Journal of Biomolecular NMR

, Volume 17, Issue 2, pp 125–136 | Cite as

A tracked approach for automated NMR assignments in proteins (TATAPRO)

  • H.S. Atreya
  • S.C. Sahu
  • K.V.R. Chary
  • Girjesh Govil
Article

Abstract

A novel automated approach for the sequence specific NMR assignments of 1HN, 13Cα, 13Cβ, 13C′/1Hα and 15N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate 1HN and 15N chemical shifts with those of 13Cα, 13Cβ and 13C′/1Hα. The information derived from such correlations is used to create a `master_list' consisting of all possible sets of 1HNi, 15Ni, 13Cαi, 13Cβi, 13C′i/1Hαi, 13Cαi−1, 13Cβi−1 and 13C′i−1/ 1Hαi−1 chemical shifts. On the basis of an extensive statistical analysis of 13Cα and 13Cβ chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master_list and also to translate the protein primary sequence into an array called pps_array. The program then uses the master_list to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assig_array, with the two-digit code assigned earlier. The assig_array is then mapped onto the pps_array for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18–42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the master_list created for the test proteins.

automated NMR assignments Borrelia burgdoferi OspA drosophila numb phosphotyrosine-binding domain Eh-CaBP Escherichia coli maltose binding protein fibroblast collagenase sequence specific resonance assignments triple resonance experiments 

