Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory

Modulation of Alzheimer’s Aβ Protofilament-Membrane Interactions by Lipid Headgroups

(2015) Florentina Tofoleanu et al.   ACS Chemical Neuroscience

Phosphoinositides regulate ion channels

(2015) Bertil Hille et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Structures of KcsA in Complex with Symmetrical Quaternary Ammonium Compounds Reveal a Hydrophobic Binding Site

(2014) Michael J. Lenaeus et al.   BIOCHEMISTRY

A Predicted Binding Site for Cholesterol on the GABAA Receptor

(2014) Jérôme Hénin et al.   BIOPHYSICAL JOURNAL

E. coli Outer Membrane and Interactions with OmpLA

(2014) Emilia L. Wu et al.   BIOPHYSICAL JOURNAL

Allosteric regulation of rhomboid intramembrane proteolysis

(2014) Elena Arutyunova et al.   EMBO JOURNAL

Evolutionary imprint of activation: The design principles of VSDs

(2014) Eugene Palovcak et al.   JOURNAL OF GENERAL PHYSIOLOGY

Disaccharides Impact the Lateral Organization of Lipid Membranes

(2014) Gemma Moiset et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Local anesthetic and antiepileptic drug access and binding to a bacterial voltage-gated sodium channel

(2014) C. Boiteux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ion conduction and conformational flexibility of a bacterial voltage-gated sodium channel

(2014) Céline Boiteux et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism

(2014) L. Chen et al.   SCIENCE

Crystal structure of a heterotetrameric NMDA receptor ion channel

(2014) E. Karakas et al.   SCIENCE

Slowing down single-molecule trafficking through a protein nanopore reveals intermediates for peptide translocation

(2014) Loredana Mereuta et al.   Scientific Reports

Omega Currents in Voltage-Gated Ion Channels: What Can We Learn from Uncovering the Voltage-Sensing Mechanism Using MD Simulations?

(2013) Mounir Tarek et al.   ACCOUNTS OF CHEMICAL RESEARCH

Aggregation of amyloids in a cellular context: modelling and experiment

(2013) Ran Friedman   BIOCHEMICAL JOURNAL

Membrane fusion and vesicular transformation induced by Alzheimer's amyloid beta

(2013) Mun'delanji C. Vestergaard et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Embedding Aβ42 in Heterogeneous Membranes Depends on Cholesterol Asymmetries

(2013) Nicoletta Liguori et al.   BIOPHYSICAL JOURNAL

Conical Lipids in Flat Bilayers Induce Packing Defects Similar to that Induced by Positive Curvature

(2013) Lydie Vamparys et al.   BIOPHYSICAL JOURNAL

Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics

(2013) Emilia L. Wu et al.   BIOPHYSICAL JOURNAL

Amphipathic Lipid Packing Sensor Motifs: Probing Bilayer Defects with Hydrophobic Residues

(2013) Stefano Vanni et al.   BIOPHYSICAL JOURNAL

Exploring cavity dynamics in biomolecular systems

(2013) Norbert Lindow et al.   BMC BIOINFORMATICS

Proteolysis inside the Membrane Is a Rate-Governed Reaction Not Driven by Substrate Affinity

(2013) Seth W. Dickey et al.   CELL

Surveying a complex potential energy landscape: Overcoming broken ergodicity using basin-sampling

(2013) David J. Wales   CHEMICAL PHYSICS LETTERS

Atomistic Visualization of Mesoscopic Whole-Cell Simulations Using Ray-Casted Instancing

(2013) Martin Falk et al.   COMPUTER GRAPHICS FORUM

Interactive Extraction and Tracking of Biomolecular Surface Features

(2013) M. Krone et al.   COMPUTER GRAPHICS FORUM

Molecular Modeling and Simulation of Membrane Lipid-Mediated Effects on GPCRs

(2013) S.K. Sadiq et al.   CURRENT MEDICINAL CHEMISTRY

Insights into Aβ Aggregation: A Molecular Dynamics Perspective

(2013) Joan-Emma Shea et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Tuning voltage-gated channel activity and cellular excitability with a sphingomyelinase

