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Title: 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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Award ID(s):
1660380 1810695
NSF-PAR ID:
10462911
Author(s) / Creator(s):
 ;  ;  ;  
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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