CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans
CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans
复制标题
DOI：
10.1021/acs.jctc.8b01066
复制
发表时间：
2019-01-01
影响因子：
5.5
通讯作者：
Im, Wonpil
中科院分区：
文献类型：
--
作者：
Lee, Jumin;Patel, Dhilon S.;Im, Wonpil
糖脂（如糖甘油脂、鞘糖脂和糖基磷脂酰肌醇）和脂聚糖（如脂多糖（LPS）、脂寡糖（LOS）、分枝杆菌脂阿拉伯甘露聚糖和支原体脂聚糖）通常存在于细胞膜表面上，并在各种细胞功能中起关键作用。在分子水平上表征它们的结构和动力学对于理解它们的生物学作用是必不可少的，但是糖脂和脂聚糖结构的系统产生是具有挑战性的，因为脂质结构和聚糖序列的巨大变化（即，碳水化合物类型及其连接）。为了促进全原子糖脂/LPS/LOS结构的生成，我们在CHARMM-GUI（http：//www.example.com）中开发了糖脂建模器和LPS建模器，CHARMM-GUI是一种基于网络的界面，其简化了复杂生物模拟系统的构建。www.charmm-gui.org此外，我们还将这些模块集成到Membrane Builder中，以便用户可以轻松构建具有各种糖脂和LPS/LOS的复杂对称或不对称生物膜系统。这些工具预计将是有用的创新和新颖的糖脂/LPS/LOS建模和模拟研究，简化繁琐和复杂的步骤，在复杂的生物系统建模，并应提供深入了解复杂的糖脂/LPS/LOS的生物膜系统的结构，动力学和潜在的机制。
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.