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Characterizing Domain Interfaces by NMR

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Protein NMR Techniques

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 278))

Abstract

The combination of chemical shift, residual dipolar coupling, and backbone relaxation data can be used to characterize the nature of a domain interface in a multidomain protein. Comparison of the parameters obtained from isolated domains and domain pairs provides insight into the composition of the interface as well as into interdomain dynamics. The interface between the 13th and 14th F3 module from fibronectin is used as an example.

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References

  1. Vitkup, D., Melamud, E., Moult, J., and Sander, C. (2001) Completeness in structural genomics. Nat. Struct. Biol. 8, 559–566.

    Article  PubMed  CAS  Google Scholar 

  2. Bork, P., Downing, A. K., Kieffer, B., and Campbell, I. D. (1996) Structure and distribution of modules in extracellular proteins. Q. Rev. Biophys. 29, 119–167.

    Article  PubMed  CAS  Google Scholar 

  3. Fischer, M. W., Losonczi, J. A., Weaver, J. L., and Prestegard, J. H. (1999) Domain orientation and dynamics in multidomain proteins from residual dipolar couplings. Biochemistry 38, 9013–9022.

    Article  PubMed  CAS  Google Scholar 

  4. Braddock, D. T., Cai, M., Baber, J. L., Huang, Y., and Clore, G. M. (2001) Rapid identification of medium-to large-scale interdomain motion in modular proteins using dipolar couplings. J. Am. Chem. Soc. 123, 8634, 8635.

    Article  PubMed  CAS  Google Scholar 

  5. Tolman, J. R. (2002) A novel approach to the retrieval of structural and dynamic information from residual dipolar couplings using several oriented media in biomolecular NMR spectroscopy. J. Am. Chem. Soc. 124, 12,020–12,030.

    Article  PubMed  CAS  Google Scholar 

  6. Lipari, G. and Szabo, A. (1982) Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules, 1: theory and range of validity. J. Am. Chem. Soc. 104, 4546–4559.

    Article  CAS  Google Scholar 

  7. Woessner, D. E. (1962) Nuclear spin relaxation in ellipsoids undergoing rotational Brownian motion. J. Chem. Phys. 37, 647–654.

    Article  CAS  Google Scholar 

  8. Bruschweiler, R., Liao, X., and Wright, P. E. (1995) Long-range motional restrictions in a multidomain zinc-finger protein from anisotropic tumbling. Science 268, 886–889.

    Article  PubMed  CAS  Google Scholar 

  9. Clore, G. M., Gronenborn, A. M., Szabo, A., and Tjandra, N. (1998) Determining the magnitude of the fully asymmetric diffusion tensor from heteronuclear relaxation data in the absence of structural information. J. Am. Chem. Soc. 120, 4889, 4890.

    Article  CAS  Google Scholar 

  10. Ghose, R., Fushman, D., and Cowburn, D. (2001) Determination of the rotational diffusion tensor of macromolecules in solution from NMR relaxation data with a combination of exact and approximate methods: application to the determination of interdomain orientation in multidomain proteins. J. Magn. Reson. 149, 204–217.

    Article  PubMed  CAS  Google Scholar 

  11. Fushman, D., Xu, R., and Cowburn, D. (1999) Direct determination of changes of interdomain orientation on ligation: use of the orientational dependence of 15N NMR relaxation in Abl SH(32). Biochemistry 38, 10,225–10,230.

    Article  PubMed  CAS  Google Scholar 

  12. Smith, S. P., Hashimoto, Y., Pickford, A. R., Campbell, I. D., and Werner, J. M. (2000) Interface characterization of the type II module pair from fibronectin. Biochemistry 39, 8374–8381.

    Article  PubMed  CAS  Google Scholar 

  13. Tugarinov, V., Liang, Z., Shapiro, Y. E., Freed, J.H., and Meirovitch, E. (2001) A structural mode-coupling approach to 15N NMR relaxation in proteins. J. Am. Chem. Soc. 123, 3055–3063.

    Article  PubMed  CAS  Google Scholar 

  14. Baber, J. L., Szabo, A., and Tjandra, N. (2001) Analysis of slow interdomain motion of macromolecules using NMR relaxation data. J. Am. Chem. Soc. 123, 3953–3959.

