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Some challenges in the computational investigations of carbohydrates

Apr 25, 2013 | 04:15 PM

Dr. Mark Santer, Max Planck Institute of Colloids and Interfaces, Potsdam Dep. of Theory & Bio Systems Research Group "Carboyhdrates & Polysaccharides"

Apart from serving as biochemical fuel or structural elements of cell walls, carbohydrates as modifications (glycosylations) of lipids and proteins are playing a broad variety of roles in the extracellular matrix of any organism. These so-called glycans are oligosaccharides composed of up to ~ 30 monomer units, and are part of many specific cell-cell recognition and communication processes. The largest part of glycan functionality, related to unspecific functions, remains to be elucidated. Carbohydrates may simply adjust the solubility of proteins or enhance the steric inter- and intramolecular interaction of biomolecules. Due to the rich conformational behavior of glycans, these cases cannot easily be accessed by experimental techniques, and computational modeling represents a valuable complementary approach. Our work is dedicated to two long term case studies to uncover the “global” picture of special classes of glycans. Glycosylphosphatidyl-Inositol (GPI) anchors are important modifications of proteins that allow their attachment to a membrane without penetrating it; they are thought to facilitate the association with lipid rafts. From the computational point of view, the proximity of three different species of biomolecules (lipids, carbohydrates, proteins) raises a series of interesting questions which we will highlight. Our second case study deals with the structure of lipopolysaccharide O-Antigen chains of gram-negative bacteria. We discuss how, starting from the analysis of small fragments, one could extrapolate to the behavior of chains consisting of a large number of repeat units and possibly develop coarse grain models.

Time & Location

Apr 25, 2013 | 04:15 PM

Seminar Room T2 (1.4.03)