Nonpolar interactions of thrombin S' subsites with its bivalent inhibitor: Methyl scan of the inhibitor linker

Biochemistry

Volumn 36, Issue 44, 1997, Pages 13494-13502

  Slon Usakiewicz, Jacek J ^a   Purisima, Enrico ^a   Tsuda, Yuko ^a,b   Sulea, Traian ^a   Pedyczak, Artur ^a,c   Féthière, James ^a   Cygler, Miroslaw ^a   Konishi, Yasuo ^a  

^a NATIONAL RESEARCH COUNCIL CANADA   (Canada)

^b KOBE GAKUIN UNIVERSITY   (Japan)

^c Connaught Laboratories Limited ^*  (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

THROMBIN; THROMBIN INHIBITOR;

ARTICLE; BLOOD CLOTTING; CRYSTAL STRUCTURE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME CONFORMATION; ENZYME INHIBITION; ENZYME INHIBITOR COMPLEX; HUMAN; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; STEREOSPECIFICITY;

ANIMALS; BINDING SITES; CATTLE; CRYSTALLOGRAPHY, X-RAY; HUMANS; MODELS, MOLECULAR; OLIGOPEPTIDES; SERINE PROTEINASE INHIBITORS; STRUCTURE-ACTIVITY RELATIONSHIP; SUBSTRATE SPECIFICITY; THROMBIN;

EID: 0030815230     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi970857h     Document Type: Article

References (52)

