Conformational changes in the NS3 protease from hepatitis C virus strain Bk monitored by limited proteolysis and mass spectrometry

Protein Science

Volumn 8, Issue 7, 1999, Pages 1445-1454

  Orrù, Stefania ^a,b   Dal Piaz, Fabrizio ^a   Casbarra, Annarita ^a   Biasiol, Gabriella ^b   De Francesco, Raffaele ^b   Steinkühler, Christian ^b   Pucci, Piero ^a  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b IRBM   (Italy)

Author keywords

Conformational analysis; Hepatitis C virus; Limited proteolysis; Mass spectrometry; NS3 protease; Selective chemical modifications

Indexed keywords

PROTEINASE; VIRUS PROTEIN;

AMINO ACID SEQUENCE; AMINO TERMINAL SEQUENCE; ARTICLE; BINDING SITE; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; ENZYME ACTIVATION; ENZYME CONFORMATION; ENZYME SUBSTRATE COMPLEX; HEPATITIS C VIRUS; MASS SPECTROMETRY; MOLECULAR INTERACTION; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN STABILITY;

EID: 0032813669     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.7.1445     Document Type: Article

References (43)

1. Bartenschlager R, Ahlborn-Laake L, Mous J, Jacobsen H. 1993. Nonstructural protein 3 of the Hepatitis C Virus encodes a serine-type proteinase required for cleavage at the NS3/4 and NS4/5 junctions. J Virol 67:3835-3844.
2. Bartenschlager R, Lohmann V, Wilkinson T, Koc JA. 1995. Complex formation between the NS3 serine-type proteinase of the Hepatitis C Virus and NS4A and its importance for polyprotein maturation. J Virol 69:7519-7528.
3. Bianchi E, Urbani A, Biasiol G, Brunetti M, Pessi A, De Francesco R, Steinkühler C. 1997. Complex formation between the Hepatitis C Virus serine protease and a synthetic NS4A cofactor peptide. Biochemistry 36:7890-7897.
4. Butkiewicz N, Wende M, Zhang R, Jubin R, Pichardo J, Smith E, Hart A, Ingram R, Durkin J, Mui P, et al. 1996. Enhancement of Hepatitis C Virus NS3 proteinase activity by association with NS4A specific synthetic peptides: Identification of the sequence and critical residues of NS4A for the cofactor activity. Virology 225:328-338.
5. Choo Q-L, Richman KH, Han HJ, Berger K, Lee C, Dong C, Colt D, Medina-Selby R, Barr PJ, Weiner AJ, et al. 1991. Genetic organization and diversity of the hepatitis C virus. Proc Natl Acad Sci USA 88:2451-2455.
6. Cohen SL, Ferrè-D'Amarè AR, Burley KS, Chait BT. 1995. Probing the solution structure of the DNA-binding protein Max by a combination of proteolysis and mass spectrometry. Protein Sci 4:82-87.
7. Cole J. 1996. Characterization of human Cytomegalovirus protease dimerization by analytical centrifugation. Biochemistry 35:15601-15610.
8. Darke PL, Cole JL, Waxman L, Hall DL, Sardana M, Kuo LC. 1996. Active human Cytomegalovirus protease is a dimer. J Biol Chem 271:7445-7449.
9. Eckart MR, Selby M, Masiarz F, Lee C, Berger K, Crawford K, Kuo C, Kuo G, Houghton M, Choo Q-L. 1993. The Hepatitis C Virus encodes a serine protease involved in the processing of the putative nonstructural proteins from the viral polyprotein precursor. Biochem Biophys Res Commun 192:399-406.
10. Failla C, Tomei L, De Francesco R. 1994. Both NS3 and NS4A are required for the proteolytic processing of Hepatitis C Virus nonstructural proteins. J Virol 68:3753-3760.
11. Failla C, Tomei L, De Francesco R. 1995. An amino-terminal domain of Hepatitis C Virus NS3 protease is essential for interaction with NS4A. J Virol 69:1769-1777.
