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J Chem Theory Comput. 2019 Jan 8;15(1):775-786. doi: 10.1021/acs.jctc.8b01066. Epub 2018 Dec 28.

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

Author information

1
Departments of Biological Sciences and Bioengineering , Lehigh University , Bethlehem , Pennsylvania 18015 , United States.
2
Department of Organic Chemistry, Arrhenius Laboratory , Stockholm University , SE-106 91 Stockholm , Sweden.
3
State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China.
4
Wellcome-Wolfson Institute for Experimental Medicine , Queen's University Belfast BT9 7BL , United Kingdom.
5
Division of Structural Biochemistry, Research Center Borstel , Airway Research Center North, Member of the German Center for Lung Research (DZL) , D-23845 Borstel , Germany.
6
N. D. Zelinsky Institute of Organic Chemistry , Russian Academy of Sciences , 119991 Moscow , Russia.
7
Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering , East China Normal University , Shanghai 200062 , China.
8
Leadership Computing Facility , Argonne National Laboratory , Argonne , Illinois 60439 , United States.
9
Department of Chemical and Biomolecular Engineering and the Biophysics Graduate Program , University of Maryland , College Park , Maryland 20742 , United States.

Abstract

Glycolipids (such as glycoglycerolipids, glycosphingolipids, and glycosylphosphatidylinositol) and lipoglycans (such as lipopolysaccharides (LPS), lipooligosaccharides (LOS), mycobacterial lipoarabinomannan, and mycoplasma lipoglycans) are typically found on the surface of cell membranes and play crucial roles in various cellular functions. Characterizing their structure and dynamics at the molecular level is essential to understand their biological roles, but systematic generation of glycolipid and lipoglycan structures is challenging because of great variations in lipid structures and glycan sequences (i.e., carbohydrate types and their linkages). To facilitate the generation of all-atom glycolipid/LPS/LOS structures, we have developed Glycolipid Modeler and LPS Modeler in CHARMM-GUI ( http://www.charmm-gui.org ), a web-based interface that simplifies building of complex biological simulation systems. In addition, we have incorporated these modules into Membrane Builder so that users can readily build a complex symmetric or asymmetric biological membrane system with various glycolipids and LPS/LOS. These tools are expected to be useful in innovative and novel glycolipid/LPS/LOS modeling and simulation research by easing tedious and intricate steps in modeling complex biological systems and shall provide insight into structures, dynamics, and underlying mechanisms of complex glycolipid-/LPS-/LOS-containing biological membrane systems.

PMID:
30525595
DOI:
10.1021/acs.jctc.8b01066
[Indexed for MEDLINE]

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