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

Journal Article · Tue Jan 01 00:00:00 EST 2019 · Journal of Chemical Theory and Computation

DOI:https://doi.org/10.1021/acs.jctc.8b01066· OSTI ID:1570434

Lee, Jumin; Patel, Dhilon S; Stahle, Jonas; Park, Sang-Jun; Kern, Nathan R; Kim, Seonghoon; Lee, Joonseong; Cheng, Xi; Valvano, Miguel A; Holst, Otto; Knirel, Yuriy A; Qi, Yifei; Jo, Sunhwan; Klauda, Jeffrey B; Widmalm, Goran; Im, Wonpil

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.

• Research Organization: Argonne National Lab. (ANL), Argonne, IL (United States)
• Sponsoring Organization: National Science Foundation (NSF); National Institutes of Health (NIH); Swedish Research Council (SRC)
• DOE Contract Number: AC02-06CH11357
• OSTI ID: 1570434
• Journal Information: Journal of Chemical Theory and Computation, Vol. 15, Issue 1
• Country of Publication: United States
• Language: English