List of works - James C Gumbart

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins

scientific article published on 13 November 2019

A Novel Approach to Simulating the Gating Transitions of Mechanosensitive Channels

scientific article published on 15 December 2020

A novel human IL2RB mutation results in T and NK cell-driven immune dysregulation

scientific article published on 30 April 2019

ATP-Dependent Signaling in Simulations of a Revised Model of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)

scientific article published on 10 April 2019

Accelerating Membrane Simulations with Hydrogen Mass Repartitioning

scientific article published on 02 July 2019

Accelerating the use of molecular modeling in the high school classroom with VMD Lite

scientific article published on 11 January 2016

Applications of the molecular dynamics flexible fitting method

scientific article

Architecture and assembly of the Gram-positive cell wall

scientific article

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

scientific article published on 6 February 2018

BamA is required for autotransporter secretion

scientific article published on 27 February 2020

Bifunctional Janus Particles as Multivalent Synthetic Nanoparticle Antibodies (SNAbs) for Selective Depletion of Target Cells

scientific article published on 04 January 2021

C-terminal kink formation is required for lateral gating in BamA

article published in the Proceedings of the National Academy of Sciences of the United States of America

Coarse-Grained Molecular Dynamics Simulations of the Bacterial Cell Wall

scientific article published on January 2016

Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape

scientific article

Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method

scientific article published on 08 March 2018

Conformational Changes of the Clamp of the Protein Translocation ATPase SecA

scientific article published on 14 May 2015

Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly

scientific article published on 26 September 2019

Constant electric field simulations of the membrane potential illustrated with simple systems

scientific article

Correction to: Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method

scientific article published on 01 June 2018

Correction: A novel human IL2RB mutation results in T and NK cell-driven immune dysregulation.

scientific article published on 14 May 2019

Coupling of calcium and substrate binding through loop alignment in the outer-membrane transporter BtuB.

scientific article

Cryo-EM structure of the ribosome–SecYE complex in the membrane environment

scientific article

DNA Scrunching in the Packaging of Viral Genomes

scientific article

Decrypting protein insertion through the translocon with free-energy calculations

scientific article published on 16 February 2016

Determination of membrane-insertion free energies by molecular dynamics simulations

scientific article published on 21 February 2012

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

scientific article

Distribution of mechanical stress in the Escherichia coli cell envelope

scientific article published on 29 September 2018

Efficient determination of protein-protein standard binding free energies from first principles

scientific article published on August 2013

Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations

scientific article

Exploring adsorption of neutral aromatic pollutants onto graphene nanomaterials via molecular dynamics simulations and theoretical linear solvation energy relationships

Exploring substrate diffusion in channels using biased molecular dynamics simulations.

scientific article published in January 2012

Fatal arrhythmias: Another reason why doctors remain cautious about chloroquine/hydroxychloroquine for treating COVID-19

scientific article published on 29 May 2020

Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields

scientific article published on 01 August 2018

Free energy of nascent-chain folding in the translocon

scientific article

Free-energy cost for translocon-assisted insertion of membrane proteins

scientific article

Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.

scientific article

IcmQ in the Type 4b Secretion System Contains an NAD+ Binding Domain

scientific article

Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA

scientific article published on 12 January 2019

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

scientific article published on 10 September 2020

Intrinsic curvature properties of photosynthetic proteins in chromatophores

scientific article

Lateral opening and exit pore formation are required for BamA function

scientific article

Living on the edge: Simulations of bacterial outer-membrane proteins

scientific article published on 27 January 2016

Mechanics of force propagation in TonB-dependent outer membrane transport

scientific article

Mechanisms of SecM-mediated stalling in the ribosome

scientific article

Membrane curvature induced by aggregates of LH2s and monomeric LH1s

scientific article published on December 2009

Membrane proteins: Where theory meets experiment.

scientific article published on 16 April 2016

Membrane thinning and lateral gating are consistent features of BamA across multiple species

scientific article published on 28 October 2020

Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter

scientific article

Molecular dynamics simulations of membrane channels and transporters

scientific article published on April 2009

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations

scientific article

Molecular dynamics simulations of proteins in lipid bilayers

scientific article

Molecular dynamics studies of the archaeal translocon

scientific article

Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface

scientific article published on 12 February 2020

Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison

scientific article published on 01 October 2020

Parametrization of macrolide antibiotics using the force field toolkit

scientific article published on 17 August 2015

Presence of substrate aids lateral gate separation in LptD

scientific article published on 25 July 2019

Producing membrane proteins one simulation at a time

scientific article published in November 2017

Protein-induced membrane curvature investigated through molecular dynamics flexible fitting

scientific article published on July 2009

Rapid parameterization of small molecules using the Force Field Toolkit

scientific article published on 02 September 2013

Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion

scientific article published on 31 January 2013

Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β-Hairpin Maquette Determined through Spectroscopy and Simulation.

