Abstract
A computer program has been developed to accurately and automatically predict the 1H and 13C chemical shifts of unassigned proteins on the basis of sequence homology. The program (called SHIFTY) uses standard sequence alignment techniques to compare the sequence of an unassigned protein against the BioMagResBank – a public database containing sequences and NMR chemical shifts of nearly 200 assigned proteins [Seavey et al. (1991) J. Biomol. NMR, 1, 217–236]. From this initial sequence alignment, the program uses a simple set of rules to directly assign or transfer a complete set of 1H or 13C chemical shifts (from the previously assigned homologues) to the unassigned protein. This ‘homologous assignment’ protocol takes advantage of the simple fact that homologous proteins tend to share both structural similarity and chemical shift similarity. SHIFTY has been extensively tested on more than 25 medium-sized proteins. Under favorable circumstances, this program can predict the 1H or 13C chemical shifts of proteins with an accuracy far exceeding any other method published to date. With the expo- nential growth in the number of assigned proteins appearing in the literature (now at a rate of more than 150 per year), we believe that SHIFTY may have widespread utility in assigning individual members in families of related proteins, an endeavor that accounts for a growing portion of the protein NMR work being done today.
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References
Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) J.Mol.Biol., 215, 403–410.
Bairoch, A. and Apweiler, R. (1996) Nucleic Acids Res., 24, 21–25.
Bartels, C., Billeter, M., Güntert, G. and Wüthrich, K. (1996) J.Biomol. NMR, 7, 207–213.
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.V., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M.J. (1977) J.Mol.Biol., 112, 535–542.
Bryant, S.H. (1996) Proteins Struct.Funct.Genet., 26, 172–185.
Dayhoff, M.O., Barker, W.C. and Hunt, L.T. (1983) Methods Enzymol., 91, 524–545.
De Dios, A.C., Pearson, J.G. and Oldfield, E. (1993) Science, 260, 1491–1495.
George, D.G., Hunt, L.R. and Barker, W.C. (1996) Methods Enzymol., 266, 41–59.
Gronwald, W., Boyko, R.F., Sönnichsen, F.D., Wishart, D.S. and Sykes, B.D. (1997) J.Biomol.NMR, 10, 165–179.
Herranz, J., Gonzalez, C., Rico, M., Nieto, J.L., Santoro, J., Jimenez, M.A., Bruix, M., Neira, J.L. and Blanco, F.J. (1992) Magn.Reson. Chem., 30, 1012–1018.
Herzberg, O. and James, M.N.G. (1988) J.Mol.Biol., 203, 761–771.
Ikura, M., Kay, L.E. and Bax, A. (1990) Biochemistry, 29, 4659–4667.
Needleman, S.B. and Wunsch, C.D. (1970) J.Mol.Biol., 48, 443–453.
Orengo, C.A., Brown, N.P. and Taylor, W.R. (1992) Proteins Struct. Funct.Genet., 14, 139–167.
Ösapay, K. and Case, D.A. (1991) J.Am.Chem.Soc., 113, 9436–9444.
Ösapay, K. and Case, D.A. (1994) J.Biomol.NMR, 4, 215–230.
Perkins, S.J. and Wüthrich, K. (1979) Biochim.Biophys.Acta, 576, 409–422.
Perkins, S.J. and Dwek, R.A. (1980) Biochemistry, 19, 245–255.
Redfield, C. and Robertson, J.P. (1991) In Computational Aspects of the Study of Biological Macromolecules by Nuclear Magnetic Resonance Spectroscopy (Eds., Hoch, J.C., Poulsen, F.M. and Redfield, C.), Plenum, New York, NY, U.S.A., pp. 303–316.
Sali, A., Overington, J.P., Johnson, M.S. and Blundell, R.L. (1990) Trends Biochem.Sci., 15, 235–240.
Seavey, B.R., Farr, E.A., Westler, W.M. and Markley, J.L. (1991) J. Biomol.NMR, 1, 217–236.
Slupsky, C.M., Reinach, F.C., Smillie, L.B. and Sykes, B.D. (1995) Protein Sci., 4, 1279–1290.
Taylor, D.A., Sack, J.S., Maune, J.F. and Beckingham, K. (1991) J. Biol.Chem., 266, 21375–21384.
Williamson, M.P., Asakura, T., Nakamura, E. and Demura, M. (1992) J.Biomol.NMR, 2, 83–98.
Wishart, D.S., Sykes, B.D. and Richards, F.M. (1991) J.Mol.Biol., 222, 311–333.
Wishart, D.S., Boyko, R.F. and Sykes, B.D. (1994) Comput.Appl. Biosci., 10, 121–132.
Wishart, D.S. and Sykes, B.D. (1994) J.Biomol.NMR, 4, 171–180.
Wishart, D.S., Bigam, C.G., Holm, A., Hodges, R.S. and Sykes, B.D. (1995a) J.Biomol.NMR, 5, 1–22.
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.
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Wishart, D.S., Watson, M.S., Boyko, R.F. et al. Automated 1H and 13C chemical shift prediction using the BioMagResBank. J Biomol NMR 10, 329–336 (1997). https://doi.org/10.1023/A:1018373822088
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DOI: https://doi.org/10.1023/A:1018373822088