X-ray structure and conformational dynamics of the HIV-1 protease in complex with the inhibitor SDZ283-910: Agreement of time-resolved spectroscopy and molecular dynamics simulations

Journal of Molecular Biology

Volumn 286, Issue 4, 1999, Pages 1147-1159

  Ringhofer, S ^a   Kallen, J ^b   Dutzler, R ^a   Billich, A ^c   Visser, A J W G ^d   Scholz, D ^c   Steinhauser, O ^a   Schreiber, H ^a   Auer, M ^c   Kungl, A J ^c  

^a UNIVERSITY OF VIENNA   (Austria)

^b NOVARTIS PHARMA AG   (Switzerland)

^c Brunnerstra e 59   (Austria)

^d WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

AIDS; HIV 1 protease; Molecular dynamics; Time resolved fluorescence; X ray crystallography

Indexed keywords

PROTEINASE; PROTEINASE INHIBITOR; SDZ 283910; UNCLASSIFIED DRUG;

ANISOTROPY; ARTICLE; CONTROLLED STUDY; DIPOLE; DRUG DESIGN; ENZYME BINDING; ENZYME CONFORMATION; FLUORESCENCE; HUMAN IMMUNODEFICIENCY VIRUS 1; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; SIMULATION; X RAY ANALYSIS;

EID: 0033525464     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1998.2533     Document Type: Article

References (47)

