Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels

Computational Modeling of Realistic Cell Membranes

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

Multiscale Simulations of Biological Membranes: The Challenge To Understand Biological Phenomena in a Living Substance

(2019) Giray Enkavi et al.   CHEMICAL REVIEWS

Ceramides bind VDAC2 to trigger mitochondrial apoptosis

(2019) Shashank Dadsena et al.   Nature Communications

Lipid-Dependent Regulation of Ion Channels and G Protein–Coupled Receptors: Insights from Structures and Simulations

(2019) Anna L. Duncan et al.   Annual Review of Pharmacology and Toxicology

Insights into Membrane Protein–Lipid Interactions from Free Energy Calculations

(2019) Robin A. Corey et al.   Journal of Chemical Theory and Computation

Atomistic basis of opening and conduction in mammalian inward rectifier potassium (Kir2.2) channels

(2019) Eva-Maria Zangerl-Plessl et al.   JOURNAL OF GENERAL PHYSIOLOGY

Cardiolipin dynamics and binding to conserved residues in the mitochondrial ADP/ATP carrier

(2018) Anna L. Duncan et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Understanding the diversity of membrane lipid composition

(2018) Takeshi Harayama et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Specific cardiolipin–SecY interactions are required for proton-motive force stimulation of protein secretion

(2018) Robin A. Corey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allostery revealed within lipid binding events to membrane proteins

(2018) John W. Patrick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lipid–Protein Interactions Are Unique Fingerprints for Membrane Proteins

(2018) Valentina Corradi et al.   ACS Central Science

Molecular Dynamics Simulations of Kir2.2 Interactions with an Ensemble of Cholesterol Molecules

(2018) Nicolas Barbera et al.   BIOPHYSICAL JOURNAL

PtdIns(4,5)P2 stabilizes active states of GPCRs and enhances selectivity of G-protein coupling

(2018) Hsin-Yung Yen et al.   NATURE

Ion channels can be allosterically regulated by membrane domains near a de-mixing critical point

(2018) Ofer Kimchi et al.   JOURNAL OF GENERAL PHYSIOLOGY

Cholesterol Interaction Sites on the Transmembrane Domain of the Hedgehog Signal Transducer and Class F G Protein-Coupled Receptor Smoothened

(2018) George Hedger et al.   STRUCTURE

Direct protein-lipid interactions shape the conformational landscape of secondary transporters

(2018) Chloe Martens et al.   Nature Communications

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

(2017) Julian Michalowsky et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic role of the tether helix in PIP 2 -dependent gating of a G protein–gated potassium channel

(2017) Emre Lacin et al.   JOURNAL OF GENERAL PHYSIOLOGY

The role of interfacial lipids in stabilizing membrane protein oligomers

(2017) Kallol Gupta et al.   NATURE

Sphingolipids: membrane microdomains in brain development, function and neurological diseases

(2017) Anne S. B. Olsen et al.   Open Biology

Protein crowding and lipid complexity influence the nanoscale dynamic organization of ion channels in cell membranes

(2017) Anna L. Duncan et al.   Scientific Reports

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

(2016) George Hedger et al.   BIOCHEMISTRY

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

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

Structural basis of control of inward rectifier Kir2 channel gating by bulk anionic phospholipids

(2016) Sun-Joo Lee et al.   JOURNAL OF GENERAL PHYSIOLOGY

TRPV1 structures in nanodiscs reveal mechanisms of ligand and lipid action

(2016) Yuan Gao et al.   NATURE

Cardiolipin binds selectively but transiently to conserved lysine residues in the rotor of metazoan ATP synthases

(2016) Anna L. Duncan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lipid agonism: The PIP2 paradigm of ligand-gated ion channels

(2015) Scott B. Hansen   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Membrane Nanoclusters—Tails of the Unexpected

(2015) Erdinc Sezgin et al.   CELL

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Identification of a Cholesterol-Binding Pocket in Inward Rectifier K + (Kir) Channels

