Abstract
Chemical shift assignment is reported for the protein ubiquitin denatured in 8M urea at pH 2. The variations in 15N chemical shifts of three different proteins (ubiquitin, disulfide reduced, carboxymethylated lysozyme, all-Ala-α-lactalbumin), all without disulfides and denatured in 8M urea at pH 2 are compared to `random coil shifts' of small model peptides (Braun et al., 1994) and to the averaged native chemical shifts taken from the BMRB database. Both parameterizations show a remarkable agreement with the averaged measured 15N chemical shifts in the three denatured proteins. Detailed analysis of these experimental 15N chemical shifts provides an estimate of the influence of nearest neighbors and conformational preferences on the chemical shift and provides a direct means to identify non-random structural preferences in denatured proteins.
Similar content being viewed by others
Explore related subjects
Discover the latest articles and news from researchers in related subjects, suggested using machine learning.References
Arcus, V.L., Vuilleumier, S., Freund, S.M., Bycroft, M. and Fersht, A.R. (1995) J. Mol. Biol., 254, 305–321.
Arcus, V.L., Vuilleumier, S., Freund, S.M., Bycroft, M. and Fersht, A.R. (1994) Proc. Natl. Acad. Sci. USA, 91, 9412–9416.
Blanco, F.J., Serrano, L. and Forman-Kay, J.D. (1998) J. Mol. Biol., 284, 1153–1164.
Braun, D., Wider, G. and Wüthrich, K. (1994) J. Am. Chem. Soc., 116, 8466–8469.
Briggs, M.S. and Roder, H. (1992) Proc. Natl. Acad. Sci. USA, 89, 2017–2021.
Brutscher, B., Brüschweiler, R. and Ernst, R.R. (1997) Biochemistry, 36, 13043–13053.
Buck, M., Schwalbe, H. and Dobson, C.M. (1995) Biochemistry, 34, 13219–13232.
Carlomagno, T., Maurer, M., Hennig, M. and Griesinger, C. (2000) J. Am. Chem. Soc., 122, 5105–5113.
Cornilescu, G., Delaglio, F. and Bax, A. (1999) J. Biomol. NMR, 13, 289–302.
Cornilescu, G., Marquardt, J.L., Ottiger, M. and Bax, A. (1999) J. Am. Chem. Soc., 120, 6836–6837.
Di Stefano, D.L. and Wand, A.L. (1987) Biochemistry, 26, 7272–7281.
Driscoll, P.C., Clore, G.M., Marion, D., Wingfield, P.T. and Gronenborn, A.M. (1990) Biochemistry, 29, 3542–3556.
Dyson, J. and Wright, P.E. (1998) Nat. Struct. Biol., 5, 499–503.
Eliezer, D., Yao, J., Dyson, H.J. and Wright, P.E. (1998) Nat. Struct. Biol., 5, 148–155.
Emsley, L. and Bodenhausen, G. (1990) Chem. Phys. Lett., 165, 469–476.
Emsley, L. and Bodenhausen, G. (1992) J. Magn. Reson., 97, 135–148.
Fiebig, K.M., Schwalbe, H., Buck, M., Smith, L.J. and Dobson, C.M. (1996) J. Phys. Chem., 100, 2661–2666.
Frank, M.K., Clore, G.M. and Gronenborn, A.M. (1995) Protein Sci., 4, 2605–2610.
Frenkiel, T., Bauer, C., Carr, M.D., Birdsall, B. and Feeney, J. (1990) J. Magn. Reson., 90, 420–425.
Fushman, D. and Cowburn, D. (1998) J. Am. Chem. Soc., 120, 7109–7110.
Fushman, D., Tjandra, N. and Cowburn, D. (1998) J. Am. Chem. Soc., 120, 10947–10952.
Glushka, J., Lee, M., Coffin, S. and Cowburn, D. (1989) J. Am. Chem. Soc., 111, 7716–7722.
Grzesiek, S., Anglister, J. and Bax, A. (1993) J. Magn. Reson., B101, 114–119.
Grzesiek, S. and Bax, A. (1992) J. Am. Chem. Soc., 114, 6291–6293.
Grzesiek, S. and Bax, A. (1993) J. Am. Chem. Soc., 115, 12593–12594.
Hennig, M., Bermel, W., Spencer, A., Dobson, C.M., Smith, L.J. and Schwalbe, H. (1999) J. Mol. Biol., 288, 705–723.
Hershko, A. and Ciechanover, A. (1998) Annu. Rev. Biochem., 67, 425–479.
Jenson, J., Goldstein, G. and Breslow, E. (1980) Biochim. Biophys. Acta, 624, 378–385.
Kay, L.E. and Bax, A. (1990) J. Magn. Reson., 86, 110–126.
Kay, L.E., Ikura, M., Tschudin, R. and Bax, A. (1990) J. Magn. Reson., 89, 496–514.
Lenkinski, R.E., Douglas, C.M., Glickson, J.D. and Goldstein, G. (1977) Biochim. Biophys. Acta, 494, 126–130.
Logan, T.M., Olejniczak, E.T., Xu, R.X. and Fesik, S.W. (1993) J. Biomol. NMR, 2, 225–231.
