Skip to main content
SpringerLink
Log in

Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles

  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

The concept of self-consistent J coupling evaluation exploits redundant structure information inherent in large sets of 3J coupling constants. Application to the protein Desulfovibrio vulgaris flavodoxin demonstrates the simultaneous refinement of torsion-angle values and related Karplus coefficients. The experimental basis includes quantitative coupling constants related to the polypeptide backbone φ torsion originating from a variety of heteronuclear 2D and 3D NMR correlation experiments, totalling 124 3J(HN,Hα), 129 3J(HN,C′), 121 3J(HN,Cβ), 128 3J(C′i−1,Hαi), 121 3J(C′i−1,C′i), and 122 3J(C′i−1,Cβi). Without prior knowledge from either X-ray crystallography or NMR data, such as NOE distance constraints, accurate φ dihedral angles are specified for 122 non-glycine and non-proline residues out of a total of 147 amino acids. Different models of molecular internal mobility are considered. The Karplus coefficients obtained are applicable to the conformational analysis of φ torsions in other polypeptides.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Similar content being viewed by others

References

  • Bax, A., Vuister, G.W., Grzesiek, S., Delaglio, F., Wang, A.C., Tschudin, R. and Zhu, G. (1994) Methods Enzymol., 239, 79–105.

    Article  Google Scholar 

  • Biamonti, C., Rios, C.B., Lyons, B.A. and Montelione, G.T. (1994) Adv. Biophys. Chem., 4, 51–120.

    Google Scholar 

  • Billeter, M., Neri, D., Otting, G., Qian, Y.Q. and Wüthrich, K. (1992) J. Biomol. NMR, 2, 257–274.

    Article  Google Scholar 

  • Blackledge, M.J., Brüschweiler, R., Griesinger, C., Schmidt, J.M., Xu, P. and Ernst, R.R. (1993) Biochemistry, 32, 10960–10974.

    Article  Google Scholar 

  • Blümel, M., Schmidt, J.M., Löhr, F. and Rüterjans, H. (1998) Eur. Biophys. J., 27, 321–334.

    Article  Google Scholar 

  • Brünger, A.T. and Karplus, M. (1991) Acc. Chem. Res., 24, 54.

    Article  Google Scholar 

  • Brünger, A.T., Adams, P.D., Clore, G.M., Gros, P., Grosse-Kunstleve, R.W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N.S., Read, R.J., Rice, L.M., Simonson, T. and Warren, G.L. (1998) Acta Crystallogr., D54, 905–921.

    Google Scholar 

  • Brüschweiler, R. and Case, D.A. (1994) J. Am. Chem. Soc., 116, 11199–11200.

    Article  Google Scholar 

  • Bystrov, V.F. (1976) Prog. NMR Spectrosc., 10, 41–81.

    Article  Google Scholar 

  • Case, D.A., Dyson, H.J. and Wright, P.E. (1994) Methods Enzymol., 239, 392–416.

    Article  Google Scholar 

  • Curley, G.P., Carr, M.C., Mayhew, S.G. and Voordouw, G. (1991) Eur. J. Biochem., 202, 1091–1100.

    Article  Google Scholar 

  • Davidson, W.C. (1959) A.E.C. Research and Development Report, ANL-5990.

  • DeMarco, A., Llinás, M. and Wüthrich, K. (1978a) Biopolymers, 17, 637–650.

    Article  Google Scholar 

  • DeMarco, A., Llinás, M. and Wüthrich, K. (1978b) Biopolymers, 17, 2727–2742.

    Article  Google Scholar 

  • DeMarco, A. and Llinás, M. (1979) Biochemistry, 18, 3846–3854.

    Article  Google Scholar 

  • Eberstadt, M., Gemmecker, G., Mierke, D.F. and Kessler, H. (1995) Angew. Chem., 107, 1813–1838; Angew. Chem. Int. Ed. Engl., 34, 1671–1695.

    Article  Google Scholar 

  • Fischman, A.J., Live, D.H., Wyssbrod, H.R., Agosta, W.C. and Cowburn, D. (1980) J. Am. Chem. Soc., 102, 2533–2539.

    Article  Google Scholar 

  • Fletcher, R. and Powell, M.J.D. (1963) Comput. J., 6, 163–168.

    MathSciNet  MATH  Google Scholar 

  • Ghisla, S. and Massey, V. (1989) Eur. J. Biochem., 181, 1–17.

    Article  Google Scholar 

  • Güntert, P., Braun, W. and Wüthrich, K. (1991) J. Mol. Biol., 217, 517–530.

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Haasnoot, C.A.G., de Leeuw, F.A.A.M. and Altona, C. (1980) Tetrahedron, 36, 2783–2792.

    Article  Google Scholar 

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

    Article  Google Scholar 

  • Hoch, J.C., Dobson, C.M. and Karplus, M. (1985) Biochemistry, 24, 3831–3841.

    Article  Google Scholar 

  • Hu, J.-S. and Bax, A. (1996) J. Am. Chem. Soc., 118, 8170–8171.

    Article  Google Scholar 

  • Hu, J.-S. and Bax, A. (1997) J. Am. Chem. Soc., 119, 6360–6368.

    Article  Google Scholar 

  • Hu, J.-S. and Bax, A. (1998) J. Biomol. NMR, 11, 199–203.

    Article  Google Scholar 

  • IUPAC-IUB Commission on Biochemical Nomenclature (1970) J. Mol. Biol., 52, 1–17; Biochemistry, 9, 3471–3479.

