Skip to main content

Studies of Protein-Ligand Interactions by NMR

  • Protocol
Protein NMR Techniques

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 60))

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 (17).

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Roberts, G. C. K. (1993) NMR of Macromolecules: A Practical Approach, Oxford University Press, Oxford, chs 6 and 7.

    Google Scholar 

  2. Handschumacher, R. E. and Armitage, I. M., eds. (1989) NMR Methods for Elucidating Macromolecule-Ligand Interactions: An Approach to Drug Design, Pergamon, Oxford.

    Google Scholar 

  3. Craik, D. J., ed. (1995) NMR in Drug Design, CRC, Boca Raton, FL.

    Google Scholar 

  4. 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.

    Google Scholar 

  5. Otting, G. (1993) Experimental NMR techniques for studies of protein-ligand interactions. Curr. Opinion Struct. Biol. 3, 760–768.

    Article  CAS  Google Scholar 

  6. 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.

    Article  PubMed  CAS  Google Scholar 

  7. Fesik, S. W. (1991) NMR studies of molecular complexes as a tool in drug design. J. Med. Chem. 34, 2937–2945.

    Article  PubMed  CAS  Google Scholar 

  8. 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.

    Google Scholar 

  9. 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.

    Google Scholar 

  10. 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.

    Google Scholar 

  11. Feeney, J. (1990) NMR studies of interactions of ligands with dihydrofolate reductase. Biochem. Pharmacol. 40, 141–152.

    Article  PubMed  CAS  Google Scholar 

  12. 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.

    Google Scholar 

  13. 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.

    Article  PubMed  CAS  Google Scholar 

  14. 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.

    Article  PubMed  CAS  Google Scholar 

  15. 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.

    Article  PubMed  CAS  Google Scholar 

  16. 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.

    Article  PubMed  CAS  Google Scholar 

  17. 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.

    Article  PubMed  CAS  Google Scholar 

  18. 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.

    Google Scholar 

  19. 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.

    CAS  Google Scholar 

  20. 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.

    Article  PubMed  CAS  Google Scholar 

  21. 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.

    Article  PubMed  CAS  Google Scholar 

  22. Neuhaus, D. and Williamson, M. (1989) The Nuclear Overhauser Effect, VCH Publishers, New York.

    Google Scholar 

  23. Wüthrich, K. (1986) NMR of Proteins and Nucleic Acids, Wiley, New York.

    Google Scholar 

  24. Dugad, L. B. and Gerig, J. T. (1988) NMR studies of carbonic anhydrase-4-fluorobenzenesulfonamide complexes. Biochemistry 27, 4310–4316.

    Article  PubMed  CAS  Google Scholar 

  25. 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.

    Article  PubMed  CAS  Google Scholar 

  26. 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.

    Article  PubMed  CAS  Google Scholar 

  27. 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.

    CAS  Google Scholar 

  28. 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.

    Google Scholar 

  29. 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.

    Article  PubMed  CAS  Google Scholar 

  30. 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.

    Article  PubMed  CAS  Google Scholar 

  31. 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.

    Article  PubMed  CAS  Google Scholar 

  32. 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.

    CAS  Google Scholar 

  33. Sykes, B. D. (1993) Determination of the conformation of bound peptides using NMR-transferred NOE techniques. Curr. Opinion Biotechnol. 4, 392–396.

    Article  CAS  Google Scholar 

  34. Campbell, A. P. and Sykes, B. D. (1991) Theoretical evaluation of the two-dimensional transferred nuclear Overhauser effect. J. Magn. Reson. 93, 77–92.

    CAS  Google Scholar 

  35. 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.

    CAS  Google Scholar 

  36. 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.

    PubMed  CAS  Google Scholar 

  37. 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.

    Article  PubMed  CAS  Google Scholar 

  38. 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.

    Article  PubMed  CAS  Google Scholar 

  39. 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.

    Article  Google Scholar 

  40. Landy, F. G. and Rao, B. D. (1989) Dynamical NOE in multiple-spin systems undergoing chemical exchange. J. Magn. Reson. 81, 371–377.

    Google Scholar 

  41. Lippens, G., Cerf, C., and Hallenga, K. (1992) Theory and experimental results of transfer NOE experiments. J. Magn. Reson. 99, 268–281.

    CAS  Google Scholar 

  42. Taga, T., Tanaka, H., Goto, T., and Tada, S. (1987) Structure of a new macrocyclic antibiotic. Acta. Cryst. C43, 751–753.

    CAS  Google Scholar 

  43. 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.

    Article  PubMed  CAS  Google Scholar 

  44. 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.

    Article  CAS  Google Scholar 

  45. 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.

    Article  PubMed  CAS  Google Scholar 

  46. 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.

    Article  Google Scholar 

  47. 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.

    Article  PubMed  CAS  Google Scholar 

  48. 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.

    Article  PubMed  CAS  Google Scholar 

  49. 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.

    Article  CAS  Google Scholar 

  50. 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.

    Article  PubMed  CAS  Google Scholar 

  51. 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.

    Article  PubMed  Google Scholar 

  52. 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.

    Article  PubMed  CAS  Google Scholar 

  53. 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.

    Article  PubMed  CAS  Google Scholar 

  54. 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.

    Article  PubMed  CAS  Google Scholar 

  55. 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.

    Article  PubMed  CAS  Google Scholar 

  56. Otting, G., Liepinsh, E., and Wuthrich, K. (1991) Protein hydration in aqueous solution. Science 254, 974–980.

    Article  PubMed  CAS  Google Scholar 

  57. 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.

    Article  CAS  Google Scholar 

  58. 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.

    Article  Google Scholar 

  59. 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.

    Article  PubMed  CAS  Google Scholar 

  60. 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.

    CAS  Google Scholar 

  61. 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.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints 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

Publish with us

Policies and ethics