scientific article published in February 2017

Regulation of the Protein-Conducting Channel by a Bound Ribosome

scientific article

Role of the Native Outer-Membrane Environment on the Transporter BtuB.

scientific article

Scalable molecular dynamics with NAMD

scientific article (publication date: December 2005)

Self-assembly of photosynthetic membranes

scientific article

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

scientific article published on 04 April 2016

Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations

scientific article published on 02 July 2019

Standard binding free energies from computer simulations: What is the best strategy?

scientific article

Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens

scientific article

Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization

scientific article

Structural basis for iron piracy by pathogenic Neisseria

scientific article

Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery

scientific article

Structural determinants of lateral gate opening in the protein translocon

scientific article published in 2007

Structural insight into the biogenesis of β-barrel membrane proteins

scientific article

Structural insight into toxin secretion by contact dependent growth inhibition transporters

scientific article published on 22 October 2020

Structure and Function of Tryptophan-Tyrosine Dyads in Biomimetic β Hairpins

scientific article published on 19 March 2019

Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin

scientific article

Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome

scientific article

Structure of the SecY channel during initiation of protein translocation

scientific article

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

scientific article published on 29 July 2020

Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19

scientific article published on 16 December 2020

Symmetry-restrained flexible fitting for symmetric EM maps

scientific article

Synergistic Biophysical Techniques Reveal Structural Mechanisms of Engineered Cationic Antimicrobial Peptides in Lipid Model Membranes

scientific article published on 13 March 2020

The Effect of (-)-Epigallocatechin-3-Gallate on the Amyloid-β Secondary Structure

scientific article published on 10 June 2020

The Mechanism of the Amidases: MUTATING THE GLUTAMATE ADJACENT TO THE CATALYTIC TRIAD INACTIVATES THE ENZYME DUE TO SUBSTRATE MISPOSITIONING

scientific article

The adaptive biasing force method: everything you always wanted to know but were afraid to ask

scientific article

The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state

scientific article

The roles of pore ring and plug in the SecY protein-conducting channel

scientific article published on 10 November 2008

The β-barrel assembly machinery in motion

scientific article

Thermodynamics of Deca-alanine Folding in Water

scientific article

Toward the rational design of macrolide antibiotics to combat resistance.

scientific article published on 17 April 2017

Transitions of Double-Stranded DNA Between the A- and B-Forms

scientific article published on 02 May 2016

Transmembrane but not soluble helices fold inside the ribosome tunnel

scientific article published in Nature Communications

Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design

scientific article published on 06 November 2020

Tyrosine, cysteine, and proton coupled electron transfer in a ribonucleotide reductase-inspired beta hairpin maquette

scientific article published on 19 July 2019

When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy

scientific article published in 2022

β-Barrel proteins tether the outer membrane in many Gram-negative bacteria

scientific article published on 02 November 2020

List of works by James C Gumbart

A Minimal Membrane Metal Transport System: Dynamics and Energetics of mer Proteins

A Novel Approach to Simulating the Gating Transitions of Mechanosensitive Channels

A novel human IL2RB mutation results in T and NK cell-driven immune dysregulation

ATP-Dependent Signaling in Simulations of a Revised Model of Cystic Fibrosis Transmembrane Conductance Regulator (CFTR)

Accelerating Membrane Simulations with Hydrogen Mass Repartitioning

Accelerating the use of molecular modeling in the high school classroom with VMD Lite

Applications of the molecular dynamics flexible fitting method

Architecture and assembly of the Gram-positive cell wall

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

BamA is required for autotransporter secretion

Bifunctional Janus Particles as Multivalent Synthetic Nanoparticle Antibodies (SNAbs) for Selective Depletion of Target Cells

C-terminal kink formation is required for lateral gating in BamA

Coarse-Grained Molecular Dynamics Simulations of the Bacterial Cell Wall

Coarse-grained simulations of bacterial cell wall growth reveal that local coordination alone can be sufficient to maintain rod shape

Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method

Conformational Changes of the Clamp of the Protein Translocation ATPase SecA

Conformational Dynamics of AcrA Govern Multidrug Efflux Pump Assembly

Constant electric field simulations of the membrane potential illustrated with simple systems

Correction to: Computed Free Energies of Peptide Insertion into Bilayers are Independent of Computational Method

Correction: A novel human IL2RB mutation results in T and NK cell-driven immune dysregulation.

