Journal of Biomolecular NMR

, Volume 18, Issue 1, pp 43–48 | Cite as

Random coil chemical shifts in acidic 8 M urea: Implementation of random coil shift data in NMRView

  • Stephan Schwarzinger
  • Gerard J.A. Kroon
  • Ted R. Foss
  • Peter E. Wright
  • H. Jane Dyson


Studies of proteins unfolded in acid or chemical denaturant can help in unraveling events during the earliest phases of protein folding. In order for meaningful comparisons to be made of residual structure in unfolded states, it is necessary to use random coil chemical shifts that are valid for the experimental system under study. We present a set of random coil chemical shifts obtained for model peptides under experimental conditions used in studies of denatured proteins. This new set, together with previously published data sets, has been incorporated into a software interface for NMRView, allowing selection of the random coil data set that fits the experimental conditions best.

chemical shift CSI denaturant NMRView peptide random coil 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Arcus, V.L., Vuilleumier, S., Freund, S.M.V., Bycroft, M. and Fersht, A.R. (1995) J. Mol. Biol., 254, 305–321.Google Scholar
  2. Braun, D., Wider, G. and Wüthrich, K. (1994) J. Am. Chem. Soc., 116, 8466–8469.Google Scholar
  3. Braunschweiler, L. and Ernst, R.R. (1983) J. Magn. Reson., 53, 521–528.Google Scholar
  4. Bundi, A. and Wüthrich, K. (1979) Biopolymers, 18, 285–297.Google Scholar
  5. Cobas, C., Cruces, J. and Sardina, F.J. (1999) Scholar
  6. Delaglio, F., Grzesiek, S., Vuister, G.W., Huang, Z., Pfeifer, J. and Bax, A. (1995) J. Biomol. NMR, 6, 277–293.Google Scholar
  7. Frank, M.K., Clore, G.M. and Gronenborn, A.M. (1995) Protein Sci., 4, 2605–2615.Google Scholar
  8. Gross, K.-H. and Kalbitzer, H.R. (1988) J. Magn. Reson., 76, 87–99.Google Scholar
  9. Grzesiek, S. and Bax, A. (1993) J. Am. Chem. Soc., 115, 12593–12594.Google Scholar
  10. Jimenez, M.A., Nieto, J.L., Rico, M., Santoro, J., Herranz, J. and Bermejo, F.J. (1986) J. Mol. Struct., 143, 435–438.Google Scholar
  11. Johnson, B.A. and Blevins, R.A. (1994) J. Chem. Phys., 29, 1012–1014.Google Scholar
  12. Logan, T.M., Thériault, Y. and Fesik, S.W. (1994) J. Mol. Biol., 236, 637–648.Google Scholar
  13. Merutka, G., Dyson, H.J. and Wright, P.E. (1995) J. Biomol. NMR, 5, 14–24.Google Scholar
  14. Neri, D., Billeter, M., Wider, G. and Wüthrich, K. (1992) Science, 257, 1559–1563.Google Scholar
  15. Pastore, A. and Saudek, V. (1990) J. Magn. Reson., 90, 165–176.Google Scholar
  16. Pervushin, K., Riek, R., Wider, G. and Wüthrich, K. (1997) Proc. Natl. Acad. Sci. USA, 94, 12366–12371.Google Scholar
  17. Plaxco, K.W., Morton, C.J., Grimshaw, S.B., Jones, J.A., Pitkeathly, M., Campbell, I.D. and Dobson, C.M. (1997) J. Biomol. NMR, 10, 221–230.Google Scholar
  18. Rance, M., Sørensen, O.W., Bodenhausen, G., Wagner, G., Ernst, R.R. and Wüthrich, K. (1983) Biochem. Biophys. Res. Commun., 117, 479–485.Google Scholar
  19. Richarz, R. and Wüthrich, K. (1978) Biopolymers, 17, 2133–2141.Google Scholar
  20. Schwalbe, H., Fiebig, K.M., Buck, M., Jones, J.A., Grimshaw, S.B., Spencer, A., Glaser, S.J., Smith, L.J. and Dobson, C.M. (1997) Biochemistry, 36, 8977–8991.Google Scholar
  21. Spera, S. and Bax, A. (1991) J. Am. Chem. Soc., 113, 5490–5492.Google Scholar
  22. Szilágyi, L. and Jardetzky, O. (1989) J. Magn. Reson., 83, 441–449.Google Scholar
  23. Thanabal, V., Omecinsky, D.O., Reily, M.D. and Cody, W.L. (1994) J. Biomol. NMR, 4, 47–59.Google Scholar
  24. Van Geet, A.L. (1970) Anal. Chem., 42, 679–680.Google Scholar
  25. Vuister, G.W. and Bax, A. (1992) J. Magn. Reson., 98, 428–435.Google Scholar
  26. Wishart, D.S., Sykes, B.D. and Richards, F.M. (1992) Biochemistry, 31, 1647–1651.Google Scholar
  27. Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995a) J. Biomol. NMR, 5, 67–81.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. (1995b) J. Biomol. NMR, 6, 135–140.Google Scholar
  29. Wishart, D.S. and Sykes, B.D. (1994) J. Biomol. NMR, 4, 171–180.Google Scholar
  30. Wishart, D.S., Sykes, B.D. and Richards, F.M. (1991) J. Mol. Biol., 222, 311–333.Google Scholar
  31. Yao, J., Dyson, H.J. and Wright, P.E. (1997) FEBS Lett., 419, 285–289.Google Scholar
  32. Zhang, O., Kay, L.E., Olivier, J.P. and Forman-Kay, J.D. (1994) J. Biomol. NMR, 4, 845–858.Google Scholar

Copyright information

© Kluwer Academic Publishers 2000

Authors and Affiliations

  • Stephan Schwarzinger
    • 1
  • Gerard J.A. Kroon
    • 1
  • Ted R. Foss
    • 1
  • Peter E. Wright
    • 1
  • H. Jane Dyson
    • 1
  1. 1.Department of Molecular Biology and Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaU.S.A.

Personalised recommendations