Abstract
NMR spectroscopy is recognized widely as an invaluable tool for the structural characterization of biological macromolecules with molecular weights of less than approx 25 kDa. The quality of structures obtainable using NMR spectroscopic methods is comparable with those derived from X-ray crystallography but, in addition, NMR offers the possibility of obtaining quantitative information on molecular flexibility. A particularly important aspect of the dynamics of macromolecules is that of ligand binding. Such binding can be accompanied by conformational changes in either the ligand, the macromolecule, or both and, in many cases, such dynamic changes are crucial to the functioning of the macromolecular system. This chapter is concerned with the use of NMR to define the nature of specific protein-ligand interactions. Although the focus is on interactions of ligands with proteins, rather than with other biological macromolecules, such as DNA or membranes, many of the techniques applicable to studies of protein-ligand interactions generally are applicable also to other macromolecular interactions. The topic of protein-ligand interactions has also been addressed from a number of different viewpoints in several other recent reviews (1–7).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Roberts, G. C. K. (1993) NMR of Macromolecules: A Practical Approach, Oxford University Press, Oxford, chs 6 and 7.
Handschumacher, R. E. and Armitage, I. M., eds. (1989) NMR Methods for Elucidating Macromolecule-Ligand Interactions: An Approach to Drug Design, Pergamon, Oxford.
Craik, D. J., ed. (1995) NMR in Drug Design, CRC, Boca Raton, FL.
Craik, D. J. and Higgins, K. A. (1989) NMR studies of ligand-macromolecule interactions, in Annual Reports tn NMR Spectroscopy, vol. 22 (Webb, G. A, ed.), Academic, London, pp. 61–138.
Otting, G. (1993) Experimental NMR techniques for studies of protein-ligand interactions. Curr. Opinion Struct. Biol. 3, 760–768.
Fesik, S. W., Zuiderweg, E. R. P., Olejniczak, E. T, and Gampe, R. T. (1990) NMR methods for determining the structures of enzyme/inhibitor complexes as an aid in drug design. Biochem. Pharmacol. 40, 161–167.
Fesik, S. W. (1991) NMR studies of molecular complexes as a tool in drug design. J. Med. Chem. 34, 2937–2945.
Feeney, J. and Birdsall, B. (1993) NMR studies of protein-ligand interactions, in NMR of Macromolecules: A Practical Approach (Roberts, G. C. K., ed.), Oxford University Press, Oxford, pp. 181–215.
Roberts, G. C. K. (1983) The interaction of substrates and inhibitors with dihydrofolate reductase, in Chemistry and Biology of Pteridines. (Blair, J. A. and de Gruyter, W., eds.), Dekker, Berlin.
Feeney, J. (1991) NMR studies of dynamic processes and multiple conformations in protein-ligand complexes, in NMR and Biomolecular Structure. (Bertini, I., Molinari, H., and Niccolai, N., eds.), VCH Publishers, New York, Oxford, pp. 189–205.
Feeney, J. (1990) NMR studies of interactions of ligands with dihydrofolate reductase. Biochem. Pharmacol. 40, 141–152.
Feeney, J. (1986) NMR studies of drug-receptor complexes antifolate drugs binding to dihydrofolate reductase, in NMR in Living Systems (Axenrod, T. and Ceccarelli, G., eds.), D. Reidel, Dordrecht, pp. 347–366.
Stone, M. J., Chandrasekhar, K., Holmgren, A., Wright, P. E., and Dyson, H. J. (1993) Comparison of backbone and tryptophan side-chain dynamics of reduced and oxidised Escherichia coli thioredoxin using 15N NMR relaxation measurements. Biochemistry 32, 426–435.
Clore, G. M., Driscoll, P. C., Wingfield, P. T., and Gronenborn, A. M. (1990) Analysis of the backbone dynamics of interleukin-1β using two-dimensional inverse detected heteronuclear 15N-1H NMR spectroscopy. Biochemistry 29, 7387–7401.
Peng, J. W. and Wagner, G. (1992) Mapping of the spectral densities of N-H bond motions in eglin-c using heteronuclear relaxation experiments. Biochemistry 31, 8571–8586.
