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1. (Article ID: 4849)
Jo S, Wu EL, Stuhlsatz D, Klauda JB, MacKerell AD, Widmalm G, Im W
Lipopolysaccharide membrane building and simulation
Methods in Molecular Biology 1273 (2015)
391-406
While membrane simulations are widely employed to study the structure and dynamics of various lipid bilayers and membrane proteins in the bilayers, simulations of lipopolysaccharides (LPS) in membrane environments have been limited due to their structural complexity, difficulties in building LPS-membrane systems, and lack of the appropriate molecular force fields. In this work, as a first step to extend CHARMM-GUI Membrane Builder to incorporate LPS molecules and to explore their structures and dynamics in membrane environments using molecular dynamics simulations, we describe step-by-step procedures to build LPS bilayer systems using CHARMM and the recently developed CHARMM carbohydrate and lipid force fields. Such procedures are illustrated by building various bilayers of Escherichia coli R1.O6 LPS and the presentation of preliminary simulation results in terms of per-LPS area and density distributions of various components along the membrane normal.
molecular, Escherichia coli, lipid A, glycan, Computational Biology, E.coli, bilayer, molecular dynamics simulation, O6 antigen, R1 core
NCBI PubMed ID: 25753722Publication DOI: 10.1007/978-1-4939-2343-4_24Journal NLM ID: 9214969Publisher: Springer
Correspondence: wonpil
ku.edu
Institutions: Department of Molecular Biosciences and Center for Computational Biology, The University of Kansas, 2030 Becker Drive, Lawrence, KS, 66045, USA, Department of Chemical and Biomolecular Engineering, The University of Maryland, 2113 Chemical and Nuclear Engineering, College Park, MD 20742, USA, Department of Organic Chemistry and Stockholm Center for Biomembrane Research, Arrhenius Laboratory, Stockholm University, S106-91 Stockholm, Sweden
Methods: MD simulations, CHARMM-GUI Membrane Builder
The publication contains the following compound(s):
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2. (Article ID: 10482)
Thapliyal RP, Bahuguna RP
An oleanolic acid based bisglycoside from Clematis montana roots
Phytochemistry 34 (1993)
861-862
Clemontanoside F, a new triterpenic bisglycoside from the roots of Clematis montana, has been characterized as 3-O-β-D-glucopyranosyl-28-O-β-D-galactopyranosyl(1→6)-[α-L-r hamnopyranosyl (1→)]-β-D-glucopyranosyl-3β-hydroxy-olean-12-en-28-oate.
The publication contains the following compound(s):
- Compound ID: 25739
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b-D-Glcp-(1-3)-+
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b-D-Galp-(1-6)-+ |
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a-L-Rhap-(1-2)-b-D-Glcp-(1-28)-Oleanolic
Oleanolic = 3β-hydroxy-olean-12-en-28-oic acid |
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Structure type: oligomer
Trivial name: clemontanoside F
Compound class: saponin glycoside
Reference(s) to other database(s): CCSD:
30981, CBank-STR:10616
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