(2013) David J. Combs et al.   JOURNAL OF GENERAL PHYSIOLOGY

Domain Swapping in the Cytoplasmic Domain of the Escherichia coli Rhomboid Protease

(2013) Christelle Lazareno-Saez et al.   JOURNAL OF MOLECULAR BIOLOGY

Local Frustration Determines Molecular and Macroscopic Helix Structures

(2013) Christopher J. Forman et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Catalysis of Na+ permeation in the bacterial sodium channel NaVAb

(2013) N. Chakrabarti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wild type and mutants of the HET-s(218-289) prion show different flexibility at fibrillar ends: A simulation study

(2013) Ran Friedman et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes

(2013) Joseph E. Goose et al.   PLoS Computational Biology

The Role of Molecular Simulations in the Development of Inhibitors of Amyloid β-Peptide Aggregation for the Treatment of Alzheimer’s Disease

(2012) Justin A. Lemkul et al.   ACS Chemical Neuroscience

The Morphology of Decorated Amyloid Fibers is Controlled by the Conformation and Position of the Displayed Protein

(2012) Christopher J. Forman et al.   ACS Nano

Thermal Unfolding of Proteins Probed at the Single Molecule Level Using Nanopores

(2012) Linda Payet et al.   ANALYTICAL CHEMISTRY

Conformational Change in Rhomboid Protease GlpG Induced by Inhibitor Binding to Its S′ Subsites

(2012) Yi Xue et al.   BIOCHEMISTRY

Oligomeric state study of prokaryotic rhomboid proteases

(2012) Padmapriya Sampathkumar et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Stability and membrane interactions of an autotransport protein: MD simulations of the Hia translocator domain in a complex membrane environment

(2012) Daniel A. Holdbrook et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Conformational dynamics and membrane interactions of the E. coli outer membrane protein FecA: A molecular dynamics simulation study

(2012) Thomas J. Piggot et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Structural Characterization and Computer-Aided Optimization of a Small-Molecule Inhibitor of the Arp2/3 Complex, a Key Regulator of the Actin Cytoskeleton

(2012) Andrew W. Baggett et al.   ChemMedChem

Probabilistic Local Features in Uncertain Vector Fields with Spatial Correlation

(2012) Christoph Petz et al.   COMPUTER GRAPHICS FORUM

Curvature, Lipid Packing, and Electrostatics of Membrane Organelles: Defining Cellular Territories in Determining Specificity

(2012) Joëlle Bigay et al.   DEVELOPMENTAL CELL

Dual Effect of Phosphatidyl (4,5)-Bisphosphate PIP2on Shaker K+Channels

(2012) Fayal Abderemane-Ali et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

(2012) Mikyung Seo et al.   Journal of Chemical Theory and Computation

Molecular Dynamics Simulations of Phosphatidylcholine Membranes: A Comparative Force Field Study

(2012) Thomas J. Piggot et al.   Journal of Chemical Theory and Computation

Free Energy Calculations Reveal the Origin of Binding Preference for Aminoadamantane Blockers of Influenza A/M2TM Pore

(2012) Paraskevi Gkeka et al.   Journal of Chemical Theory and Computation

Regulation of voltage-gated potassium channels by PI(4,5)P2

(2012) Martin Kruse et al.   JOURNAL OF GENERAL PHYSIOLOGY

Ion Channels as Therapeutic Targets: A Drug Discovery Perspective

(2012) Sharan K. Bagal et al.   JOURNAL OF MEDICINAL CHEMISTRY

Molecular Dynamics Simulations of Lipid Membrane Electroporation

(2012) Lucie Delemotte et al.   JOURNAL OF MEMBRANE BIOLOGY

Molecular Interactions of Alzheimer's Aβ Protofilaments with Lipid Membranes

(2012) Florentina Tofoleanu et al.   JOURNAL OF MOLECULAR BIOLOGY

Predictions for Cholesterol Interaction Sites on the A2A Adenosine Receptor

(2012) Ji Young Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Nanopore-Based, Single-Molecule Exploration of Copper Binding to an Antimicrobial-Derived, Histidine-Containing Chimera Peptide