Wishart, D. S., Sykes, B. D., and Richards, F. M. (1991) Relationship between nuclear magnetic resonance chemical shift and protein secondary structure. J. Mol. Biol. 222, 311–333.
Wishart, D. S. and Sykes, B. D. (1994) The 13C chemical shift index a simple method for the identification of protein secondary structure using 13C chemical-shift data. J. Biomol. NMR 4, 171–180.
London, R. E. (1980) Intramolecular dynamics of proteins and peptides as monitored by nuclear magnetic resonance measurements, in Magnetic Resonance in Biology, vol. 1 (Cohen, J. S., ed.), Wiley, New York, pp. 1–69.
McCain, D. C., Ulrich, E. L., and Markley, J. L. (1988) NMR relaxation study of internal motions in staphylococcal nuclease. J. Magn. Reson. 80, 296–305.
Ando, M. E., Gerig, J. T., and Luk, K. F. S. (1986) Motion at the active site of ((4-fluorophenyl)sulphonyl-)chymotrypsin. Biochemistry 25, 4772–4778.
Cheng, J.-W., Lepre, C. A., and Moore, J. M. (1994) 15N NMR relaxation studies of the FK506 binding protein: dynamic effects of ligand binding and applications for calcineurin recognition. Biochemistry 33, 4093–4100.
Neuhaus, D. and Williamson, M. (1989) The Nuclear Overhauser Effect, VCH Publishers, New York.
Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York.
Dugad, L. B. and Gerig, J. T. (1988) NMR studies of carbonic anhydrase-4-fluorobenzenesulfonamide complexes. Biochemistry 27, 4310–4316.
Hyde, E. I., Birdsall, B., Roberts, G. C. K., Feeney, J., and Burgen, A. S. V. (1980) Phosphorus-31 nuclear magnetic resonance studies of the binding of oxidised coenzymes to Lactobacillus casei dihydrofolate reductase. Biochemistry 19, 3746–3754.
Theriault, Y., Logan, T. M., Meadows, R., Yu, L., Olejniczak, E. T., Holzman, T. F., Simmer, R. L., and Fesik, S. W. (1993) Solution structure of the cyclosporin A/cyclophilin complex by NMR. Nature 361, 88–91.
Feeney, J., Batchelor, J. G., Albrand, J. P., and Roberts, G. C. K. (1979) The effects of intermediate exchange processes on the estimation of equilibrium binding constants by NMR. J. Magn. Reson. 33, 519–529.
Pavlopoulos, S., Rose, M., Wickham, G., and Craik, D. J. A. 1H NMR analysis of the interaction between terephthalamide derivatives and the oligonucleotide duplex d(GGTAATTACC2. Anticancer Drug Design, in press.
Embrey, K. J., Searle, M. S., and Craik, D. J. (1993) Interaction of Hoechst 33258 with the minor groove of the A + T-rich DNA duplex d(GGTAATTACC)2 studied in solution by NMR spectroscopy. Eur. J. Biochem. 211, 437–447.
Searle, M. S. and Embrey, K. J. (1990) Sequence-specific interaction of Hoechst 33258 with the minor groove of an adenine-tract DNA duplex studied in solution by 1H NMR spectroscopy. Nucleic Acids Res. 18, 3753–3762.
Otting, G. and Wuthrich, K. (1990) Heteronuclear filters in two-dimensional [1H,1H]-NMR spectroscopy combined use with isotope labeling for studies of macromolecular conformation and intermolecular interactions. Q. Rev. Biophys. 23, 39–96.
London, R. E., Perlman, M. E., and Davis, D. G. (1992) Relaxation matrix analysis of the transferred nuclear Overhauser effect for finite exchange rates. J. Magn. Reson. 97, 79–98.
Sykes, B. D. (1993) Determination of the conformation of bound peptides using NMR-transferred NOE techniques. Curr. Opinion Biotechnol. 4, 392–396.
