Molecular and Structural Characterization of the Domain 2 of Hepatitis C Virus Non-structural Protein 5A

  • Liang, Yu (Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University) ;
  • Kang, Cong Bao (Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University) ;
  • Yoon, Ho Sup (Division of Structural and Computational Biology, School of Biological Sciences, Nanyang Technological University)
  • Received : 2006.02.02
  • Accepted : 2006.05.29
  • Published : 2006.08.31

Abstract

Hepatitis C virus (HCV) non-structural protein 5A protein (NS5A), which consists of three functional domains, is involved in regulating viral replication, interferon resistance, and apoptosis. Recently, the three-dimensional structure of the domain 1 was determined. However, currently the molecular basis for the domains 2 and 3 of HCV NS5A is yet to be defined. Toward this end, we expressed, purified the domain 2 of the NS5A (NS5A-D2), and then performed biochemical and structural studies. The purified domain 2 was active and was able to bind NS5B and PKR, biological partners of NS5A. The results from gel filtration, CD analysis, 1D $^1H$ NMR and 2D $^1H-^{15}N$ heteronuclear single quantum correlation (HSQC) spectroscopy indicate that the domain 2 of NS5A appears to be flexible and disordered.

Keywords

References

  1. Adler, A. J., Greenfield, N. J., and Fasman, G. D. (1973) Circular dichroism and optical rotatory dispersion of proteins and polypeptides. Methods Enzymol. 27, 675−735 https://doi.org/10.1016/S0076-6879(73)27030-1
  2. Blight, K. J., Kolykhalov, A. A., and Rice, C. M. (2000) Efficient initiation of HCV RNA replication in cell culture. Science 290, 1972−1974 https://doi.org/10.1126/science.290.5498.1972
  3. Bode, W., Schwager, P., and Huber, R. (1978) The transition of bovine trypsinogen to a trypsin-like state upon strong ligand binding. The refined crystal structures of the bovine trypsi trypsinogen-pancreatic trypsin inhibitor complex and of its ternary complex with Ile-Val at 1.9 A resolution. J. Mol. Biol. 118, 99−112 https://doi.org/10.1016/0022-2836(78)90246-2
  4. Brass, V., Bieck, E., Montserret, R., Wolk, B., Hellings, J. A., et al. (2002) Moradpour, An amino-terminal amphipathic alpha-helix mediates membrane association of the hepatitis C virus nonstructural protein 5A. J. Biol. Chem. 277, 8130−8139 https://doi.org/10.1074/jbc.M111289200
  5. Chung, Y. L., Sheu, M. L., and Yen, S. H. (2003) Hepatitis C virus NS5A as a potential viral Bcl-2 homologue interacts with Bax and inhibits apoptosis in hepatocellular carcinoma. Int. J. Cancer 107, 65−73 https://doi.org/10.1002/ijc.11303
  6. Dunker, A. K., Lawson, J. D., Brown, C. J., Williams, R. M., Romero, P., et al. (2001) Intrinsically disordered protein. J. Mol. Graph. Model 19, 26−59
  7. Gale, M. J. Jr, Korth, M. J., Tang, N. M., Tan, S. L., Hopkins, D. A., et al. (1997) Evidence that hepatitis C virus resistance to interferon is mediated through repression of the PKR protein kinase by the nonstructural 5A protein. Virology 230, 217−227 https://doi.org/10.1006/viro.1997.8493
  8. Gale, M. Jr., Kwieciszewski, B., Dossett, M., Nakao, H., and Katze, M. G. (1999) Antiapoptotic and oncogenic potentials of hepatitis C virus are linked to interferon resistance by viral repression of the PKR protein kinase. J. Virol. 73, 6506−6516
  9. Huang, L., Sineva, E. V., Hargittai, M. R., Sharma, S. D., Suthar, M., et al. (2004) Purification and characterization of hepatitis C virus non-structural protein 5A expressed in Escherichia coli. Protein Expr. Purif. 37, 144−153 https://doi.org/10.1016/j.pep.2004.05.005
  10. Liu, J., Tan, H., and Rost, B. (2002) Loopy proteins appear conserved in evolution. J. Mol. Biol. 322, 53−64
