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Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems

The European physical journal. B, Condensed matter physics, 2021-07, Vol.94 (7), p.144-144, Article 144

2021

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Human cellular model systems of β-thalassemia enable in-depth analysis of disease phenotype

Nature communications, 2023-10, Vol.14 (1), p.6260-6260, Article 6260

2023

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ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer

Scientific reports, 2021-05, Vol.11 (1), p.10591-10591, Article 10591

2021

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Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2

Nature communications, 2022-01, Vol.13 (1), p.222-222, Article 222

2022

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Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion

eLife, 2022-04, Vol.11

2022

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The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour

Computational and structural biotechnology journal, 2022-01, Vol.20, p.139-147

2022

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Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study

Journal of chemical information and modeling, 2017-02, Vol.57 (2), p.256-266

2017

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Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex

PLoS computational biology, 2011-08, Vol.7 (8), p.e1002128-e1002128

2011

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Resistance to the "last resort" antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes

Chemical communications (Cambridge, England), 2020-06, Vol.56 (5), p.6874-6877

2020

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Identification and validation of novel microtubule suppressors with an imidazopyridine scaffold through structure-based virtual screening and docking

RSC medicinal chemistry, 2022-08, Vol.13 (8), p.929-943

2022

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Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus

Redox biology, 2018-06, Vol.16, p.209-214

2018

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Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site

PLoS computational biology, 2014-12, Vol.10 (12), p.e1004010-e1004010

2014

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Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: Molecular dynamics studies of HlyB

Protein science, 2011-07, Vol.20 (7), p.1220-1230

2011

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Insights into the Molecular Mechanism of an ABC Transporter: Conformational Changes in the NBD Dimer of MJ0796

The journal of physical chemistry. B, 2010-04, Vol.114 (16), p.5486-5496

2010

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Molecular mechanisms of chaperone‐directed protein folding: Insights from atomistic simulations

Protein science, 2024-03, Vol.33 (3), p.e4880-n/a

2024

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The Role of Lys147 in the Interaction between MPSA-Gold Nanoparticles and the α‑Hemolysin Nanopore

Langmuir, 2012-11, Vol.28 (44), p.15643-15650

2012

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Decrypting Allostery in Membrane-Bound K‑Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations

Journal of the American Chemical Society, 2024-01, Vol.146 (1), p.901-919

2024

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A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors

Biophysical journal, 2021-03, Vol.120 (6), p.983-993

2021

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On the Use of Different Dielectric Constants for Computing Individual and Pairwise Terms in Poisson−Boltzmann Studies of Protein Ionization Equilibrium

The journal of physical chemistry. B, 2005-08, Vol.109 (30), p.14691-14706

2005

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Signal Propagation in the ATPase Domain of Mycobacterium tuberculosis DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations

Biochemistry (Easton), 2024-05, Vol.63 (11), p.1493-1504

2024

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Heme binding to the SARS-CoV-2 spike glycoprotein

The Journal of biological chemistry, 2023-08, Vol.299 (8), p.105014-105014, Article 105014

2023

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An expandable, modular de novo protein platform for precision redox engineering

Proceedings of the National Academy of Sciences - PNAS, 2023-08, Vol.120 (31), p.e2306046120-e2306046120

2023

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Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations

Structure (London), 2019-07, Vol.27 (7), p.1171-1183.e3

2019

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SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid

Journal of molecular cell biology, 2023-08, Vol.15 (3)

2023

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Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations

Biochimica et biophysica acta, 2016-06, Vol.1857 (6), p.759-771

2016

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Dynamical nonequilibrium molecular dynamics reveals the structural basis for allostery and signal propagation in biomolecular systems

Human cellular model systems of β-thalassemia enable in-depth analysis of disease phenotype

ATP hydrolysis and nucleotide exit enhance maltose translocation in the MalFGK2E importer

Structural insights in cell-type specific evolution of intra-host diversity by SARS-CoV-2

Rate-limiting transport of positively charged arginine residues through the Sec-machinery is integral to the mechanism of protein secretion

The fatty acid site is coupled to functional motifs in the SARS-CoV-2 spike protein and modulates spike allosteric behaviour

Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study

Inter-domain communication mechanisms in an ABC importer: a molecular dynamics study of the MalFGK2E complex

Resistance to the "last resort" antibiotic colistin: a single-zinc mechanism for phosphointermediate formation in MCR enzymes

Identification and validation of novel microtubule suppressors with an imidazopyridine scaffold through structure-based virtual screening and docking

Regulation of the mechanism of Type-II NADH: Quinone oxidoreductase from S. aureus

Exploring O2 diffusion in A-type cytochrome c oxidases: molecular dynamics simulations uncover two alternative channels towards the binuclear site

Structural consequences of ATP hydrolysis on the ABC transporter NBD dimer: Molecular dynamics studies of HlyB

Insights into the Molecular Mechanism of an ABC Transporter: Conformational Changes in the NBD Dimer of MJ0796

Molecular mechanisms of chaperone‐directed protein folding: Insights from atomistic simulations

The Role of Lys147 in the Interaction between MPSA-Gold Nanoparticles and the α‑Hemolysin Nanopore

Decrypting Allostery in Membrane-Bound K‑Ras4B Using Complementary In Silico Approaches Based on Unbiased Molecular Dynamics Simulations

A potential interaction between the SARS-CoV-2 spike protein and nicotinic acetylcholine receptors

On the Use of Different Dielectric Constants for Computing Individual and Pairwise Terms in Poisson−Boltzmann Studies of Protein Ionization Equilibrium

Signal Propagation in the ATPase Domain of Mycobacterium tuberculosis DNA Gyrase from Dynamical-Nonequilibrium Molecular Dynamics Simulations

Heme binding to the SARS-CoV-2 spike glycoprotein

An expandable, modular de novo protein platform for precision redox engineering

Identification of the Initial Steps in Signal Transduction in the α4β2 Nicotinic Receptor: Insights from Equilibrium and Nonequilibrium Simulations

SARS-CoV-2 spike variants differ in their allosteric responses to linoleic acid

Coupling between protonation and conformation in cytochrome c oxidase: Insights from constant-pH MD simulations

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