Refining the treatment of membrane proteins by coarse-grained models

Mechanisms of Integral Membrane Protein Insertion and Folding

(2015) Florian Cymer et al.   JOURNAL OF MOLECULAR BIOLOGY

Dissecting the role of the γ-subunit in the rotary–chemical coupling and torque generation of F1-ATPase

(2015) Shayantani Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Energetics of Membrane Protein Folding

(2014) Karen G. Fleming   Annual Review of Biophysics

Ion-Induced Defect Permeation of Lipid Membranes

(2014) Igor Vorobyov et al.   BIOPHYSICAL JOURNAL

Modeling gating charge and voltage changes in response to charge separation in membrane proteins

(2014) I. Kim 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

Coarse-grained simulations of the gating current in the voltage-activated Kv1.2 channel

(2014) Ilsoo Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Perspective on the Martini model

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

The Different Interactions of Lysine and Arginine Side Chains with Lipid Membranes

(2013) Libo Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulating the pulling of stalled elongated peptide from the ribosome by the translocon

(2013) A. Rychkova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Membrane protein thermodynamic stability may serve as the energy sink for sorting in the periplasm

(2013) C. Preston Moon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Measuring membrane protein stability under native conditions

(2013) Y.-C. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An effective Coarse-grained model for biological simulations: Recent refinements and validations

(2013) Spyridon Vicatos et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch

(2012) Armando J. de Jesus et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Determination of Membrane-Insertion Free Energies by Molecular Dynamics Simulations

(2012) James Gumbart et al.   BIOPHYSICAL JOURNAL

Exploring the nature of the translocon-assisted protein insertion

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

Realistic simulation of the activation of voltage-gated ion channels

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

Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase

(2012) S. Mukherjee 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

Coarse-Grained (Multiscale) Simulations in Studies of Biophysical and Chemical Systems

(2011) Shina C.L. Kamerlin et al.   Annual Review of Physical Chemistry

The role of membrane thickness in charged protein–lipid interactions

(2011) Libo B. Li et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Coarse grained model for exploring voltage dependent ion channels

(2011) Anatoly Dryga et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Outer membrane phospholipase A in phospholipid bilayers: A model system for concerted computational and experimental investigations of amino acid side chain partitioning into lipid bilayers

(2011) Patrick J. Fleming et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Coarse-grained models for protein aggregation

(2011) Chun Wu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

Electrostatic origin of the mechanochemical rotary mechanism and the catalytic dwell of F1-ATPase

(2011) S. Mukherjee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers

(2011) C. P. Moon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Free-energy cost for translocon-assisted insertion of membrane proteins

(2011) James Gumbart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular Simulation Approaches to Membrane Proteins

(2011) Phillip J. Stansfeld et al.   STRUCTURE

Coarse Grained Modeling and Approaches to Protein Folding

(2010) Carlo Guardiani et al.   Current Bioinformatics

A Look at Arginine in Membranes

(2010) Kalina Hristova et al.   JOURNAL OF MEMBRANE BIOLOGY

Arginine in Membranes: The Connection Between Molecular Dynamics Simulations and Translocon-Mediated Insertion Experiments

(2010) Eric V. Schow et al.   JOURNAL OF MEMBRANE BIOLOGY

Determining Peptide Partitioning Properties via Computer Simulation

(2010) Jakob P. Ulmschneider et al.   JOURNAL OF MEMBRANE BIOLOGY

On the energetics of translocon-assisted insertion of charged transmembrane helices into membranes

(2010) Anna Rychkova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

One-microsecond molecular dynamics simulation of channel gating in a nicotinic receptor homologue

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

Computational analysis of membrane proteins: the largest class of drug targets

(2009) Yalini Arinaminpathy et al.   DRUG DISCOVERY TODAY

Insights from Coarse-Grained Gō Models for Protein Folding and Dynamics

(2009) Ronald Hills et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The role of lipid composition for insertion and stabilization of amino acids in membranes

(2009) Anna C. V. Johansson et al.   JOURNAL OF CHEMICAL PHYSICS

Torque generation and elastic power transmission in the rotary FOF1-ATPase

(2009) Wolfgang Junge et al.   NATURE

Multiscale simulations of protein landscapes: Using coarse-grained models as reference potentials to full explicit models

(2009) Benjamin M. Messer et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Effective approach for calculations of absolute stability of proteins using focused dielectric constants

(2009) Spyridon Vicatos et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Lipids on the move: Simulations of membrane pores, domains, stalks and curves

(2008) Siewert J. Marrink et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Does Arginine Remain Protonated in the Lipid Membrane? Insights from Microscopic pKa Calculations

(2008) Jejoong Yoo et al.   BIOPHYSICAL JOURNAL

Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations

(2008) Justin L. MacCallum et al.   BIOPHYSICAL JOURNAL

The MARTINI Coarse-Grained Force Field: Extension to Proteins

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

A Continuum Method for Determining Membrane Protein Insertion Energies and the Problem of Charged Residues

(2008) Seungho Choe et al.   JOURNAL OF GENERAL PHYSIOLOGY

Peptide Folding Using Multiscale Coarse-Grained Models

(2008) Ian F. Thorpe et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane

(2008) Igor Vorobyov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Potential of Mean Force and pKaProfile Calculation for a Lipid Membrane-Exposed Arginine Side Chain

(2008) Libo Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Titratable Amino Acid Solvation in Lipid Membranes as a Function of Protonation State

(2008) Anna C. V. Johansson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modest stabilization by most hydrogen-bonded side-chain interactions in membrane proteins

(2008) Nathan HyunJoong Joh et al.   NATURE

Sensing voltage across lipid membranes

(2008) Kenton J. Swartz   NATURE