Campbell, A. P. and Sykes, B. D. (1991) Theoretical evaluation of the two-dimensional transferred nuclear Overhauser effect. J. Magn. Reson. 93, 77–92.
Clore, G. M. and Gronenbom, A. M. (1982) Theory and applications of the transferred nuclear Overhauser effect to the study of the conformations of small ligands bound to proteins. J. Magn. Reson. 48, 402–417.
Clore, G. M., Gronenborn, A. M., Birdsall, B., Feeney, J., and Roberts, G. C. K. (1984) 19F NMR studies of 3′,5′-difluoromethotrexate binding to Lactobacillus casei dihydrofolate reductase. Molecular motion and coenzyme-induced conformational changes. Biochem. J. 217, 659–666.
Searle, M. S., Forster, M. J., Birdsall, B., Roberts, G. C. K., Feeney, J., Cheung, H. T. A., Kompis, I., and Geddes, A. J. (1988) Dynamics of trimethoprim bound to dihydrofolate reductase. Proc. Natl. Acad. Sci. USA 85, 3787–3791.
Rajagopalan, J. S., Taylor, K. M., and Jaffe, E. K. (1993) 13C NMR studies of the enzyme-product complex of Bacillus subtilis chorismate mutase. Biochemistry 32, 3965–3972.
Lippins, G., Hallenga, K., Van Belle, D., Wodak, S. J., Nirmala, N. R., Hill, P., Russell, K. C., Smith, D. D., and Hruby, V. J. (1993) Transfer nuclear Overhauser effect study of the conformation of oxytocin bound to bovine neurophysin I. Biochemistry 32, 9423–9434.
Landy, F. G. and Rao, B. D. (1989) Dynamical NOE in multiple-spin systems undergoing chemical exchange. J. Magn. Reson. 81, 371–377.
Lippens, G., Cerf, C., and Hallenga, K. (1992) Theory and experimental results of transfer NOE experiments. J. Magn. Reson. 99, 268–281.
Taga, T., Tanaka, H., Goto, T., and Tada, S. (1987) Structure of a new macrocyclic antibiotic. Acta. Cryst. C43, 751–753.
Bierer, B. E., Somers, P. K., Wandless, T. J., Burakoff, S. J., and Schreiber, S. L. (1990) Probing immunosuppressant action with a non-natural immunophilin ligand. Science 250, 556–559.
Karuso, P., Kessler, H., and Mierke, D. F. (1990) Solution structure of FK506 from nuclear magnetic resonance and molecular dynamics. J. Am. Chem. Soc. 112, 9434–9437.
Fesik, S. W., Gampe, R. T., Jr., Holzman, T. F., Egan, D. A., Edalji, R., Luly, J. R., Simmer, R., Helfrich, R., Klahore, V., and Rich, D. H. (1990) Isotope-edited NMR of cyclosporin A bound to cyclophilin evidence for a trans 9,10-amide bond. Science 250, 1406–1409.
Fesik, S. W., Gampe, R. T., Jr., Eaton, H. L., Gemmecker, G., Olejniczak, E. T., Neri, P., Holzman, T. F., Egan, D. H., Edalji, R., Simmer, R., Helfrich, R., Hochlowski, J., and Jackson, M. (1991) NMR studies of [U-13C]cyclosporin A bound to cyclophilin bound confirmation and portions of cyclosporin involved in binding. Biochemistry 31, 6574–6583.
Weber, C., Wider, G., von Freyberg, K., Truber, R., Braun, W., Widner, H., and Wuthrich, K. (1991) The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution. Biochemistry 30, 6563–6574.
Rosen, M. K., Standaert, R. F., Galat, A., Nakatsuka, M., and Schreiber, S. L. (1990). Inhibition of FKBP rotamase activity by immunosuppressant FK506:twisted amide surrogate. Science 248, 863–866.
Wandless, T. J., Michnick, S. W., Rosen, M. K., Karplus, M., and Schreiber, S. L. (1991) FK506 and rapamycin binding to FKBP common elements in immunophilin-ligand complexation. J. Am. Chem. Soc. 113, 2339–2341.
