An approach to global fold determination using limited NMR data from larger proteins selectively protonated at specific residue types
Tóm tắt
A combination of calculation and experiment is used to demonstrate that the global fold of larger proteins can be rapidly determined using limited NMR data. The approach involves a combination of heteronuclear triple resonance NMR experiments with protonation of selected residue types in an otherwise completely deuterated protein. This method of labelling produces proteins with α-specific deuteration in the protonated residues, and the results suggest that this will improve the sensitivity of experiments involving correlation of side-chain (1H and 13C) and backbone (1H and 15N) amide resonances. It will allow the rapid assignment of backbone resonances with high sensitivity and the determination of a reasonable structural model of a protein based on limited NOE restraints, an application that is of increasing importance as data from the large number of genome sequencing projects accumulates. The method that we propose should also be of utility in extending the use of NMR spectroscopy to determine the structures of larger proteins.
Tài liệu tham khảo
Arrowsmith, C., Pachter, R., Altman, R. and Jardetzky, O. (1991) Eur. J. Biochem., 202, 53–66.
Bax, A. and Grzesiek, S. (1993) Acc. Chem. Res., 26, 131–138.
Broadhurst, R.W., Hardman, C.H., Thomas, J.O. and Laue, E.D. (1995) Biochemistry, 34, 16608–16617.
Brünger, A.T. (1992) X-PLOR Manual v. 3.0, Yale University, New Haven, CT, U.S.A.
Clore, G.M. and Gronenborn, A. (1991) Science, 252, 795–796.
Clowes, R.T., Boucher, W., Hardman, C.H., Domaille, P.J. and Laue, E.D. (1993) J. Biomol. NMR, 3, 349–354.
Crespi, H.L., Rosenberg, R.M. and Katz, J.J. (1968) Science, 161, 795–796.
FarmerII, B.T. and Venters, R.A. (1995) J. Am. Chem. Soc., 117, 4187–4188.
Grzesiek, S. and Bax, A. (1992a) J. Magn. Reson., 99, 201–207.
Grzesiek, S. and Bax, A. (1992b) J. Am. Chem. Soc., 114, 6291–6293.
Grzesiek, S. and Bax, A. (1993) J. Biomol. NMR, 3, 185–204.
Grzesiek, S., Anglister, J., Ren, H. and Bax, A. (1993) J. Am. Chem. Soc., 115, 4369–4370.
Grzesiek, S., Wingfield, P., Stahl, S., Kaufman, J.D. and Bax, A. (1995) J. Am. Chem. Soc., 117, 9594–9595.
Kraulis, P.J. (1991) J. Appl. Crystallogr., 24, 946–950.
Kraulis, P.J., Domaille, P.J., Campbell-Burk, S.L., VanAken, T. and Laue, E.D. (1994) Biochemistry, 33, 3515–3531.
Laue, E.D., Mayger, M.R., Skilling, J. and Staunton, J. (1986) J. Magn. Reson., 68, 14–29.
LeMaster, D.M. and Richards, F.M. (1988) Biochemistry, 27, 142–150.
LeMaster, D.M. (1990) Q. Rev. Biophys., 23, 133–174.
Logan, T.M., Olejniczak, E.T., Xu, R.X. and Fesik, S.W. (1992) FEBS Lett., 314, 413–418.
Markley, J.L., Potter, I. and Jardetzky, O. (1968) Science, 161, 1249–1251.
Markus, M.A., Dayie, K.T., Matsudaira, P. and Wagner, G. (1994) J. Magn. Reson., A105, 192–195.
Montelione, G.T., Lyons, B.A., Emerson, S.D. and Tashiro, M. (1992) J. Am. Chem. Soc., 114, 10974–10975.
Nietlispach, D., Clowes, R.T., Broadhurst, R.W., Ito, Y., Keeler, J., Kelly, M., Ashurst, J., Oschkinat, H., Domaille, P.J. and Laue, E.D. (1996) J. Am. Chem. Soc., 118, 407–415.
Nilges, M. (1995) J. Mol. Biol., 245, 645–660.
Oldfield, E. (1995) J. Biomol. NMR, 5, 217–225.
Spera, S. and Bax, A. (1991) J. Am. Chem. Soc., 113, 5490–5492.
Tjandra, N., Feller, S.E., Pastor, R.W. and Bax, A. (1995) J. Am. Chem. Soc., 117, 12562–12566.
Tolman, J.R., Flanagan, J.M., Kennedy, M.A. and Prestegard, J.H. (1995) Proc. Natl. Acad. Sci. USA, 92, 9279–9283.
Torchia, D.A., Sparks, S.W. and Bax, A. (1988) J. Am. Chem. Soc., 110, 2320–2321.
Venters, R.A., Metzler, W.J., Spicer, L.D., Mueller, L. and FarmerII, B.T. (1995) J. Am. Chem. Soc., 117, 9592–9593.
Vuister, G.W., Kim, S.-J., Wu, C. and Bax, A. (1994) J. Am. Chem. Soc., 116, 9206–9210.
Wang, A.C., Lodi, P.J., Qin, J., Vuister, G.W., Gronenborn, A.M. and Clore, G.M. (1994) J. Magn. Reson., B105, 196–198.
Wishart, D.S. and Sykes, B.D. (1994) Methods Enzymol., 239, 363–392.
Yamazaki, T., Lee, W., Revington, M., Mattiello, D.L., Dahlquist, F.W., Arrowsmith, C.H. and Kay, L.E. (1994a) J. Am. Chem. Soc., 116, 6464–6465.
Yamazaki, T., Lee, W., Arrowsmith, C.H., Muhandiram, D.R. and Kay, L.E. (1994b) J. Am. Chem. Soc., 116, 11655–11666.