Conformation of heparin pentasaccharide bound to antithrombin III

The interaction, in aqueous solution, of the synthetic pentasaccharide AGA* IA(M) (GlcN,6-SO(3)alpha1-4GlcA beta1-4GlcN,3,6-SO(3)alpha1-4IdoA,2-SO3(alp ha)1-4GlcN,6-SO(3)alpha OMe; where GlcN,6-SO3 is 2-deoxy-2-sulpliamino-alph a -D-glucopyranosyl 6-sulphate, IdoA is L-iduronic acid and IdoA2-SO3 is L- iduronic acid 2-sulphate), which exactly reproduces the structure of the sp ecific binding sequence of heparin and heparan sulphate for antithrombin II I, has been studied by NMR. In the presence of antithrombin there were mark ed changes in the chemical shifts and nuclear Overhauser effects (NOEs), co mpared with the free state. On the basis of the optimized geometry of the p entasaccharide the transferred NOEs were interpreted with full relaxation a nd conformational exchange matrix analysis. An analysis of the three-dimens ional structures of the pentasaccharide in the free state, and in the compl ex, revealed the binding to be accompanied by dihedral angle variation at t he A-G and I-A(M) (where G, I, A and A(M) are beta -D-glucuronic acid, 2-O- sulphated alpha -L-iduronic acid, N,6-O-sulphated alpha -D-glucosamine and the alpha -methyl-glycoside of A respectively) glycosidic linkages. Evidenc e is also provided that the protein drives the conformation of the 2-O-sulp hated iduronic acid residue towards the skewed S-2(0) form.