Calmodulin Target Database

  • Kyoko L. Yap
  • Justin Kim
  • Kevin Truong
  • Marc Sherman
  • Tao Yuan
  • Mitsuhiko Ikura


The intracellular calcium sensor protein calmodulin (CaM) interacts with a large number of proteins to regulate their biological functions in response to calcium stimulus. This molecular recognition process is diverse in its mechanism, but can be grouped into several classes based on structural and sequence information. We have developed a web-based database ( for this family of proteins containing CaM binding sites or, as we propose to call it herein, CaM recruitment signaling (CRS) motifs. At present the CRS motif found in approximately 180 protein sequences in the databases can be divided into four subclasses, each subclass representing a distinct structural mode of molecular recognition involving CaM. The database can predict a putative CRS location within a given protein sequence, identify the subclass to which it may belong, and structural and biophysical parameters such as hydrophobicity, hydrophobic moment, and propensity for a -helix formation.

calcium signaling EF-hand protein molecular recognition protein-protein interaction 


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  1. 1.
    Williams, R.J.P. (1999) in: Calcium as a cellular regulator, pp. 3–629 (Carafoli, E. and Klee, C.B., Eds.) Oxford University Press, Oxford.Google Scholar
  2. 2.
    James, P., Vorherr, T. and Carafoli, E. (1995) Trends Biochem Sci 20, 38–42.PubMedCrossRefGoogle Scholar
  3. 3.
    Zhang, M. and Yuan, T. (1998) Biochem Cell Biol 76, 313–23.PubMedCrossRefGoogle Scholar
  4. 4.
    O'Neil, K.T. and DeGrado, W.F. (1990) Trends Biochem Sci 15, 59–64.PubMedCrossRefGoogle Scholar
  5. 5.
    Crivici, A. and Ikura, M. (1995) Annu Rev Biophys Biomol Struct 24, 85–116.PubMedCrossRefGoogle Scholar
  6. 6.
    Porumb, T., Crivici, A., Blackshear, P.J. and Ikura, M. (1997) Eur Biophys J 25, 239–47.PubMedCrossRefGoogle Scholar
  7. 7.
    Dasgupta, M., Honeycutt, T. and Blumenthal, D.K. (1989) J Biol Chem 264, 17156–63.PubMedGoogle Scholar
  8. 8.
    Barnes, J.A. and Gomes, A.V. (1995) Mol Cell Biochem 149–150, 17–27.PubMedCrossRefGoogle Scholar
  9. 9.
    Ikura, M., Clore, G.M., Gronenborn, A.M., Zhu, G., Klee, C.B. and Bax, A. (1992) Science 256, 632–8.PubMedGoogle Scholar
  10. 10.
    Meador, W.E., Means, A.R. and Quiocho, F.A. (1992) Science 257, 1251–5.PubMedGoogle Scholar
  11. 11.
    Meador, W.E., Means, A.R. and Quiocho, F.A. (1993) Science 262, 1718–21.PubMedGoogle Scholar
  12. 12.
    Afshar, M., Caves, L.S., Guimard, L., Hubbard, R.E., Calas, B., Grassy, G. and Haiech, J. (1994) J Mol Biol 244, 554–71.PubMedCrossRefGoogle Scholar
  13. 13.
    Rhoads, A.R. and Friedberg, F. (1997) Faseb J 11, 331–40.PubMedGoogle Scholar
  14. 14.
    Cheney, R.E. and Mooseker, M.S. (1992) Curr Opin Cell Biol 4, 27–35.PubMedCrossRefGoogle Scholar
  15. 15.
    Ruan, J., Xie, Q., Hutchinson, N., Cho, H., Wolfe, G.C. and Nathan, C. (1996) J Biol Chem 271, 22679–86.PubMedCrossRefGoogle Scholar
  16. 16.
    Nevalainen, L.T., Aoyama, T., Ikura, M., Crivici, A., Yan, H., Chua, N.H. and Nairn, A.C. (1997) Biochem J 321, 107–15.PubMedGoogle Scholar
  17. 17.
    Yuan, T. and Vogel, H.J. (1998) J Biol Chem 273, 30328–35.PubMedCrossRefGoogle Scholar
  18. 18.
    Onions, J., Hermann, S. and Grundstrom, T. (2000) Biochemistry 39, 4366–74.PubMedCrossRefGoogle Scholar
