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

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 webbased 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.

Annexin A4 trimers are recruited by high membrane curvatures in Giant Plasma Membrane Vesicles

“…30 The membrane is composed of 680 lipid molecules, 20% POPS and 80% POPC, constructed using CHARMM-GUI. 25 The structure was immersed in a periodic box of TIP3P atomistic water 31 with 70k water molecules and 1.5 mM salt (405 K + , 287 Cl − ) corresponding to the physiological condition. 18 Ca +2…”

K-PAM: A unified platform to distinguishKlebsiellaspecies K- and O-antigen types, model antigen structures and identify hypervirulent strains

“…LPS models that correspond to O-antigens, namely, O1, O2, O2aeh, O3, O4, O5, O7, O8 and O12 (modeled using CHARMM-GUI [59]) that has been deposited in the repository can be accessed through O-antigen menu bar. The LPS structures can either be visualized in the Jsmol applet or be downloaded.…”

CHARMM‐GUI DEER facilitator for spin‐pair distance distribution calculations and preparation of restrained‐ensemble molecular dynamics simulations

“…[4,5] The reMD method uses a global ensemble-based energy restraint to force the spin-spin distance distribution histograms calculated from a multiple-copy MD simulation to match those obtained from EPR/DEER experiments. For the available spin labels in DEER Facilitator, their best conformations are searched and linked to a particular site of a protein system through PDB Reader & Manipulator [32] and can be also used in various CHARMM-GUI modules such as Solution Builder, [33,34] Membrane Builder, [35][36][37][38] Nanodisc Builder, [39] HMMM Builder, [40] Monolayer Builder, and Micelle Builder. [4] The reMD simulation method is implemented in NAMD [19] and CHARMM [20] program packages.…”