12. Glocker MO, Bacher C, Fielder W, Suckau D, Przybylski K. 1994. Molecular characterisation of surface topology in protein tertiary structures by amino-acylation and mass spectrometric peptide mapping. Bioconj Chem 5:583-590.
13. Grakoui A, McCourt DW, Wychowski C, Feinstone SM, Rice CM. 1993. Characterisation of the Hepatitis C Virus-encoded serine proteinase: Determination of proteinase-dependent polyprotein cleavage sites. J Virol 67:2832-2843.
14. Hijikata M, Mizushima H, Akagi T, Mori S, Kakiuchi N, Kato N, Tanaka T, Kimura K, Shimotohno K. 1993. Two distinct proteinase activities required for the processing of a putative nonstructural precursor protein of Hepatitis C Virus. J Virol 67:4665-4675.
15. Houghton M, Weiner A, Han J, Kuo G, Choo Q-L. 1991. Molecular biology of the Hepatitis C Viruses: Implications for diagnosis, development and control of viral disease. Hepatology 14:381-388.
16. Kato N, Hijikata M, Oostuyama Y, Nagawaka M, Ohkoshi S, Sugimura T, Shimotohno K. 1990. Molecular cloning of the human Hepatitis C Virus genome from Japanese patients with non-A, non-B hepatitis. Proc Natl Acad Sci USA 87:9524-9528.
17. Kim JL, Morgenstern KA, Lin C, Fox T, Dwyer MD, Landro JA, Chambers SP, Markland W, Lepre CA, O'Malley ET, et al. 1996. Crystal structure of the Hepatitis C Virus NS3 protease domain complexed with a synthetic NS4A cofactor peptide. Cell 57:343-355.
18. Koch JO, Lohmann V, Herian U, Bartenschlager R. 1996. In vitro studies on the activation of the Hepatitis C Virus NS3 protease by the NS4A cofactor. Virology 221:54-66
19. Komoda Y, Hijikata M, Tanji Y, Hirowatari Y, Mizushima H, Kimura K, Shimotohono K. 1994. Processing of Hepatitis C viral polyprotein in Escherichia coli. Gene 145:221-226.
20. Lin C, Pragai BM, Grakoui A, Xu J, Rice CM. 1994. Hepatitis C Virus NS3 serine proteinase: Trans-cleavage requirements and processing kinetics. J Virol 68:8147-8157.
21. Lin C, Thomson JA, Rice CM. 1995. A central region in the Hepatitis C Virus NS4A protein allows formation of an active NS3-NS4A serine proteinase complex in vivo and in vitro. J Virol 69:4373-4380.
22. Love RA, Parge HE, Wickersham JA, Hostomsky Z, Habuka N, Moomaw EW, Adachi T, Hostomska Z. 1996. The crystal structure of Hepatitis C Virus NS3 proteinase reveals a trysin-like fold and a structural zinc binding site. Cell 87:331-342.
23. Margosiak SA, Vanderpool DL, Sisson W, Pinko C, Kan CC. 1996. Dimerization of the human Cytomegalovirus protease: Kinetic and biochemical characterisation of the catalytic homodimer. Biochemistry 55:5300-5307.
24. Mori A, Yamada J, Kimura T, Koide T, Yuasa S, Yamada E, Miyamura T. 1996. Enzymatic characterisation of purified NS3 serine proteinase of Hepatitis C Virus expressed in Escherichia coli. FEBS Lett 378:31-42.
25. Pizzi E, Tramontano A, Tomei L, La Monica N, Failla C, Sardana M, Wood T, De Francesco R. 1994. Molecular modelling of the specificity pocket of the Hepatitis C Virus protease: Implications for substrate recognition. Proc Natl Acad Sci USA 91:888-892.
26. Priev A, Almagor A, Yedgar S, Gavish B. 1996. Glycerol decreases the volume and compressibility of protein interior. Biochemistry 35:2061-2066.
27. Satoh S, Tanji Y, Hijikata M, Kimura K, Shimotohno K. 1995. The N-terminal region of Hepatitis C Virus nonstructural protein 3 (NS3) is essential for stable complex formation with NS4A. J Virol 69:4255-4260.