(2012) Loredana Mereuta et al.   LANGMUIR

Crystal structure of the channelrhodopsin light-gated cation channel

(2012) Hideaki E. Kato et al.   NATURE

Architectural and thermodynamic principles underlying intramembrane protease function

(2012) Rosanna P Baker et al.   Nature Chemical Biology

Membrane-Sensitive Conformational States of Helix 8 in the Metabotropic Glu2 Receptor, a Class C GPCR

(2012) Agostino Bruno et al.   PLoS One

Alzheimer Aβ peptide interactions with lipid membranes

(2012) Florentina Tofoleanu et al.   Prion

PIP2 controls voltage-sensor movement and pore opening of Kv channels through the S4-S5 linker

(2012) A. A. Rodriguez-Menchaca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanism of Voltage Gating in Potassium Channels

(2012) M. O. Jensen et al.   SCIENCE

Crystal Structure of the Human K2P TRAAK, a Lipid- and Mechano-Sensitive K+ Ion Channel

(2012) S. G. Brohawn et al.   SCIENCE

Structural Basis for Allosteric Regulation of GPCRs by Sodium Ions

(2012) W. Liu et al.   SCIENCE

Similarities between protein folding and granular jamming

(2012) Prasanth P Jose et al.   Nature Communications

Molecular Dynamics Simulations of Voltage-Gated Cation Channels: Insights on Voltage-Sensor Domain Function and Modulation

(2012) Lucie Delemotte et al.   Frontiers in Pharmacology

A partially folded structure of amyloid-beta(1–40) in an aqueous environment

(2011) Subramanian Vivekanandan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Hydrogen bond dynamics in membrane protein function

(2011) Ana-Nicoleta Bondar et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Quantitative Modeling of Membrane Deformations by Multihelical Membrane Proteins: Application to G-Protein Coupled Receptors

(2011) Sayan Mondal et al.   BIOPHYSICAL JOURNAL

Crystal Structure of the Mammalian GIRK2 K+ Channel and Gating Regulation by G Proteins, PIP2, and Sodium

(2011) Matthew R. Whorton et al.   CELL

Uncovering the intimate relationship between lipids, cholesterol and GPCR activation

(2011) Joanne Oates et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Voronoi-Based Extraction and Visualization of Molecular Paths

(2011) N. Lindow et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Catalytic Mechanism of Rhomboid Protease GlpG Probed by 3,4-Dichloroisocoumarin and Diisopropyl Fluorophosphonate

(2011) Yi Xue et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Perspectives on: Ion selectivity

(2011) Olaf S. Andersen   JOURNAL OF GENERAL PHYSIOLOGY

Origins of ion selectivity in potassium channels from the perspective of channel block

(2011) Crina M. Nimigean et al.   JOURNAL OF GENERAL PHYSIOLOGY

Surfactant Effects on Amyloid Aggregation Kinetics

(2011) Ran Friedman et al.   JOURNAL OF MOLECULAR BIOLOGY

Insights into Substrate Gating in H. influenzae Rhomboid

(2011) Cory L. Brooks et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure of Rhomboid Protease in a Lipid Environment

(2011) Kutti R. Vinothkumar   JOURNAL OF MOLECULAR BIOLOGY

Electroporation of the E. coli and S. Aureus Membranes: Molecular Dynamics Simulations of Complex Bacterial Membranes

(2011) Thomas J. Piggot et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free Energy Calculations on the Two Drug Binding Sites in the M2 Proton Channel

(2011) Ruo-Xu Gu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamics of Unfolded Protein Transport through an Aerolysin Pore

(2011) Manuela Pastoriza-Gallego et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In Silico Partitioning and Transmembrane Insertion of Hydrophobic Peptides under Equilibrium Conditions

(2011) Jakob P. Ulmschneider et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Specific Binding of Adamantane Drugs and Direction of Their Polar Amines in the Pore of the Influenza M2 Transmembrane Domain in Lipid Bilayers and Dodecylphosphocholine Micelles Determined by NMR Spectroscopy

