Integrating hydrogen–deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins

Deuteros: software for rapid analysis and visualization of data from differential hydrogen deuterium exchange-mass spectrometry

(2019) Andy M C Lau et al.   BIOINFORMATICS

Computational Modeling of Realistic Cell Membranes

(2019) Siewert J. Marrink et al.   CHEMICAL REVIEWS

Structural insight into substrate and inhibitor discrimination by human P-glycoprotein

(2019) Amer Alam et al.   SCIENCE

Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions

(2018) Leslie A. Salas-Estrada et al.   BIOPHYSICAL JOURNAL

Identifying key membrane protein lipid interactions using mass spectrometry

(2018) Kallol Gupta et al.   Nature Protocols

Lipid bilayer composition modulates the unfolding free energy of a knotted α-helical membrane protein

(2018) M. R. Sanders et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conformational analysis of complex protein states by hydrogen/deuterium exchange mass spectrometry (HDX-MS): Challenges and emerging solutions

(2018) Esben Trabjerg et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

A direct interaction of cholesterol with the dopamine transporter prevents its out-to-inward transition

(2018) Talia Zeppelin et al.   PLoS Computational Biology

Substrate-modulated unwinding of transmembrane helices in the NSS transporter LeuT

(2018) Patrick S. Merkle et al.   Science Advances

Microscopic view of lipids and their diverse biological functions

(2018) Po-Chao Wen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Evidence for a Partially Stalled γ Rotor in F1-ATPase from Hydrogen–Deuterium Exchange Experiments and Molecular Dynamics Simulations

(2018) Angela Murcia Rios et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Chemical Additives Enable Native Mass Spectrometry Measurement of Membrane Protein Oligomeric State within Intact Nanodiscs

(2018) James E. Keener et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Mechanisms of GPCR Signaling: A Structural Perspective

(2017) Vsevolod Gurevich et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Conformational dynamics of a neurotransmitter:sodium symporter in a lipid bilayer

(2017) Suraj Adhikary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ligand-induced conformational dynamics of theEscherichia coliNa+/H+antiporter NhaA revealed by hydrogen/deuterium exchange mass spectrometry

(2017) Martin Lorenz Eisinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Membrane cholesterol access into a G-protein-coupled receptor

(2017) Ramon Guixà-González et al.   Nature Communications

Integrating mass spectrometry with MD simulations reveals the role of lipids in Na+/H+ antiporters

(2017) Michael Landreh et al.   Nature Communications

Shared Molecular Mechanisms of Membrane Transporters

(2016) David Drew et al.   Annual Review of Biochemistry

Drugging Membrane Protein Interactions

(2016) Hang Yin et al.   Annual Review of Biomedical Engineering

Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations

(2016) George Hedger et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Conformational insight into multi-protein signaling assemblies by hydrogen–deuterium exchange mass spectrometry

(2016) Rane A Harrison et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action

(2016) Yuan Gao et al.   NATURE

A saposin-lipoprotein nanoparticle system for membrane proteins

(2016) Jens Frauenfeld et al.   NATURE METHODS

NMR as a tool to investigate the structure, dynamics and function of membrane proteins

(2016) Binyong Liang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Lipids modulate the conformational dynamics of a secondary multidrug transporter

(2016) Chloé Martens et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nanodiscs for structural and functional studies of membrane proteins

(2016) Ilia G Denisov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Load-dependent destabilization of the γ-rotor shaft in FOF1ATP synthase revealed by hydrogen/deuterium-exchange mass spectrometry

(2016) Siavash Vahidi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NMR as a tool to investigate the structure, dynamics and function of membrane proteins

(2016) Binyong Liang et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Lipids modulate the conformational dynamics of a secondary multidrug transporter

(2016) Chloé Martens et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Nanodiscs for structural and functional studies of membrane proteins

(2016) Ilia G Denisov et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol

(2016) Moutusi Manna et al.   eLife

Probing the Lipid Annular Belt by Gas-Phase Dissociation of Membrane Proteins in Nanodiscs

(2015) Michael T. Marty et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Probing the dynamic regulation of peripheral membrane proteins using hydrogen deuterium exchange-MS (HDX-MS)

(2015) O. Vadas et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Effective Application of Bicelles for Conformational Analysis of G Protein-Coupled Receptors by Hydrogen/Deuterium Exchange Mass Spectrometry

(2015) Nguyen Minh Duc et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The role of lipids in mechanosensation

(2015) Christos Pliotas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

How amide hydrogens exchange in native proteins

(2015) Filip Persson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying the stabilizing effects of protein–ligand interactions in the gas phase

(2015) Timothy M. Allison et al.   Nature Communications

The role of lipids in mechanosensation

(2015) Christos Pliotas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Biomedical applications of ion mobility-enhanced data-independent acquisition-based label-free quantitative proteomics

(2014) Ute Distler et al.   Expert Review of Proteomics

Membrane proteins bind lipids selectively to modulate their structure and function

(2014) Arthur Laganowsky et al.   NATURE

Ion mobility–mass spectrometry of a rotary ATPase reveals ATP-induced reduction in conformational flexibility

(2014) Min Zhou et al.   Nature Chemistry

Global structural changes of an ion channel during its gating are followed by ion mobility mass spectrometry

(2014) Albert Konijnenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Benchmarking all-atom simulations using hydrogen exchange

(2014) John J. Skinner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mass spectrometry reveals synergistic effects of nucleotides, lipids, and drugs binding to a multidrug resistance efflux pump

(2013) J. Marcoux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure of a bacterial homologue of glucose transporters GLUT1–4

(2012) Linfeng Sun et al.   NATURE

Molecular recognition of a single sphingolipid species by a protein’s transmembrane domain

(2012) F.-Xabier Contreras et al.   NATURE

Dynamics of a bacterial multidrug ABC transporter in the inward- and outward-facing conformations

(2012) S. Mehmood et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

OPM database and PPM web server: resources for positioning of proteins in membranes

(2011) Mikhail A. Lomize et al.   NUCLEIC ACIDS RESEARCH

Mass Spectrometry of Intact V-Type ATPases Reveals Bound Lipids and the Effects of Nucleotide Binding

(2011) M. Zhou et al.   SCIENCE

Ligand-Dependent Perturbation of the Conformational Ensemble for the GPCR β2 Adrenergic Receptor Revealed by HDX

(2011) Graham M. West et al.   STRUCTURE

Conformational Analysis of Membrane Proteins in Phospholipid Bilayer Nanodiscs by Hydrogen Exchange Mass Spectrometry

(2010) Christine M. Hebling et al.   ANALYTICAL CHEMISTRY

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

(2010) Jeffery B. Klauda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Membrane protein assembly into Nanodiscs

(2009) Timothy H. Bayburt et al.   FEBS LETTERS

Lipids and membrane protein structures

(2008) C HUNTE et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY