Journal of the Korean Magnetic Resonance Society (한국자기공명학회논문지)

Korean Magnetic Resonance Society (한국자기공명학회)
권호 표지
DOI QR코드

DOI QR Code

Backbone 1H, 15N, and 13C Resonance Assignment and Secondary Structure Prediction of HP1298 from Helicobacter pylori

  • Kim, Won-Je (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University) ;
  • Lim, Jong-Soo (Advanced Analysis Center, Korea Institute of Science and Technology (KIST)) ;
  • Son, Woo-Sung (Department of Chemistry and Biochemistry University of California) ;
  • Ahn, Hee-Chul (Advanced Analysis Center, Korea Institute of Science and Technology (KIST)) ;
  • Lee, Bong-Jin (Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University)
  • Published : 2008.12.20
Download PDF
⟨ Previous Next ⟩

Abstract

HP1298 (Swiss-Prot ID ; P65108) is an 72-residue protein from Helicobacter pylori strain 26695. The function of HP1298 was identified as Translation initiation factor IF-l based on sequence homology, and HP1298 is included in IF-l family. Here, we report the sequence-specific backbone resonance assignments of HP1298. About 97% of all the $^{1}HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances could be assigned unambiguously. We could predict the secondary structure of HP1298, 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 HP1298 consists of six $\beta$-strands. This study is a prerequisite for determining the solution structure of HP1298 and investigating the structure-function relationship of HP1298. Assigned chemical shift can be used for the study on interaction between HP1298 and other Helicobacter pylori proteins.

Keywords

References

  1. J. G. Kusters, M. M. Gerrits, J. A. Van Strijp, and C. M. Vandenbroucke-Grauls, Coccoid forms of Helicobacter pylori are the morphologic manifestation of cell death, Infect. Immun. 65, 3672-3679 (1997).
  2. P. W. O`Toole, M. C. Lane, and S. Porwollil, Helicobacter pylori motility, Microbes Infect. 2, 1207-1214 (2000). https://doi.org/10.1016/S1286-4579(00)01274-0
  3. M. J. Blaser, Helicobacter pylori and the pathogenesis of gastroduodenal inflammation, J. Infect. Dis. 161, 626-633 (1990). https://doi.org/10.1093/infdis/161.4.626
  4. D. Forman, D. G. Newell, F. Fullerton, J. W. Yarnell, A. R. Stacey, N. Wald, and F. Sitas, Association between infection with Helicobacter pylori and risk of gastric cancer: evidence from a prospective investigation, Br. Med. J. 302, 1302-1305 (1991). https://doi.org/10.1136/bmj.302.6788.1302
  5. J. Parsonnet, S. Hansen, and L. Rodriguez, et al. Helicobacter pylori infection and gastric lymphoma, N. Engl. Med. 330, 1267-1271 (1994). https://doi.org/10.1056/NEJM199405053301803
  6. F. T. Jean, W. Owen, R. K. Anthony, A. C. Rebecca, G. S. Granger, D. F. Robert, A. K. Karen, P. K. Hans, G. Steven, A. D. Brian, N. Karen, Q. John, Z. Lixin, F. K. Ewen, G. Anna, M. Keith, M. F. Lisa, L. Norman, D. A. Mark, K. H. Erin, E. B. Douglas, M. W. Jeanine, F. Claire, B. Cheryl, W. Larry, W. Erik, S. H. William, B. Mark, D. K. Peter, O. S, Hamilton, M. F. Claire, and V. Craig, The complete genome sequence of the gastric pathogen Helicobacter pylori, Nature 388:7, 539-547 (1997). https://doi.org/10.1038/41483
  7. R. A. Alm, L. S. King, D. T. Moir, B. L. King, E. D. Brown, P. C. Doig, D. R. Smith, B. Noonan, B. C. Guild, B. L. deJonge, G. Carmel, P. J. Tummino, A. Caruso, M. Uria- Nickelsen, D. M. Mills, C. Ives, R. Gibson, D. Merberg, S. D. Mills, Q. Jiang, D. E. Taylor, G. F. Vovis, and T. J. Trust, Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen, Helicobacter pylori. Nature 397, 176-180 (1999). https://doi.org/10.1038/16495
  8. I. G. Boneca, H. de Reuse, J. C. Epinat, M. Pupin, A. Labigne, and I. Moszer, A revised annotation and comparative analysis of Helicobacter pylori genomes, Nucleic Acids Res. 31, 1704-1714 (2003). https://doi.org/10.1093/nar/gkg250
  9. G. Bodenhausen, and D. J. Ruben, Heteronuclear 2D correlation spectra with double inphase transfer steps, Chem. Phys. Letters 69, 185-189 (1980). https://doi.org/10.1016/0009-2614(80)80041-8
  10. M. Wittekind, and L. Mueller, 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. B 101, 214-217 (1993). https://doi.org/10.1006/jmrb.1993.1036
  11. T. Yamazaki, W. Lee, M. Revington, D. L. Mattiello, F. W. Dahlquist, C. H. Arrowsmith, and L. E. Kay, 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 (1994). https://doi.org/10.1021/ja00093a069
  12. D.G. Reid, "Protein NMR Techniques." Humana Press, New Jersey, 1997.
  13. F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer, and A. Bax, NMRPipe: a multidimensional spectral processing system based on UNIX pipes, J. Biomol. NMR 6, 277-293 (1995)
  14. B. A. Johnson, and R. A. Blevins, NMRView: A computer program for the visualization and analysis of NMR data, J. Biomol. NMR 4, 603-614 (1994). https://doi.org/10.1007/BF00404272
  15. D. S. Wishart, and B. D. Sykes, 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 (1994).
  16. C. Gabriel, D. Frank, and A. Bax, Protein backbone angle restraints from searching a database for chemical shift and sequence homology, J. Biomol. NMR 13, 289-302 (1995).
  17. W. J. Metzler, K. L. Constantine, M. S. Friedrichs, A. J. Bell, E. G. Ernst, T. B. Lavoie, and L. Muller, Characterization of the three-dimensional solution structure of human profiling: $^1H,^{13}C$, and $^{15}N$ NMR assignments and global folding pattern, Biochemistry 32, 6201-6211 (1993).
  18. S. Spera, and A. Bax, Empirical correlation between protein backbone conformation and C.alpha. and C.beta. $^{13}C$ nuclear magnetic resonance chemical shifts, J. Am. Chem. Soc. 113, 5490-5492 (1991). https://doi.org/10.1021/ja00014a071
  19. D. S. Wishart, B. D. Sykes, and F. M. Richards, Relationship between nuclear magnetic resonance chemical shift and protein secondary structure, J. Mol. Biol. 222, 311-333 (1991). https://doi.org/10.1016/0022-2836(91)90214-Q
  20. W. J. Fairbrother, A. G. Palmer, M. Rance, J. Reizer, M. H. Saier, and P. E. Wright, Assignment of the aliphatic proton and carbon-13 resonances of the Bacillus subtilis glucose permease IIA domain using double- and triple-resonance heteronuclear threedimensional NMR spectroscopy, Biochemistry 31, 4413-4425 (1992). https://doi.org/10.1021/bi00133a005