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Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

Chemical reviews, 2020-09, Vol.120 (18), p.10298-10335

2020

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Organization and Dynamics of Receptor Proteins in a Plasma Membrane

Journal of the American Chemical Society, 2015-11, Vol.137 (46), p.14694-14704

2015

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Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs

Nature communications, 2020-07, Vol.11 (1), p.3752-14, Article 3752

2020

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Reduced lateral mobility of lipids and proteins in crowded membranes

PLoS computational biology, 2013-04, Vol.9 (4), p.e1003033-e1003033

2013

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Structures of the otopetrin proton channels Otop1 and Otop3

Nature structural & molecular biology, 2019-06, Vol.26 (6), p.518-525

2019

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Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

Journal of the American Chemical Society, 2016-08, Vol.138 (33), p.10611-10622

2016

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Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5‑HT3 Receptor Channel

ACS nano, 2020-08, Vol.14 (8), p.10480-10491

2020

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Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1

Science (American Association for the Advancement of Science), 2010-04, Vol.328 (5977), p.470-473

2010

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Biomimetic Phospholipid Membrane Organization on Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Simulation Study

ACS nano, 2017-02, Vol.11 (2), p.1613-1625

2017

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A lipid gating mechanism for the channel-forming O antigen ABC transporter

Nature communications, 2019-02, Vol.10 (1), p.824-824, Article 824

2019

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A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates

Proceedings of the National Academy of Sciences - PNAS, 2019-07, Vol.116 (28), p.13989-13995

2019

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Bendix: intuitive helix geometry analysis and abstraction

Bioinformatics, 2012-08, Vol.28 (16), p.2193-2194

2012

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Designing biomimetic pores based on carbon nanotubes

Proceedings of the National Academy of Sciences - PNAS, 2012-05, Vol.109 (18), p.6939-6944

2012

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Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes

Biochemistry (Easton), 2016-11, Vol.55 (45), p.6238-6249

2016

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Structural basis for cannabinoid-induced potentiation of alpha1-glycine receptors in lipid nanodiscs

Nature communications, 2022-08, Vol.13 (1), p.4862-4862, Article 4862

2022

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Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes

PLoS computational biology, 2016-07, Vol.12 (7), p.e1005028-e1005028

2016

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Structural insights into the Venus flytrap mechanosensitive ion channel Flycatcher1

Nature communications, 2022-02, Vol.13 (1), p.850-850, Article 850

2022

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Voltage Gating of a Biomimetic Nanopore: Electrowetting of a Hydrophobic Barrier

ACS nano, 2017-02, Vol.11 (2), p.1840-1847

2017

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Structure and dynamics of the membrane-bound cytochrome P450 2C9

PLoS computational biology, 2011-08, Vol.7 (8), p.e1002152-e1002152

2011

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Insertion and Assembly of Membrane Proteins via Simulation

Journal of the American Chemical Society, 2006-03, Vol.128 (8), p.2697-2704

2006

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Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations

PLoS computational biology, 2021-09, Vol.17 (9), p.e1008807-e1008807

2021

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LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins

Nature communications, 2023-11, Vol.14 (1), p.7774-7774, Article 7774

2023

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Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics

Journal of the American Chemical Society, 2016-09, Vol.138 (36), p.11633-11642

2016

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Membrane Perturbation by Carbon Nanotube Insertion: Pathways to Internalization

Small (Weinheim an der Bergstrasse, Germany), 2013-11, Vol.9 (21), p.3639-3646

2013

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Atomistic mechanism of transmembrane helix association

PLoS computational biology, 2020-06, Vol.16 (6), p.e1007919-e1007919

2020

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Water in Nanopores and Biological Channels: A Molecular Simulation Perspective

Organization and Dynamics of Receptor Proteins in a Plasma Membrane

Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs

Reduced lateral mobility of lipids and proteins in crowded membranes

Structures of the otopetrin proton channels Otop1 and Otop3

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

Electric Field Induced Wetting of a Hydrophobic Gate in a Model Nanopore Based on the 5‑HT3 Receptor Channel

Molecular Basis of Alternating Access Membrane Transport by the Sodium-Hydantoin Transporter Mhp1

Biomimetic Phospholipid Membrane Organization on Graphene and Graphene Oxide Surfaces: A Molecular Dynamics Simulation Study

A lipid gating mechanism for the channel-forming O antigen ABC transporter

A heuristic derived from analysis of the ion channel structural proteome permits the rapid identification of hydrophobic gates

Bendix: intuitive helix geometry analysis and abstraction

Designing biomimetic pores based on carbon nanotubes

Lipid-Loving ANTs: Molecular Simulations of Cardiolipin Interactions and the Organization of the Adenine Nucleotide Translocase in Model Mitochondrial Membranes

Structural basis for cannabinoid-induced potentiation of alpha1-glycine receptors in lipid nanodiscs

Multiscale Simulations Suggest a Mechanism for the Association of the Dok7 PH Domain with PIP-Containing Membranes

Structural insights into the Venus flytrap mechanosensitive ion channel Flycatcher1

Voltage Gating of a Biomimetic Nanopore: Electrowetting of a Hydrophobic Barrier

Structure and dynamics of the membrane-bound cytochrome P450 2C9

Insertion and Assembly of Membrane Proteins via Simulation

Membrane-binding mechanism of the EEA1 FYVE domain revealed by multi-scale molecular dynamics simulations

LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins

Roles of Interleaflet Coupling and Hydrophobic Mismatch in Lipid Membrane Phase-Separation Kinetics

Membrane Perturbation by Carbon Nanotube Insertion: Pathways to Internalization

Atomistic mechanism of transmembrane helix association

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