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Glycobiology Advance Access originally published online on December 4, 2008
Glycobiology 2009 19(4):344-355; doi:10.1093/glycob/cwn137
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© The Author 2008. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Atomic-resolution conformational analysis of the GM3 ganglioside in a lipid bilayer and its implications for ganglioside–protein recognition at membrane surfaces

Mari L DeMarco and Robert J Woods1

Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602-4712, USA

1 To whom correspondence should be addressed: Tel: +1-706-542-4454; Fax: +1-706-542-4412; e-mail: rwoods{at}ccrc.uga.edu

Received on September 26, 2008; revised on November 25, 2008; accepted on November 26, 2008

Eukaryotic cells depend on external surface markers, such as gangliosides, to recognize and bind various other molecules as part of normal growth and maturation. The localization of gangliosides in the outer leaflet of the plasma membrane, also make them targets for pathogens trying to invade the host cells. Since ganglioside-mediated interactions are critical to both beneficial and pathological processes, much effort has been directed at determining the 3D structures of their carbohydrate head groups; however, technical difficulties have generally prevented the characterization of the head group in intact membrane-bound gangliosides. Determining the 3D structure and presentation of gangliosides at the surface of membranes is important in understanding how cells interact with their local environment. Here, we employ all-atom explicit solvent molecular dynamics (MD) simulations, using the GLYCAM06 force field, to model the conformation and dynamics of ganglioside GM3 ({alpha}-Neu5Ac-(2-3)-β-Gal-(1-4)-β-Glc-ceramide) in a DMPC lipid bilayer. By comparison with MD simulations of the carbohydrate head-group fragment of GM3 alone, it was possible to quantify and characterize the extent of changes in head-group presentation and dynamics associated with membrane anchoring. The accuracy of data from the MD simulations was determined by comparison to NMR and crystallographic data for the head group in solution and for GM3 in membrane-mimicking environments. The experimentally consistent model of GM3, in a lipid bilayer, was then used to model the recognition of GM3 at the cell surface by known protein receptors.

Key words: glycoplipid / molecular dynamics / recognition / sialoadhesin / wheat germ agglutinin


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