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

文献类型：期刊论文

作者Lee, Jumin1,2; Patel, Dhilon S.1,2; Stahle, Jonas3; Park, Sang-Jun1,2; Kern, Nathan R.1,2; Kim, Seonghoon1,2; Lee, Joonseong1,2; Cheng, Xi4; Valvano, Miguel A.5; Holst, Otto6
刊名JOURNAL OF CHEMICAL THEORY AND COMPUTATION
出版日期2019
卷号15期号:1页码:775-786
ISSN号1549-9618
DOI10.1021/acs.jctc.8b01066
通讯作者Im, Wonpil(wonpil@lehigh.edu)
英文摘要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.
WOS关键词MOLECULAR-DYNAMICS SIMULATIONS ; GUILLAIN-BARRE-SYNDROME ; HUMAN PERIPHERAL-NERVE ; ADDITIVE FORCE-FIELD ; ANTIGEN CHAIN-LENGTH ; OUTER-MEMBRANE ; REGULATORY PROTEIN ; LIPID-COMPOSITION ; GLYCAN READER ; O-ANTIGENS
资助项目NSF[MCB-1727508] ; NSF[DBI-1707207] ; NSF[DBI-1660380] ; NSF[IIA-1664696] ; NSF[MCB-1149187] ; NIH[U54 GM087519] ; NIH[R01 GM103695] ; XSEDE[MCB070009] ; Swedish Research Council[2013-4859] ; Swedish Research Council[2017-03703]
WOS研究方向Chemistry ; Physics
语种英语
出版者AMER CHEMICAL SOC
WOS记录号WOS:000455558200068
源URL[http://119.78.100.183/handle/2S10ELR8/290766]  
专题新药研究国家重点实验室
通讯作者Im, Wonpil
作者单位1.Lehigh Univ, Dept Biol Sci, Bethlehem, PA 18015 USA
2.Lehigh Univ, Dept Bioengn, Bethlehem, PA 18015 USA
3.Stockholm Univ, Dept Organ Chem, Arrhenius Lab, SE-10691 Stockholm, Sweden
4.Chinese Acad Sci, State Key Lab Drug Res, Shanghai Inst Mat Med, 555 Zuchongzhi Rd, Shanghai 201203, Peoples R China
5.Queens Univ Belfast, Wellcome Wolfson Inst Expt Med, Belfast BT9 7BL, Antrim, North Ireland
6.German Ctr Lung Res DZL, Div Struct Biochem, Res Ctr Borstel, Airway Res Ctr North, D-23845 Borstel, Germany
7.Russian Acad Sci, ND Zelinsky Inst Organ Chem, Moscow 119991, Russia
8.East China Normal Univ, Shanghai Engn Res Ctr Mol Therapeut & New Drug De, Sch Chem & Mol Engn, Shanghai 200062, Peoples R China
9.Argonne Natl Lab, Leadership Comp Facil, 9700 S Cass Ave, Argonne, IL 60439 USA
10.Univ Maryland, Dept Chem & Biomol Engn, College Pk, MD 20742 USA
推荐引用方式
GB/T 7714		 Lee, Jumin,Patel, Dhilon S.,Stahle, Jonas,et al. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans[J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION,2019,15(1):775-786.
APA Lee, Jumin.,Patel, Dhilon S..,Stahle, Jonas.,Park, Sang-Jun.,Kern, Nathan R..,...&Im, Wonpil.(2019).CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans.JOURNAL OF CHEMICAL THEORY AND COMPUTATION,15(1),775-786.
MLA Lee, Jumin,et al."CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans".JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15.1(2019):775-786.

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来源：上海药物研究所

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