Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior

Watkins, Laura C.; DeGrado, William F.; Voth, Gregory A.

doi:10.1021/jacs.1c09281

Title: Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior

Authors:

^[1];

^[2];

^[1]

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States
Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, California 94158, United States

Publication Date:: Wed Jan 05 00:00:00 EST 2022

Sponsoring Org.:: USDOE

OSTI Identifier:: 1858799

Grant/Contract Number:: FG02-97ER25308

Resource Type:: Published Article

Journal Name:: Journal of the American Chemical Society

Additional Journal Information:: Journal Name: Journal of the American Chemical Society Journal Volume: 144 Journal Issue: 2; Journal ID: ISSN 0002-7863

Publisher:: American Chemical Society

Country of Publication:: United States

Language:: English

Citation Formats


                    Watkins, Laura C., DeGrado, William F., and Voth, Gregory A. Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.  United States: N. p., 2022. 
Web.  doi:10.1021/jacs.1c09281.

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                    Watkins, Laura C., DeGrado, William F., & Voth, Gregory A. Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.  United States.  https://doi.org/10.1021/jacs.1c09281

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                    Watkins, Laura C., DeGrado, William F., and Voth, Gregory A. Wed .  
"Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior".  United States.  https://doi.org/10.1021/jacs.1c09281.

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@article{osti_1858799,

  title        = {Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior},

  author       = {Watkins, Laura C. and DeGrado, William F. and Voth, Gregory A.},

  abstractNote = {},

  doi          = {10.1021/jacs.1c09281},

  journal      = {Journal of the American Chemical Society},

  number       = 2,

  volume       = 144,

  place        = {United States},

  year         = {Wed Jan 05 00:00:00 EST 2022},

  month        = {Wed Jan 05 00:00:00 EST 2022}

}

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Citation Formats

Multiscale Reactive Molecular Dynamics for Absolute p K a Predictions and Amino Acid Deprotonation journal, May 2014

Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel journal, June 2014

Density-functional exchange-energy approximation with correct asymptotic behavior journal, September 1988

Selective proton permeability and pH regulation of the influenza virus M2 channel expressed in mouse erythroleukaemia cells. journal, July 1996

Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale journal, September 2020

Fast Parallel Algorithms for Short-Range Molecular Dynamics journal, March 1995

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states journal, December 2014

Solid-state NMR characterization of conformational plasticity within the transmembrane domain of the influenza A M2 proton channel journal, December 2007

The Influenza M2 Cytoplasmic Tail Changes the Proton-Exchange Equilibria and the Backbone Conformation of the Transmembrane Histidine Residue to Facilitate Proton Conduction journal, April 2015

Differences in conductance of M2 proton channels of two influenza viruses at low and high pH journal, January 2003

Toward Theoretical Analyis of Long-Range Proton Transfer Kinetics in Biomolecular Pumps † journal, January 2006

Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue journal, October 1995

Promoting transparency and reproducibility in enhanced molecular simulations journal, July 2019

Conformational plasticity of the influenza A M2 transmembrane helix in lipid bilayers under varying pH, drug binding, and membrane thickness journal, January 2011

Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel journal, November 2013

Proton Association Constants of His 37 in the Influenza-A M2 18–60 Dimer-of-Dimers journal, September 2014

Proton movement and coupling in the POT family of peptide transporters journal, November 2017

Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach journal, April 2005

Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel journal, July 2009

PLUMED 2: New feathers for an old bird journal, February 2014

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction journal, November 2015

Multiscale Kinetic Modeling Reveals an Ensemble of Cl – /H + Exchange Pathways in ClC-ec1 Antiporter journal, January 2018

Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics journal, September 2020

The M2 Proton Channels of Influenza A and B Viruses journal, April 2006

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models journal, October 2015

A hybrid Gaussian and plane wave density functional scheme journal, October 1997

Insight into the Mechanism of the Influenza A Proton Channel from a Structure in a Lipid Bilayer journal, October 2010

Mechanism for Proton Conduction of the M2 Ion Channel of Influenza A Virus journal, March 2000

Acid activation mechanism of the influenza A M2 proton channel journal, October 2016

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu journal, April 2010

Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport journal, November 2015

Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus journal, August 2010

The Curious Case of the Hydrated Proton journal, August 2011

Dynamic Short Hydrogen Bonds in Histidine Tetrad of Full-Length M2 Proton Channel Reveal Tetrameric Structural Heterogeneity and Functional Mechanism journal, December 2015

Mechanisms of Proton Conduction and Gating in Influenza M2 Proton Channels from Solid-State NMR journal, October 2010

