Design of P1' and P3' residues of trivalent thrombin inhibitors and their crystal structures

Biochemistry

Volumn 39, Issue 9, 2000, Pages 2384-2391

  Slon Usakiewicz, Jacek J ^a   Sivaraman, J ^a   Li, Yunge ^a   Cygler, Miroslaw ^a   Konishi, Yasuo ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

FIBRINOGEN; THROMBIN; THROMBIN INHIBITOR;

ARTICLE; BINDING AFFINITY; BINDING SITE; BLOOD CLOTTING; CRYSTAL STRUCTURE; CRYSTALLIZATION; HUMAN; MOLECULAR RECOGNITION; PEPTIDE SYNTHESIS; PRIORITY JOURNAL; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; AMINO ACIDS; ANTITHROMBINS; BINDING SITES; BINDING, COMPETITIVE; CRYSTALLIZATION; HUMANS; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN BINDING; PROTEIN CONFORMATION; SERINE PROTEINASE INHIBITORS; STRUCTURE-ACTIVITY RELATIONSHIP; THROMBIN;

EID: 0034092880     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi992419b     Document Type: Article

References (39)

1. Laudano, A. P., Cottrell, B. A., and Doolittle, R. F. (1983) Ann. N. Y. Acad Sci. 27, 315-329.
2. Vu, T.-K. H., Hung, D. T., Wheaton, V. I., and Coughlin, S. R. (1991) Cell 64, 1057-1068.
3. Schechter, I., and Berger, A. (1967) Biochem. Biophys. Res. Commun. 27, 157-162.
4. Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R., and Hofsteenge, J. (1989) EMBO J. 8, 3467-3475.
5. Blombäck, B., Blombäck, M., Hessel, B., and Iwanaga, S. (1967) Nature 215, 1445-1448.
6. Le Bonniec, B. F., Myles, T., Johnson, T., Knight, C. G., Tapparelli, C., and Stone, S. R. (1996) Biochemistry 35, 7114-7122.
7. Martin, P. D., Robertson, W., Turk, D., Huber, R., Bode, W., and Edwards, B. F. P. (1992) J. Biol. Chem. 267, 7911-7920.
8. Rezaie, A. R., and Olson S. T. (1997) Biochemistry 36, 1026-1033.
9. Maraganore, J. M., Bourdon, P., Jablonsky, J., Ramachandran, K. I., and Fenton, J. W. II (1990) Biochemistry 29, 7095-7101.
10. DiMaio, J., Gibbs, B., Munn, D., Lefebvre, J., Ni, F., and Konishi, Y. (1990) J. Biol. Chem. 265, 21698-21703.
11. Bourdon, P., Jablonski, J.-A., Chao, B. H., and Maraganore, J. M. (1991) FEBS Lett. 294, 163-166.
12. DiMaio, J., Ni, F., Gibbs, B., and Konishi, Y. (1991) FEBS Lett. 282, 47-52.
13. DiMaio, J., Gibbs, B., Lefebvre, J., Konishi, Y., Munn, D., Yue, S.-Y., and Hornberger, W. (1992) J. Med. Chem. 35, 3331-3341.
14. Kline, T., Hammond, C., Bourdon, P., and Maraganore, J. M. (1991) Biochem. Biophys. Res. Commun. 177, 1049-1055.
15. Krishnan, R., Tulinsky, A., Vlasuk, G. P., Pearson, D., Vallar, P., Bergum, P., Brunck, T. K., and Ripka, W. C. (1996) Protein Sci. 5, 422-433.
16. Lombardi, A., Nastri, F., Morte, R. D., Rossi, A., De Rosa, A., Staiano, N., Redone, C., and Pavone, V. (1996) J. Med. Chem. 39, 2008-2017.
