ArticleChemPlusChem2024
CHARMM-GUI Membrane Builder for Lipid Droplet Modeling and Simulation.
Article in ChemPlusChem, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Article
- Tutorial for Atomistic and Coarse-Grained Simulations of Membrane-Nanoplastic Interactions Using GROMACS.The journal of physical chemistry. B · 2026Article
- A conserved vesicular circuit enables metabolic adaptation and maintains systemic heme homeostasis.bioRxiv : the preprint server for biology · 2026Article
- Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution across Different Lipid Environments.Biomacromolecules · 2026Article
- Omega-3 DHA as a blank canvas: A molecular approximation to how lipid mediators modulate LGR6 in inflammation resolution.Protein science : a publication of the Protein Society · 2026Article
- Mixed-Solvent MD suite: modular tools for building and analyzing mixed-solvent molecular dynamics systems.Journal of computer-aided molecular design · 2026Article
- Article
- Coarse-Grained Simulations of Mycobacterial Outer Membranes Reveal Fluidity-Dependent PDIM Redistribution Across Different Lipid Environments.bioRxiv : the preprint server for biology · 2026Article
- Membrane Remodeling Activity of Dengue Virus NS4A and NS1 Proteins: A Computational Perspective.The Journal of membrane biology · 2026Article
- Multiscale Computational Dissection of CCRL2-Mediated Chemerin Presentation.Journal of chemical information and modeling · 2025Article
- Molecular dynamics of the pathogenic KCNQ2 variant G256W reveal mechanisms of channel dysfunction in epileptic encephalopathy.bioRxiv : the preprint server for biology · 2025Article
- CHARMM-GUIJournal of chemical information and modeling · 2025Article
- DHRS7 Integrates NADPbioRxiv : the preprint server for biology · 2025Article
- Virtual screening and molecular dynamics of anti-Alzheimer compounds fromFrontiers in chemistry · 2025Article
- Physicochemical Properties of Seed Oil Blends and Their Potential for the Creation of Synthetic Oleosomes with Modulated Polarities.ACS omega · 2024Article
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4 authors.
Funding
Abstract
Lipid droplets (LDs) are organelles that are necessary for eukaryotic and prokaryotic metabolism and energy storage. They have a unique structure consisting of a spherical phospholipid monolayer encasing neutral lipids such as triacylglycerol (TAG). LDs have garnered increased interest for their implications in disease and for drug delivery applications. Consequently, there is an increased need for tools to study their structure, composition, and dynamics in biological contexts. In this work, we utilize CHARMM-GUI Membrane Builder to simulate and analyze LDs with and without a plant LD protein, oleosin. The results show that Membrane Builder can generate biologically relevant all-atom LD systems with relatively short equilibration times using a new TAG library having optimized headgroup parameters. TAG molecules originally inserted into a lipid bilayer aggregate in the membrane center, forming a TAG-only core flanked by two monolayers. The TAG-only core thickness stably grows with increasing TAG mole fraction. A 70 % TAG system has a core that is thick enough to house oleosin without its interactions with the distal leaflet or disruption of its secondary structure. We hope that Membrane Builder can aid in the future study of LD systems, including their structure and dynamics with and without proteins.
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