Structure and mechanism of the M2 proton channel of influenza A virus journal, January 2008

A pH-Dependent Conformational Ensemble Mediates Proton Transport through the Influenza A/M2 Protein journal, November 2010

Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter journal, March 2016

Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs journal, June 2021

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density journal, January 1988

A Theory for the Proton Transport of the Influenza Virus M2 Protein: Extensive Test against Conductance Data journal, February 2011

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase journal, June 2016

A second generation multistate empirical valence bond model for proton transport in aqueous systems journal, September 2002

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase journal, May 2017

Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel journal, June 2019

Relativistic separable dual-space Gaussian pseudopotentials from H to Rn journal, August 1998

Histidines, heart of the hydrogen ion channel from influenza A virus: Toward an understanding of conductance and proton selectivity journal, April 2006

Multidimensional replica-exchange method for free-energy calculations journal, October 2000

Asp44 Stabilizes the Trp41 Gate of the M2 Proton Channel of Influenza A Virus journal, November 2013

Influence of residue 44 on the activity of the M2 proton channel of influenza A virus journal, January 2005

Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins journal, January 2016

Local conformational dynamics regulating transport properties of a Cl − /H + antiporter journal, October 2019

Influence of amantadine resistance mutations on the pH regulatory function of the M2 protein of influenza A viruses journal, December 1992

pH-Dependent Conformation, Dynamics, and Aromatic Interaction of the Gating Tryptophan Residue of the Influenza M2 Proton Channel from Solid-State NMR journal, April 2013

“Proton Holes” in Long-Range Proton Transfer Reactions in Solution and Enzymes: A Theoretical Analysis journal, December 2006

The Grotthuss mechanism journal, October 1995

Viroporins: structure and biological functions journal, July 2012

Backbone Structure of the Amantadine-Blocked Trans-Membrane Domain M2 Proton Channel from Influenza A Virus journal, June 2007

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics journal, September 2012

The Gate of the Influenza Virus M 2 Proton Channel Is Formed by a Single Tryptophan Residue journal, August 2002

Activation and Proton Transport Mechanism in Influenza A M2 Channel journal, November 2013

Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux journal, November 2018

VMD: Visual molecular dynamics journal, February 1996

Structural basis for proton conduction and inhibition by the influenza M2 protein: Structure and Function of the TM Domain of M2 journal, October 2012

Multiscale reactive molecular dynamics journal, December 2012

Multiscale Reactive Molecular Dynamics for Absolute p K _a Predictions and Amino Acid Deprotonation
journal, May 2014

Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel
journal, June 2014

Density-functional exchange-energy approximation with correct asymptotic behavior
journal, September 1988

Selective proton permeability and pH regulation of the influenza virus M2 channel expressed in mouse erythroleukaemia cells.
journal, July 1996

Multiscale Simulation Reveals Passive Proton Transport Through SERCA on the Microsecond Timescale
journal, September 2020

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995

Statistically optimal analysis of state-discretized trajectory data from multiple thermodynamic states
journal, December 2014

Solid-state NMR characterization of conformational plasticity within the transmembrane domain of the influenza A M2 proton channel
journal, December 2007

The Influenza M2 Cytoplasmic Tail Changes the Proton-Exchange Equilibria and the Backbone Conformation of the Transmembrane Histidine Residue to Facilitate Proton Conduction
journal, April 2015

Differences in conductance of M2 proton channels of two influenza viruses at low and high pH
journal, January 2003

Toward Theoretical Analyis of Long-Range Proton Transfer Kinetics in Biomolecular Pumps ^†
journal, January 2006

Activation of the M2 ion channel of influenza virus: a role for the transmembrane domain histidine residue
journal, October 1995

Promoting transparency and reproducibility in enhanced molecular simulations
journal, July 2019

Conformational plasticity of the influenza A M2 transmembrane helix in lipid bilayers under varying pH, drug binding, and membrane thickness
journal, January 2011

Benchmark Study of the SCC-DFTB Approach for a Biomolecular Proton Channel
journal, November 2013

Proton Association Constants of His 37 in the Influenza-A M2 _18–60 Dimer-of-Dimers
journal, September 2014

Proton movement and coupling in the POT family of peptide transporters
journal, November 2017

Quickstep: Fast and accurate density functional calculations using a mixed Gaussian and plane waves approach
journal, April 2005

Identification of the functional core of the influenza A virus A/M2 proton-selective ion channel
journal, July 2009

