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Title: 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 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.

Authors:
; ; ; ; ; ; ; ; ; ; ; ; ; ; ;
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Science Foundation (NSF); National Institutes of Health (NIH); Swedish Research Council (SRC)
OSTI Identifier:
1570434
DOE Contract Number:  
AC02-06CH11357
Resource Type:
Journal Article
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 15; Journal Issue: 1
Country of Publication:
United States
Language:
English

Citation Formats

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, and Im, Wonpil. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. United States: N. p., 2019. Web. doi:10.1021/acs.jctc.8b01066.
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. CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans. United States. doi:10.1021/acs.jctc.8b01066.
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, and Im, Wonpil. Tue . "CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans". United States. doi:10.1021/acs.jctc.8b01066.
@article{osti_1570434,
title = {CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans},
author = {Lee, Jumin and Patel, Dhilon S and Stahle, Jonas and Park, Sang-Jun and Kern, Nathan R and Kim, Seonghoon and Lee, Joonseong and Cheng, Xi and Valvano, Miguel A and Holst, Otto and Knirel, Yuriy A and Qi, Yifei and Jo, Sunhwan and Klauda, Jeffrey B and Widmalm, Goran and Im, Wonpil},
abstractNote = {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.},
doi = {10.1021/acs.jctc.8b01066},
journal = {Journal of Chemical Theory and Computation},
number = 1,
volume = 15,
place = {United States},
year = {2019},
month = {1}
}