Model of a Ternary Complex between Activated Factor VII, Tissue Factor and Factor IX

Summary

Upon binding to tissue factor, FVIIa triggers coagulation by activating vitamin K-dependent zymogens, factor IX (FIX) and factor X (FX). To understand recognition mechanisms in the initiation step of the coagulation cascade, we present a three-dimensional model of the ternary complex between FVIIa:TF:FIX. This model was built using a full-space search algorithm in combination with computational graphics. With the known crystallographic complex FVIIa:TF kept fixed, the FIX docking was performed first with FIX Gla-EGF1 domains, followed by the FIX protease/EGF2 domains. Because the FIXa crystal structure lacks electron density for the Gla domain, we constructed a chimeric FIX molecule that contains the Gla-EGF1 domains of FVIIa and the EGF2-protease domains of FIXa. The FVIIa:TF:FIX complex has been extensively challenged against experimental data including site-directed mutagenesis, inhibitory peptide data, haemophilia B database mutations, inhibitor antibodies and a novel exosite binding inhibitor peptide. This FVIIa:TF:FIX complex provides a powerful tool to study the regulation of FVIIa production and presents new avenues for developing therapeutic inhibitory compounds of FVIIa:TF:substrate complex.

Keywords

Protein-protein interaction - haemostasis - coagulation cascade - haemophilia - extrinsic pathway - comparative modeling - homology modelling

• References

• 1 Lawson JH, Butenas S, Mann KG. The evaluation of complex-dependent alterations in human factor VIIa. J Biol Chem 1992; 267: 4834-43.
• 2 Osterud B, Rapaport SI. Activation of factor IX by the reaction product of tissue factor and factor VII: additional pathway for initiating blood coagulation. Proc Natl Acad Sci USA 1977; 74: 5260-4.
• 3 Cooper DN, Millar DS, Wacey A, Banner DW, Tuddenham EG. Inherited factor VII deficiency: molecular genetics and pathophysiology. Thromb Haemost 1997; 78: 151-60.
• 4 Yamamoto M, Nakagaki T, Kisiel W. Tissue factor-dependent autoactivation of human blood coagulation factor VII. J Biol Chem 1992; 267: 19089-94.
• 5 Ellison EH, Castellin FJ. Adsorption of vitamin K-dependent blood coagulation proteins to spread phospholipid monolayers as determined from combined measurements of the surface pressure and surface protein concentration. Biochemistry 1998; 37: 7997-8003.
• 6 Marmur JD, Thiruvikraman SV, Fyfe BS, Guha A, Sharma SK, Ambrose JA, Fallon JT, Nemerson Y, Taubman MB. Identification of active tissue factor in human coronary atheroma. Circulation 1996; 94: 1226-32.
• 7 Hasenstab D, Lea H, Hart CE, Lok S, Clowes AW. Tissue factor over-expression in rat arterial neointima models thrombosis and progression of advanced atherosclerosis. Circulation 2000; 101: 2651-7.
• 8 Westmuckett AD, Lupu C, Goulding DA, Das S, Kakkar VV, Lupu F. In situ analysis of tissue factor-dependent thrombin generation in human atherosclerotic vessels. Thromb Haemost 2000; 84: 904-11.
• 9 Asakura H, Kamikubo Y, Goto A, Shiratori Y, Yamazaki M, Jokaji H, Saito M, Uotani C, Kumabashiri I, Morishita E. et al. Role of tissue factor in disseminated intravascular coagulation. Thromb Res 1995; 80: 217-24.
• 10 Semeraro N, Colucci M. Tissue factor in health and disease. Thromb Haemost 1997; 78: 759-64.
• 11 Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res 2000; 28: 235-42.
• 12 Janin J. Protein-protein recognition. Prog Biophys Mol Biol 1995; 64: 145-66.
• 13 Sternberg MJ, Gabb HA, Jackson RM. Predictive docking of protein and protein-DNA complexes. Curr Opin Struct Biol 1998; 08: 250-6.
• 14 Strynadka NC, Eisenstein M, Katchalski-Katzir E, Shoichet BK, Kuntz ID, Abagyan R, Totrov M, Janin J, Cherfils J, Zimmerman F, Olson A, Duncan B, Rao M, Jackson R, Sternberg M, James MN. Molecular docking programs successfully predict the binding of a beta-lactamase inhibitory protein to TEM-1 beta-lactamase. Nat Struct Biol 1996; 03: 233-9.
• 15 Goodsell DS, Olson AJ. Automated docking of substrates to proteins by simulated annealing. Proteins 1990; 08: 195-202.
• 16 Jiang F, Kim SH. “Soft docking”: matching of molecular surface cubes. J Mol Biol 1991; 219: 79-102.