PLUMED 2: New feathers for an old bird
journal, February 2014

High-resolution structures of the M2 channel from influenza A virus reveal dynamic pathways for proton stabilization and transduction
journal, November 2015

Multiscale Kinetic Modeling Reveals an Ensemble of Cl ^– /H ⁺ Exchange Pathways in ClC-ec1 Antiporter
journal, January 2018

Influenza A M2 Inhibitor Binding Understood through Mechanisms of Excess Proton Stabilization and Channel Dynamics
journal, September 2020

The M2 Proton Channels of Influenza A and B Viruses
journal, April 2006

PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models
journal, October 2015

A hybrid Gaussian and plane wave density functional scheme
journal, October 1997

Insight into the Mechanism of the Influenza A Proton Channel from a Structure in a Lipid Bilayer
journal, October 2010

Mechanism for Proton Conduction of the M2 Ion Channel of Influenza A Virus
journal, March 2000

Acid activation mechanism of the influenza A M2 proton channel
journal, October 2016

A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu
journal, April 2010

Role of Presolvation and Anharmonicity in Aqueous Phase Hydrated Proton Solvation and Transport
journal, November 2015

Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus
journal, August 2010

The Curious Case of the Hydrated Proton
journal, August 2011

Dynamic Short Hydrogen Bonds in Histidine Tetrad of Full-Length M2 Proton Channel Reveal Tetrameric Structural Heterogeneity and Functional Mechanism
journal, December 2015

Mechanisms of Proton Conduction and Gating in Influenza M2 Proton Channels from Solid-State NMR
journal, October 2010

Structure and mechanism of the M2 proton channel of influenza A virus
journal, January 2008

A pH-Dependent Conformational Ensemble Mediates Proton Transport through the Influenza A/M2 Protein
journal, November 2010

Multiscale Simulations Reveal Key Aspects of the Proton Transport Mechanism in the ClC-ec1 Antiporter
journal, March 2016

Cryo-EM structure of SARS-CoV-2 ORF3a in lipid nanodiscs
journal, June 2021

Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
journal, January 1988

A Theory for the Proton Transport of the Influenza Virus M2 Protein: Extensive Test against Conductance Data
journal, February 2011

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase
journal, June 2016

A second generation multistate empirical valence bond model for proton transport in aqueous systems
journal, September 2002

Understanding the essential proton-pumping kinetic gates and decoupling mutations in cytochrome c oxidase
journal, May 2017

Proton-Induced Conformational and Hydration Dynamics in the Influenza A M2 Channel
journal, June 2019

Relativistic separable dual-space Gaussian pseudopotentials from H to Rn
journal, August 1998

Histidines, heart of the hydrogen ion channel from influenza A virus: Toward an understanding of conductance and proton selectivity
journal, April 2006

Multidimensional replica-exchange method for free-energy calculations
journal, October 2000

Asp44 Stabilizes the Trp41 Gate of the M2 Proton Channel of Influenza A Virus
journal, November 2013

Influence of residue 44 on the activity of the M2 proton channel of influenza A virus
journal, January 2005

Computationally Efficient Multiscale Reactive Molecular Dynamics to Describe Amino Acid Deprotonation in Proteins
journal, January 2016

Local conformational dynamics regulating transport properties of a Cl ⁻ /H ⁺ antiporter
journal, October 2019

Influence of amantadine resistance mutations on the pH regulatory function of the M2 protein of influenza A viruses
journal, December 1992

pH-Dependent Conformation, Dynamics, and Aromatic Interaction of the Gating Tryptophan Residue of the Influenza M2 Proton Channel from Solid-State NMR
journal, April 2013

“Proton Holes” in Long-Range Proton Transfer Reactions in Solution and Enzymes: A Theoretical Analysis
journal, December 2006

The Grotthuss mechanism
journal, October 1995

Viroporins: structure and biological functions
journal, July 2012

Backbone Structure of the Amantadine-Blocked Trans-Membrane Domain M2 Proton Channel from Influenza A Virus
journal, June 2007

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics
journal, September 2012

The Gate of the Influenza Virus M ₂ Proton Channel Is Formed by a Single Tryptophan Residue
journal, August 2002

Activation and Proton Transport Mechanism in Influenza A M2 Channel
journal, November 2013

Modulating the Chemical Transport Properties of a Transmembrane Antiporter via Alternative Anion Flux
journal, November 2018

VMD: Visual molecular dynamics
journal, February 1996

Structural basis for proton conduction and inhibition by the influenza M2 protein: Structure and Function of the TM Domain of M2
journal, October 2012

Multiscale reactive molecular dynamics
journal, December 2012