Advertisement

Journal of Biomolecular NMR

, Volume 11, Issue 1, pp 45–57 | Cite as

Chemical shift homology in proteins

  • Barbara C.M. Potts
  • Walter J. Chazin
Article

Abstract

The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of Cα protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins.

chemical shift protein structural homology resonance assignments secondary chemical shift sequence homology 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Adman, E.T. (1991) Adv. Protein Chem., 42, 145–197.Google Scholar
  2. Carlström, G. and Chazin, W.J.(1993) J. Mol. Biol., 227, 415–430.Google Scholar
  3. Eklund, H., Gleason, F.K. and Holmgren, A. (1991) Proteins Struct.Funct. Genet., 11, 13–28.Google Scholar
  4. Gippert, G.P. (1995) Ph.D. Thesis, The Scripps Research Institute, La Jolla, CA,U.S.A.Google Scholar
  5. Gronenborn, A.M. and Clore, G.M. (1994) J. Biomol. NMR, 4, 455–458.Google Scholar
  6. Jamin, N., Gabrielsen, O.S., Gilles, N., Lirsac, P. and Toma, F. (1993) Eur. J. Biochem., 216, 147–154.Google Scholar
  7. Kofman, V., Farver, O., Pecht, I. and Goldfarb, D. (1996) J. Am. Chem. Soc., 118, 1201–1206.Google Scholar
  8. Kretsinger, R.H., Tolbert, D., Nakayama, S. and Pearson, W. (1991) In Novel Calcium-Binding Proteins (Ed., Heizmann, C.W.), Springer, New York, NY, U.S.A., pp. 17–37.Google Scholar
  9. Kuriyan, J. and Cowburn, D. (1993) Curr. Opin. Struct. Biol.,3, 828–837.Google Scholar
  10. Kuszewski, J., Qin, J., Gronenborn, A.M. and Clore, G.M. (1995) J. Magn. Reson.,106, 92–96.Google Scholar
  11. Lee, M.S., Mortishire-Smith, R.J. and Wright, P.E. (1992) FEBS Lett., 309, 29–32.Google Scholar
  12. Mortishire-Smith, R.J., Lee, M.S., Bolinger, L. and Wright, P.E. (1992) FEBS Lett., 296, 11–15.Google Scholar
  13. Ogata, K., Hojo, H., Aimoto, S., Nakai, T., Nakamura, H., Sarai, A., Ishii, S. and Nishimura, Y. (1992) Proc. Natl. Acad. Sci. USA, 89, 6428–6432.Google Scholar
  14. Oldfield, E. (1995) J. Biomol. NMR, 5, 217–225.Google Scholar
  15. Ösapay, K., Theriault, Y., Wright, P.E. and Case, D.A. (1994) J. Mol. Biol., 244, 183–197.Google Scholar
  16. Potts, B.C., Carlström, G., Okazaki, K., Hidaka, H. and Chazin, W.J. (1996) Protein Sci., 5, 2162–2174.Google Scholar
  17. Press, W., Flannery, B.P., Teukolsky, S.A. and Vetterling, W.T. (1986) Numerical Recipes, Cambridge University Press, New York, NY.Google Scholar
  18. Redfield, C. and Dobson, C.M. (1990) Biochemistry, 29, 7201–7214.Google Scholar
  19. Seavey, B.R., Farr, E.A., Westler, W.M. and Markley, J.L. (1991) J. Biomol. NMR, 1, 217–236.Google Scholar
  20. Skelton, N.J., Aspiras, F., Ogez, J.and Schall, T.J. (1995) Biochemistry, 34, 5329–5342.Google Scholar
  21. Spera, S. and Bax, A. (1991) J. Am. Chem. Soc.,113, 5490–5492.Google Scholar
  22. Sykes, A.G. (1991) Adv. Inorg. Chem., 36, 377–408.Google Scholar
  23. Szilagyi, L. (1995)Prog. NMR Spectrosc., 27, 325–443.Google Scholar
  24. Williamson, M.P., Kikuchi, J. and Tetsuo, A. (1995) J. Mol. Biol.,247, 541–546.Google Scholar
  25. Wishart, D.S., Sykes, B.D. and Richards, F.M. (1991) J. Mol. Biol., 222, 311–333.Google Scholar
  26. Wishart, D.S., Sykes, B.D. and Richards, F.M. (1992) Biochemistry, 31, 1647–1651.Google Scholar
  27. Wishart, D.S.and Sykes, B.D. (1994) J. Biomol. NMR, 4, 171–180.Google Scholar
  28. Wishart, D.S., Bigam, C.G., Yao, J., Abildgaard, F., Dyson, H.J., Oldfield, E., Markley, J.L. and Sykes, B.D. (1995) J. Biomol. NMR, 6, 135–140.Google Scholar
  29. Wittekind, M., Reizer, J., Deutscher, J., Saier, M.H. and Klevit, R.E. (1989) Biochemistry, 28, 9908–9912.Google Scholar

Copyright information

© Kluwer Academic Publishers 1998

Authors and Affiliations

  • Barbara C.M. Potts
    • 1
  • Walter J. Chazin
    • 1
  1. 1.Department of Molecular BiologyThe Scripps Research InstituteLa JollaU.S.A

Personalised recommendations