The mechanism of an inhibitory antibody on TF-initiated blood coagulation revealed by the crystal structures of human tissue factor, Fab 5G9 and TF·5G9 complex

Journal of Molecular Biology

Volumn 275, Issue 5, 1998, Pages 873-894

  Huang, Mingdong ^a   Syed, Rashid ^a,b   Stura, Enrico A ^a   Stone, Martin J ^a,c   Stefanko, Randy S ^a   Ruf, Wolfram ^a   Edgington, Thomas S ^a   Wilson, Ian A ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b AMGEN INC   (United States)

^c INDIANA UNIVERSITY   (United States)

Author keywords

Antibody antigen interactions; Blood coagulation mechanism

Indexed keywords

ARGININE; IMMUNOGLOBULIN F(AB) FRAGMENT; LYSINE; MONOCLONAL ANTIBODY; PROTEINASE; THROMBOPLASTIN; TYROSINE;

ANTIGEN ANTIBODY COMPLEX; ANTIGEN RECOGNITION; ARTICLE; BLOOD CLOTTING; COMPLEMENTARITY DETERMINING REGION; CONTROLLED STUDY; CRYSTAL STRUCTURE; HUMAN; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN STRUCTURE;

EID: 0032488808     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1512     Document Type: Article

References (56)

1. Amit, A. G., Mariuzza, R. A., Phillips, S. E. & Poljak, R. J. (1986). Three-dimensional structure of an antigen-antibody complex at 2.8 Å resolution. Science, 233, 747-753.
2. Arevalo, J. H., Stura, E. A., Taussig, M. J. & Wilson, I. A. (1993). Three-dimensional structure of an anti-steroid Fab′ and progesterone-Fab′ complex. J. Mol. Biol. 231, 103-118.
3. Ban, N., Escobar, C., Garcia, R., Hasel, K., Day, J., Greenwood, A. & McPherson, A. (1994). Crystal structure of an idiotype-anti-idiotype Fab complex. Proc. Natl Acad. Sci. USA, 91, 1604-1608.
4. Banner, D. W., D'Arcy, A., Chene, C., Winkler, F. K., Guha, A., Konigsberg, W. H., Nemerson, Y. & Kirchhofer, D. (1996). The crystal structure of the complex of blood coagulation factor VIIa with soluble tissue factor. Nature, 380, 41-46.
5. Bazan, J. F. (1990). Structural design and molecular evolution of a cytokine receptor superfamily. Proc. Natl Acad. Sci. USA, 87, 6934-6938.
6. Bernstein, F. C., Koetzle, T. F., Williams, G. J., Meyer, E. F., Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1978). The Protein Data Bank: a computer-based archival file for macromolecular structures. Arch. Biochem. Biophys. 185, 584-591.
7. Bhat, T. N., Bentley, G. A., Boulot, G., Greene, M. I., Tello, D., Dall'Acqua, W., Souchon, H., Schwarz, F. P., Mariuzza, R. A. & Poljak, R. J. (1994). Bound water molecules and conformational stabilization help mediate an antigen-antibody association. Proc. Natl Acad. Sci. USA, 91, 1089-1093.
8. Bizebard, T., Gigant, B., Rigolet, P., Rasmussen, B., Diat, O., Bosecke, P., Wharton, S. A., Skehel, J. J. & Knossow, M. (1995). Structure of influenza virus haemagglutinin complexed with a neutralizing antibody. Nature, 376, 92-94.
9. Bossart-Whitaker, P., Chang, C. Y., Novotny, J., Benjamin, D. C. & Sheriff, S. (1995). The crystal structure of the antibody N10-staphylococcal nuclease complex at 2.9 Å resolution. J. Mol. Biol. 253, 559-575.
10. Braden, B. C. & Poljak, R. J. (1995). Structural features of the reactions between antibodies and protein antigens. FASEB J. 9, 9-16.
11. Braden, B. C., Souchon, H., Eisele, J. L., Bentley, G. A., Bhat, T. N., Navaza, J. & Poljak, R. J. (1994). Three-dimensional structures of the free and the antigen-complexed Fab from monoclonal anti-lysozyme antibody D44.1. J. Mol. Biol. 243, 767-781.
12. Braden, B. C., Fields, B. A., Ysern, X., Dall'Acqua, W., Goldbaum, F. A., Poljak, R. J. & Mariuzza, R. A. (1996). Crystal structure of an Fv-Fv idiotope-anti-idiotope complex at 1.9 Å resolution. J. Mol. Biol. 264, 137-151.
13. Brocklehurst, S. M. & Perham, R. N. (1993). Prediction of the three-dimensional structures of the biotiny-lated domain from yeast pyruvate carboxylase and of the lipoylated H-protein from the pea leaf glycine cleavage system: a new automated method for the prediction of protein tertiary structure. Protein Sci. 2, 626-639.
