The impact of physiologically relevant temperatures on physical properties of thylakoid membranes: a molecular dynamics study

Current Trends and Changes in Use of Membrane Molecular Dynamics Simulations within Academia and the Pharmaceutical Industry

(2023) Stephan L. Watkins   Membranes

Phase Transition and Phase Separation in Realistic Thylakoid Lipid Membrane of Marine Algae in All-Atom Simulations

(2023) Arun K. Rathod et al.   Journal of Chemical Information and Modeling

Biosynthesis and the Roles of Plant Sterols in Development and Stress Responses

(2022) Yinglin Du et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural and functional roles of non-bilayer lipid phases of chloroplast thylakoid membranes and mitochondrial inner membranes

(2022) Győző Garab et al.   PROGRESS IN LIPID RESEARCH

Assessing the Role of Lipids in the Molecular Mechanism of Membrane Proteins

(2021) Léni Jodaitis et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Mechanistic Understanding from Molecular Dynamics in Pharmaceutical Research 2: Lipid Membrane in Drug Design

(2021) Tomasz Róg et al.   Pharmaceuticals

The fluid-mosaic membrane theory in the context of photosynthetic membranes: Is the thylakoid membrane more like a mixed crystal or like a fluid?

(2020) Christian Wilhelm et al.   JOURNAL OF PLANT PHYSIOLOGY

Molecular Dynamics Simulations of Membrane Permeability

(2019) Richard M. Venable et al.   CHEMICAL REVIEWS

Lipid fingerprints and cofactor dynamics of light-harvesting complex II in different membranes

(2019) Sebastian Thallmair et al.   BIOPHYSICAL JOURNAL

Dynamics of Liposomes in the Fluid Phase

(2019) Sudipta Gupta et al.   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

Lipidomic studies of membrane glycerolipids in plant leaves under heat stress

(2019) Yasuhiro Higashi et al.   PROGRESS IN LIPID RESEARCH

Curvature increases permeability of the plasma membrane for ions, water and the anti-cancer drugs cisplatin and gemcitabine

(2019) Semen Yesylevskyy et al.   Scientific Reports

Fine tuning of the photosystem II major antenna mobility within the thylakoid membrane of higher plants

(2019) Vangelis Daskalakis et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

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

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

The role of nonbilayer phospholipids in mitochondrial structure and function

(2017) Writoban Basu Ball et al.   FEBS LETTERS

On the Calculation of Acyl Chain Order Parameters from Lipid Simulations

(2017) Thomas J. Piggot et al.   Journal of Chemical Theory and Computation

Lipid remodelling: Unravelling the response to cold stress in Arabidopsis and its extremophile relative Eutrema salsugineum

(2017) Cristina Barrero-Sicilia et al.   PLANT SCIENCE

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

(2017) Floris J. Van Eerden et al.   Nature Communications

Molecular dynamics simulations of membrane proteins and their interactions: from nanoscale to mesoscale

(2016) Matthieu Chavent et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane

(2016) Floris J. van Eerden et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Role of membrane glycerolipids in photosynthesis, thylakoid biogenesis and chloroplast development

(2016) Koichi Kobayashi   JOURNAL OF PLANT RESEARCH

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

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

MEMBPLUGIN: studying membrane complexity in VMD

(2014) Ramon Guixà-González et al.   BIOINFORMATICS

CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations

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

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

(2013) Sander Pronk et al.   BIOINFORMATICS

Characterizing the binding of annexin V to a lipid bilayer using molecular dynamics simulations

(2013) Zhuxi Chen et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Improved Parameters for the Martini Coarse-Grained Protein Force Field

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

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

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

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

(2009) Sunhwan Jo et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

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

Response of isolated thylakoid membranes with altered fluidity to short term heat stress

(2009) Maya Velitchkova et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

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

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