17. Skordalakes, E., Elgendy, S., Goodwill, C. A., Green, D., Scully, M. F., Kakkar, V. V., Freyssinet, J.-M., Dodson, G., and Deadman, J. J. (1998) Biochemistry 37, 14420-14427.
18. Lombardi, A., De Simone, G., Nastri, F., Galdiero, S., Morte, R. D., Staiano, N., Pedone, C., Bolognesi, M., and Pavone, V. (1999) Protein Sci. 8, 91-95.
19. Rehse, P. H., Steinmetzer, T., Li, Y., Konishi, Y., and Cygler, M. (1995) Biochemistry 34, 11537-11544.
20. Tsuda, Y., Cygler, M., Gibbs, B. F., Pedyczak, A., Féthière, J., Yue, S.-Y., and Konishi, Y. (1994) Biochemistry 33, 14443-14451.
21. Slon-Usakiewicz, J. J. Purisima, E., Tsuda, Y., Sulea, T., Pedyczak, A., Féthière, J., Cygler, M., and Konishi, Y. (1997) Biochemistry 36, 13494-13502.
22. Szewczuk, Z., Gibbs, B. F., Yue, S.-Y., Purisima, E., Zdanow, A., Cygler, M., and Konishi, Y. (1993) Biochemistry 32, 3396-3404.
23. Szewcsuk, Z., Gibbs, B. F., Yue, S.-Y., Purisima, E., and Konishi, Y. (1992) Biochemistry 31, 9132-9140.
24. Segel, I. H. (1975) Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems, pp 100-160, John Wiley & Sons, New York.
25. Otwinowski, Z. (1993) Proceeding of the CCP4 Study Weekend: "Data Collection and Processing", Jan29-30, 1993, pp 56-62, SERC Daresbury Laboratory, England (compiled by Sawyer, L., Isaacs, N., and Bailey, S.).
26. Minor, W. (1993) XDISPLAY Program, Purdue University.
27. Zdanov, A., Wu, S., DiMaio, J., Konishi, Y., Li, Y., Wu, X., Edwards, B. F. P., Martin, P. D., and Cygler, M. (1993) Proteins 17, 252-265.
28. Jones, T. A., Zhou, J. Y., Cowan, S. W., and Kjeldgaard, M. (1991) Acta Crstallogr. A47, 110-119.
29. Brunger, A. T. (1993) X-plor version 3.1, Yale University, New Haven, CT.
30. Okuyama, K., and Ohuchi, S. (1996) Biopolymers 40, 85-103.
31. Féthière, J., Tsuda, Y., Coulombe, R., Konishi, Y., and Cygler, M. (1996) Protein Sci. 5, 1174-1183.
32. Skrzypczak-Jankun, E., Carperos, V. E., Ravichandran, K. G., Tulinsky, A., Westbrook, M., and Maraganore, J. M. (1991) J. Mol. Biol. 221, 1379-1393.
33. Qiu, X., Padmanabhan, K. P., Carperos, V. E., Tulinsky, A., Kline, T., Maraganore, J. M., and Fenton, J. W., II (1992) Biochemistry 31, 11689-11697.
34. Stephens, A. W., Siddiqui, A., and Hirsh, C. H. W. (1988) J. Biol. Chem. 263, 3639-3645.
35. Theunissen, H. J. M., Dijiikema, R., Grootenhuis, P. D. J., Swinkels, J. C., DePoorter, T. L., Carati, P., and Visser, A. (1993) J. Biol. Chem. 268, 9035-9040.
36. Wnendt, S., Janocha, E., Steffens, G. J., and Strassburger, W. (1997) Protein Eng. 10, 169-173.
37. Stubbs, M. T., and Bode, W. (1993) Thrombin Res. 69, 1-58.
38. Matthews, J. H., Krishnan, R., Costanzo, M. J., Maryanoff, B. E., and Tulinsky, A. (1996) Biophys. J. 71, 2830-2839.
39. St. Charles, R., Matthews, J. H., Zhang, E., and Tulinsky, A. (1999) J. Med. Chem. 42, 1376-1383.