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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‐GUIMembrane Builderto simulate and analyze LDs with and without a plant LD protein, oleosin. The results show thatMembrane Buildercan 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 thatMembrane Buildercan aid in the future study of LD systems, including their structure and dynamics with and without proteins.
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CHARMM‐GUI Nanodisc Builder for modeling and simulation of various nanodisc systems
Nanodiscs are discoidal protein–lipid complexes that have wide applications in membrane protein studies. Modeling and simulation of nanodiscs are challenging due to the absence of structures of many membrane scaffold proteins (MSPs) that wrap around the membrane bilayer. We have developed CHARMM‐GUINanodisc Builder(http://www.charmm-gui.org/input/nanodisc) to facilitate the setup of nanodisc simulation systems by modeling the MSPs with defined size and known structural features. A total of 11 different nanodiscs with a diameter from 80 to 180 Å are made available in both the all‐atom CHARMM and two coarse‐grained (PACE and Martini) force fields. The usage of theNanodisc Builderis demonstrated with various simulation systems. The structures and dynamics of proteins and lipids in these systems were analyzed, showing similar behaviors to those from previous all‐atom and coarse‐grained nanodisc simulations. We expect theNanodisc Builderto be a convenient and reliable tool for modeling and simulation of nanodisc systems. © 2019 Wiley Periodicals, Inc.
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- PAR ID:
- 10462911
- Publisher / Repository:
- Wiley Blackwell (John Wiley & Sons)
- Date Published:
- Journal Name:
- Journal of Computational Chemistry
- Volume:
- 40
- Issue:
- 7
- ISSN:
- 0192-8651
- Page Range / eLocation ID:
- p. 893-899
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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