Excessive aggregation of membrane proteins in the Martini model

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

G Protein–Coupled Receptor Heteromers

(2016) Ivone Gomes et al.   Annual Review of Pharmacology and Toxicology

Alternative packing of EGFR transmembrane domain suggests that protein–lipid interactions underlie signal conduction across membrane

(2016) Eduard V. Bocharov et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Efficient preparation and analysis of membrane and membrane protein systems

(2016) Matti Javanainen et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Interplay of G Protein-Coupled Receptors with the Membrane: Insights from Supra-Atomic Coarse Grain Molecular Dynamics Simulations

(2016) Xavier Periole   CHEMICAL REVIEWS

Martini straight: Boosting performance using a shorter cutoff and GPUs

(2016) Djurre H. de Jong et al.   COMPUTER PHYSICS COMMUNICATIONS

Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association

(2016) Jan Domański et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Changes in the Epidermal Growth Factor Receptor: Role of the Transmembrane Domain Investigated by Coarse-Grained MetaDynamics Free Energy Calculations

(2016) Mickaël Lelimousin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes

(2016) C. Arnarez et al.   Chemical Science

Membrane omega-3 fatty acids modulate the oligomerisation kinetics of adenosine A2A and dopamine D2 receptors

(2016) Ramon Guixà-González et al.   Scientific Reports

De novo design of transmembrane helix–helix interactions and measurement of stability in a biological membrane

(2015) Anthony Nash et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

High-Throughput Simulations of Dimer and Trimer Assembly of Membrane Proteins. The DAFT Approach

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field

(2015) Yifei Qi et al.   Journal of Chemical Theory and Computation

Organization and Dynamics of Receptor Proteins in a Plasma Membrane

(2015) Heidi Koldsø et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Supramolecular assemblies underpin turnover of outer membrane proteins in bacteria

(2015) Patrice Rassam et al.   NATURE

Nothing to Sneeze At: A Dynamic and Integrative Computational Model of an Influenza A Virion

(2015) Tyler Reddy et al.   STRUCTURE

MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes

(2015) Phillip J. Stansfeld et al.   STRUCTURE

Preferred Supramolecular Organization and Dimer Interfaces of Opioid Receptors from Simulated Self-Association

(2015) Davide Provasi et al.   PLoS Computational Biology

Dimerization of the EphA1 Receptor Tyrosine Kinase Transmembrane Domain: Insights into the Mechanism of Receptor Activation

(2014) Matthieu Chavent et al.   BIOCHEMISTRY

Cholesterol Modulates the Dimer Interface of the β2-Adrenergic Receptor via Cholesterol Occupancy Sites

(2014) Xavier Prasanna et al.   BIOPHYSICAL JOURNAL

Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems

(2014) Matthieu Chavent et al.   FARADAY DISCUSSIONS

Potential of mean force analysis of the self-association of leucine-rich transmembrane α-helices: Difference between atomistic and coarse-grained simulations

(2014) Manami Nishizawa et al.   JOURNAL OF CHEMICAL PHYSICS

Differential Stability of the Crystallographic Interfaces of Mu- and Kappa-Opioid Receptors

(2014) Jennifer M. Johnston et al.   PLoS One

The Free Energy Landscape of Dimerization of a Membrane Protein, NanC

(2014) Thomas A. Dunton et al.   PLoS Computational Biology

Glycophorin A transmembrane domain dimerization in plasma membrane vesicles derived from CHO, HEK 293T, and A431 cells

(2013) Sarvenaz Sarabipour et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Free energy of WALP23 dimer association in DMPC, DPPC, and DOPC bilayers

(2013) Norberto Castillo et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Multiscale modelling to understand the self-assembly mechanism of human β2-adrenergic receptor in lipid bilayer

(2013) Anirban Ghosh et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Toward Optimized Potential Functions for Protein–Protein Interactions in Aqueous Solutions: Osmotic Second Virial Coefficient Calculations Using the MARTINI Coarse-Grained Force Field

(2013) Austin C. Stark et al.   Journal of Chemical Theory and Computation

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

Membrane Driven Spatial Organization of GPCRs

(2013) Sayan Mondal et al.   Scientific Reports

Reduced Lateral Mobility of Lipids and Proteins in Crowded Membranes

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

Anomalous and normal diffusion of proteins and lipids in crowded lipid membranes

(2012) Matti Javanainen et al.   FARADAY DISCUSSIONS

Improved Parameters for the Martini Coarse-Grained Protein Force Field

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

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

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

Characterization of the motion of membrane proteins using high-speed atomic force microscopy

(2012) Ignacio Casuso et al.   Nature Nanotechnology

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

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

Making Structural Sense of Dimerization Interfaces of Delta Opioid Receptor Homodimers

(2011) Jennifer M. Johnston et al.   BIOCHEMISTRY

Transmembrane helix–helix interactions are modulated by the sequence context and by lipid bilayer properties

(2011) Florian Cymer et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Aggregation of Model Membrane Proteins, Modulated by Hydrophobic Mismatch, Membrane Curvature, and Protein Class

(2011) Daniel L. Parton et al.   BIOPHYSICAL JOURNAL

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

Lessons from Free Energy Simulations of δ-Opioid Receptor Homodimers Involving the Fourth Transmembrane Helix

(2010) Davide Provasi et al.   BIOCHEMISTRY

Self-Association of Models of Transmembrane Domains of ErbB Receptors in a Lipid Bilayer

(2010) Anupam Prakash et al.   BIOPHYSICAL JOURNAL

Lipid-Modulated Sequence-Specific Association of Glycophorin A in Membranes

(2010) Lorant Janosi et al.   BIOPHYSICAL JOURNAL

g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation Estimates

(2010) Jochen S. Hub et al.   Journal of Chemical Theory and Computation

Measuring the Energetics of Membrane Protein Dimerization in Mammalian Membranes

(2010) Lirong Chen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The structural basis for intramembrane assembly of an activating immunoreceptor complex

(2010) Matthew E Call et al.   NATURE IMMUNOLOGY

Lipid-mediated interactions tune the association of glycophorin A helix and its disruptive mutants in membranes

(2010) Durba Sengupta et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Method to measure strong protein-protein interactions in lipid bilayers using a steric trap

(2010) H. Hong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

Structural Basis for Dimerization of the BNIP3 Transmembrane Domain,

(2009) Endah S. Sulistijo et al.   BIOCHEMISTRY

Energetics of ErbB1 Transmembrane Domain Dimerization in Lipid Bilayers

(2009) Lirong Chen et al.   BIOPHYSICAL JOURNAL

The structure of the integrin αIIbβ3 transmembrane complex explains integrin transmembrane signalling

(2009) Tong-Lay Lau et al.   EMBO JOURNAL

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

Transmembrane domain of EphA1 receptor forms dimers in membrane-like environment

(2008) Elena O. Artemenko et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Spatial Structure and pH-dependent Conformational Diversity of Dimeric Transmembrane Domain of the Receptor Tyrosine Kinase EphA1

(2008) Eduard V. Bocharov et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The MARTINI Coarse-Grained Force Field: Extension to Proteins

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