The aim of this project is to develop and test methodologies for conformational studies of free and bound GAGs. Gas phase conformations of heparin-derived oligosaccharides were studied by using Ion Mobility Mass Spectrometry (IMMS) and molecular modelling. Gas phase conformations were modelled using the AMBER force field. Their theoretical collision cross-sections were compared with the IMMS data and a good agreement was obtained. The gas phase conformations of heparin oligosaccharides were more compact than those observed in solution or crystal structures of heparin-protein complexes. This was attributed to the effects of sodium cations interacting with the negatively charged sulphate and carboxyl groups of oligosaccharides. Adiabatic maps of dihedral angles vs. potential energy of disaccharide fragments of the tetrasaccharides were calculated in the absence of the sodium cations. New NMR methods for the measurement of scalar and dipolar <sup>1</sup>H-<sup>1</sup>H coupling constants and <sup>13</sup>C-<sup>13</sup>C coupling constants in natural abundance <sup>13</sup>C samples were developed. Performance of these methods was tested extensively. Solution conformation of the fully sulphated heparin-derived tetrasaccharide was studied by NMR spectroscopy. <sup>1</sup>H-<sup>1</sup>H scalar coupling constants were used to characterize the dynamic equilibria of flexible monosaccharide rings. <sup>1</sup>H-<sup>1</sup>H and <sup>1</sup>H-<sup>13</sup>C RDCs were used in the study of the conformation of the glycosidic linkages. RDC-refined structures were obtained from molecular dynamics with explicit water and sodium cations. Interactions of the heparin-derived fully sulphated tetrasaccharide with factor H modules, fH~19, 20 and fH~7, were studied using AUTODOCK. Conformation of a spin-labelled heparin-derived fully sulphated disaccharide was studied by NMR and molecular modelling.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:653011 |
| Date | January 2007 |
| Creators | Jin, Lan |
| Publisher | University of Edinburgh |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://hdl.handle.net/1842/12304 |
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