Logan, T.M., Theriault, Y. and Fesik, S.W. (1994) J. Mol. Biol., 236, 637–648.
Ludvigsen, S., Andersen, K.V. and Poulsen, F.M. (1991) J. Mol. Biol., 217, 731–736.
Marion, D., Driscoll, P.C., Kay, L.E., Wingfield, P.T., Bax, A., Gronenborn, A.M. and Clore, G.M. (1989a) Biochemistry, 28, 6150–6156.
Marion, D., Kay, L.E., Sparks, S.W., Torchia, D.A. and Bax, A. (1989b) J. Am. Chem. Soc., 111, 1515–1517.
Merutka, G., Dyson, H.J. and Wright, P.E. (1995) J. Biomol. NMR, 5, 14–24.
Nash, D.P. and Jonas, J. (1997) Biochem. Biophys. Res. Commun., 238, 289–291.
Neri, D., Billeter, M., Wider, G. and Wüthrich, K. (1992a) Science, 257, 1559–1563.
Neri, D., Wider, G. and Wüthrich, K. (1992b) Proc. Natl. Acad. Sci. USA, 89, 4397–4401.
Pardi, A., Billeter, M. and Wüthrich, K. (1984) J. Mol. Biol., 180, 741–751.
Penkett, C.J., Redfield, C., Dodd, I., Hubbard, J., McBay, D.L., Mossakowska, D.E., Smith, R.A., Dobson, C.M. and Smith, L.J. (1997) J. Mol. Biol., 274, 152–159.
Penkett, C.J., Redfield, C., Jones, J.A., Dodd, I., Hubbard, J., Smith, R.A., Smith, L.J. and Dobson, C.M. (1998) Biochemistry, 37, 17054–17067.
Peti, W., Hennig, M., Smith, L.J. and Schwalbe, H. (2000) J. Am. Chem. Soc., 122, 12017–12018.
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.
Redfield, C., Schulman, B.A., Milhollen, M.A., Kim, P.S. and Dobson, C.M. (1999) Nat. Struct. Biol., 6, 948–952.
Sattler, M., Schleucher, J. and Griesinger, C. (1999) Prog. NMR Spectrosc., 34, 93–158.
Schneider, D.M., Dellwo, M.J. and Wand, A.J. (1992) Biochemistry, 31, 3645–3652.
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.
Shortle, D. (1996) Curr. Opin. Struct. Biol., 6, 24–30.
Smith, L.J., Bolin, K.A., Schwalbe, H., MacArthur, M.W., Thornton, J.M. and Dobson, C.M. (1996a) J. Mol. Biol., 255, 494–506.
Smith, L.J., Fiebig, K.M., Schwalbe, H. and Dobson, C.M. (1996b) Fold. Des., 1, R95–106.
Spera, S. and Bax, A. (1991) J. Am. Chem. Soc., 113, 5490–5492.
Thanabal, V., Omecinsky, D.O., Reily, M.D. and Cody, W.L. (1994) J. Biomol. NMR, 4, 47–59.
Tjandra, N., Feller, S.E., Pastor, R.W. and Bax, A. (1995) J. Am. Chem. Soc., 117, 12562–12566.
Tjandra, N., Szabo, A. and Bax, A. (1996) J. Am. Chem. Soc., 118, 6986–6991.
Vijay-Kumar, S., Bugg, C.E. and Cook, W.J. (1987) J. Mol. Biol., 194, 531–544.
Vuister, G.W. and Bax, A. (1993) J. Am. Chem. Soc., 115, 7772–7777.
Weber, P.L., Brown, S.C. and Mueller, L. (1987) Biochemistry, 26, 7282–7290.
Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995a) J. Biomol. NMR, 5, 67–81.
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.
Wishart, D.S. and Nip, A.M. (1998) Biochem. Cell Biol., 76, 153–163.
Wishart, D.S. and Sykes, B.D. (1994a) J. Biomol. NMR, 4, 171–180.
Wishart, D.S. and Sykes, B.D. (1994b) Methods Enzymol., 239, 363–392.
Wishart, D.S., Sykes, B.D. and Richards, F.M. (1992) Biochemistry, 31, 1647–1651.
Wishart, D.S., Sykes, B.D. and Richards, F.M. (1991a) J. Mol. Biol., 222, 311–333.
Wishart, D.S., Sykes, B.D. and Richards, F.M. (1991b) FEBS Lett., 293, 72–80.
Wishart, D.S., Watson, M.S., Boyko, R.F. and Sykes, B.D. (1997) J. Biomol. NMR, 10, 329–336.
Wittekind, M. and Mueller, L. (1993) J. Magn. Reson., B101, 201–205.
Wong, K.B., Freund, S.M. and Fersht, A.R. (1996) J. Mol. Biol., 259, 805–818.
Yang, D. and Kay, L.E. (1996) J. Mol. Biol., 263, 369–382.
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Peti, W., Smith, L.J., Redfield, C. et al. Chemical shifts in denatured proteins: Resonance assignments for denatured ubiquitin and comparisons with other denatured proteins. J Biomol NMR 19, 153–165 (2001). https://doi.org/10.1023/A:1008307323283
Issue Date:
DOI: https://doi.org/10.1023/A:1008307323283