• 17 Cherfils J, Duquerroy S, Janin J. Protein-protein recognition analyzed by docking simulation. Proteins 1991; 11: 271-80.
• 18 Totrov M, Abagyan R. Detailed ab initio prediction of lysozyme-antibody complex with 1.6 A accuracy. Nat Struct Biol 1994; 01: 259-63.
• 19 Jackson RM, Gabb HA, Sternberg MJ. Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J Mol Biol 1998; 276: 265-85.
• 20 Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. Molecular surface recognition: determination of geometric fit between proteins and their ligands by correlation techniques. Proc Natl Acad Sci USA 1992; 89: 2195-9.
• 21 Walls PH, Sternberg MJ. New algorithm to model protein-protein recognition based on surface complementarity. Applications to antibody-antigen docking. J Mol Biol 1992; 228: 277-97.
• 22 Helmer-Citterich M, Tramontano A. PUZZLE: a new method for automated protein docking based on surface shape complementarity. J Mol Biol 1994; 235: 1021-31.
• 23 Gabb HA, Jackson RM, Sternberg MJ. Modelling protein docking using shape complementarity, electrostatics and biochemical information. J Mol Biol 1997; 272: 106-20.
• 24 Vakser IA, Matar OG, Lam CF. A systematic study of low-resolution recognition in protein-protein complexes. Proc Natl Acad Sci USA 1999; 96: 8477-82.
• 25 Mandell JG, Roberts VA, Pique ME, Kotlovyi V, Mitchell JC, Nelson E, Tsigelny I, Ten Eyck LF. Protein docking using continuum electrostatics and geometric fit. Protein Eng 2001; 14: 105-13.
• 26 Camacho CJ, Gatchell DW, Kimura SR, Vajda S. Scoring docked conformations generated by rigid-body protein-protein docking. Proteins 2000; 40: 525-37.
• 27 Nelsestuen GL, Ostrowski BG. Membrane association with multiple calcium ions: vitamin-K-dependent proteins, annexins and pentraxins. Curr Opin Struct Biol 1999; 09: 433-7.
• 28 Banner DW, D’Arcy A, Chène C, Winkler FK, Guha A, Konigsberg WH, Nemerson Y, Kirchhofer D. The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature 1996; 380: 41-6.
• 29 Brandstetter H, Bauer M, Huber R, Lollar P, Bode W. X-ray structure of clotting factor IXa: Active site and module structure related to Xase activity and hemophilia B. Proc Natl Acad Sci USA 1995; 92: 9796-800.
• 30 Zhong D, Smith KJ, Birktoft JJ, Bajaj SP. First epidermal growth factorlike domain of human blood coagulation factor IX is required for its activation by factor VIIa/tissue factor but not by factor XIa. Proc Natl Acad Sci USA 1994; 91: 3574-8.
• 31 Chang JY, Monroe DM, Stafford DW, Brinkhous KM, Roberts HR. Replacing the first epidermal growth factor-like domain of factor IX with that of factor VII enhances activity in vitro and in canine hemophilia B. J Clin Invest 1997; 100: 886-92.
• 32 Ruf W, Shobe J, Rao SM, Dickinson CD, Olson A, Edgington TS. Importance of factor VIIa Gla-domain residue Arg-36 for recognition of the macromolecular substrate factor X Gla-domain. Biochemistry 1999; 38: 1957-66.
• 33 Leonard BJ, Clarke BJ, Sridhara S, Kelley R, Ofosu FA, Blajchman MA. Activation and active site occupation alter conformation in the region of the first epidermal growth factor-like domain of human factor VII. J Biol Chem 2000; 275: 34894-900.
• 34 Jacobs M, Freedman SJ, Furie BC, Furie B. Membrane binding properties of the factor IX gamma-carboxyglutamic acid-rich domain prepared by chemical synthesis. J Biol Chem 1994; 269: 25494-501.
• 35 Sunnerhagen M, Forsén S, Hoffrén A-M, Drakenberg T, Teleman O, Stenflo J. Structure of the Ca2+-free GLA domain sheds light on membrane binding of blood coagulation proteins. Nat Struct Biol 1995; 02: 504-9.
• 36 Freedman SJ, Blostein MD, Baleja JD, Jacobs M, Furie BC, Furie B. Identification of the phospholipid binding site in the vitamin K-dependent blood coagulation protein factor IX. J Biol Chem 1996; 271: 16227-36.