  11. Lohmann, V., Korner, F., Dobierzewska, A., and Bartenschlager, R. (2001) Mutations in hepatitis C virus RNAs conferring cell culture adaptation. J. Virol. 75, 1437−1449 https://doi.org/10.1128/JVI.75.3.1437-1449.2001
  12. Miller, R. H. and Purcell, R. H. (1990) Hepatitis C virus shares amino acid sequence similarity with pestiviruses and flaviviruses as well as members of two plant virus supergroups. Proc. Natl. Acad. Sci. USA 87, 2057−2061
  13. Ohsawa, M., Shingu, N., Miwa, H., Yoshihara, H., Kubo, M., et al. (1999) Risk of non-Hodgkin's lymphoma in patients with hepatitis C virus infection. Int. J. Cancer 80, 237−239 https://doi.org/10.1002/(SICI)1097-0215(19990118)80:2<237::AID-IJC12>3.0.CO;2-I
  14. Okuda, K. (1998) Hepatitis C and hepatocellular carcinoma. J. Gastroenterol. Hepatol. 13, 294–298 https://doi.org/10.1111/j.1440-1746.1998.tb00538.x
  15. Page, R., Peti, W., Wilson, I. A., Stevens, R. C., and Wüthrich, K. (2005) NMR screening and crystal quality of bacterially expressed prokaryotic and eukaryotic proteins in a structural genomics pipeline. Proc. Natl. Acad. Sci. USA 102, 1901−1905
  16. Pawlotsky, J. M. and Germanidis, G. (1999) The non-structural 5A protein of hepatitis C virus. J. Viral. Hepat. 6, 343−356 https://doi.org/10.1046/j.1365-2893.1999.00185.x
  17. Penin, F., Brass, V., Appel, N., Ramboarina, S., Montserret, R., et al. (2002) an amino-terminal amphipathic alpha-helix mediates membrane association of the hepatitis C virus nonstructural protein 5A. J. Biol. Chem. 277, 8130−8139
  18. Qin, W., Yamashita, T., Shirota, Y., Lin, Y., Wei, W., et al. (2001) Mutational analysis of the structure and functions of hepatitis C virus RNA-dependent RNA polymerase. Hepatology 33, 728−737 https://doi.org/10.1053/jhep.2001.22765
  19. Shimakami, T., Hijikata, M., Luo, H., Ma, Y. Y., Kaneko, S., et al. (2004) Effect of interaction between hepatitis C virus NS5A and NS5B on hepatitis C virus RNA replication with the hepatitis C virus replicon. J. Virol. 78, 2738−2748 https://doi.org/10.1128/JVI.78.6.2738-2748.2004
  20. Shirota, Y., Luo, H., Qin, W., Kaneko, S., Yamashita, T., et al. (2002) Hepatitis C virus (HCV) NS5A binds RNA-dependent RNA polymerase (RdRP) NS5B and modulates RNAdependent RNA polymerase activity. J. Biol. Chem. 277, 11149−11155 https://doi.org/10.1074/jbc.M111392200
  21. Tellinghuisen, T. L., Marcotrigiano, J., Gorbalenya, A. E., and Rice, C. M. (2004) The NS5A protein of hepatitis C virus is a zinc metalloprotein. J. Biol. Chem. 279, 48576−48587 https://doi.org/10.1074/jbc.M407787200
  22. Tellinghuisen, T. L., Marcotrigiano, J., and Rice, C. M. (2005) Structure of the zinc-binding domain of an essential component of the hepatitis C virus replicase. Nature 435, 374−379 https://doi.org/10.1038/nature03580
  23. Tompa, P. (2002) Intrinsically unstructured proteins. Trends Biochem. Sci. 27, 527−533 https://doi.org/10.1016/S0968-0004(02)02169-2
  24. Trepo, C., Berthillon, P., and Vitvitski, L. (1998) HCV and lymphoproliferative diseases. Ann. Oncol. 9, 469−470 https://doi.org/10.1023/A:1008298228620
  25. Uversky, V. N. (2002) Natively unfolded proteins: a point where biology waits for physics. Protein Sci. 11, 739−756 https://doi.org/10.1110/ps.4210102
  26. Wright, P. E. and Dyson, H. J. (1999) Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293, 321−331 https://doi.org/10.1006/jmbi.1999.3110
  27. Yamashita, T., Kaneko, S., Shirota, Y., Qin, W., Nomura, T., et al. (1998) RNA-dependent RNA polymerase activity of the soluble recombinant hepatitis C virus NS5B protein truncated at the C-terminal region. J. Biol. Chem. 273, 15479−15486 https://doi.org/10.1074/jbc.273.25.15479