    Article  Google Scholar 

  • Jardetzky, O. (1980) Biochim. Biophys. Acta, 621, 227–232.

    Google Scholar 

  • Karimi-Nejad, Y., Schmidt, J.M., Rüterjans, H., Schwalbe, H. and Griesinger, C. (1994) Biochemistry, 33, 5481–5492.

    Article  Google Scholar 

  • Karplus, M. (1963) J. Am. Chem. Soc., 85, 2870–2871.

    Article  Google Scholar 

  • Knauf, M.A., Löhr, F., Curley, G.P., O'Farrell, P., Mayhew, S.G., Muller, F. and Rüterjans, H. (1993) Eur. J. Biochem., 213, 167–184.

    Article  Google Scholar 

  • Knauf, M.A., Löhr, F., Blümel, M., Mayhews, S.G. and Rüterjans, H. (1996) Eur. J. Biochem., 238, 423–434.

    Article  Google Scholar 

  • Kuboniwa, H., Grzesiek, S., Delaglio, F. and Bax, A. (1994) J. Biomol. NMR, 4, 871–878.

    Article  Google Scholar 

  • Löhr, F. and Rüterjans, H. (1995) J. Biomol. NMR, 5, 25–36.

    Article  Google Scholar 

  • Löhr, F. (1996) Ph.D. Thesis, University of Frankfurt am Main, Germany.

  • Löhr, F., Blümel, M., Schmidt, J.M. and Rüterjans, H. (1997) J. Biomol. NMR, 10, 107–118.

    Article  Google Scholar 

  • Löhr, F. and Rüterjans, H. (1999) J. Biomol. NMR, 13, 263–274.

    Article  Google Scholar 

  • Ludvigsen, S., Andersen, K.V. and Poulsen, F.M. (1991) J. Mol. Biol., 217, 731–736.

    Article  Google Scholar 

  • Mayhew, S.G. and Ludwig, M.L. (1975) In The Enzymes (Ed., Boyer, P.D.), Vol. 12, 3rd ed., Academic Press, New York, NY, pp. 57–118.

    Google Scholar 

  • Mayhew, S.G. and Tollin, G. (1992) In Chemistry and Biochemistry of flavoenzymes (Ed., Müller, F.), Vol. 3, 3rd ed., CRC Press, Boca Raton, FL, pp. 389–426.

    Google Scholar 

  • Mierke, D.F. and Kessler, H. (1992) Biopolymers, 32, 1277–1282.

    Article  Google Scholar 

  • Pardi, A., Billeter, M. and Wüthrich, K. (1984) J. Mol. Biol., 180, 741–751.

    Article  Google Scholar 

  • Roberts, G.C.K. (Ed.) (1993) NMR of Macromolecules: A Practical Approach, Oxford University Press, Oxford, U.K.

    Google Scholar 

  • Schmidt, J.M., Ernst, R.R., Aimoto, S. and Kainosho, M. (1995) J. Biomol. NMR, 6, 95–105.

    Article  Google Scholar 

  • Schmidt, J.M., Löhr, F. and Rüterjans, H. (1996) J. Biomol. NMR, 7, 142–152.

    Article  Google Scholar 

  • Schmidt, J.M. (1997a) J. Magn. Reson., 124, 298–309.

    Article  ADS  Google Scholar 

  • Schmidt, J.M. (1997b) J. Magn. Reson., 124, 310–322.

    Article  ADS  Google Scholar 

  • Stone, M. (1974) J. R. Stat. Soc., B36, 111–147.

    Google Scholar 

  • van Gunsteren, W.F. and Berendsen, H.J.C. (1985) In Molecular Dynamics and Protein Structure, (Ed., Herman, J.), Polycrystal Book Service, Western Springs, IL, pp. 5–14.

    Google Scholar 

  • Vuister, G.W. and Bax, A. (1993) J Am. Chem. Soc., 115, 7772–7777.

    Article  Google Scholar 

  • Wang, A.C. and Bax, A. (1995) J. Am. Chem. Soc., 117, 1810–1813.

    Article  Google Scholar 

  • Wang, A.C. and Bax, A. (1996) J. Am. Chem. Soc., 118, 2483–2494.

    Article  Google Scholar 

  • Watt, W., Tulinsky, A., Swenson, R.P. and Watenpaugh, K.D. (1991) J. Mol. Biol., 218, 195–208.

    Article  Google Scholar 

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

    Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Institut für Biophysikalische Chemie, Johann Wolfgang Goethe-Universität, Biozentrum N230, Marie-Curie-Strasse 9, D-60439, Frankfurt am Main, Germany

    Jürgen M. Schmidt, Markus Blümel, Frank Löhr & Heinz Rüterjans

Authors
  1. Jürgen M. Schmidt
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Markus Blümel
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Frank Löhr
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Heinz Rüterjans
    View author publications

    You can also search for this author in PubMed Google Scholar

Electronic Supplementary Material

Rights and permissions

Reprints and permissions

About this article

Cite this article

Schmidt, J.M., Blümel, M., Löhr, F. et al. Self-consistent 3J coupling analysis for the joint calibration of Karplus coefficients and evaluation of torsion angles. J Biomol NMR 14, 1–12 (1999). https://doi.org/10.1023/A:1008345303942

Download citation

  • Issue Date:

  • DOI: https://doi.org/10.1023/A:1008345303942

Search

Navigation