Computational ‘microscopy’ of cellular membranes

Molecular dynamics simulations of large macromolecular complexes

(2015) Juan R Perilla et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Adaptive Lipid Packing and Bioactivity in Membrane Domains

(2015) Erdinc Sezgin et al.   PLoS One

A Highly Tilted Membrane Configuration for the Prefusion State of Synaptobrevin

(2014) Andrew E. Blanchard et al.   BIOPHYSICAL JOURNAL

E. coli Outer Membrane and Interactions with OmpLA

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

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

(2014) Emilia L. Wu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

α-Synuclein-Induced Membrane Remodeling Is Driven by Binding Affinity, Partition Depth, and Interleaflet Order Asymmetry

(2014) Anthony R. Braun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Lipid Organization of the Plasma Membrane

(2014) Helgi I. Ingólfsson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Lipid landscapes and pipelines in membrane homeostasis

(2014) Joost C.M. Holthuis et al.   NATURE

Lipid Membranes as Solvents for Carbon Nanoparticles

(2014) Jonathan Barnoud et al.   PHYSICAL REVIEW LETTERS

Expansion of the fusion stalk and its implication for biological membrane fusion

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

Sodium recognition by the Na+/Ca2+exchanger in the outward-facing conformation

(2014) Fabrizio Marinelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polyunsaturated phospholipids facilitate membrane deformation and fission by endocytic proteins

(2014) M. Pinot et al.   SCIENCE

Ion permeation in K+ channels occurs by direct Coulomb knock-on

(2014) D. A. Kopfer et al.   SCIENCE

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

Atomistic simulations indicate cardiolipin to have an integral role in the structure of the cytochrome bc1 complex

(2013) Sanja Pöyry et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

(2013) Sander Pronk et al.   BIOINFORMATICS

Understanding the Role of Amphipathic Helices in N-BAR Domain Driven Membrane Remodeling

(2013) Haosheng Cui et al.   BIOPHYSICAL JOURNAL

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Cardiolipin-dependent formation of mitochondrial respiratory supercomplexes

(2013) Eugenia Mileykovskaya et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

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

Recovery from slow inactivation in K+ channels is controlled by water molecules

(2013) Jared Ostmeyer et al.   NATURE

Linear aggregation of proteins on the membrane as a prelude to membrane remodeling

(2013) M. Simunovic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiscale Simulations Reveal Conserved Patterns of Lipid Interactions with Aquaporins

(2013) Phillip J. Stansfeld et al.   STRUCTURE

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

(2013) C. Arnarez et al.   Scientific Reports

Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes

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

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models

(2013) Per Larsson et al.   PLoS Computational Biology

Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics Simulations

(2013) Hang Yu et al.   PLoS Computational Biology

Modeling and Simulation of Ion Channels

(2012) Christopher Maffeo et al.   CHEMICAL REVIEWS

To milliseconds and beyond: challenges in the simulation of protein folding

(2012) Thomas J Lane et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors

(2012) Djurre H. de Jong et al.   FARADAY DISCUSSIONS

Arrangement of the Respiratory Chain Complexes inSaccharomyces cerevisiaeSupercomplex III2IV2Revealed by Single Particle Cryo-Electron Microscopy

(2012) Eugenia Mileykovskaya et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Cardiolipin-dependent Reconstitution of Respiratory Supercomplexes from PurifiedSaccharomyces cerevisiaeComplexes III and IV

(2012) Soledad Bazán et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains

(2012) Wei Han et al.   Journal of Chemical Theory and Computation

Predictions for Cholesterol Interaction Sites on the A2A Adenosine Receptor

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

Structural Determinants of the Supramolecular Organization of G Protein-Coupled Receptors in Bilayers

(2012) Xavier Periole et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Flexibility of a Eukaryotic Lipidome – Insights from Yeast Lipidomics

(2012) Christian Klose et al.   PLoS One

Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae

(2012) K. M. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular driving forces defining lipid positions around aquaporin-0

(2012) C. Aponte-Santamaria et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organization, dynamics, and segregation of Ras nanoclusters in membrane domains

(2012) L. Janosi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the Relative Stability of Dimer Interfaces in G Protein-Coupled Receptors

(2012) Jennifer M. Johnston et al.   PLoS Computational Biology

Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles

(2012) Benjamin A. Hall et al.   PLoS Computational Biology

Arrangement of electron transport chain components in bovine mitochondrial supercomplex I1III2IV1

(2011) Thorsten Althoff et al.   EMBO JOURNAL

Definition and testing of the GROMOS force-field versions 54A7 and 54B7

(2011) Nathan Schmid et al.   EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS

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

An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0

(2011) Alpeshkumar K. Malde et al.   Journal of Chemical Theory and Computation

Membrane protein sequestering by ionic protein–lipid interactions

(2011) Geert van den Bogaart et al.   NATURE

Pathway and mechanism of drug binding to G-protein-coupled receptors

(2011) Ron O. Dror et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Membrane lipidome of an epithelial cell line

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

Interaction of complexes I, III, and IV within the bovine respirasome by single particle cryoelectron tomography

(2011) N. V. Dudkina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes

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

Concerted Interconversion between Ionic Lock Substates of the β2 Adrenergic Receptor Revealed by Microsecond Timescale Molecular Dynamics

(2010) Tod D. Romo et al.   BIOPHYSICAL JOURNAL

Reconstruction of atomistic details from coarse-grained structures

(2010) Andrzej J. Rzepiela et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Zwitterionic Lipid Assemblies: Molecular Dynamics Studies of Monolayers, Bilayers, and Vesicles Using a New Coarse Grain Force Field

(2010) Wataru Shinoda et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Dual-resolution molecular dynamics simulation of antimicrobials in biomembranes

(2010) M. Orsi et al.   Journal of the Royal Society Interface

Cholesterol Induces Specific Spatial and Orientational Order in Cholesterol/Phospholipid Membranes

(2010) Hector Martinez-Seara et al.   PLoS One

Role of phospholipids in respiratory cytochrome bc1 complex catalysis and supercomplex formation

(2009) Tina Wenz et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

New Insights into BAR Domain-Induced Membrane Remodeling

(2009) Gary S. Ayton et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Order of lipid phases in model and plasma membranes

(2009) H.-J. Kaiser et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Discovery Through the Computational Microscope

(2009) Eric H. Lee et al.   STRUCTURE

Respiratory Active Mitochondrial Supercomplexes

(2008) Rebeca Acín-Pérez et al.   MOLECULAR CELL

Membrane lipids: where they are and how they behave

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

Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution

(2007) Matej Praprotnik et al.   Annual Review of Physical Chemistry