Crystal Structures of Native and Thrombin-Complexed Heparin Cofactor II Reveal a Multistep Allosteric Mechanism

Crystal structures of native and thrombin-complexed heparin cofactor II reveal a multistep allosteric mechanism Trevor P. Baglin†, Robin W. Carrell†, Frank C. Church‡, Charles T. Esmon§, and James A. Huntington†¶ †Department of Haematology, Cambridge Institute for Medical Research, Wellcome Trust͞MRC Building, Hills Road, Cambridge CB2 2XY, United Kingdom; ‡Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599-7035; and §Cardiovascular Biology Research Program, Oklahoma Medical Research Foundation, Howard Hughes Medical Institute, and Department of Pathology and Biochemistry and Molecular Cell Biology, University of Oklahoma Health Science Center, Oklahoma City, OK 73104 Edited by Earl W. Davie, University of Washington, Seattle, WA, and approved June 24, 2002 (received for review April 17, 2002) The serine proteases sequentially activated to form a fibrin clot are native inhibitory serpins with a fully exposed reactive center loop inhibited primarily by members of the serpin family, which use a and a five-stranded ␤-sheet A (Fig. 1a). unique ␤-sheet expansion mechanism to trap and destroy their The reactive center-loop sequence of HCII implies specificity targets. Since the discovery that serpins were a family of serine for chymotrypsin, with a leucine in the critical P1 position (where protease inhibitors there has been controversy as to the role of the scissile bond is denoted P1–P1Ј; ref. 9), yet it is a specific conformational change in their mechanism. It now is clear that inhibitor of thrombin, which normally requires a P1 arginine. protease inhibition depends entirely on rapid serpin ␤-sheet ex- The specificity of HCII for thrombin is conferred by a highly pansion after proteolytic attack. The regulatory advantage af- acidic hirudin-like N-terminal tail, which becomes available after forded by the conformational mobility of serpins is demonstrated GAG binding for interaction with the anion-binding exosite I of here by the structures of native and S195A thrombin-complexed thrombin (10–14). A mechanism for HCII activation has been heparin cofactor II (HCII). HCII inhibits thrombin, the final protease proposed (11, 15) whereby the N-terminal tail is sequestered in of the coagulation cascade, in a glycosaminoglycan-dependent the native structure through an interaction with the highly basic manner that involves the release of a sequestered hirudin-like heparin binding region, and activation is brought about through N-terminal tail for interaction with thrombin. The native structure the competitive displacement of the acidic tail of HCII by of HCII resembles that of native antithrombin and suggests an heparin or similar anionic GAGs. Here we describe, in turn, the alternative mechanism of allosteric activation, whereas the struc- crystallographic structures of native and S195A thrombin- ture of the S195A thrombin–HCII complex defines the molecular complexed HCII. The native structure displays unexpected basis of allostery. Together, these structures reveal a multistep homology to AT, which provides a previously uncharacterized allosteric mechanism that relies on sequential contraction and mechanism for sequestration and release of the acidic tail, and expansion of the central ␤-sheet of HCII. the Michaelis complex between HCII and thrombin defines the molecular basis of activation. Together, these structures reveal a multistep mechanism that depends on the sequential contraction he predominant protease inhibitors of the higher organisms, ␤ Tthe serpins (1, 2), have evolved a complex mechanism that and expansion of -sheet A and demonstrate the degree to which was revealed recently by the crystallographic structure of a the complicated serpin mechanism of protease inhibition has serpin–protease complex (3). This dramatic mechanism amounts been exploited by evolution to effect regulatory control. to a race between proteolysis and the incorporation of the Methods serpin-reactive center loop into its main ␤-sheet (␤-sheet A). The Native HCII. HCII was purified as described (16). Crystals were dependence of the serpin inhibitory mechanism on ␤-sheet obtained from Hampton Crystal Screen Cryo 6 (Hampton expansion renders serpins highly susceptible to both loss-of- Research, Riverside, CA) and were generally very thin plates function and gain-of-function diseases but additionally allows for that diffracted poorly. Crystals were shown to contain intact a range of mechanisms for the modulation of serpin activity. HCII by SDS͞PAGE, although some degradation, presumably Thus, serpins typically are found controlling tightly regulated N-terminal cleavage, was observed in older crystals. A data set physiological pathways such as blood coagulation. Antithrombin was collected on