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Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation

Chemical reviews, 2019-07, Vol.119 (13), p.7737-7832

2019

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String method solution of the gating pathways for a pentameric ligand-gated ion channel

Proceedings of the National Academy of Sciences - PNAS, 2017-05, Vol.114 (21), p.E4158-E4167

2017

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Elucidating factors important for monovalent cation selectivity in enzymes: E. coli β-galactosidase as a model

Physical chemistry chemical physics : PCCP, 2015-04, Vol.17 (16), p.10899-10909

2015

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Evidence for a third sodium-binding site in glutamate transporters suggests an ion/substrate coupling model

Proceedings of the National Academy of Sciences - PNAS, 2010-08, Vol.107 (31), p.13912-13917

2010

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Identification of Electric-Field-Dependent Steps in the Na+,K+-Pump Cycle

Biophysical journal, 2014-09, Vol.107 (6), p.1352-1363

2014

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QM/MM calculations with deMon2k

Molecules, 2015-03, Vol.20 (3), p.4780-4812

2015

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The Membrane Dipole Potential and the Roles of Interfacial Water and Lipid Hydrocarbon Chains

The journal of physical chemistry. B, 2024-10, Vol.128 (39), p.9482-9499

2024

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Simulating ion channel activation mechanisms using swarms of trajectories

Journal of computational chemistry, 2020-02, Vol.41 (5), p.387-401

2020

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Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter Glt(Ph)

Physical chemistry chemical physics : PCCP, 2013-02, Vol.15 (7), p.2397-2404

2013

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Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter GltPh

Physical chemistry chemical physics : PCCP, 2013-02, Vol.15 (7), p.2397-244

2013

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Application of the String and 2D Hamiltonian Replica Exchange Umbrella Sampling Methods for the Study of Conformational Changes in the Bacterial Aspartate Transporter Glt(Ph)

Biophysical journal, 2016-02, Vol.110 (3), p.523a-523a

2016

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Involvement of alpha-subunit N-termini in the mechanism and regulation of the Na+,K+- and H+,K+-ATPases

Biophysical journal, 2023-02, Vol.122 (3), p.529a-529a

2023

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Ion Modulation of Gating in Aspartate Transporter GltPh: Insights from MD Simulations and Free Energy Computations

Biophysical journal, 2012-01, Vol.102 (3), p.519a-519a

2012

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Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations

Journal of chemical theory and computation, 2013-09, Vol.9 (9), p.4165-4175

2013

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Ion selectivity in channels and transporters

The Journal of general physiology, 2011-05, Vol.137 (5), p.415-426

2011

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Cholesterol depletion inhibits Na+,K+-ATPase activity in a near-native membrane environment

The Journal of biological chemistry, 2019-04, Vol.294 (15), p.5956-5969

2019

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Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter Glt sub(Ph)

Physical chemistry chemical physics : PCCP, 2013-01, Vol.15 (7), p.2397-2404

2013

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Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter GItPh

Physical chemistry chemical physics : PCCP, 2013, Vol.15 (7), p.2397-2404

2013

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Na+, K+ and Tl+ hydration from QM/MM computations and MD simulations with a polarizable force field

Interdisciplinary sciences : computational life sciences, 2010-03, Vol.2 (1), p.12-20

2010

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Gating Pathways for a Pentameric Ligand-Gated Ion Channel Solved by Atomistic String Method Simulations

Biophysical journal, 2017-02, Vol.112 (3), p.475a-475a

2017

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On the Molecular Mechanism of Ion-Modulated Gating in Secondary Transporters

Biophysical journal, 2013-01, Vol.104 (2), p.408a-408a

2013

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Allosteric Gating Pathways for the Pentameric Ligand-Gated Ion Channel Glic

Biophysical journal, 2016-02, Vol.110 (3), p.456a-456a

2016

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Effects of Lipid Composition on Biological Membrane Electrostatics

Biophysical journal, 2014-01, Vol.106 (2), p.80a-80a

2014

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The voltage-sensitive dye RH421 detects a Na+,K+-ATPase conformational change at the membrane surface

Biochimica et biophysica acta. Biomembranes, 2017-05, Vol.1859 (5), p.813-823

2017

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Atomistic models of ion and solute transport by the sodium-dependent secondary active transporters

Biochimica et biophysica acta, 2012-02, Vol.1818 (2), p.337-347

2012

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Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation

String method solution of the gating pathways for a pentameric ligand-gated ion channel

Elucidating factors important for monovalent cation selectivity in enzymes: E. coli β-galactosidase as a model

Evidence for a third sodium-binding site in glutamate transporters suggests an ion/substrate coupling model

Identification of Electric-Field-Dependent Steps in the Na+,K+-Pump Cycle

QM/MM calculations with deMon2k

The Membrane Dipole Potential and the Roles of Interfacial Water and Lipid Hydrocarbon Chains

Simulating ion channel activation mechanisms using swarms of trajectories

Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter Glt(Ph)

Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter GltPh

Application of the String and 2D Hamiltonian Replica Exchange Umbrella Sampling Methods for the Study of Conformational Changes in the Bacterial Aspartate Transporter Glt(Ph)

Involvement of alpha-subunit N-termini in the mechanism and regulation of the Na+,K+- and H+,K+-ATPases

Ion Modulation of Gating in Aspartate Transporter GltPh: Insights from MD Simulations and Free Energy Computations

Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations

Ion selectivity in channels and transporters

Cholesterol depletion inhibits Na+,K+-ATPase activity in a near-native membrane environment

Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter Glt sub(Ph)

Role of protein matrix rigidity and local polarization effects in the monovalent cation selectivity of crystallographic sites in the Na-coupled aspartate transporter GItPh

Na+, K+ and Tl+ hydration from QM/MM computations and MD simulations with a polarizable force field

Gating Pathways for a Pentameric Ligand-Gated Ion Channel Solved by Atomistic String Method Simulations

On the Molecular Mechanism of Ion-Modulated Gating in Secondary Transporters

Allosteric Gating Pathways for the Pentameric Ligand-Gated Ion Channel Glic

Effects of Lipid Composition on Biological Membrane Electrostatics

The voltage-sensitive dye RH421 detects a Na+,K+-ATPase conformational change at the membrane surface

Atomistic models of ion and solute transport by the sodium-dependent secondary active transporters

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