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. 1993 Oct;2(10):1630–1642. doi: 10.1002/pro.5560021009

Changes in interactions in complexes of hirudin derivatives and human alpha-thrombin due to different crystal forms.

J P Priestle 1, J Rahuel 1, H Rink 1, M Tones 1, M G Grütter 1
PMCID: PMC2142260  PMID: 8251938

Abstract

The three-dimensional structures of D-Phe-Pro-Arg-chloromethyl ketone-inhibited thrombin in complex with Tyr-63-sulfated hirudin (ternary complex) and of thrombin in complex with the bifunctional inhibitor D-Phe-Pro-Arg-Pro-(Gly)4-hirudin (CGP 50,856, binary complex) have been determined by X-ray crystallography in crystal forms different from those described by Skrzypczak-Jankun et al. (Skrzypczak-Jankun, E., Carperos, V.E., Ravichandran, K.G., & Tulinsky, A., 1991, J. Mol. Biol. 221, 1379-1393). In both complexes, the interactions of the C-terminal hirudin segments of the inhibitors binding to the fibrinogen-binding exosite of thrombin are clearly established, including residues 60-64, which are disordered in the earlier crystal form. The interactions of the sulfate group of Tyr-63 in the ternary complex structure explain why natural sulfated hirudin binds with a 10-fold lower K(i) than the desulfated recombinant material. In this new crystal form, the autolysis loop of thrombin (residues 146-150), which is disordered in the earlier crystal form, is ordered due to crystal contacts. Interactions between the C-terminal fragment of hirudin and thrombin are not influenced by crystal contacts in this new crystal form, in contrast to the earlier form. In the bifunctional inhibitor-thrombin complex, the peptide bond between Arg-Pro (P1-P1') seems to be cleaved.

