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Glycobiology Advance Access originally published online on April 4, 2008
Glycobiology 2008 18(6):426-440; doi:10.1093/glycob/cwn026
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© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Review

Structural glycobiology: A game of snakes and ladders

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 November 1, 2007; revised on March 19, 2008; accepted on March 19, 2008

Oligo- and polysaccharides are infamous for being extremely flexible molecules, populating a series of well-defined rotational isomeric states under physiological conditions. Characterization of this heterogeneous conformational ensemble has been a major obstacle impeding high-resolution structure determination of carbohydrates and acting as a bottleneck in the effort to understand the relationship between the carbohydrate structure and function. This challenge has compelled the field to develop and apply theoretical and experimental methods that can explore conformational ensembles by both capturing and deconvoluting the structural and dynamic properties of carbohydrates. This review focuses on computational approaches that have been successfully used in combination with experiment to detail the three-dimensional structure of carbohydrates in a solution and in a complex with proteins. In addition, emerging experimental techniques for three-dimensional structural characterization of carbohydrate–protein complexes and future challenges in the field of structural glycobiology are discussed. The review is divided into five sections: (1) The complexity and plasticity of carbohydrates, (2) Predicting carbohydrate–protein interactions, (3) Calculating relative and absolute binding free energies for carbohydrate–protein complexes, (4) Emerging and evolving techniques for experimental characterization of carbohydrate–protein structures, and (5) Current challenges in structural glycoscience.

Key words: Binding free energy / docking / molecular dynamics / nomenclature / oxidative footprinting


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