(2011) Sarah D. Cady et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Principles of activation and permeation in an anion-selective Cys-loop receptor

(2011) Ryan E. Hibbs et al.   NATURE

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

(2011) Scott B. Hansen et al.   NATURE

The crystal structure of a voltage-gated sodium channel

(2011) Jian Payandeh et al.   NATURE

Finite-size scaling at the jamming transition: Corrections to scaling and the correlation-length critical exponent

(2011) Daniel Vågberg et al.   PHYSICAL REVIEW E

Jamming, Yielding, and Rheology of Weakly Vibrated Granular Media

(2011) Joshua A. Dijksman et al.   PHYSICAL REVIEW LETTERS

On the selective ion binding hypothesis for potassium channels

(2011) I. Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intermediate states of the Kv1.2 voltage sensor from atomistic molecular dynamics simulations

(2011) L. Delemotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fibril elongation mechanisms of HET-s prion-forming domain: Topological evidence for growth polarity

(2011) Marco Baiesi et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The importance of solvation in the design of ligands targeting membrane proteins

(2011) Angel González et al.   MedChemComm

The rhomboid protease family: a decade of progress on function and mechanism

(2011) Sinisa Urban et al.   GENOME BIOLOGY

Coupling of Retinal, Protein, and Water Dynamics in Squid Rhodopsin

(2010) Eduardo Jardón-Valadez et al.   BIOPHYSICAL JOURNAL

Potential role of caveolin-1-positive domains in the regulation of the acetylcholine receptor's activable pool: Implications in the pathogenesis of a novel congenital myasthenic syndrome

(2010) Carlos Baez et al.   Channels

Energy landscapes: some new horizons

(2010) David J Wales   CURRENT OPINION IN STRUCTURAL BIOLOGY

The structural basis for catalysis and substrate specificity of a rhomboid protease

(2010) Kutti R Vinothkumar et al.   EMBO JOURNAL

Evaluations of the Absolute and Relative Free Energies for Antidepressant Binding to the Amino Acid Membrane Transporter LeuT with Free Energy Simulations

(2010) Chunfeng Zhao et al.   Journal of Chemical Theory and Computation

Inhibition of peptide aggregation by lipids: Insights from coarse-grained molecular simulations

(2010) Andrew Hung et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Transmembrane Structures for Alzheimer’s Aβ1−42Oligomers

(2010) Birgit Strodel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanism and Kinetics of Peptide Partitioning into Membranes from All-Atom Simulations of Thermostable Peptides

(2010) Martin B. Ulmschneider et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Investigation of Single-Molecule Kinetics Mediated by Weak Hydrogen Bonds within a Biological Nanopore

(2010) Alina Asandei et al.   LANGMUIR

Rigorous Free Energy Calculations in Structure-Based Drug Design

(2010) Julien Michel  et al.   Molecular Informatics

Deciphering ionic current signatures of DNA transport through a nanopore

(2010) Aleksei Aksimentiev   Nanoscale

Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers

(2010) Sarah D. Cady et al.   NATURE

Structural mechanism of C-type inactivation in K+ channels

(2010) Luis G. Cuello et al.   NATURE

G protein-coupled receptors: novel targets for drug discovery in cancer

(2010) Rosamaria Lappano et al.   NATURE REVIEWS DRUG DISCOVERY

Channelopathies linked to plasma membrane phosphoinositides

(2010) Diomedes E. Logothetis et al.   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Lateral opening of a translocon upon entry of protein suggests the mechanism of insertion into membranes

(2010) P. F. Egea et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coexistence of two adamantane binding sites in the influenza A M2 ion channel

(2010) M. R. Rosenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The force network ensemble for granular packings

(2010) Brian P. Tighe et al.   Soft Matter

Jamming of frictional spheres and random loose packing

(2010) Leonardo E. Silbert   Soft Matter

Dynamics of SecY Translocons with Translocation-Defective Mutations

(2010) Ana-Nicoleta Bondar et al.   STRUCTURE

Impaired Processing of Human Pro-Islet Amyloid Polypeptide Is Not a Causative Factor for Fibril Formation or Membrane Damage in Vitro