• 37 Ten Eyck LF, Mandell J, Roberts VA, Pique ME. In: Proceedings of the 1995 ACM/IEEE Supercomputing Conference, San Diego. December 3-8, 1995. Hayes A, Simmons M. eds. IEEE Computer Society Press; Los Alamitos, CA: http://www.supercomp.org/sc95/proceedings/636_LTEN/ SC95.HTM
• 38 Roberts VA, Pique ME. Definition of the interaction domain for cytochrome c on cytochrome c oxidase. III. Prediction of the docked complex by a complete, systematic search. J Biol Chem 1999; 274: 38051-60.
• 39 Brünger AT. Book X-PLOR Manual. Version 3.0. New Haven: Yale University Press; 1992
• 40 Brooks B, Bruccoleri R, Olafson B, States D, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and molecular dynamics calculations. J Comp Chem 1983; 04: 187-217.
• 41 O’Hara PJ, Grant FJ, Haldeman BA, Gray CL, Insley MY, Hagen FS, Murray MJ. Nucleotide sequence of the gene coding for human factor VII, a vitamin K-dependent protein participating in blood coagulation. Proc Natl Acad Sci USA 1987; 84: 5158-62.
• 42 Yoshitake S, Schach BG, Foster DC, Davie EW, Kurachi K. Nucleotide sequence of the gene for human factor IX (antihemophilic factor B). Biochemistry 1985; 24: 3736-50.
• 43 Leytus SP, Foster DC, Kurachi K, Davie EW. Gene for human factor X: A blood coagulation factor whose gene organization is essentially identical with that of factor IX and protein C. Biochemistry 1986; 25: 5098-102.
• 44 Pellequer JL, Gale AJ, Getzoff ED, Griffin JH. Three-dimensional model of the coagulation factor Va bound to activated protein C. Thromb Haemost 2000; 84: 849-57.
• 45 Zhang E, St Charles RE, Tulinsky A. Structure of extracellular tissue factor complexed with factor VIIa inhibited with a BPTI mutant. J Mol Biol 1999; 285: 2089-104.
• 46 Perera L, Darden TA, Pedersen LG. Modeling human zymogen factor IX. Thromb Haemost 2001; 85: 596-603.
• 47 Kirchhofer D, Lipari MT, Moran P, Eigenbrot C, Kelley RF. The tissue factor region that interacts with substrates factor IX and Factor X. Biochemistry 2000; 39: 7380-7.
• 48 Kumar A, Blumenthal DK, Fair DS. Identification of molecular sites on factor VII which mediate its assembly and function in the extrinsic pathway activation complex. J Biol Chem 1991; 266: 915-21.
• 49 Mathur A, Zhong D, Sabharwal AK, Smith KJ, Bajaj SP. Interaction of factor IXa with factor VIIIa. Effects of protease domain Ca2+ binding site, proteolysis in the autolysis loop, phospholipid, and factor X. J Biol Chem 1997; 272: 23418-26.
• 50 Chang J, Jin J, Lollar P, Bode W, Brandstetter H, Hamaguchi N, Straight DL, Stafford DW. Changing residue 338 in human factor IX from arginine to alanine causes an increase in catalytic activity. J Biol Chem 1998; 273: 12089-94.
• 51 Kolkman JA, Mertens K. Insertion loop 256-268 in coagulation factor IX restricts enzymatic activity in the absence but not in the presence of factor VIII. Biochemistry 2000; 39: 7398-405.
• 52 Celie PH, Lenting PJ, Mertens K. Hydrophobic contact between the two epidermal growth factor-like domains of blood coagulation factor IX contributes to enzymatic activity. J Biol Chem 2000; 275: 229-34.
• 53 Shobe J, Dickinson CD, Ruf W. Regulation of the catalytic function of coagulation factor VIIa by a conformational linkage of surface residue Glu 154 to the active site. Biochemistry 1999; 38: 2745-51.
• 54 Ruf W. Factor VIIa residue Arg290 is required for efficient activation of the macromolecular substrate factor X. Biochemistry 1994; 33: 11631-6.
• 55 Wu PC, Hamaguchi N, Yu YS, Shen MC, Lin SW. Hemophilia B with mutations at glycine-48 of factor IX exhibited delayed activation by the factor VIIa-tissue factor complex. Thromb Haemost 2000; 84: 626-34.
• 56 Hertzberg MS, Facey SL, Hogg PJ. An Arg/Ser substitution in the second epidermal growth factor-like module of factor IX introduces an O-linked carbohydrate and markedly impairs activation by factor XIa and factor VIIa/ Tissue factor and catalytic efficiency of factor IXa. Blood 1999; 94: 156-63.
• 57 Huang Q, Neuenschwander PF, Rezaie AR, Morrissey JH. Substrate recognition by tissue factor-factor VIIa. Evidence for interaction of residues Lys165 and Lys166 of tissue factor with the 4-carboxyglutamate-rich domain of factor X. J Biol Chem 1996; 271: 21752-7.