Coupling of calcium and substrate binding through loop alignment in the outer-membrane transporter BtuB.

Cryo-EM structure of the ribosome–SecYE complex in the membrane environment

DNA Scrunching in the Packaging of Viral Genomes

Decrypting protein insertion through the translocon with free-energy calculations

Determination of membrane-insertion free energies by molecular dynamics simulations

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations.

Distribution of mechanical stress in the Escherichia coli cell envelope

Efficient determination of protein-protein standard binding free energies from first principles

Escherichia coli peptidoglycan structure and mechanics as predicted by atomic-scale simulations

Exploring adsorption of neutral aromatic pollutants onto graphene nanomaterials via molecular dynamics simulations and theoretical linear solvation energy relationships

Exploring substrate diffusion in channels using biased molecular dynamics simulations.

Fatal arrhythmias: Another reason why doctors remain cautious about chloroquine/hydroxychloroquine for treating COVID-19

Folding free energy landscapes of β-sheets with non-polarizable and polarizable CHARMM force fields

Free energy of nascent-chain folding in the translocon

Free-energy cost for translocon-assisted insertion of membrane proteins

Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD.

IcmQ in the Type 4b Secretion System Contains an NAD+ Binding Domain

Identification of Binding Sites for Efflux Pump Inhibitors of the AcrAB-TolC Component AcrA

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

Intrinsic curvature properties of photosynthetic proteins in chromatophores

Lateral opening and exit pore formation are required for BamA function

Living on the edge: Simulations of bacterial outer-membrane proteins

Mechanics of force propagation in TonB-dependent outer membrane transport

Mechanisms of SecM-mediated stalling in the ribosome

Membrane curvature induced by aggregates of LH2s and monomeric LH1s

Membrane proteins: Where theory meets experiment.

Membrane thinning and lateral gating are consistent features of BamA across multiple species

Molecular Basis for the Activation of a Catalytic Asparagine Residue in a Self-Cleaving Bacterial Autotransporter

Molecular dynamics simulations of membrane channels and transporters

Molecular dynamics simulations of membrane proteins under asymmetric ionic concentrations

Molecular dynamics simulations of proteins in lipid bilayers

Molecular dynamics studies of the archaeal translocon

Outer membrane protein size and LPS O-antigen define protective antibody targeting to the Salmonella surface

Parameterization of a drug molecule with a halogen σ-hole particle using ffTK: Implementation, testing, and comparison

Parametrization of macrolide antibiotics using the force field toolkit

Presence of substrate aids lateral gate separation in LptD

Producing membrane proteins one simulation at a time

Protein-induced membrane curvature investigated through molecular dynamics flexible fitting

Rapid parameterization of small molecules using the Force Field Toolkit

Reconciling the roles of kinetic and thermodynamic factors in membrane-protein insertion

Redox-Driven Conformational Dynamics in a Photosystem-II-Inspired β-Hairpin Maquette Determined through Spectroscopy and Simulation.

Regulation of the Protein-Conducting Channel by a Bound Ribosome

Role of the Native Outer-Membrane Environment on the Transporter BtuB.

Scalable molecular dynamics with NAMD

Self-assembly of photosynthetic membranes

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

Stable calcium-free myocilin olfactomedin domain variants reveal challenges in differentiating between benign and glaucoma-causing mutations

Standard binding free energies from computer simulations: What is the best strategy?

Structural and Functional Characterization of the LPS Transporter LptDE from Gram-Negative Pathogens

Structural and biophysical characterization of an epitope-specific engineered Fab fragment and complexation with membrane proteins: implications for co-crystallization

Structural basis for iron piracy by pathogenic Neisseria

Structural basis for substrate selection by the translocation and assembly module of the β-barrel assembly machinery

Structural determinants of lateral gate opening in the protein translocon

Structural insight into the biogenesis of β-barrel membrane proteins

Structural insight into toxin secretion by contact dependent growth inhibition transporters

Structure and Function of Tryptophan-Tyrosine Dyads in Biomimetic β Hairpins

Structure and Misfolding of the Flexible Tripartite Coiled-Coil Domain of Glaucoma-Associated Myocilin

Structure of Monomeric Yeast and Mammalian Sec61 Complexes Interacting with the Translating Ribosome

Structure of the SecY channel during initiation of protein translocation