14. Brünger, A. T. (1992a). Free R-value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472-474.
15. Brünger, A. T. (1992b). X-PLOR, Version 3.1: A System for X-ray Crystallography and NMR, Yale University Press, New Haven, CT.
16. Brünger, A. T., Kuriyan, J. & Karplus, M. (1987). Crystallographic R-factor refinement by molecular dynamics. Science, 235, 458-460.
17. Brünger, A. T., Krukowski, A. & Erickson, J. W. (1990). Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallog. sect. A, 46, 585-593.
18. Carter, P. J., Winter, G., Wilkinson, A. J. & Fersht, A. R. (1984). The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Cell, 38, 835-840.
19. Case, D. A. & Karplus, M. (1979). Dynamics of ligand binding to heme proteins. J. Mol. Biol. 132, 343-368.
20. CCP4 (1994). The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D, 50, 760-763.
21. Chacko, S., Silverton, E. W., Kam-Morgan, L., Smith-Gill, S. J., Cohen, G. H. & Davies, D. R. (1995). Structure of an antibody-lysozyme complex: unexpected effect of a conservative mutation. J. Mol. Biol. 245, 261-274.
22. Chitarra, V., Alzari, O. M., Bentley, G. A., Bhat, T. N., Eisele, J. L., Houdusse, A., Lescar, J., Souchon, H. & Poljak, R. J. (1993). Three-dimensional structure of a heteroclitic antigen-antibody cross-reaction complex. Proc. Natl Acad. Sci. USA, 90, 7711-7715.
23. Chothia, C., Lesk, A. M., Tramontano, A., Levitt, M., Smith-Gill, S. J., Air, G., Sheriff, S., Padlan, E. A., Davies, D., Tulip, W. R., Colman, P. M., Spinelli, S., Alzari, P. M. & Poljak, R. J. (1989). Conformations of immunoglobulin hypervariable regions. Nature, 342, 877-883.
24. Clackson, T. & Wells, J. A. (1995). A hot spot of binding energy in a hormone-receptor interface. Science, 267, 383-386.
25. Cohen, G. H., Sheriff, S. & Davies, D. R. (1996). Refined structure of the monoclonal antibody HyHEL-5 with its antigen hen egg-white lyzozyme. Acta Crystallog. sect. D, 52, 315-326.
26. Connolly, M. L. (1983). Solvent-accessible surfaces of proteins and nucleic acids. Science, 221, 709-713.
27. Covell, D. G. & Wallqvist, A. (1997). Analysis of protein-protein interactions and the effects of amino acid mutations on their energetics: the importance of water molecules in the binding epitope. J. Mol. Biol. 269, 281-297.
28. Cowtan, K. (1994). Joint CCP4 and ESF-EACBM Newsletter on Protein Crystallography, 31, 34-38.
29. Davies, D. R. & Cohen, G. H. (1996). Interactions of protein antigens with antibodies. Proc. Natl Acad. Sci. USA, 93, 7-12.
30. Davies, D. R., Padlan, E. A. & Sheriff, S. (1990). Antibody-antigen complexes. Annu. Rev. Biochem. 59, 439-473.
31. DeLand, A. L. & Brünger, A. T. (1995). The direct rotation function: rotational Patterson correlation search applied to molecular replacement. Acta Crystallog. sect. D, 51, 740-748.
32. Dickinson, C. D., Kelly, C. R. & Ruf, W. (1996). Identification of surface residues mediating tissue factor binding and catalytic function of the serine protease factor Vila. Proc. Natl Acad. Sci. USA, 93, 14379-14384.
33. Edgington, T. S., Mackman, N., Fan, S. T. & Ruf, W. (1992). Cellular immune and cytokine pathways resulting in tissue factor expression and relevance to septic shock. Nouv. Rev. Fr. Hematol. 34(Suppl.), S15-S27.
34. Ferrin, T. E., Huang, C. C., Jarvis, L. E. & Langridge, R. (1988). The Midas display system. J. Mol. Graph. 6, 13-27.
35. Fersht, A. R., Shi, J.-P., Knill-Jones, J., Lowe, D. M., Wilkinson, A. T., Blow, D. M., Brick, P., Carter, P., Ware, M. M. Y. & Winter, G. (1985). Hydrogen bonding and biological specificity analysed by protein engineering. Nature, 314, 235-238.