(2014) Oliver Fürst et al.   BIOPHYSICAL JOURNAL

Phosphoinositide regulation of inward rectifier potassium (Kir) channels

(2014) Oliver Fürst et al.   Frontiers in Physiology

Cholesterol binding to ion channels

(2014) Irena Levitan et al.   Frontiers in Physiology

Interplay Between Lipid Modulators of Kir2 Channels: Cholesterol and PIP2

(2014) Avia Rosenhouse-Dantsker et al.   Computational and Structural Biotechnology Journal

Cholesterol sensitivity of KIR2.1 depends on functional inter-links between the N and C termini

(2013) Avia Rosenhouse-Dantsker et al.   Channels

Identification of Novel Cholesterol-binding Regions in Kir2 Channels

(2013) Avia Rosenhouse-Dantsker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evidence for Cardiolipin Binding Sites on the Membrane-Exposed Surface of the Cytochrome bc1

(2013) Clement Arnarez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Secondary anionic phospholipid binding site and gating mechanism in Kir2.1 inward rectifier channels

(2013) Sun-Joo Lee et al.   Nature Communications

Identification of cardiolipin binding sites on cytochrome c oxidase at the entrance of proton channels

(2013) C. Arnarez et al.   Scientific Reports

Simulation-Based Prediction of Phosphatidylinositol 4,5-Bisphosphate Binding to an Ion Channel

(2012) Matthias R. Schmidt et al.   BIOCHEMISTRY

Distant Cytosolic Residues Mediate a Two-way Molecular Switch That Controls the Modulation of Inwardly Rectifying Potassium (Kir) Channels by Cholesterol and Phosphatidylinositol 4,5-Bisphosphate (PI(4,5)P2)

(2012) Avia Rosenhouse-Dantsker et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Cholesterol regulates prokaryotic Kir channel by direct binding to channel protein

(2011) Dev K. Singh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Dual-Mode Phospholipid Regulation of Human Inward Rectifying Potassium Channels

(2011) Wayland W.L. Cheng et al.   BIOPHYSICAL JOURNAL

Cholesterol Sensitivity of KIR2.1 Is Controlled by a Belt of Residues around the Cytosolic Pore

(2011) Avia Rosenhouse-Dantsker et al.   BIOPHYSICAL JOURNAL

From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations

(2011) Phillip J. Stansfeld et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Membrane protein sequestering by ionic protein–lipid interactions

(2011) Geert van den Bogaart et al.   NATURE

Structural basis of PIP2 activation of the classical inward rectifier K+ channel Kir2.2

(2011) Scott B. Hansen et al.   NATURE

Enantioselective Protein-Sterol Interactions Mediate Regulation of Both Prokaryotic and Eukaryotic Inward Rectifier K+ Channels by Cholesterol

(2011) Nazzareno D'Avanzo et al.   PLoS One

Cell Membranes: The Lipid Perspective

(2011) Ünal Coskun et al.   STRUCTURE

Automatic Lip-Contour Extraction and Mouth-Structure Segmentation in Images

(2010) Juan-Bernardo Gómez-Mendoza et al.   COMPUTING IN SCIENCE & ENGINEERING

Direct and Specific Activation of Human Inward Rectifier K+Channels by Membrane Phosphatidylinositol 4,5-Bisphosphate

(2010) Nazzareno D'Avanzo et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Lipid map of the mammalian cell

(2010) G. van Meer et al.   JOURNAL OF CELL SCIENCE

PIP2-Binding Site in Kir Channels: Definition by Multiscale Biomolecular Simulations

(2009) Phillip J. Stansfeld et al.   BIOCHEMISTRY

Direct Regulation of Prokaryotic Kir Channel by Cholesterol

(2009) Dev K. Singh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Community detection in graphs

(2009) Santo Fortunato   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Membrane lipids: where they are and how they behave

(2008) Gerrit van Meer et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY