N.m.r. and molecular-modelling studies of the solution conformation of heparin

Abstract

The solution conformations of heparin and de-N-sulphated, re-N-acetylated heparin have been determined by a combination of n.m.r. spectroscopic and molecular-modelling techniques. The 1H- and 13C-n.m.r. spectra of these polysaccharides have been assigned. Observed 1H-1H nuclear Overhauser enhancements (n.O.e.s) have been simulated using the program NOEMOL [Forster, Jones and Mulloy (1989) J. Mol. Graph. 7, 196-201] for molecular models derived from conformational-energy calculations; correlation times for the simulations were chosen to fit experimentally determined 13C spin-lattice relaxation times. In order to achieve good agreement between calculated and observed 1H-1H n.O.e.s it was necessary to assume that the reorientational motion of the polysaccharide molecules was not isotropic, but was that of a symmetric top. The resulting model of heparin in solution is similar to that determined in the fibrous state by X-ray-diffraction techniques [Nieduszynski, Gardner and Atkins (1977) Am. Chem. Soc. Symp. Ser. 48, 73-80].

The Kaposi's sarcoma-associated herpesvirus complement control protein (KCP) binds to heparin and cell surfaces via positively charged amino acids in CCP1–2

“…Approaching heparin molecules in solution can therefore bind with only small torsional changes on its stable conformation, which is consistent with previous observations of experimental heparin structures (PDB code 1hpn) or co-crystallysed complexes (eg. PDB codes 1rid, 1bfc and 1e0o) (Faham et al, 1996;Ganesh et al, 2004;Mulloy et al, 1993;Pellegrini et al, 2000).…”

“…To abbreviate calculation time of docking simulations the CCP1 and CCP2 domains of each KCP models (extended and bent forms) were represented by a series of energy grid potentials that are approximations of the proteins' properties. Five different properties were taken into account, namely van der Waals potential (with carbon and hydrogen probes), electrostatic potential, hydrogen bonding potential and hydrophobic potential (Fernandez-Recio et al, 2002;Totrov, 2001) The heparin molecule (PDB code 1hpn) (Mulloy et al, 1993) was represented explicitly (all-atoms) and full flexibility was allowed during the docking around the rotatable bonds. The Merck Molecular Force Field parameters were assigned to atoms of both the KCP models and heparin.…”

Structural specificity of heparin binding in the fibroblast growth factor family of proteins

“…HSGAG disaccharides (I 2S H NS,6S ;) with the iduronic acid in the 2 S 0 and 1 C 4 and the glucosamine in the 4 C 1 ring conformations were modeled by using the bond lengths, bond angles, and ring geometries obtained from the cocrystal structures. Using the NANDH program (30), the glycosidic linkage torsions were explored to generate oligosaccharides (hexa-and octasaccharides) of unbound HSGAG satisfying the 2 1 -helical symmetry with an axial rise of 8.4-8.7 Å per unit [consistent with fiber diffraction and NMR data (12,14)]. From these oligosaccharide structures, one structure for each iduronate ring conformation was chosen as the reference ''unbound'' HSGAG structure.…”

“…Further, the N position of the glucosamine can also be acetylated. Similar to DNA and fibrous proteins like collagen, HSGAGs adopt a helical structure (12)(13)(14)(15). The topology and geometry of a HSGAG structure is governed by the backbone torsion angles, which include both the intermonosaccharide glycosidic torsion angles and the pyranose ring torsion angles.…”

Chlorination and oxidation of heparin and hyaluronan by hypochlorous acid and hypochlorite anions: effect of sulfate groups on reaction pathways and kinetics

“…In contrast to heparin, 100% yields were found at all pHs chloramide yield as found in the model compound. The 3-dimensional structure of heparin [31,32] shows that the 6-O-sulphate group is closer to the N-sulphate group than is the 2-O-sulphate group in the ioduronic acid moiety and is therefore likely to produce a greater negative electrostatic effect on the rate of reaction of OCl -with the N-sulphate group. This effect is clearly sufficient to allow an oxidation step to be preferred in 40% of the OCl -reaction with heparin at pH8.5, in contrast to no oxidation in the D-glucosamine-2-N-sulphate model compound.…”