a single frozen crystal at the SRS Daresbury (AT) and heparin cofactor II (HCII) have independently (4, 5) Station 14.1 (Cheshire, U.K.) on an ADSC image plate. The evolved mechanisms by which they circulate in an inert state until crystal diffraction was nonisotropic, and significant decay was activated by binding to cell surface glycosaminoglycans (GAGs). observed during data collection. The data were processed using AT and HCII thus are allosterically activated toward factor Xa MOSFLM, SCALA, and TRUNCATE (17) and were of reasonable and thrombin, respectively, the final two proteases in the blood quality to a resolution limit of 2.35 Å (Table 1). The structure of coagulation cascade. native HCII was solved by molecular replacement (MolRep; ref. The structure and mechanism of activation of AT has been 18) using native plasminogen activator inhibitor-1 (PDB ID code well characterized. Its fold is similar to that of the rest of the 1DVN), native AT (PDB ID code 1EO5), latent AT (PDB ID serpin family with the single and important exception that the code 1EO5), and pentasaccharide-activated AT (PDB ID code reactive center loop is constrained through partial incorporation ␤ 1AZX) as search models. Comparison of the relative scores for into -sheet A (refs. 6 and 7; Fig. 1a). The native conformation the molecular replacement solutions clearly indicated that the of AT thus renders it incapable of forming a productive recog- nition complex (Michaelis complex) with factor Xa, and only as the result the conformational changes brought about through the This paper was submitted directly (Track II) to the PNAS office. interaction with a specific heparin pentasaccharide sequence Abbreviations: AT, antithrombin; HCII, heparin cofactor II; GAG, glycosaminoglycan. does AT become an efficient inhibitor of factor Xa. Pentasac- Data deposition: The atomic coordinates and structure factors have been deposited in the charide binding results in secondary structural changes in the Protein Data Bank, www.rcsb.org (PDB ID codes 1JMJ and 1JMO for native and S195A heparin binding region and the expulsion of the reactive center thrombin-complexed HCII, respectively). BIOCHEMISTRY loop (8) such that activated AT resembles all the other known ¶To whom reprint requests should be addressed. E-mail: [email protected]. www.pnas.org͞cgi͞doi͞10.1073͞pnas.162232399 PNAS ͉ August 20, 2002 ͉ vol. 99 ͉ no. 17 ͉ 11079–11084 Downloaded by guest on September 26, 2021 Fig. 1. The AT-like structure of native HCII. (a) The native structure of AT is different from all other know serpins with the partial incorporation of the reactive center loop (yellow) into ␤-sheet A (red), resulting in an unfavorable orientation of the reactive center arginine side chain (red, space-filling). Binding of heparin (ball-and-stick) to helix D (cyan) results in the expulsion of the reactive center loop from ␤-sheet A and its freeing for the formation of a productive Michaelis complex. (b) The structure of native HCII resembles that of native AT, with its reactive center loop partially inserted into ␤-sheet A. (c) Stereo depiction of the electron density for the entire reactive center loop contoured at 1␴.(d) The high degree of conservation of heparin binding residues on helix D (cyan) and helix A (green) with AT indicates a similar mode of binding and suggests similar conformational changes in response to binding. (e) A stereo representation of the crystallographic dimer of HCII formed by the antiparallel ␤-sheet interaction between strands 1C (orange) of each monomer. This contact is the probable cause of the displacement of the acidic N-terminal tail (magenta). The bottom monomer is molecule A. best solution was for native AT and that two monomers occupied models. The C-terminal half of HCII (residues 282–480) was the asymmetric unit. A homology model of HCII was generated subsequently positioned with the solutions for thrombin and the on the native AT template by using SWISSMODEL (19), which then N-terminal fraction fixed. Molecular replacement attempts with was subjected to rigid-body refinement and coordinate refine- native HCII were unsuccessful even with the thrombin solution ment with simulated annealing by using CNS (20). The Rfree set fixed using both MOLREP and AMORE (24). The final refined was chosen randomly from a subset of reflections unrelated by model was obtained as described above. Solvent-flattened maps noncrystallographic symmetry. Iterative rounds of rebuilding in were calculated by using DM because of the unusually high XTALVIEW (21) and refinement with CNS resulted in an Rfactor and solvent content (72%). Processing and refinement statistics are Rfree of 20.8 and 24.7, respectively (Table 1). Because the twofold given in Table 1. Figures were made by using MOLSCRIPT

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