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Korean Society for Biochemistry and Molecular Biology (생화학분자생물학회)
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Backbone 1H, 15N, and 13C Resonance Assignment and Secondary Structure Prediction of HP0495 from Helicobacter pylori

  • Seo, Min-Duk (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University) ;
  • Park, Sung-Jean (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University) ;
  • Kim, Hyun-Jung (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University) ;
  • Seok, Seung-Hyeon (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University) ;
  • Lee, Bong-Jin (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University)
  • Published : 2007.09.30
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Abstract

HP0495 (Swiss-Prot ID; Y495_HELPY) is an 86-residue hypothetical protein from Helicobacter pylori strain 26695. The function of HP0495 cannot be identified based on sequence homology, and HP0495 is included in a fairly unique sequence family. Here, we report the sequencespecific backbone resonance assignments of HP0495. About 97% of all the $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances were assigned unambiguously. We could predict the secondary structure of HP0495, by analyzing the deviation of the $^{13}C{\alpha}$ and $^{13}C{\beta}$ shemical shifts from their respective random coil values. Secondary structure prediction shows that HP0495 consists of two $\alpha$-helices and four $\beta$-strands. This study is a prerequisite for determining the solution structure of HP0495 and investigating the protein-protein interaction between HP0495 and other Helicobacter pylori proteins.

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References

  1. Alm, R. A., King, L. S., Moir, D. T., King, B. L., Brown, E. D., Doig, P. C., Smith, D. R., Noonan, B., Guild, B. C., deJonge, B. L., Carmel, G., Tummino, P. J., Caruso, A., Uria-Nickelsen, M., Mills, D. M., Ives, C., Gibson, R., Merberg, D., Mills, S. D., Jiang, Q., Taylor, D. E., Vovis, G. F. and Trust, T. J. (1999) Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397, 176-180. https://doi.org/10.1038/16495
  2. Blaser, M. J. (1990) Helicobacter pylori and the pathogenesis of gastroduodenal inflammation. J. Infect. Dis. 161, 626-633. https://doi.org/10.1093/infdis/161.4.626
  3. Bodenhausen, G. and Ruben, D. J. (1980) Heteronuclear 2D correlation spectra with double in-phase transfer steps. Chem. Phys. Letters 69, 185-189. https://doi.org/10.1016/0009-2614(80)80041-8
  4. Boneca, I. G., de Reuse, H., Epinat, J. C., Pupin, M., Labigne, A. and Moszer, I. (2003) A revised annotation and comparative analysis of Helicobacter pylori genomes. Nucleic Acids Res. 31, 1704-1714. https://doi.org/10.1093/nar/gkg250
  5. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J. and Bax, A. (1995) NMRPipe: a multidimensional spectral processing system based on UNIX pipes. J. Biomol. NMR 6, 277-293 https://doi.org/10.1007/BF00197809
  6. Fairbrother, W. J., Palmer, A. G., Rance, M., Reizer, J., Saier, M. H. and Wright, P. E. (1992) Assignment of the aliphatic proton and carbon-13 resonances of the Bacillus subtilis glucose permease IIA domain using double- and triple-resonance heteronuclear three-dimensional NMR spectroscopy. Biochemistry 31, 4413-4425. https://doi.org/10.1021/bi00133a005
  7. Forman, D., Newell, D. G., Fullerton, F., Yarnell, J. W., Stacey, A. R., Wald, N. and Sitas, F. (1991) Association between infection with Helicobacter pylori and risk of gastric cancer: evidence from a prospective investigation. Br. Med. J. 302, 1302-1305. https://doi.org/10.1136/bmj.302.6788.1302
  8. Gabriel, C., Frank, D. and Bax, A. (1995) Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13, 289-302. https://doi.org/10.1023/A:1008392405740
  9. Jean-F. T., Owen, W., Anthony, R. K., Rebecca, A. C., Granger G. S., Robert, D. F., Karen, A. K., Hans, P. K., Steven, G., Brian, A. D., Karen, N., John, Q., Lixin, Z., Ewen, F. K., Anna, G., Keith, M., Lisa, M. F., Norman, L., Mark, D. A., Erin, K. H., Douglas, E. B., Jeanine, M. W., Claire, F., Cheryl, B., Larry, W., Erik, W., William, S. H., Mark, B., Peter, D. K., Hamilton, O. S., Claire, M. F. and Craig, V. (1997) The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388, 539-547 https://doi.org/10.1038/41483
  10. Johnson, B. A. and Blevins, R. A. (1994) NMRView: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603-614. https://doi.org/10.1007/BF00404272
  11. Kusters, J. G., Gerrits, M. M., Van Strijp, J. A. and Vandenbroucke-Grauls, C. M. (1997) Coccoid forms of Helicobacter pylori are the morphologic manifestation of cell death. Infect. Immun. 65, 3672-3679.
  12. Metzler, W. J., Constantine, K. L., Friedrichs, M. S., Bell, A. J., Ernst, E. G., Lavoie, T. B. and Muller, L. (1993) Characterization of the three-dimensional solution structure of human profiling: 1H, 13C, and 15N NMR assignments and global folding pattern. Biochemistry 32, 6201-6211.
  13. O'Toole, P. W., Lane, M. C. and Porwollil, S. (2000) Helicobacter pylori motility. Microbes Infect. 2, 1207-1214. https://doi.org/10.1016/S1286-4579(00)01274-0
  14. Parsonnet, J., Hansen, S., Rodriguez, L., Gelb, A. B., Warnke, R. A., Jellum, E., Orentreich, N., Vogelman, J. H. and Friedman, G. D. (1994) Helicobacter pylori infection and gastric lymphoma. N. Engl. J. Med. 330, 1267-1271. https://doi.org/10.1056/NEJM199405053301803
  15. Reid, D. G. (1997) Protein NMR Techniques. Humana Press: New Jersey, USA.
  16. Spera, S. and Bax, A. (1991) Empirical correlation between protein backbone conformation and C.alpha. and C.beta. 13C nuclear magnetic resonance chemical shifts. J. Am. Chem. Soc. 113, 5490-5492. https://doi.org/10.1021/ja00014a071
  17. Wishart, D. S., Sykes, B. D. and Richards, F. M. (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol. 222, 311-333. https://doi.org/10.1016/0022-2836(91)90214-Q
  18. Wishart, D. S. and Sykes, B. D. (1994) The $^{13}C$ chemical-shift index: a simple method for the identification of protein secondary structure using $^{13}C$ chemical-shift data. J. Biomol. NMR. 4, 171-180.
  19. Wittekind, M. and Mueller, L. (1993) HNCACB, a highsensitivity 3D NMR experiment to correlate amide proton and nitrogen resonances with the ${\alpha}-carbon$ and ${\beta}-carbon$ resonances in proteins. J. Magn. Reson. ser. 101, 214-217. https://doi.org/10.1006/jmrb.1993.1036
  20. Yamazaki, T., Lee, W., Revington, M., Mattiello, D. L., Dahlquist, F. W., Arrowsmith, C. H. and Kay, L. E. (1994) An HNCA pulse scheme for the backbone assignment of $^{15}N,\;^{13}C,\;^2H$ labeled proteins: application to a 37-kDa trp repressor-DNA complex. J. Am. Chem. Soc. 116, 6464-6465. https://doi.org/10.1021/ja00093a069

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