri Jul 01 00:00:00 EDT 2011},

  month        = {Fri Jul 01 00:00:00 EDT 2011}

}

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Similar Records

Title: Glu-286 Rotation and Water Wire Reorientation Are Unlikely the Gating Elements for Proton Pumping in Cytochrome c Oxidase

Citation Formats

Energy diagrams and mechanism for proton pumping in cytochrome c oxidase journal, September 2007

Analyzing Free Energy Relationships for Proton Translocations in Enzymes: Carbonic Anhydrase Revisited journal, January 2004

The X-ray Crystal Structures of Wild-type and EQ(I-286) Mutant Cytochrome c Oxidases from Rhodobacter sphaeroides journal, August 2002

Energy Transduction: Proton Transfer Through the Respiratory Complexes journal, June 2006

p K a Analysis for the Zinc-Bound Water in Human Carbonic Anhydrase II: Benchmark for “Multiscale” QM/MM Simulations and Mechanistic Implications journal, May 2007

Microscopic p K a Analysis of Glu286 in Cytochrome c Oxidase ( Rhodobacter sphaeroides ): Toward a Calibrated Molecular Model journal, February 2009

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

Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome c Oxidase journal, February 2004

Properties of Arg481 Mutants of the aa 3 -Type Cytochrome c Oxidase from Rhodobacter sphaeroides Suggest That neither R481 nor the Nearby D-Propionate of Heme a 3 Is Likely To Be the Proton Loading Site of the Proton Pump journal, August 2009

Kinetic models of redox-coupled proton pumping journal, February 2007

Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase journal, September 2007

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation journal, December 2007

Grand canonical Monte Carlo simulations of water in protein environments journal, October 2004

Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties journal, September 1998

Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations journal, June 1997

Proton Transfer in Carbonic Anhydrase Is Controlled by Electrostatics Rather than the Orientation of the Acceptor † journal, February 2008

Cytochrome c oxidase: exciting progress and remaining mysteries journal, October 2008

Proton-Coupled Electron Transfer in Cytochrome Oxidase journal, December 2010

Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase journal, April 2008

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins † journal, April 1998

Charge parameterization of the metal centers in cytochrome c oxidase journal, April 2008

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science journal, November 2008

Storage of an Excess Proton in the Hydrogen-Bonded Network of the D-Pathway of Cytochrome c Oxidase: Identification of a Protonated Water Cluster journal, March 2007

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase journal, October 2009

Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction journal, October 2007

SCC-DFTB: What Is the Proper Degree of Self-Consistency? † journal, July 2007

CHARMM: The biomolecular simulation program journal, July 2009

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types journal, June 2010

Computer simulation of explicit proton translocation in cytochrome c oxidase: The D-pathway journal, April 2005

Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes journal, April 2006

Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase journal, May 2008

Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II journal, May 2009

Proton pumping mechanism and catalytic cycle of cytochrome c oxidase: Coulomb pump model with kinetic gating journal, April 2004

Intricate Role of Water in Proton Transport through Cytochrome c Oxidase journal, October 2010

The barrier for proton transport in aquaporins as a challenge for electrostatic models: The role of protein relaxation in mutational calculations journal, June 2006

Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations journal, August 2004

Calculated Proton Uptake on Anaerobic Reduction of Cytochrome c Oxidase: Is the Reaction Electroneutral? journal, June 2006

THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method journal, October 1992

Water clusters in nonpolar cavities journal, November 2004

Polymorphic transitions in single crystals: A new molecular dynamics method journal, December 1981

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) journal, March 2011

p K a Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols journal, August 2005

Quantum Chemical Studies of Proton-Coupled Electron Transfer in Metalloenzymes journal, December 2010

Water-gated mechanism of proton translocation by cytochrome c oxidase journal, June 2003

Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation journal, June 1998

On the convergence improvement in the metadynamics simulations: A Wang-Landau recursion approach journal, May 2007

A smooth particle mesh Ewald method journal, November 1995

The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase journal, January 2011

A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method journal, January 2001

Kinetic gating of the proton pump in cytochrome c oxidase journal, August 2009

On the treatment of electrostatic interactions in biomolecular simulation journal, January 1991

Generalized solvent boundary potential for computer simulations journal, February 2001

Computer Simulation of Proton Solvation and Transport in Aqueous and Biomolecular Systems journal, February 2006

Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water journal, May 2011

Energy diagrams and mechanism for proton pumping in cytochrome c oxidase
journal, September 2007