• 58 Dittmar S, Ruf W, Edgington TS. Influence of mutations in tissue factor on the fine specificity of macromolecular substrate activation. Biochem J 1997; 321: 787-93.
• 59 Ruf W, Miles DJ, Rehemtulla A, Edgington TS. Tissue factor residues 157-167 are required for efficient proteolytic activation of factor X and factor VII. J Biol Chem 1992; 267: 22206-10.
• 60 Ruf W, Edgington TS. An anti-tissue factor monoclonal antibody which inhibits TF.VIIa complex is a potent anticoagulant in plasma. Thromb Haemost 1991; 66: 529-33.
• 61 Kirchhofer D, Eigenbrot C, Lipari MT, Moran P, Peek M, Kelley RF. The tissue factor region that interacts with factor Xa in the activation of factor VII. Biochemistry 2001; 40: 675-82.
• 62 Kirchhofer D, Moran P, Chiang N, Kim J, Riederer MA, Eigenbrot C, Kelley RF. Epitope location on tissue factor determines the anticoagulant potency of monoclonal anti-tissue factor antibodies. Thromb Haemost 2000; 84: 1072-81.
• 63 Huang M, Syed R, Stura EA, Stone MJ, Stefanko RS, Ruf W, Edgington TS, Wilson IA. The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF.G9 complex. J Mol Biol 1998; 275: 873-94.
• 64 Dickinson CD, Shobe J, Ruf W. Influence of cofactor binding and active site occupancy on the conformation of the macromolecular substrate exosite of factor VIIa. J Mol Biol 1998; 277: 959-71.
• 65 Dennis MS, Eigenbrot C, Skelton NJ, Ultsch MH, Santell L, Dwyer MA, O’Connell MP, Lazarus RA. Peptide exosite inhibitors of factor VIIa as anticoagulants. Nature 2000; 404: 465-70.
• 66 Rusconi CP, Yeh A, Lyerly HK, Lawson JH, Sullenger BA. Blocking the initiation of coagulation by RNA aptamers to factor VIIa. Thromb Haemost 2000; 84: 841-8.
• 67 Pawashe AB, Golino P, Ambrosio G, Migliaccio F, Ragni M, Pascucci I, Chiariello M, Bach R, Garen A, Konigsberg WK. et al. A monoclonal antibody against rabbit tissue factor inhibits thrombus formation in stenotic injured rabbit carotid arteries. Circ Res 1994; 74: 56-63.
• 68 Biemond BJ, Levi M, ten Cate H, Soule HR, Morris LD, Foster DL, Bogowitz CA, van der Poll T, Buller HR, ten Cate JW. Complete inhibition of endotoxin-induced coagulation activation in chimpanzees with a monoclonal Fab fragment against factor VII/VIIa. Thromb Haemost 1995; 73: 223-30.
• 69 Feuerstein GZ, Patel A, Toomey JR, Bugelski P, Nichols AJ, Church WR, Valocik R, Koster P, Baker A, Blackburn MN. Antithrombotic efficacy of a novel murine antihuman factor IX antibody in rats. Arterioscler Thromb Vasc Biol 1999; 19: 2554-62.
• 70 Kirchhofer D, Tschopp TB, Baumgartner HR. Active site-blocked factors VIIa and IXa differentially inhibit fibrin formation in a human ex vivo thrombosis model. Arterioscler Thromb Vasc Biol 1995; 15: 1098-106.
• 71 Taylor FB, Chang AC, Peer G, Li A, Ezban M, Hedner U. Active site inhibited factor VIIa (DEGR VIIa) attenuates the coagulant and interleukin-6 and -8, but not tumor necrosis factor, responses of the baboon to LD100 Escherichia coli. Blood 1998; 91: 1609-15.
• 72 Ghrib F, Leger P, Ezban M, Kristensen A, Cambus J, Boneu B. Anti-thrombotic and haemorrhagic effects of active site-inhibited factor VIIa in rats. Br J Haematol 2001; 112: 506-12.
• 73 Himber J, Kirchhofer D, Riederer M, Tschopp TB, Steiner B, Roux SP. Dissociation of antithrombotic effect and bleeding time prolongation in rabbits by inhibiting tissue factor function. Thromb Haemost 1997; 78: 1142-9.
• 74 Bullens S, Smith N, Rowell TJ, Chen C, Hanson S, Bunting S. Safety and efficacy of a humanized anti-tissue factor antibody F(ab’)2 fragment. Thromb Haemost. 2001 abstract 1388..
• 75 Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Cryst 1991; 24: 946-50.
• 76 Merritt EA, Bacon DJ. Raster3D: Photorealistic molecular graphics. Meth Enzymol 1997; 277: 505-24.