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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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Probing the structure of nanodiscs using surface-induced dissociation mass spectrometry
In the study of membrane proteins and antimicrobial peptides, nanodiscs have emerged as a valuable membrane mimetic to solubilze these molecules in a lipid bilayer. We present the structural characterization of nanodiscs using native mass spectrometry and surface-induced dissociation, which are powerful tools in structural biology.
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- Award ID(s):
- 1845230
- PAR ID:
- 10212783
- Date Published:
- Journal Name:
- Chemical Communications
- Volume:
- 56
- Issue:
- 100
- ISSN:
- 1359-7345
- Page Range / eLocation ID:
- 15651 to 15654
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D0CC05531J