Analyzing Free Energy Relationships for Proton Translocations in Enzymes: Carbonic Anhydrase Revisited
journal, January 2004

The X-ray Crystal Structures of Wild-type and EQ(I-286) Mutant Cytochrome c Oxidases from Rhodobacter sphaeroides
journal, August 2002

Energy Transduction: Proton Transfer Through the Respiratory Complexes
journal, June 2006

p K _a Analysis for the Zinc-Bound Water in Human Carbonic Anhydrase II: Benchmark for “Multiscale” QM/MM Simulations and Mechanistic Implications
journal, May 2007

Microscopic p K _a Analysis of Glu286 in Cytochrome c Oxidase ( Rhodobacter sphaeroides ): Toward a Calibrated Molecular Model
journal, February 2009

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

Electrostatic Study of the Proton Pumping Mechanism in Bovine Heart Cytochrome c Oxidase
journal, February 2004

Properties of Arg481 Mutants of the aa ₃ -Type Cytochrome c Oxidase from Rhodobacter sphaeroides Suggest That neither R481 nor the Nearby D-Propionate of Heme a ₃ Is Likely To Be the Proton Loading Site of the Proton Pump
journal, August 2009

Kinetic models of redox-coupled proton pumping
journal, February 2007

Dynamics of the glutamic acid 242 side chain in cytochrome c oxidase
journal, September 2007

P-LINCS: A Parallel Linear Constraint Solver for Molecular Simulation
journal, December 2007

Grand canonical Monte Carlo simulations of water in protein environments
journal, October 2004

Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties
journal, September 1998

Atomic Radii for Continuum Electrostatics Calculations Based on Molecular Dynamics Free Energy Simulations
journal, June 1997

Proton Transfer in Carbonic Anhydrase Is Controlled by Electrostatics Rather than the Orientation of the Acceptor ^†
journal, February 2008

Cytochrome c oxidase: exciting progress and remaining mysteries
journal, October 2008

Proton-Coupled Electron Transfer in Cytochrome Oxidase
journal, December 2010

Glutamic acid 242 is a valve in the proton pump of cytochrome c oxidase
journal, April 2008

All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins ^†
journal, April 1998

Charge parameterization of the metal centers in cytochrome c oxidase
journal, April 2008

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
journal, November 2008

Storage of an Excess Proton in the Hydrogen-Bonded Network of the D-Pathway of Cytochrome c Oxidase: Identification of a Protonated Water Cluster
journal, March 2007

Mechanism and energetics by which glutamic acid 242 prevents leaks in cytochrome c oxidase
journal, October 2009

Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method: Third-Order Expansion of the Density Functional Theory Total Energy and Introduction of a Modified Effective Coulomb Interaction
journal, October 2007

SCC-DFTB: What Is the Proper Degree of Self-Consistency? ^†
journal, July 2007

CHARMM: The biomolecular simulation program
journal, July 2009

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010

Computer simulation of explicit proton translocation in cytochrome c oxidase: The D-pathway
journal, April 2005

Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes
journal, April 2006

Electrostatic basis for the unidirectionality of the primary proton transfer in cytochrome c oxidase
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Elucidation of the Proton Transport Mechanism in Human Carbonic Anhydrase II
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Intricate Role of Water in Proton Transport through Cytochrome c Oxidase
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Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
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Calculated Proton Uptake on Anaerobic Reduction of Cytochrome c Oxidase: Is the Reaction Electroneutral?
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THE weighted histogram analysis method for free-energy calculations on biomolecules. I. The method
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Water clusters in nonpolar cavities
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Polymorphic transitions in single crystals: A new molecular dynamics method
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p K _a Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations: A Quantitative Test of QM/MM Protocols
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Quantum Chemical Studies of Proton-Coupled Electron Transfer in Metalloenzymes
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Water-gated mechanism of proton translocation by cytochrome c oxidase
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Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
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On the convergence improvement in the metadynamics simulations: A Wang-Landau recursion approach
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A smooth particle mesh Ewald method
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The identity of the transient proton loading site of the proton-pumping mechanism of cytochrome c oxidase
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A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method
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Kinetic gating of the proton pump in cytochrome c oxidase
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On the treatment of electrostatic interactions in biomolecular simulation
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Generalized solvent boundary potential for computer simulations
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Computer Simulation of Proton Solvation and Transport in Aqueous and Biomolecular Systems
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Application of the SCC-DFTB Method to Neutral and Protonated Water Clusters and Bulk Water
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