1. Bajusz, S., Széll, E., Badgy, D., Barabás, E., Horváth, G., Diószegi, M., Fittler, Z., Szabó, G. A., Juhász, A., Tomori, E., & Szilágyi, G. (1990) J. Med. Chem. 33, 1729-1735.
2. Bajusz, S., Barabás, E., Fauszt, I., Feher, A., Horváth, G., Juhász, A., Szabó, G. A., & Széll, E. (1996) Semin. Thromb. Hemostasis 22, 243-246.
3. Blamback, B., Blamback, M., Hessel, B., & Iwanaga, S. (1967) Nature 215, 1445-1448.
4. Bode, W., Mayr, I., Baumann, U., Huber, R., Stone, S. R., & Hofsteenge, J. (1989) EMBO J. 8, 3467-3475.
5. Bode, W., Turk, D., & Sturzebecher, J. (1990) Eur. J. Biochem. 193, 175-182.
6. Bode, W., Turk, D., & Karshikov, A. (1992) Protein Sci. 1, 426-471.
7. Boobyer, D. N. A., Goodford, P. J., McWhinnie, P. M., & Wade, R. C. (1989) J. Med. Chem. 32, 1083-1094.
8. Brandstetter, H., Turk, D., Hoeffken, H. W., Grosse, D., Stürzebecher, J., Martin, P. D., Edwards, B. F. P., & Bode, W. (1992) J. Mol. Biol. 226, 1085-1099.
9. Brourdon, P., Jablonski, J.-A., Chao, B. H., & Maraganore, J. M. (1991) FEBS Lett. 294, 163-166.
10. Chang, J. Y. (1990) J. Biol. Chem. 265, 22159-22166.
11. Chaturvedi, D. N., Knittel, J. J., Hruby, V. J., Castrucci, A. M., & Hadley, M. E. (1984) J. Med. Chem. 27, 1406-1410.
12. Costanzo, M. J., Maryanoff, B. E., Hecker, L. R., Schott, M. R., Yabut, S. C. Zhang, H.-C., Andrade-Gordon, P., Kauffman, J. A., Lewis, J. M., Krishnan, R., & Tulinsky, A. (1996) J. Med. Chem. 39, 3039-3043.
13. DiMaio, J., Gibbs, B., Munn, D., Lefebvre, J., Ni, F., & Konishi, Y. (1990) J. Biol. Chem. 265, 21698-21703.
14. DiMaio, J., Ni, F., Gibbs, B., & Konishi, Y. (1991) FEBS Lett. 282, 47-52.
15. DiMaio, J., Gibbs, B., Lefebvre, J., Konishi, Y., Munn, D., Yue, S.-Y., & Hornberger, W. (1992) J. Med. Chem. 35, 3331-3341.
16. Fenton, J. W., II, & Bing, D. H. (1986) Semin. Thromb. Hemostasis 12, 200-208.
17. Féthière, J., Tsuda, Y., Coulombe, R., Konishi, Y., & Cygler, M. (1996) Protein Sci. 5, 1174-1183.
18. Goodford, P. J. (1985) J. Med. Chem. 28, 849-857.
19. Hopfner, K.-P., Ayala, Y., Szewczuk, Z., Konishi, Y., & Cera, E. D. (1993) Biochemistry 32, 2947-2953.
20. IMSL, International Mathematical Statistical Library (1987) Library Reference Manual, version 1.0, 9th ed., IMSL, Houston, TX.
21. Jackman, M. P., Parry, M. A. A., Hofsteenge, J., & Stone, S. R. (1992)7. Biol. Chem. 267, 15375-15383.
22. Kettner, C., Mersinger, L., & Knabb, R. (1990) J. Biol. Chem. 265, 18289-18297.
23. Kettner, M. P., & Shaw, E. (1979) Thromb. Res. 14, 969-973.
24. Kikumoto, R., Tamao, Y., Tezuka, T., Tonomura, S., Hara, H., Ninomiya, K., Hijikata, A., & Okamoto, S. (1984) Biochemistry 23, 85-90.
25. Krishnan, R., Tulinsky, A., Vlasuk, G. P., Pearson, D., Vallar, P., Bergum, P., Brunck, T. K., & Ripka, W. C. (1996) Protein Sci. 5, 422-433.
26. Liem, R. K. H., & Scheraga, H. A. (1914) Arch. Biochem. Biophys. 160, 333-339.
27. Mao, S. J. T., Yates, M. T., Owen, T. J., & Krestenansky, J. L. (1988) Biochemistry 27, 8170-8173.
28. Maraganore, J. M., Bourdon, P., Jablonsky, J., Ramachandran, K. L., & Fenton, J. W., II (1990) Biochemistry 29, 7095-7101.
29. Markwardt, F. (1970) Methods Enzymol. 19, 924-932.
30. More, J. J., Garbow, B. S., & Hillstrom, K. E. (1980) Argonne National Labs Report ANL-80-74, Argonne National Labs, Argonne, IL.
31. Nienaber, V. L., & Amparo, E. C. (1996) J. Am. Chem. Soc. 118, 6807-6810.
32. Qiu, X., Padmanabhan, K. P., Carperos, V. E., Tulinsky, A., Kline, T., Maraganore, J. M., & Fenton, J. W., II (1992) Biochemistry 31, 11689-11697.
33. Rehse, P. H., Steinmetzer, T., Li, Y., Konishi, Y., & Cygler, M. (1995) Biochemistry 34, 11537-11544.
34. Rydel, T. J., Ravichandran, K. G., Tulinsky, A., Bode, W., Huber, R., Roitsch, C., & Fenton, J. W., II (1990) Science 249, 277-280.
35. Rydel, T. J., Tulinsky, A., Bode, W., & Huber, R. (1991) J. Mol. Biol. 227, 583-601.
36. Schechter, I., & Berger, A. (1967) Biochem. Biophys. Res. Commun. 27, 157-162.
37. Segel, I. H. (1975) Enzyme Kinetics: Behavior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems, pp 100-160, John Wiley & Sons.
38. Smith, G. F., Shuman, R. T., Craft, T. J., Gifford, D. S., Kurz, K. D., Jones, N. D., Chirgadze, N., Hermann, R. B., Coffman, W. J., Sandusky, G. E., Roberts, E., & van Jackson, C. (1996) Semin. Thromb. Hemostasis 22, 173-183.
39. Stone, S. R., & Hofsteenge, J. (1986) Biochemistry 25, 4622-4628.
40. Stouten, P. F. W., Frömmel, C., Nakamura, H., & Sander, C. (1993) Mol. Simul. 10, 91-120.
41. Sturzebecher, J., Markwardt, F., Voigt, B., Wagner, G., & Walsmann, P. (1983) Thromb. Res. 29, 635-642.
42. Szewczuk, Z., Gibbs, B. F., Yue, S.-Y., Purisima, E., & Konishi, Y. (1992) Biochemistry 31, 9132-9140.
43. Szewczuk, Z., Gibbs, B. F., Yue, S.-Y., Purisima, E., Zdanow, A., Cygler, M., & Konishi, Y. (1993) Biochemistry 32, 3396-3404.
44. Tsuda, Y., Cygler, M., Gibbs, B. F., Pedyczak, A., Féthière, J., Yue, S.-Y., & Konishi, Y. (1994) Biochemistry 33, 14443-14451.
45. Tsuda, Y., Szewczuk, Z., Wang, J., Yue, S.-Y., Purisima, E., & Konishi, Y. (1995) Biochemistry 34, 8708-8714.
46. Tucker, T. J., Lumma, W. C., Mulichak, A. M., Chen, Z., Naylor-Olsen, A. M., Lewis, S. D., Lucas, R., Freidinger, R. M., & Kuo, L. C. (1997) J. Med. Chem. 40, 830-832.
47. Weiner, S. J., Kollman, P. A., Nguyen, D. T., & Case, D. A. (1986) J. Comput. Chem. 7, 230-252.
48. Witting, J. I., Bourdon, P., Brezniak, D. V., Maraganore, J. M., & Fenton, J. W., II (1992a) Biochem. J. 283, 737-743.
49. Witting, J. I., Bourdon, P., Maraganore, J. M., & Fenton, J. W., II (1992b) Biochem. J. 287, 663-664.
50. Yue, S.-Y., DiMaio, J., Szewczuk, Z., Purisima, E., Ni, F., & Konishi, Y. (1992) Protein Eng. 5, 77-85.
51. Zdanov, A., Wu, S., DiMaio, J., Konishi, Y., Li, Y., Wu, X., Edwards, B. F. P., Martin, P. D., & Cygler, M. (1993) Proteins 17, 252-265.
52. Zuckermann, R. N., Kerr, J. M., Kent, S. B. H., & Moos, W. H. (1992) J. Am. Chem. Soc. 114, 10646-10647.