1. Allen M. P., Tildesley D. J. Computer Simulation of Liquids. 1987;Clarendon Press, Oxford.
2. Appelt K. Crystal structures of HIV-1 protease-inhibitor complexes. Persp. Drug Discov. Design. 1:1993;23-48.
3. Axelsen P. H., Gratton E., Prendergast F. G. Experimentally verifying molecular dynamics simulations through fluorescence anisotropy measurements. Biochemistry. 30:1991;1173-1179.
4. Bardi J. S., Luque I., Freire E. Structure-based thermodynamic analysis of HIV-1 protease inhibitors. Biochemistry. 36:1997;6588-6596.
5. Berendsen H. J. C., Postma J., van Gunsteren W. F., DiNola A., Haak J. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:1984;3684-3690.
6. Billich A., Hammerschmid F., Winkler G. Purification, assay and kinetic features of HIV-1 proteinase. Biol. Chem. Hoppe-Seyler. 371:1990;265-272.
7. Billich A., Charpiot B., Fricker G., Gstach H., Lehr P., Peichl P., Scholz D., Rosenwirth B. HIV proteinase inhibitors containing 2-aminobenzylstatine as a novel scissile bond replacement: biochemical and pharmacological characterization. Antiviral Res. 25:1994;215-233.
8. Billich A., Scholz D., Charpiot B., Gstach H., Lehr P., Peichl P., Rosenwirth B. Potent and orally bioavailable HIV-1 proteinase inhibitors containing the 2-aminobenzylstatine moiety. Antiviral Chem. Chemother. 6:1995;327-336.
9. Brünger A. T. X-PLOR Manual 3.l. 1992;Yale University Press, New Haven.
10. Budimir J., Skinner J. L. Kinetic Ising model for polymer dynamics. II. Generalized transition rates and the Williams-Watts function. J. Chem. Phys. 82:1985;5232-5241.
11. Collins J. R., Burt S. K., Erickson J. W. Flap opening in HIV-1 protease simulated by 'activated' molecular dynamics. Nature Struct. Biol. 2:1995;334-338.
12. Cross A. J., Fleming G. R. Analysis of time-resolved fluorescence anisotropy decays. Biophys. J. 46:1984;45-56.
13. Debouck C. The HIV-1 protease as a therapeutic target for AIDS. Res. Hum. Retroviruses. 8:1992;153-164.
14. De Clercq E. Toward improved anti-HIV chemotherapy: therapeutic strategies for intervention with HIV infections. J. Med. Chem. 38:1995;2491-2517.
15. Dreyer G., Boehm J., Chenera B., DesJarlais R., Hassell A., Meek T., Tomaszek T. A symmetric inhibitor binds HIV-1 protease asymmetrically. Biochemistry. 32:1993;937-947.
16. Eftink M. Fluorescence techniques for studying protein structure. Suelter C. H. Methods of Biochemical Analysis. 1991;127-205 John Wiley & Sons, New York.
17. Erickson J., Neidhart D. J., Vandrie J., Kempf D. J., Wang X. C., Norbeck D. W., Plattner J. J., Rittenhouse J. W., Turon M., Wideburg N., Kohibrenner W. E., Simmer R., Helfrich R., Paul D. A., Knigge M. Design, activity, and 2.8 Å crystal structure of a C2 symmetric inhibitor complexed to HIV-1 protease. Science. 249:1990;527-533.
18. Ewald P. Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys. 64:1921;253-287.
19. Fitzgerald P. M., Springer J. P. Structure and function of retroviral proteases. Annu. Rev. Biophys. Biomol. Struct. 20:1991;299-320.
20. Gustchina A., Weber I. T. Comparison of inhibitor binding in HIV-1 protease and in non-viral aspartic proteases: the role of the flap. FEBS Letters. 269:1990;269-272.
21. Harte W. E., Swaminathan S., Mansuri M. M., Martin J. C., Rosenberg I. E., Beveridge D. L. Domain communication in the dynamical structure of human immunodeficiency virus 1 protease. Proc. Natl Acad. Sci. USA. 87:1990;8864-8868.
22. Ichiye T., Karplus M. Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study. Biochemistry. 22:1983;2884-2893.
23. Jones T. A., Zou J.-Y., Cowan S. W., Kjeldgraad M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A. 47:1991;110-119.
24. Karplus M., McCammon J. A. Dynamics of proteins: elements and function. Annu. Rev. Biochem. 53:1983;263-300.
25. Klafter J., Blumen A. Models for dynamically controlled relaxation. Chem. Phys. Letters. 119:1985;377-382.
26. Kungl A. J., Visser N. V., van Hoek A., Visser A. J. W. G., Billich A., Schilk A., Gstach H., Auer M. Time-resolved fluorescence anisotropy of HIV-1 protease inhibitor complexes correlates with inhibitory activity. Biochemistry. 37:1998;2778-2786.
27. Lapatto R., Blundell T., Hemmings A., Overington J., Wilderspin A., Wood S., Merson J. R., Whittle P. J., Danley D. E., Geoghegan K. F., Hawrylik S. J., Lee S. E., Scheld K. G., Hobart P. M. X-ray analysis of HIV-1 proteinase at 2.7 Angstroms resolution confirms structural homology among retroviral enzymes. Nature. 342:1989;299-302.
28. Lee B., Richards F. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
29. Messerschmidt A., Pflugrath J. W. Crystal orientation and X-ray pattern prediction routines for area detector diffractometer systems in macromolecular crystallography. Appl. Crystallog. 20:1987;306-315.
30. Nicholson L. K., Yamazaki T., Torchia D. A., Grzesiek S., Bax A., Stahl S. J., Kaufman J. D., Wingfield P. T., Lam P. Y. S., Jadhav P. K., Hodge C. N., Domaille P. J., Chang C.-H. Flexibility and function in HIV-1 protease. Nature Struct. Biol. 2:1995;274-280.
31. Norberg J., Nilsson L. Stacking-unstacking of the dinucleoside monophosphate guanyl-3′,5′-uridine studied with molecular dynamics. Biophys. J. 67:1994;812-824.
32. O'Connor D. V., Phillips D. Time-Correlated Single Photon Counting. 1984;Academic Press, London.
33. Palmer R. G., Stein D. L., Abrahams E., Anderson P. W. Models of hierachically constrained dynamics for glassy relaxation. Phys. Rev. Letters. 53:1984;958-961.
34. Richards A. D., Phylip L. H., Farmerie W. G., Scarborough P. E., Alvarez A., Dunn B. M., Hirel P. H., Konvalinka J., Strop P., Pavlickova L. Sensitive, soluble chromogenic substrates for HIV-1 proteinase. J. Biol. Chem. 265:1990;7733-7736.
35. Ringe D. X-ray structures of retroviral proteases and their inhibitor-bound complexes. Methods Enzymol. 241:1994;157-177.
36. Schreiber H., Steinhauser O., Schuster P. Parallel molecular dynamics of biomolecules. Parallel Comp. 18:1992;557-573.
37. Seelmeier S., Schmidt H., Turk V., von der Helm K. Human immunodeficiency virus has an aspartic-type protease that can be inhibited by pepstatin A. Proc. Natl Acad. Sci. USA. 85:1988;6612-6616.
38. Umezawa H., Aoyagi T., Morishima H., Matsuzaki M., Hamada M., Takeuchi T. Pepstatin, a new pepsin inhibitor produced by Actinomycetes. J. Antibiot. 23:1970;259-262.
39. van Gunsteren W. F., Berendsen H. J. C. Algorithms for molecular dynamics and constrained dynamics. Mol. Phys. 34:1977;1311-1327.
40. van Gunsteren W. F., Berendsen H. J. C. The GROMOS User Manual. 1986.
41. van Hoek K., Vos K., Visser A. J. W. G. Ultrasensitive time-resolved polarized fluorescence spectroscopy as a tool in biology and medicine. IEEE J. Quantum Electron. QE-23:1987;1812-1820.
42. Venable R., Brooks B., Carson F. Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamics. Proteins: Struct. Funct. Genet. 15:1993;374-384.
43. Visser A. J. W. G., Kulinski T., van Hoek A. Fluorescence lifetime measurements of pseudoazulenes using picosecond-resolved single photon counting. J. Mol. Struct. 175:1988;111-116.
44. Visser A. J. W. G., van Engelen J., Visser N. V., van Hoek A., Hilhorst R., Freedman R. B. Fluorescence dynamics of staphylococcal nuclease in aqueous solution and reversed micelles. Biochim. Biophys. Acta. 1204:1994;225-234.
45. Williams G., Watts D. C. Non-symmetrical dielectric relaxation behaviour arising from a simple empirical decay function. Trans. Faraday Soc. 66:1970;80-85.
46. Wlodawer A., Miller M., Jaskolski M., Sathynarayana B., Baldwin E., Weber I., Selk L., Clawson L., Schneider J., Kent S. Conserved folding in retroviral protease: crystal structure of a synthetic HIV-1 protease. Science. 245:1989;616-621.
47. Yamamoto Y., Tanaka J. Polarized absorption spectra of crystals of indole and its related compounds. Bull. Chem. Soc. Japan. 45:1972;1362-1366.