36. Fields, B. A., Goldbaum, F. A., Ysern, X., Poljak, R. J. & Mariuzza, R. A. (1995). Molecular basis of antigen mimicry by an anti-idiotope. Nature, 374, 739-742.
37. Fischmann, T. O., Bentley, G. A., Bhat, T. N., Boulot, G., Mariuzza, R. A., Phillips, S. E., Tello, D. & Poljak, R. J. (1991). Crystallographic refinement of the three-dimensional structure of the Fab D1.3 lysozyme complex at 2.5 A resolution. J. Biol. Chem. 266, 12915-12920.
38. Fitzgerald, P. M. D. (1988). MERLOT, an integrated package of computer programs for the determination of crystal structures by molecular replacement. J. Appl. Crystallog. 21, 273-278.
39. Furey, W. & Swaminathan, S. (1990). "PHASES" - a program package for the processing and analysis of diffraction data from macromolecules. PA33, Am. Crystallog. Assoc. Abstr. ser. 2, 18, 73.
40. Furey, W. & Swaminathan, S. (1997). PHASES-95: a program package for the processing and analysis of diffraction data from macromolecules. In Methods in Enzymology: Macromolecular Crystallography, Part B (Carter, C. & Sweet, R., eds), p. 277, Academic Press, Orlando, FL.
41. Gelin, B. R. & Karplus, M. (1979). Side-chain torsional potentials: effect of dipeptide, protein, and solvent environment. Biochemistry, 18, 1256-1268.
42. Harlos, K., Martin, D. M., O'Brien, D. P., Jones, E. Y., Stuart, D. I., Polikarpov, I., Miller, A., Tuddenham, E. G. & Boys, C. W. G. (1994). Crystal structure of the extracellular region of human tissue factor. Nature, 370, 662-666.
43. Harrison, S. C. (1968). A point-focusing camera for single-crystal diffraction. J. Appl. Crystallog. 1, 84-90.
44. Herron, J. N., He, X. M., Ballard, D. W., Blier, P. R., Pace, P. E., Bothwell, A. L., Voss, E. W., Jr & Edmundson, A. B. (1991). An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex. Proteins: Struct. Funct. Genet. 11, 159-175.
45. Herzberg, O., Chen, C. C., Kapadia, G., McGuire, M., Carroll, L. J., Noh, S. J. & Dunaway-Mariano, D. (1996). Swiveling-domain mechanism for enzymatic phosphotransfer between remote reaction sites. Proc. Natl Acad. Sci. USA, 93, 2653-2657.
46. Horovitz, A. (1996). Double-mutant cycles: a powerful tool for analyzing protein structure and function. Fold. Design, 1, R121-R126.
47. Howard, A. J., Gilliland, G. L., Finzel, B. C., Poulus, T. L., Ohlendorf, D. H. & Salemme, F. R. (1987). The use of an imaging proportional counter in macromolecular crystallography. J. Appl. Crystallog. 20, 383-387.
48. Huang, C. C., Pettersen, E. F., Klein, T. E. & Langridge, R. (1991). CONIC: a fast renderer for space-filling molecules with shadows. J. Mol. Graph. 9, 230-236.
49. Huber, R. (1985). In Proceedings of the Daresbury Study Weekend, pp. 58-61, Daresbury Laboratory, Daresbury, Warrington WA4 4AD, UK.
50. Jones, S. & Thornton, J. M. (1996). Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA, 93, 13-20.
51. Jones, T. A. (1978). A graphics model building and refinement system for macromolecules. J. Appl. Crystallog. 11, 268-272.
52. Jones, T. A. (1982). FRODO: a graphics fitting program for macromolecules. In Computational Chemistry (Sayre, D., ed.), pp. 303-317, Clarendon Press, Oxford.
53. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Improved methods for building protein models in electron density maps and the locations of errors in three models. Acta Crystallog. sect. A, 47, 110-119.
54. Kabat, E. A., Wu, T. T., Perry, H. M., Gottesman, K. S. & Foeller, C. (1991). Sequences of Proteins of Immunological Interest, 5th edit., National Institutes of Health, Bethesda.
55. Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Crystallog. sect. A, 32, 922-923.
56. Kelley, R. F., Costas, K. E., O'Connell, M. P. & Lazarus, R. A. (1995). Analysis of the factor Vila binding site on human tissue factor: effects of tissue factor mutations on the kinetics and thermodynamics of binding. Biochemistry, 34, 10383-10392.