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Selected References

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  1. Bagdy D., Barabas E., Gráf L., Petersen T. E., Magnusson S. Hirudin. Methods Enzymol. 1976;45:669–678. doi: 10.1016/s0076-6879(76)45057-7. [DOI] [PubMed] [Google Scholar]
  2. Banner D. W., Hadváry P. Crystallographic analysis at 3.0-A resolution of the binding to human thrombin of four active site-directed inhibitors. J Biol Chem. 1991 Oct 25;266(30):20085–20093. [PubMed] [Google Scholar]
  3. Betz A., Hofsteenge J., Stone S. R. Role of interactions involving C-terminal nonpolar residues of hirudin in the formation of the thrombin-hirudin complex. Biochemistry. 1991 Oct 15;30(41):9848–9853. doi: 10.1021/bi00105a006. [DOI] [PubMed] [Google Scholar]
  4. Bode W., Mayr I., Baumann U., Huber R., Stone S. R., Hofsteenge J. The refined 1.9 A crystal structure of human alpha-thrombin: interaction with D-Phe-Pro-Arg chloromethylketone and significance of the Tyr-Pro-Pro-Trp insertion segment. EMBO J. 1989 Nov;8(11):3467–3475. doi: 10.1002/j.1460-2075.1989.tb08511.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bode W., Turk D., Karshikov A. The refined 1.9-A X-ray crystal structure of D-Phe-Pro-Arg chloromethylketone-inhibited human alpha-thrombin: structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships. Protein Sci. 1992 Apr;1(4):426–471. doi: 10.1002/pro.5560010402. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bourdon P., Jablonski J. A., Chao B. H., Maraganore J. M. Structure-function relationships of hirulog peptide interactions with thrombin. FEBS Lett. 1991 Dec 9;294(3):163–166. doi: 10.1016/0014-5793(91)80659-q. [DOI] [PubMed] [Google Scholar]
  7. Braun P. J., Dennis S., Hofsteenge J., Stone S. R. Use of site-directed mutagenesis to investigate the basis for the specificity of hirudin. Biochemistry. 1988 Aug 23;27(17):6517–6522. doi: 10.1021/bi00417a048. [DOI] [PubMed] [Google Scholar]
  8. Brezniak D. V., Brower M. S., Witting J. I., Walz D. A., Fenton J. W., 2nd Human alpha- to zeta-thrombin cleavage occurs with neutrophil cathepsin G or chymotrypsin while fibrinogen clotting activity is retained. Biochemistry. 1990 Apr 10;29(14):3536–3542. doi: 10.1021/bi00466a017. [DOI] [PubMed] [Google Scholar]
  9. Brünger A. T., Kuriyan J., Karplus M. Crystallographic R factor refinement by molecular dynamics. Science. 1987 Jan 23;235(4787):458–460. doi: 10.1126/science.235.4787.458. [DOI] [PubMed] [Google Scholar]
  10. Clore G. M., Sukumaran D. K., Nilges M., Zarbock J., Gronenborn A. M. The conformations of hirudin in solution: a study using nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J. 1987 Feb;6(2):529–537. doi: 10.1002/j.1460-2075.1987.tb04785.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. DiMaio J., Gibbs B., Munn D., Lefebvre J., Ni F., Konishi Y. Bifunctional thrombin inhibitors based on the sequence of hirudin45-65. J Biol Chem. 1990 Dec 15;265(35):21698–21703. [PubMed] [Google Scholar]
  12. Dodt J., Köhler S., Baici A. Interaction of site specific hirudin variants with alpha-thrombin. FEBS Lett. 1988 Feb 29;229(1):87–90. doi: 10.1016/0014-5793(88)80803-2. [DOI] [PubMed] [Google Scholar]
  13. Dodt J., Köhler S., Schmitz T., Wilhelm B. Distinct binding sites of Ala48-hirudin1-47 and Ala48-hirudin48-65 on alpha-thrombin. J Biol Chem. 1990 Jan 15;265(2):713–718. [PubMed] [Google Scholar]
  14. Folkers P. J., Clore G. M., Driscoll P. C., Dodt J., Köhler S., Gronenborn A. M. Solution structure of recombinant hirudin and the Lys-47----Glu mutant: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study. Biochemistry. 1989 Mar 21;28(6):2601–2617. doi: 10.1021/bi00432a038. [DOI] [PubMed] [Google Scholar]
  15. Grütter M. G., Fendrich G., Huber R., Bode W. The 2.5 A X-ray crystal structure of the acid-stable proteinase inhibitor from human mucous secretions analysed in its complex with bovine alpha-chymotrypsin. EMBO J. 1988 Feb;7(2):345–351. doi: 10.1002/j.1460-2075.1988.tb02819.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Haruyama H., Wüthrich K. Conformation of recombinant desulfatohirudin in aqueous solution determined by nuclear magnetic resonance. Biochemistry. 1989 May 16;28(10):4301–4312. doi: 10.1021/bi00436a027. [DOI] [PubMed] [Google Scholar]
  17. Jackson C. M., Nemerson Y. Blood coagulation. Annu Rev Biochem. 1980;49:765–811. doi: 10.1146/annurev.bi.49.070180.004001. [DOI] [PubMed] [Google Scholar]
  18. Karshikov A., Bode W., Tulinsky A., Stone S. R. Electrostatic interactions in the association of proteins: an analysis of the thrombin-hirudin complex. Protein Sci. 1992 Jun;1(6):727–735. doi: 10.1002/pro.5560010605. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Maraganore J. M., Chao B., Joseph M. L., Jablonski J., Ramachandran K. L. Anticoagulant activity of synthetic hirudin peptides. J Biol Chem. 1989 May 25;264(15):8692–8698. [PubMed] [Google Scholar]
  20. Noé G., Hofsteenge J., Rovelli G., Stone S. R. The use of sequence-specific antibodies to identify a secondary binding site in thrombin. J Biol Chem. 1988 Aug 25;263(24):11729–11735. [PubMed] [Google Scholar]
  21. Qiu X., Padmanabhan K. P., Carperos V. E., Tulinsky A., Kline T., Maraganore J. M., Fenton J. W., 2nd Structure of the hirulog 3-thrombin complex and nature of the S' subsites of substrates and inhibitors. Biochemistry. 1992 Dec 1;31(47):11689–11697. doi: 10.1021/bi00162a004. [DOI] [PubMed] [Google Scholar]
  22. Rydel T. J., Ravichandran K. G., Tulinsky A., Bode W., Huber R., Roitsch C., Fenton J. W., 2nd The structure of a complex of recombinant hirudin and human alpha-thrombin. Science. 1990 Jul 20;249(4966):277–280. doi: 10.1126/science.2374926. [DOI] [PubMed] [Google Scholar]
  23. Rydel T. J., Tulinsky A., Bode W., Huber R. Refined structure of the hirudin-thrombin complex. J Mol Biol. 1991 Sep 20;221(2):583–601. doi: 10.1016/0022-2836(91)80074-5. [DOI] [PubMed] [Google Scholar]
  24. Schechter I., Berger A. On the size of the active site in proteases. I. Papain. Biochem Biophys Res Commun. 1967 Apr 20;27(2):157–162. doi: 10.1016/s0006-291x(67)80055-x. [DOI] [PubMed] [Google Scholar]
  25. Skrzypczak-Jankun E., Carperos V. E., Ravichandran K. G., Tulinsky A., Westbrook M., Maraganore J. M. Structure of the hirugen and hirulog 1 complexes of alpha-thrombin. J Mol Biol. 1991 Oct 20;221(4):1379–1393. [PubMed] [Google Scholar]
  26. Stone S. R., Dennis S., Hofsteenge J. Quantitative evaluation of the contribution of ionic interactions to the formation of the thrombin-hirudin complex. Biochemistry. 1989 Aug 22;28(17):6857–6863. doi: 10.1021/bi00443a012. [DOI] [PubMed] [Google Scholar]
  27. Stone S. R., Hofsteenge J. Kinetics of the inhibition of thrombin by hirudin. Biochemistry. 1986 Aug 12;25(16):4622–4628. doi: 10.1021/bi00364a025. [DOI] [PubMed] [Google Scholar]
  28. Stubbs M. T., Oschkinat H., Mayr I., Huber R., Angliker H., Stone S. R., Bode W. The interaction of thrombin with fibrinogen. A structural basis for its specificity. Eur J Biochem. 1992 May 15;206(1):187–195. doi: 10.1111/j.1432-1033.1992.tb16916.x. [DOI] [PubMed] [Google Scholar]
  29. Vitali J., Martin P. D., Malkowski M. G., Robertson W. D., Lazar J. B., Winant R. C., Johnson P. H., Edwards B. F. The structure of a complex of bovine alpha-thrombin and recombinant hirudin at 2.8-A resolution. J Biol Chem. 1992 Sep 5;267(25):17670–17678. [PubMed] [Google Scholar]
  30. Yue S. Y., DiMaio J., Szewczuk Z., Purisima E. O., Ni F., Konishi Y. Characterization of the interactions of a bifunctional inhibitor with alpha-thrombin by molecular modelling and peptide synthesis. Protein Eng. 1992 Jan;5(1):77–85. doi: 10.1093/protein/5.1.77. [DOI] [PubMed] [Google Scholar]

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