  19. 19.
    Schiffer, M. and Edmundson, A.B. (1967) Biophys J 7, 121–135.PubMedCrossRefGoogle Scholar
  20. 20.
    Kyte, J. and Doolittle, R.F. (1982) J Mol Biol 157, 105–32.PubMedCrossRefGoogle Scholar
  21. 21.
    Eisenberg, D., Weiss, R.M. and Terwilliger, T.C. (1982) Nature 299, 371–4.PubMedCrossRefGoogle Scholar
  22. 22.
    Eisenberg, D., Schwarz, E., Komaromy, M. and Wall, R. (1984) J Mol Biol 179, 125–42.PubMedCrossRefGoogle Scholar
  23. 23.
    Erickson-Viitanen, S. and DeGrado, W.F. (1987) Methods Enzymol 139, 455–78.PubMedCrossRefGoogle Scholar
  24. 24.
    Osawa, M., Tokumitsu, H., Swindells, M.B., Kurihara, H., Orita, M., Shibanuma, T., Furuya, T. and Ikura, M. (1999) Nature Struct Biol 6, 819–24.PubMedCrossRefGoogle Scholar
  25. 25.
    Elshorst, B. et al. (1999) Biochemistry 38, 12320–32.PubMedCrossRefGoogle Scholar
  26. 26.
    Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Nucleic Acids Res 25, 3389–402.PubMedCrossRefGoogle Scholar
  27. 27.
    Bateman, A., Birney, E., Durbin, R., Eddy, S.R., Howe, K.L. and Sonnhammer, E.L. (2000) Nucleic Acids Res 28, 263–6.PubMedCrossRefGoogle Scholar
  28. 28.
    Schultz, J., Milpetz, F., Bork, P. and Ponting, C.P. (1998) Proc Natl Acad Sci U S A 95, 5857–64.PubMedCrossRefGoogle Scholar
  29. 29.
    Eddy, S.R. (1998) Bioinformatics 14, 755–63.PubMedCrossRefGoogle Scholar
  30. 30.
    Bairoch, A. and Apweiler, R. (2000) Nucleic Acids Res 28, 45–8.PubMedCrossRefGoogle Scholar
  31. 31.
    Copley, R.R., Schultz, J., Ponting, C.P. and Bork, P. (1999) Curr Opin Struct Biol 9, 408–15.PubMedCrossRefGoogle Scholar
  32. 32.
    Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. and Thornton, J.M. (1997) Structure 5, 1093–108.PubMedCrossRefGoogle Scholar
  33. 33.
    Holm, L. and Sander, C. (1996) Science 273, 595–603.PubMedGoogle Scholar
  34. 34.
    Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) J Mol Biol 247, 536–40.PubMedCrossRefGoogle Scholar
  35. 35.
    Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucleic Acids Res 28, 235–42.PubMedCrossRefGoogle Scholar
  36. 36.
    Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Rapp, B.A. and Wheeler, D.L. (2000) Nucleic Acids Res 28, 15–8.PubMedCrossRefGoogle Scholar
  37. 37.
    Vogel, H.J. and Zhang, M. (1995) Mol Cell Biochem 149–150, 3–15.PubMedCrossRefGoogle Scholar
  38. 38.
    Yuan, T., Yap, K.L. and Ikura, M. (2000) in: Topics in Biological Inorganic Chemistry: Calcium Homeostasis, Vol. 3 (Carafoli, E. and Krebs, J., Eds.) Springer-Verlag, Heidelberg.Google Scholar
  39. 39.
    Felts, K., Wyborski, D., Bauer, J. and Vaillancourt, P. (1999) Strategies 12, 24–27.Google Scholar
  40. 40.
    Miyawaki, A., Llopis, J., Heim, R., McCaffery, J.M., Adams, J.A., Ikura, M. and Tsien, R.Y. (1997) Nature 388, 882–7.PubMedCrossRefGoogle Scholar

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • Kyoko L. Yap
    • 1
  • Justin Kim
    • 1
  • Kevin Truong
    • 1
  • Marc Sherman
    • 1
  • Tao Yuan
    • 1
  • Mitsuhiko Ikura
    • 2
  1. 1.Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical BiophysicsUniversity of TorontoTorontoCanada
  2. 2.Division of Molecular and Structural Biology, Ontario Cancer Institute and Department of Medical BiophysicsUniversity of TorontoTorontoCanada

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