A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics

Abstract

The chemical shift difference (δ[13Cβ] − δ[13Cγ]) is a reference-independent indicator of the Xaa-Pro peptide bond conformation. Based on a statistical analysis of the 13C chemical shifts of 1033 prolines from 304 proteins deposited in the BioMagRes database, a software tool was created to predict the probabilities for cis or trans conformations of Xaa-Pro peptide bonds. Using this approach, the conformation at a given Xaa-Pro bond can be identified in a simple NOE-independent way immediately after obtaining its NMR resonance assignments. This will allow subsequent structure calculations to be initiated using the correct polypeptide chain conformation.

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References

  1. Badger, J., Kumar, R.A., Yip, P. and Szalma, S. (1999) Proteins, 35, 25–33.

    Google Scholar 

  2. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucl. Acids Res., 28, 235–242.

    Google Scholar 

  3. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O. Shimanouchi, T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535–542.

    Google Scholar 

  4. Bronstein, I.N. and Semendjajew, K.A. (1985) Taschenbuch der Mathematik, Teubner Verlag, Leipzig.

  5. Brünger, A.T.(1992) X-Plor, Version 3.1: A system for X-Ray Crystallography and NMR, Yale University Press, New Haven.

  6. Dorman, D.E. and Bovey, F.A. (1973) J. Org. Chem., 38, 2379–2383 and references cited therein.

    Google Scholar 

  7. Giessner-Prettre, C., Cung, M.T. and Marraud, M. (1987)Eur. J. Biochem., 163, 79–87.

    Google Scholar 

  8. Haasnoot, C.A.G., de Leeuw, F.A.A.M., deLeeuw, H.P.M. and Altona, C. (1981) Biopolymers, 20, 1211–1245.

    Google Scholar 

  9. Herrmann, T., Güntert, P. and Wüthrich, K. (2002) J. Mol. Biol., 319, 209–227.

    Google Scholar 

  10. Jabs, A., Weiss, M.S.and Hilgenfeld, R. (1999) J. Mol. Biol., 286, 291–304.

    Google Scholar 

  11. Kang, Y.K. (1996) J. Phys.Chem., 100, 11589–11595.

    Google Scholar 

  12. Linge, J.P., O'Donoghue, S.I. and Nilges, M. (2001) Meth.Enzymol., 339, 71–90.

    Google Scholar 

  13. London, R.E. (1978) J. Am. Chem. Soc., 100, 2678–2685.

    Google Scholar 

  14. Milner-White, E.J., Bell, L.H. and Maccallum, P.H. (1992) J. Mol. Biol., 228, 725–734.

    Google Scholar 

  15. Güntert, P., Mumenthaler, C. and Wüthrich, K. (1997) J. Mol. Biol., 273, 283–298.

    Google Scholar 

  16. Nilges, M., Macias, M.J., O'Donoghue, S.I. and Oschkinat, H. (1997) J. Mol. Biol., 269, 408–422.

    Google Scholar 

  17. Ramachandran, G. N. and Sasisekharan, V. (1968) Adv. Prot. Chem., 23,283–437.

    Google Scholar 

  18. Schmidt, J.M., Brüschweiler, R., Ernst, R.R., Dunbrack, R.L., Joseph, D. and Karplus, M. (1993) J. Am. Chem. Soc., 115, 8747–8756.

    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. Siemion, I.Z., Wieland, T. and Pook, K.-H. (1975) Angew. Chem., 87, 712–714.

    Google Scholar 

  21. Stanczyk, S.M., Bolton, P.H., Dell'Acqua, M. and Gerlt, J.A. (1989) J. Am. Chem. Soc., 111, 8317–8318.

    Google Scholar 

  22. Torchia, D.A., Sparks, S.W., Young, P.E. and Bax, A. (1989) J. Am. Chem. Soc., 111,8315–8317.

    Google Scholar 

  23. Weiss, M.S., Jabs, A. and Hilgenfeld, R. (1998) Nat. Struct. Biol., 5,676.

    Google Scholar 

  24. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York, NY.

    Google Scholar 

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Correspondence to Dirk Labudde.

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Schubert, M., Labudde, D., Oschkinat, H. et al. A software tool for the prediction of Xaa-Pro peptide bond conformations in proteins based on 13C chemical shift statistics. J Biomol NMR 24, 149–154 (2002). https://doi.org/10.1023/A:1020997118364

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  • 13C chemical shifts
  • cis peptide bond
  • peptide bond conformation
  • proline
  • protein structure