Petros, A. M., Gampe, R. T., Jr., Gemmecker, G., Neri, P., Holzman, T. F., Edalji, R., Hochlowski, J., Jackson, M., McAlpine, J., Luly, J. R., Pilot-Matias, T., Pratt, S., and Fesik, S. W. (1991) Studies of an FK-506 analog, asomycin, bound to FKBP conformation and regions of asomycin involved in binding. J. Med. Chem. 34, 2925–2928.
van Duyne, G. D., Standaert, R. F., Karplus, P. A., Schreiber, S. L., and Clardy, J. (1991) Atomic structure of FKBP-FK506, an immunophilin-immunosuppressant complex. Science 252, 839–842.
Michnick, S. W., Rosen, M. K., Wandless, T. J., Karplus, M., and Schreiber, S. L. (1991) Solution structure of FKBP, a rotamase enzyme and receptor for FK506 and rapamycin. Science 252, 836–839.
Moore, J. W., Peattie, D. A., Fitzgibbon, M. J., and Thomson, J. A. (1991) Solution structure of the major binding protein for the immunosuppressant FK506. Nature 351, 248–250.
Meadows, R. P., Nettesheim, D. G., Xu, R. X., Olejniczak, E. T., Petros, A. M., Holzman, T. F., Severin, J., Gubbins, E., Smith, H., and Fesik, S. W. (1993) Three-dimensional structure of the FK506 binding protein/ascomycin complex in solution by heteronuclear three-and four-dimensional NMR. Biochemistry 32, 754–765.
Cheng, J.-W., Lepre, C. A., Chambers, S. P., Fulghum, J. R., Thomson, J. A., and Moore, J. M. (1993) 15N NMR relaxation studies of the FK506 binding protein: backbone dynamics of the uncomplexed receptor. Biochemistry 32, 9000–9010.
Otting, G., Liepinsh, E., and Wuthrich, K. (1991) Protein hydration in aqueous solution. Science 254, 974–980.
Grzesiek, S., Bax, A., Nicholson, L. K., Yamazaki, T., Wingfield, P., Stahl, S. J., Eyermann, C. J., Torchia, D. A., Hodge, C. N., Lam, P. Y. S., Jadhau, P. K., and Chang, C. M. (1994) NMR evidence for the displacement of a conserved interior water molecule in HIV protease by a non-peptide cyclic urea-based inhibitor. J. Am. Chem. Soc. 116, 1581,1582.
Clore, G. M., Bax, A., Wingfield, P. T., and Gronenborn, A. M. (1990) Identification and localisation of bound internal water in the solution structure of interleukin 1β by heteronuclear three-dimensional 1H rotating frame Overhauser 15N-1H multiple quantum coherence NMR spectroscopy. Biochemistry 28, 5671–5676.
Otting, G., Liepinsh, B. T., Farmer, B. T., and Wüthrich, K. (1991) Protein hydration studied with homonuclear 3D 1H NMR experiments. J. Biomol. NMR 1, 209–215.
Messerle, B. A., Wader, G., Otting, G., Weber, G., and Wuthrich, K. (1989) Solvent suppression using a spin lock in 2D and 3D NMR spectroscopy with H2O solutions. J. Magn. Reson. 85, 608–613.
Qi, P. X., Urbauer, J. L., Fuentes, E. J., Leopold, M. F., and Wand, A. J. (1994) Structural water in oxidized and reduced horse heart cytochrome C. Nature Struct. Biol. 1, 378–382.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 1997 Humana Press Inc.
About this protocol
Cite this protocol
Craik, D.J., Wilce, J.A. (1997). Studies of Protein-Ligand Interactions by NMR. In: Reid, D.G. (eds) Protein NMR Techniques. Methods in Molecular Biology™, vol 60. Humana Press. https://doi.org/10.1385/0-89603-309-0:195
Download citation
DOI: https://doi.org/10.1385/0-89603-309-0:195
Publisher Name: Humana Press
Print ISBN: 978-0-89603-309-2
Online ISBN: 978-1-59259-546-4
eBook Packages: Springer Protocols