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

• DOI: 10.1021/acs.jctc.8b01066
• Publication Date: 2018-12-11T18:43:31Z
• Authors: Jumin Lee; Dhilon S. Patel; Jonas Ståhle; Sang-Jun Park; Nathan R. Kern; Seonghoon Kim; Joonseong Lee; Xi Cheng; Miguel A. Valvano; Otto Holst; Yuriy A. Knirel; Yifei Qi; Sunhwan Jo; Jeffery B. Klauda; Göran Widmalm; Wonpil Im
• Keywords: Lipopolysaccharides; 0301 basic medicine; 570; Glycosylphosphatidylinositols; Cell Membrane; CD59 Antigens; Molecular Dynamics Simulation; Campylobacter jejuni; User-Computer Interface; 03 medical and health sciences; Bacterial Proteins; Escherichia coli; Humans; Computer Simulation; Glycolipids

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