Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes

Native-like membrane models of E. coli polar lipid extract shed light on the importance of lipid composition complexity

(2021) Kristyna Pluhackova et al.   BMC BIOLOGY

CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides

(2021) Ya Gao et al.   Journal of Chemical Information and Modeling

Influences of Vibrio cholerae Lipid A Types on LPS Bilayer Properties

(2021) Emanuel Luna et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Location and Conformational Ensemble of Menaquinone and Menaquinol, and Protein–Lipid Modulations in Archaeal Membranes

(2021) Shasha Feng et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Impact of Increased Membrane Realism on Conformational Sampling of Proteins

(2021) Austin T. Weigle et al.   Journal of Chemical Theory and Computation

Developing initial conditions for simulations of asymmetric membranes: a practical recommendation

(2021) Soohyung Park et al.   BIOPHYSICAL JOURNAL

Molecular Simulations of Gram-Negative Bacterial Membranes Come of Age

(2020) Wonpil Im et al.   Annual Review of Physical Chemistry

Capturing biologically complex tissue-specific membranes at different levels of compositional complexity

(2020) Helgi I Ingólfsson et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Emerging Diversity in Lipid–Protein Interactions

(2019) Valentina Corradi et al.   CHEMICAL REVIEWS

Membrane Lipid Composition: Effect on Membrane and Organelle Structure, Function and Compartmentalization and Therapeutic Avenues

(2019) Doralicia Casares et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Role of Cardiolipin in Mitochondrial Function and Dynamics in Health and Disease: Molecular and Pharmacological Aspects

(2019) Giuseppe Paradies et al.   Cells

Phospholipid subcellular localization and dynamics

(2018) Yanbo Yang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Understanding the diversity of membrane lipid composition

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

Perspective: Computational modeling of accurate cellular membranes with molecular resolution

(2018) Jeffery B. Klauda   JOURNAL OF CHEMICAL PHYSICS

CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans

(2018) Jumin Lee et al.   Journal of Chemical Theory and Computation

Mass Spectrometric Approaches for the Analysis of Phytosterols in Biological Samples

(2017) George Gachumi et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Simulations of simple linoleic acid-containing lipid membranes and models for the soybean plasma membranes

(2017) Xiaohong Zhuang et al.   JOURNAL OF CHEMICAL PHYSICS

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

An extensive simulation study of lipid bilayer properties with different head groups, acyl chain lengths, and chain saturations

(2016) Xiaohong Zhuang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Important roles for membrane lipids in haloarchaeal bioenergetics

(2016) Matthias Y. Kellermann et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Bilayer Properties of Lipid A from Various Gram-Negative Bacteria

(2016) Seonghoon Kim et al.   BIOPHYSICAL JOURNAL

Membrane curvature in cell biology: An integration of molecular mechanisms

(2016) Iris K. Jarsch et al.   JOURNAL OF CELL BIOLOGY

CHARMM-GUI 10 years for biomolecular modeling and simulation

(2016) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Influence of Cholesterol on Phospholipid Bilayer Structure and Dynamics

(2016) Christopher T. Boughter et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Lipid composition in a strain of Bacillus subtilis, a producer of iturin A lipopeptides that are active against uropathogenic bacteria

(2016) Przemysław Bernat et al.   WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY

Structure, Dynamics, and Phase Behavior of DOPC/DSPC Mixture Membrane Systems: Molecular Dynamics Simulation Studies

(2016) Seonghan Kim et al.   BULLETIN OF THE KOREAN CHEMICAL SOCIETY

Modeling Yeast Organelle Membranes and How Lipid Diversity Influences Bilayer Properties

(2015) Viviana Monje-Galvan et al.   BIOCHEMISTRY

Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations

(2015) Floris J. van Eerden et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Probing the importance of lipid diversity in cell membranes via molecular simulation

(2015) Pouyan Khakbaz et al.   CHEMISTRY AND PHYSICS OF LIPIDS

Lipid-protein interplay and lateral organization in biomembranes

(2015) Thomas K.M. Nyholm   CHEMISTRY AND PHYSICS OF LIPIDS

Mechanical properties of lipid bilayers from molecular dynamics simulation

(2015) Richard M. Venable et al.   CHEMISTRY AND PHYSICS OF LIPIDS

How Tolerant are Membrane Simulations with Mismatch in Area per Lipid between Leaflets?

(2015) Soohyung Park et al.   Journal of Chemical Theory and Computation

Long-Time-Step Molecular Dynamics through Hydrogen Mass Repartitioning

(2015) Chad W. Hopkins et al.   Journal of Chemical Theory and Computation

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

(2015) Jumin Lee et al.   Journal of Chemical Theory and Computation

E. coli Outer Membrane and Interactions with OmpLA

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

Geometrical Membrane Curvature as an Allosteric Regulator of Membrane Protein Structure and Function

(2014) Asger Tonnesen et al.   BIOPHYSICAL JOURNAL

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

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

Preferred Orientations of Phosphoinositides in Bilayers and Their Implications in Protein Recognition Mechanisms

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

Lipid Organization of the Plasma Membrane

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

Structural adaptations of proteins to different biological membranes

(2013) Irina D. Pogozheva et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Local Partition Coefficients Govern Solute Permeability of Cholesterol-Containing Membranes

(2013) Florian Zocher 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

Lipids of mitochondria

(2013) Susanne E. Horvath et al.   PROGRESS IN LIPID RESEARCH

Membrane models of E. coli containing cyclic moieties in the aliphatic lipid chain

(2012) Kunal R. Pandit et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Thermal Adaptation of the Archaeal and Bacterial Lipid Membranes

(2012) Yosuke Koga   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

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

Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study

(2010) Joseph B. Lim et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Cholesterol, the central lipid of mammalian cells

(2010) Frederick R Maxfield et al.   CURRENT OPINION IN CELL BIOLOGY

Biological Function of the Cellular Lipid BMP—BMP as a Key Activator for Cholesterol Sorting and Membrane Digestion

(2010) Hichem D. Gallala et al.   NEUROCHEMICAL RESEARCH

Phylogenetic Distribution of Fungal Sterols

(2010) John D. Weete et al.   PLoS One

Mechanisms of Lipid Transport Involved in Organelle Biogenesis in Plant Cells

(2009) Christoph Benning   Annual Review of Cell and Developmental Biology

CHARMM-GUI Membrane Builder for Mixed Bilayers and Its Application to Yeast Membranes

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

Menaquinone as pool quinone in a purple bacterium

(2009) B. Schoepp-Cothenet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrophobic thickness, lipid surface area and polar region hydration in monounsaturated diacylphosphatidylcholine bilayers: SANS study of effects of cholesterol and β-sitosterol in unilamellar vesicles

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

Lipid Bilayer Structure Determined by the Simultaneous Analysis of Neutron and X-Ray Scattering Data

(2008) Norbert Kučerka et al.   BIOPHYSICAL JOURNAL

Elasticity, Strength, and Water Permeability of Bilayers that Contain Raft Microdomain-Forming Lipids

(2008) W. Rawicz et al.   BIOPHYSICAL JOURNAL

CHARMM-GUI: A web-based graphical user interface for CHARMM

(2008) Sunhwan Jo et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Membrane lipids: where they are and how they behave

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