(2009) Lucie Khemtémourian et al.   BIOCHEMISTRY

Binding Hot Spots and Amantadine Orientation in the Influenza A Virus M2 Proton Channel

(2009) Gwo-Yu Chuang et al.   BIOPHYSICAL JOURNAL

Membrane permeabilization by Islet Amyloid Polypeptide

(2009) Maarten F.M. Engel   CHEMISTRY AND PHYSICS OF LIPIDS

The Lateral Gate of SecYEG Opens during Protein Translocation

(2009) David J. F. du Plessis et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Soluble Protofibrils as Metastable Intermediates in Simulations of Amyloid Fibril Degradation Induced by Lipid Vesicles

(2009) Ran Friedman et al.   Journal of Physical Chemistry Letters

Initial Response of the Potassium Channel Voltage Sensor to a Transmembrane Potential

(2009) Werner Treptow et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Pore architecture and ion sites in acid-sensing ion channels and P2X receptors

(2009) Eric B. Gonzales et al.   NATURE

Mechanism of potassium-channel selectivity revealed by Na+ and Li+ binding sites within the KcsA pore

(2009) Ameer N Thompson et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Simulations of rigid bodies in an angle-axis framework

(2009) Dwaipayan Chakrabarti et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Critical Scaling and Aging in Cooling Systems Near the Jamming Transition

(2009) David A. Head   PHYSICAL REVIEW LETTERS

Jamming Transition as Probed by Quasistatic Shear Flow

(2009) Claus Heussinger et al.   PHYSICAL REVIEW LETTERS

Rhomboid Protease Dynamics and Lipid Interactions

(2009) Ana-Nicoleta Bondar et al.   STRUCTURE

PIP2 Is a Necessary Cofactor for Ion Channel Function: How and Why?

(2008) Byung-Chang Suh et al.   Annual Review of Biophysics

How Translocons Select Transmembrane Helices

(2008) Stephen H. White et al.   Annual Review of Biophysics

Growth of β2-microglobulin-related amyloid fibrils by non-esterified fatty acids at a neutral pH

(2008) Kazuhiro Hasegawa et al.   BIOCHEMICAL JOURNAL

Excursion of a single polypeptide into a protein pore: simple physics, but complicated biology

(2008) Mohammad M. Mohammad et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

Energy landscapes for diffusion: Analysis of cage-breaking processes

(2008) Vanessa K. de Souza et al.   JOURNAL OF CHEMICAL PHYSICS

Amyloid Aggregation on Lipid Bilayers and Its Impact on Membrane Permeability

(2008) Ran Friedman et al.   JOURNAL OF MOLECULAR BIOLOGY

Removal of phospho-head groups of membrane lipids immobilizes voltage sensors of K+ channels

(2008) Yanping Xu et al.   NATURE

Structural basis for the function and inhibition of an influenza virus proton channel

(2008) Amanda L. Stouffer et al.   NATURE

Structure of a complex of the ATPase SecA and the protein-translocation channel

(2008) Jochen Zimmer et al.   NATURE

Conformational transition of Sec machinery inferred from bacterial SecYE structures

(2008) Tomoya Tsukazaki et al.   NATURE

Embedded cholesterol in the nicotinic acetylcholine receptor

(2008) G. Brannigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Amantadine-induced conformational and dynamical changes of the influenza M2 transmembrane proton channel

(2008) S. D. Cady et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of the outer membrane protein OprF ofPseudomonas aeruginosain a lipopolysaccharide membrane by computer simulation

(2008) T.P. Straatsma et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

A Specific Cholesterol Binding Site Is Established by the 2.8 Å Structure of the Human β2-Adrenergic Receptor

(2008) Michael A. Hanson et al.   STRUCTURE

Protein Translocation Across the Bacterial Cytoplasmic Membrane

(2007) Arnold J.M. Driessen et al.   Annual Review of Biochemistry

Nanopore Analysis of a Small 86-Residue Protein

(2007) Radu Stefureac et al.   Small

Structure of the transmembrane region of the M2 protein H+ channel

(2002) Junfeng Wang et al.   PROTEIN SCIENCE