SCHOOL OF Chemistry

Professor Rob Woods, Ph.D., FRSC.

Career Synopsis: 1985  B.Sc. (Honors, Engineering Chemistry) Queen's University, Kingston, Ontario, Canada 1990  Teaching Assistant, ACS Short Course in Molecular Modeling, The University of North Carolina 1990  Ph.D. (Computational and Carbohydrate Chemistry)  School of Graduate Studies and Research, Queen's University 1991-1992 Associate Member Linacre College, Oxford, UK. 1993  Associate Member Corpus Christi College, Oxford, UK 1990-1991 Postdoctoral Fellow, Laboratory for Molecular Modeling, The University of North Carolina 1991-1994 Postdoctoral Fellow, Glycobiology Institute, Oxford, UK 1994-1995 Term Scientist, Institute for Biological Sciences, NRC of Canada, Ottawa, Canada 1996-Present Member, Computational Center for Molecular Structure and Design, Department of Chemistry, The University of Georgia, Athens

  Research interests and Publications:

 
Predicted structure of glycosylated human Erythropoietin.

Prof..Woods's research examines the relationships between the conformations of carbohydrate molecules and biological recognition and activity, particularly the mechanisms involved in carbohydrate recognition in immunological events. Significant alterations in the biological activities of peptides and proteins often accompany the covalent attachment of an oligosaccharide (glycosylation) to one or more of their amino acid residues. Approximately 60% of all mammalian proteins are glycosylated, and the glycoproteins that are generated by glycosylation are also frequently found attached to the cell surfaces of bacteria, fungi, and parasites. But the roles of oligosaccharide moieties are extremely diverse. In mucins, for example, the carbohydrate component of a glycoprotein may be present in a largely structural capacity, whereas in human chorionic gonadotropin or tissue plasminogen activator it alters the functioning of the protein. The carbohydrate component may also be the part of the glycoprotein recognized by the immune system, directly affecting antibody-antigen interactions, self- and non-self-recognition, and auto-immune disorders.

The Woods's group utilizes the computational techniques of molecular dynamics and free energy perturbation simulations to study the conformational properties of oligosaccharides and carbohydrate-protein complexes. The computational methods are complimented by experimental techniques, such as NMR spectroscopy, X-ray crystallography. The computational simulations use the all-atom AMBER force field for proteins and nucleic acids and a novel set of parameters developed by Dr. Woods's group for use with carbohydrates, GLYCAM. The GLYCAM parameters make it possible to probe the interatomic interactions responsible for oligosaccharide and glycoprotein dynamics and compare these directly with experimental NMR data that are often consistent with numerous possible conformations. These parameters are currently suitable for all biologically relevant N- and O-linkages in oligo- and polysaccharides and glycoproteins.

Current research projects using these techniques include examinations of bacterial antigen-antibody interactions, as well as carbohydrate-lectin interactions. Carbohydrate antigens associated with Salmonella paratyphi B and group B Streptococcus are being studied to understand the energetic contributions hydrophobic and hydrophilic interactions make to antibody binding energy. More applied aspects of the research include the screening of synthetic combinatorial peptide libraries for peptides that bind to carbohydrate receptor proteins (antibodies and lectins) and their subsequent co-crystallization with the receptor. Peptides are characteristically more antigenic than carbohydrates, and the Woods laboratory's interest in carbohydrate mimics is driven by a desire to produce non-carbohydrate molecules that can either act as anti-bacterial vaccines or inhibit auto-immune reactions. This research is supported by the National Institutes of Health and the National Science Foundation.

  See CALCULATING CARBOHYDRATES - CHEMICAL & Engineering News (Cover Story)

Some Recent Publications:

49. Kadirvelraj, R., B.L. Foley, J.D. Dyekjær and R.J. Woods. 2008. Involvement of Water in Carbohydrate-Protein Binding: Concanavalin A Revisited. J. Am. Chem. Soc. In Press.

48. Yongye, A.B., J. Gonzalez-Outeriño, J.Glushka, V. Schutlheis, and R.J. Woods. 2008. The Conformational Properties of Methyl a-(2,8)- di/trisialoside. Implications for anti- Neisseria meningitidis Vaccine Design. Biochemistry In Press.

