Antithrombin structures and the heparin pentasaccharide

• Main Author: Jin, L.
• Published: University of Cambridge 1998
• Subjects: 547.7
• Online Access: http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.605606

Antithrombin, the major inhibitor of blood coagulation, is relatively inactive until it binds to, and is achieved by the heparan sidechains that line the microvasculature. The binding specifically occurs to a core pentasaccharide, present both in the heparans and in their therapeutic derivative heparin. This specific binding can cause antithrombin's conformational change which is required for activation. The crystal structure of a dimer of inhibitory(I) and latent(I) antithrombin, each in complex with the high-affinity pentasaccharide, was solved at 2.9A resolution. To achieve this, a new approach to the effective crystallisation of antithrombin was developed involving equal-molar mixing of inhibitory and latent antithrombin, in this case, in the additional presence of the heparin pentasaccharide. The structure elucidated, for the first time, the binding details and accompanying conformational change of antithrombin which is fundamental for activation. The pentasaccharide binds to antithrombin by hydrogen-bonding or salt-bridging of its sulphates and carboxylates to Arg129 and Lys125 on the D-helix, to Asn45, Arg46 and Arg47 on the A-helix, to Lys114 and Glu113 on the new induced P-helix and to LKys11 and Arg13 in a cleft formed by the amino-terminus. Inhibitory activation results from a shift in the main β-sheet of the molecule(the A-sheet) from a partially six-stranded to a five-stranded form with extrusion of the reactive loop to give a more exposed orientation. There is a tilting and elongation of the D-helix with the formation of a new 2-turn P-helix between the C and D helices. Comparing the concomitant conformational changes at the heparin binding site of the I and L molecules also explains structurally both the initial tight binding of antithrombin to the heparans and the subsequent release of the antithrombin/protease complex into the circulation. The clear definition of the binding site and interaction details has given a new insight into the molecular pathology of antithrombin deficiency and provides a structural basis for developing heparin analogues which are more specific towards their intended target, antithrombin, and therefore less likely to exhibit side-effects.