28. Scaloni A, Miraglia N, Orrù S, Amodeo P, Motta A, Marino G, Pucci P. 1998. Topology of Calmodulin-Melittin complex. J Mol Biol 277:945-958.
29. Shoji I, Suzuki T, Chieda S, Sato M, Harada T, Chiba T, Matsuura Y, Miyamura T. 1995. Proteolytic activity of NS3 serine proteinase of Hepatitis C Virus efficiently expressed in Escherichia coli. Hepatology 22:1648-1655.
30. Steinkühler C, Biasiol G, Brunetti M, Urbani A, Koch U, Cortese R, Pessi A, De Francesco R. 1998. Product inhibition of the Hepatitis C Virus NS3 protease. Biochemistry 37:8899-8905.
31. Steinkühler C, Tomei L, De Francesco R. 1996a. In vitro activity of Hepatitis C Virus protease NS3 purified from recombinant baculovirus-infected Sf9 cells. J Biol Chem 271:6367-6373.
32. Steinkühler C, Urbani A, Tomei L, Sardana M, Bianchi E, Pessi A, De Francesco R. 1996b. Activity of purified Hepatitis C Virus protease NS3 on peptide substrates. J Virol 70:6694-6700.
33. Suckau D, Mark M, Przybylski M. 1992. Protein surface topology-probing by selective chemical modification and mass spectrometric peptide mapping. Proc Nail Acad Sci USA 89:5630-5634.
34. Suzuki T, Sato M, Chieda S, Shoji I, Harada T, Yamakawa Y, Watabe S, Matsuura Y, Miyamura T. 1995. In vivo and in vitro trans-cleavage activity of Hepatitis C Virus serine proteinase expressed by recombinant baculoviruses. J Gen Virol 76:3021-3029.
35. Takamizawa A, Mori C, Fuke I, Manabe S, Murakame S, Fujita J, Onoshi E, Andoh T, Yoshida Y, Okayama H. 1991. Structure and organisation of the Hepatitis C Virus genome isolated from human carriers. J Virol 65:1105-1113.
36. Tanji Y, Hijikata M, Hirowatari Y, Shimotohno K. 1995. Hepatitis C virus-encoded nonstructural protein NS4A has versatile functions in viral protein processing. J Virol 69:1575-1581.
37. Timasheff SN. 1993. The control of protein stability and association by weak interaction with water: How do solvents affect these processes. Annu Rev Biophys Biomol Struct 22:67-97.
38. Tomei L, Failla C, Santolini E, De Francesco R, La Monica N. 1993. NS3 is a serine protease required for processing of Hepatitis C Virus polyprotein. J Virol 67:4017-4026.
39. Tomei L, Failla C, Vitale RL, Bianchi E, De Francesco R. 1996. A central Hydrophobic domain of the Hepatitis C Virus NS4A protein is required and sufficient for the activation of the NS3 protease. J Gen Virol 77:1065-1070.
40. Urbani A, Bianchi E, Narjes F, Tramontano A, De Francesco R, Steinkühler C, Pessi A. 1997. Substrate specificity of the Hepatitis C Virus serine protease NS3. J Biol Chem 272:9204-9209.
41. Yan Y, Li Y, Sardana V, Cole JL, Sardana M, Steinkühler C, Tomei L, De Francesco R, Kuo LC, Chen Z. 1998. Complex of NS3 protease and NS4A peptide of BK strain Hepatitis C Virus: A 2.2 Å resolution structure in a hexagonal crystal form. Protein Sci 7:837-847.
42. Zappacosta F, Ingallinella P, Scaloni A, Pessi A, Bianchi E, Sollazzo M, Tramontano A, Marino G, Pucci P. 1997. Surface topology of Minibody by selective chemical modification and mass spectrometry. Protein Sci 6:1901-1909.
43. Zappacosta F, Pessi A, Bianchi E, Venturini S, Sollazzo M, Tramontano A, Marino G, Pucci P. 1996. Probing the tertiary structure of proteins by limited proteolysis and mass spectrometry: The case of Miniboby. Protein Sci 5:802-813.