47. Charvatova, O., B.L. Foley, M. Bern, J. Sharp, R. Orlando and R.J. Woods. 2008. Quantifying Protein Interface Footprinting by Hydroxyl Radical Oxidation and Molecular Dynamics Simulation: Application to Galectin-1. J. Am. Soc. Mass Spectrom. doi:10.1016/j.jasms.2008.07.013.

46. DeMarco, M.L. and R.J. Woods. 2008. Bridging Structural Biology and Glycobiology: A Game of Snakes and Ladders. (Invited Review) Glycobiology 18, 426-440.

45. Yongye, A.B., B.L. Foley and R.J. Woods. 2008. On achieving experimental accuracy from molecular dynamics simulations of flexible molecules: aqueous glycerol. J. Phys. Chem. B 112, 2634 -2639.

44. Seo, M., N. Castillo, R. Ganzynkowicz, C.R. Daniels, R.J. Woods, P.-N. Roy and T.L. Lowary. 2008. An approach for the simulation and modeling of flexible rings.  Application to the α-D-arabinofuranoside ring, a key constituent of polysaccharides from Mycobacterium tuberculosis. J. Chem. Theory Comput. 4, 184-191.

43. Pedatella, S., M. De Nisco, B. Ernst, A. Guaragna, B. Wagner, R.J. Woods and G. Palumbo. 2007. New Sialyl Lewis ^x Mimic Containing an α-Substituted β ³-Amino Acid Spacer. Carbohydr. Res. 343, 31-38.

42. Tessier, M.B., M.L. DeMarco, A.B. Yongye and R.J. Woods. 2007. Extension of the GLYCAM06 Biomolecular Force Field to Lipids, Lipid Bilayers and Glycolipids. Molecular Simulation 34, 349-364.

41. Kirschner, K.N., A.B. Yongye, S.M. Tschampel, J. Gonzalez-Outeriño, C.R. Daniels, B.L. Foley and R.J. Woods. 2008. GLYCAM06: A Generalizable Biomolecular Force Field. Carbohydrates. J. Comput. Chem. 29, 622-655.

40. Tschampel, S.M., M.R. Kennerty and R.J. Woods. 2007. A TIP5P-Consistent Treatment of Electrostatics for Biomolecular Simulations. J. Chem. Theory Comput. 3, 1721-1733.

39. Seyfried, N.T., J.A. Atwood, III, A. Almond, A.J. Day, R. Orlando and R.J. Woods. 2007. Fourier transform mass spectrometry to monitor hyaluronan–protein interactions: use of hydrogen/deuterium amide exchange, Rapid Commun. Mass Spectrom. 21, 121-131.

38. Elking, D., T. Darden and R.J. Woods. 2006. Gaussian induced dipole polarization model. J. Comput. Chem. 28, 1261-1274.

37. Kadirvelraj, R., M.L. Beckham, M.G. Ford, J. Gonzalez-Outeriño and R.J. Woods. 2006. Understanding the bacterial polysaccharide antigenicity of Streptococcus agalactiae versus Streptococcus pneumoniae. Proc. Natl. Acad. Sci. USA. 103, 8149-8154.

36. Kawatkar, S.P., D.A. Kuntz, R.J. Woods, D.R. Rose and G.-J. Boons. 2006. Structural basis of the inhibition of golgi α-mannosidase II by mannostatin A and the role of the thiomethyl moiety in ligand-protein interactions. J. Am. Chem. Soc. 128, 8310-8319.

35. Gonzalez-Outeiriño, J., K.N. Kirschner, S. Thobhani and R.J. Woods. 2006. Reconciling solvent effects on rotamer populations in carbohydrates: a joint MD and NMR analysis. Can. J. Chem. 84, 569-579.

34. Case, D.A., T. Cheatham, T. Darden, H. Gohlke, R. Luo, K.H. Merz, Jr., A. Onufriev, C. Simmerling, B. Wang and R.J. Woods. 2005. The AMBER biomolecular simulation programs. J. Comput. Chem. 26, 1668-1688.

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