The computed properties of the interatomic interactions in three complimentary examples of carbohydrate-protein complex, will provide insight into the roles played by hydrophilicity, hydrophobicity, solvation and induced fit in determining binding affinities. This approach will provide insight into the fundamental physical requirements for carbohydrate antigenicity. Experimental techniques may be used to provide ligand binding affinities, however, a computational approach must be employed for an interpretation of the experimental values in terms of discreet energetic components; e.g., electrostatic, hydrogen-bond, steric, or van der Waals contributions. Further, a computational approach enables the prediction of the effect of point mutations on binding energies. There are two categories of carbohydrate-protein interactions: those in which a compact group of sugars is recognized, such for the O-antigen of the polysaccharides from Salmonella paratyphi B (SPB), and those in which an extended epitope of 10-20 sugars is present, as in the capsular polysaccharides from group B Streptococcus (GBS) and in the interaction between polylactosamine (PL) and the S-type lectin Galectin-1.
Aim 1 of this proposal is to apply the techniques of molecular dynamics (MD) simulation and free energy perturbation (FEP) to the well-characterized Salmonella-Fab system, to establish the ability of these calculations to reproduce the reported experimental geometries and interaction energies. The rigidity of the SPB ligands in this complex facilitates the accurate computation of relative binding energies. Antigenicity-enhancing interactions will be quantified.
Aim 2 is to apply MD in the determination of the solution conformations of oligosaccharide fragments of PL and in the docking of these ligands to the X-ray structure of Galectin-1. The relatively simple morphology of the PL ligands facilitates a determination of the extent to which binding induces conformational changes in the receptor or ligand.
Aim 3 is to determine the conformations of structurally related polysaccharides from GBS. The conformational properties of the capsular polysaccharides will be examined in order to explain the lack of mAb cross-reactivities among serotypes. Based on the results from the branched oligosaccharide (Aim1), and the linear polysaccharide (Aim 2), a model for the branched GBS capsular polysaccharides will be proposed. The role played by charge complimentarity, between the anionic polsaccharides and the protein will be assessed through FEP calculations. A better understanding of the conformational properties of the serotypes may provide a basis for rational vaccine design.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM055230-05
Application #
6363277
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Flicker, Paula F
Project Start
1997-03-01
Project End
2003-02-28
Budget Start
2001-03-01
Budget End
2003-02-28
Support Year
5
Fiscal Year
2001
Total Cost
$175,606
Indirect Cost
Name
University of Georgia
Department
Type
Organized Research Units
DUNS #
City
Athens
State
GA
Country
United States
Zip Code
30602
DeMarco, Mari L; Woods, Robert J (2011) From agonist to antagonist: structure and dynamics of innate immune glycoprotein MD-2 upon recognition of variably acylated bacterial endotoxins. Mol Immunol 49:124-33
Kadirvelraj, Renuka; Grant, Oliver C; Goldstein, Irwin J et al. (2011) Structure and binding analysis of Polyporus squamosus lectin in complex with the Neu5Ac{alpha}2-6Gal{beta}1-4GlcNAc human-type influenza receptor. Glycobiology 21:973-84
Frank, Aaron T; Ramsook, Caleen B; Otoo, Henry N et al. (2010) Structure and function of glycosylated tandem repeats from Candida albicans Als adhesins. Eukaryot Cell 9:405-14
Woods, Robert J; Tessier, Matthew B (2010) Computational glycoscience: characterizing the spatial and temporal properties of glycans and glycan-protein complexes. Curr Opin Struct Biol 20:575-83
Charvatova, Olga; Foley, B Lachele; Bern, Marshall W et al. (2008) Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1. J Am Soc Mass Spectrom 19:1692-705
Kadirvelraj, Renuka; Foley, B Lachele; Dyekjaer, Jane D et al. (2008) Involvement of water in carbohydrate-protein binding: concanavalin A revisited. J Am Chem Soc 130:16933-42
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Bosques, Carlos J; Tschampel, Sarah M; Woods, Robert J et al. (2004) Effects of glycosylation on peptide conformation: a synergistic experimental and computational study. J Am Chem Soc 126:8421-5
Gonzalez-Outeirino, Jorge; Glushka, John; Siriwardena, Aloysius et al. (2004) The structure and conformational behavior of sulfonium salt glycosidase inhibitors in solution: a combined quantum mechanical NMR approach. J Am Chem Soc 126:6866-7
Tschampel, Sarah M; Woods, Robert J (2003) Quantifying the role of water in protein-carbohydrate interactions. J Phys Chem A 107:9175-81

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