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References

  1. Bartels, C., Billeter, M., Güntert, P. and Wüthrich, K. (1996) J. Biomol. NMR, 7, 207-213.Google Scholar
  2. Bax, A. and Grzesiek, S. (1993) Acc. Chem. Res., 26, 131-138.Google Scholar
  3. Buchler, N.E.G., Zuiderweg, E.R.P., Wang, H. and Goldstein, R.A. (1997) J. Magn. Reson., 125, 34-42.Google Scholar
  4. Choy, W.Y., Sanctuary, B.C. and Zhu, G. (1997) J. Chem. Inf. Comput. Sci., 37, 1086-1094.Google Scholar
  5. Clubb, R.T., Thanabal, V. and Wagner, G. (1992a) J. Magn. Reson., 97, 213-217.Google Scholar
  6. Clubb, R.T., Thanabal, V. and Wagner, G. (1992b) J. Biomol. NMR, 2, 203-210.Google Scholar
  7. Clubb, R.T. and Wagner, G. (1992) J. Biomol. NMR, 2, 389-394.Google Scholar
  8. Friedrichs, M.S., Mueller, L. and Wittekind, M. (1994) J. Biomol. NMR, 4, 703-726.Google Scholar
  9. Gardner, K.H. and Kay, L.E. (1998) Annu. Rev. Biophys. Biomol. Struct., 27, 357-406.Google Scholar
  10. Gardner, K.H., Zhang, X., Gehring, K. and Kay, L.E. (1998) J. Am. Chem. Soc., 120, 11738-11748.Google Scholar
  11. Gronwald, W., Willard, L., Jellard, T., Boyko, R.F., Rajarathnam, K., Wishart, D.S., Sönnichsen, F.D. and Sykes, B.D. (1998) J. Biomol. NMR, 12, 395-405.Google Scholar
  12. Grzesiek, S. and Bax, A. (1992) J. Am. Chem. Soc., 114, 6291-6293.Google Scholar
  13. Grzesiek, S. and Bax, A. (1993) J. Biomol. NMR, 3, 185-204.Google Scholar
  14. Hare, B.J. and Prestegard, H. (1994) J. Biomol. NMR, 4, 35-46.Google Scholar
  15. Ikura, M., Kay, L.E. and Bax, A. (1990) Biochemistry, 29, 4659-4667.Google Scholar
  16. Kay, L.E., Ikura, M., Tschudin, R. and Bax, A. (1990) J. Magn. Reson., 89, 496-514.Google Scholar
  17. Li, K.-B. and Sanctuary, B.C. (1997) J. Chem. Inf. Comput. Sci., 37, 467-477.Google Scholar
  18. Li, S.C., Zwahlen, C., Vincent, S.J., McGlade, C.J., Kay, L.E., Pawson, T. and Forman-Kay, J.D. (1998) Nat. Struct. Biol., 5, 1075-1083.Google Scholar
  19. Leutner, M., Gschwind, R.M., Liermann, J., Schwarz, C., Gemmecker, G. and Kessler, H. (1998) J. Biomol. NMR, 11, 31-43.Google Scholar
  20. Loria, J.P., Rance, M. and Palmer, A.G. (1999) J. Magn. Reson., 141, 180-184.Google Scholar
  21. Lukin, J.A., Gove, A.P., Talukdar, S.N. and Ho, C. (1997) J. Biomol. NMR, 9, 151-166.Google Scholar
  22. Meadows, R.P., Olejniczak, E.T. and Fesik, S.W. (1994) J. Biomol. NMR, 4, 79-96.Google Scholar
  23. Metzler, W.J., Constantine, K.L., Friedrichs, M.S., Bell, A.J., Ernst, E.G., Lavoie, T.B. and Mueller, L. (1993) Biochemistry, 32, 13818-13829.Google Scholar
  24. Montelione, G.T., Rios, C.B., Swapna, G.V.T. and Zimmerman, D.E. (1999) In Biological Magnetic Resonance, Volume 17: Structure, Computation and Dynamics in Protein NMR (Eds., Krishna, R. and Berliner, L.), Plenum Press, New York, NY, pp. 81-130.Google Scholar
  25. Moseley, H.N.B. and Montelione, G.T. (1999) Curr. Opin. Struct. Biol., 9, 635-642.Google Scholar
  26. Moy, F.J., Pisano, M.R., Chandra, P.K., Urbano, C., Killar, L.M., Sung, M.L. and Powers, R. (1997) J. Biomol. NMR, 10, 9-19.Google Scholar
  27. Olson Jr., J.B. and Markley, J.L. (1994) J. Biomol. NMR, 4, 385-410.Google Scholar
  28. Pham, T.-N. and Koide, S. (1998) J. Biomol. NMR, 11, 407-414.Google Scholar
  29. Sahu, S.C., Atreya, H.S., Chauhan, S., Bhattacharya, A., Chary, K.V.R. and Govil, G. (1999) J. Biomol. NMR, 14, 93-94.Google Scholar
  30. Salzmann, M., Pervushin, K., Wider, G., Senn, H. and Wüthrich, K. (1998) Proc. Natl. Acad. Sci. USA, 95, 13585-13590.Google Scholar
  31. Salzmann, M., Wider, G., Pervushin, K., Senn, H. and Wüthrich, K. (1999) J. Am. Chem. Soc., 121, 844-848.Google Scholar
  32. Seavey, B.R., Farr, E.A., Westler, W.M. and Markley, J.L. (1991) J. Biomol. NMR, 1, 217-236.Google Scholar
  33. Wittekind, M. and Mueller, L. (1993) J. Magn. Reson., B101, 201-205.Google Scholar
  34. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY.Google Scholar
  35. Zimmerman, D.E., Kulikowski, C., Wang, L.L., Lyons, B.A. and Montelione, G.T. (1994) J. Biomol. NMR, 4, 241-256.Google Scholar
  36. Zimmerman, D.E., Kulikowski, C.A., Huang, Y., Feng, W., Tashiro, M., Shimotakahara, S., Chien, C., Powers, R. and Montelione, G.T. (1997) J. Mol. Biol., 269, 592-610.Google Scholar

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • H.S. Atreya
    • 1
  • S.C. Sahu
    • 1
  • K.V.R. Chary
    • 1
  • Girjesh Govil
    • 1
  1. 1.Department of Chemical SciencesTata Institute of Fundamental ResearchMumbai India

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