Abstract
Application of a modified ePHOGSY and other novel NMR experiments to an H2O-DMSO solution of the protein FKBP12 identified the presence of one molecule of DMSO bound in the substrate binding site. It occupies the same spatial region occupied by the pipecolidine moiety of the immunosuppressive drugs FK506 and Rapamycin complexed to the protein. The binding constant KD for this DMSO molecule was only 275 mM. A substructure search of small molecules similar to DMSO resulted in the identification of molecules with improved binding affinity. This work represents a clear example of the powerful interplay of molecular modelling and NMR.
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Allen, K.N., Bellamacina, C.R., Ding, X., Jeffery, C.J., Mattos, C., Petsko, G.A. and Ringe, D. (1996) J. Phys. Chem., 100, 2605–2611.
Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, Jr., E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535–542.
Boyd, J. and Soffe, N. (1989) J. Magn. Reson., 85, 406–413.
Brünger, A.T. (1992) X-PLOR (Version 3.1) Manual, Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT.
Burkhard, P. (1995) Ph.D. Thesis, University of Basel, Switzerland.
Burkhard, P., Hommel, U., Sanner, M. and Walkinshaw, M. (1999) J. Mol. Biol., in press.
Clark, M., Cramer III, R.D. and Van Opdenbosch, N. (1989) J. Comput. Chem., 10, 982–1012.
Dalvit, C. and Hommel, U. (1995) J. Magn. Reson., B109, 334–338.
Dalvit, C. and Böhlen, J.-M. (1996) J. Magn. Reson., B111, 76–80.
Dalvit, C. (1998) J. Biomol. NMR, 11, 437–444.
Dalvit, C., Shapiro, G., Böhlen, J.-M. and Parella, T. (1999) Magn. Reson. Chem., 37, 7–14.
Douzou, P. and Petsko G.A. (1984) Adv. Protein Chem., 36, 245–361.
Drobny, G., Pines, A., Sinton, S., Weitekamp, D.P. and Wemmer, D. (1979) Symp. Faraday Soc., 13, 49–55.
Dwek, R.A. (1973) Nuclear Magnetic Resonance (N.M.R.) in Biochemistry, Clarendon Press, Oxford.
Ernst, R.R., Bodenhausen, G. and Wokaun, A. (1987) Principles of Nuclear Magnetic Resonance in One and Two Dimensions, Clarendon Press, Oxford.
Hwang, T.-L. and Shaka, A.J. (1995) J. Magn. Reson., A112, 275–279.
Lehmann, M.S., Mason, S.A. and McIntyre, G.J. (1985) Biochemistry, 24, 5862–5869.
Lehmann, M.S. and Stansfield, R.F.D. (1989) Biochemistry, 28, 7028–7033.
Liepinsh, E. and Otting, G. (1997) Nat. Biotechnol., 15, 264–268.
Marion, D. and Wüthrich, K. (1983) Biochem. Biophys. Res. Commun., 113, 967–974.
Mattos, C. and Ringe, D. (1996) Nat. Biotechnol., 14, 595–599.
Momany, F.A. and Rone, R. (1992) J. Comput. Chem., 13, 883–900.
Mori, S., Berg, J.M. and Van Zijl, P.C.M. (1996) J. Biomol. NMR, 7, 77–82.
Otting, G. (1997) Prog. NMR Spectrosc., 31, 259–285.
Patt, S.L. (1992) J. Magn. Reson., 96, 94–102.
Pearlman, R.S. (1998) CONCORD/Stereoplex User's Manual, distributed by Tripos Inc., St. Louis, MO, U.S.A.
Ponstingl, H. and Otting, G. (1997) J. Biomol. NMR, 9, 441–444.
Rosen, M.K., Michnick, S.W., Karplus, M. and Schreiber, S.L. (1991) Biochemistry, 30, 4774–4789.
Shuker, S.B., Hajduk, P.J., Meadows, R.P. and Fesik, S.W. (1996) Science, 274, 1531–1534.
Sklenár, V. (1995) J. Magn. Reson., A114, 132–135.
Van Duyne, G.D., Standaert, R.F., Schreiber, S.L. and Clardy, J. (1991) J. Am. Chem. Soc., 113, 7433–7434.
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Dalvit, C., Floersheim, P., Zurini, M. et al. Use of organic solvents and small molecules for locating binding sites on proteins in solution*. J Biomol NMR 14, 23–32 (1999). https://doi.org/10.1023/A:1008378929578
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DOI: https://doi.org/10.1023/A:1008378929578