    Article  PubMed  CAS  Google Scholar 

  15. Ingham, K. C., Brew, S. A., and Atha, D. H. (1990) Interaction of heparin with fibronectin and isolated fibronectin domains. Biochem. J. 272, 605–611.

    PubMed  CAS  Google Scholar 

  16. Mould, A. P. and Humphries, M. J. (1991) Identification of a novel recognition sequence for the integrin alpha 4 beta 1 in the COOH-terminal heparin-binding domain of fibronectin. EMBO J. 10, 4089–4095.

    PubMed  CAS  Google Scholar 

  17. Sharma, A., Askari, J. A., Humphries, M. J., Jones, E. Y., and Stuart, D. I. (1999) Crystal structure of a heparin-and integrin-binding segment of human fibronectin. EMBO J. 18, 1468–1479.

    Article  PubMed  CAS  Google Scholar 

  18. Johnson, B. A. and Blevins, R. A. (1994) NMRView—a computer-program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603–614.

    Article  CAS  Google Scholar 

  19. Dosset, P., Hus, J. C., Blackledge, M., and Marion, D. (2000) Efficient analysis of macromolecular rotational diffusion from heteronuclear relaxation data. J. Biomol. NMR 16, 23–28.

    Article  PubMed  CAS  Google Scholar 

  20. Garcia de la Torre, J., Huertas, M. L., and Carrasco, B. (2000) HYDRONMR: prediction of NMR relaxation of globular proteins from atomic-level structures and hydrodynamic calculations. J. Magn. Reson. 147, 138–146.

    Article  Google Scholar 

  21. Zweckstetter, M. and Bax, A. (2001) Characterization of molecular alignment in aqueous suspensions of Pf1 bacteriophage. J. Biomol. NMR 20, 365–377.

    Article  PubMed  CAS  Google Scholar 

  22. Dosset, P., Hus, J. C., Marion, D., and Blackledge, M. (2001) A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings. J. Biomol. NMR 20, 223–231.

    Article  PubMed  CAS  Google Scholar 

  23. Koradi, R., Billeter, M., and Wuthrich, K. (1996) MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graph. 14, 51–55.

    Article  PubMed  CAS  Google Scholar 

  24. Driscoll, P. C., Clore, G. M., Marion, D., Wingfield, P. T., and Gronenborn, A. M. (1990) Complete resonance assignment for the polypeptide backbone of interleukin 1 beta using three-dimensional heteronuclear NMR spectroscopy. Biochemistry 29, 3542–3556.

    Article  PubMed  CAS  Google Scholar 

  25. Lerche, M. H., Meissner, A., Poulsen, F. M., and Sorensen, O. W. (1999) Pulse sequences for measurement of one-bond (15)N-(1)H coupling constants in the protein backbone. J. Magn. Reson. 140, 259–263.

    Article  PubMed  CAS  Google Scholar 

  26. Bax, A., Kontaxis, G., and Tjandra, N. (2001) Dipolar couplings in macromolecular structure determination. Meth. Enzymol. 339, 127–174.

    Article  PubMed  CAS  Google Scholar 

  27. Clore, G. M. and Garret, D. S. (1999) R-factor, free R, and complete cross-validation for dipolar coupling refinement of NMR structures. J. Am. Chem. Soc. 121, 9008–9012.

    Article  CAS  Google Scholar 

  28. Werner, J. M., Campbell, I. D., and Downing, A. K. (2002) Shape and dynamics of a calcium-binding protein investigated by nitrogen-15 NMR relaxation. In Methods in Molecular Biology, vol. 173: Calcium-Binding Protein Protocols, vol. 2 (Vogel, H. J. ed.). Humana, Totowa, NJ, pp. 285–300.

    Google Scholar 

  29. Kay, L. E., Torchia, D. A., and Bax, A. (1989) Backbone dynamics of proteins as studied by 15N inverse detected heteronuclear NMR-spectroscopy—application to staphylococcal nuclease. Biochemistry 28, 8972–8979.

    Article  PubMed  CAS  Google Scholar 

  30. Farrow, N. A., Zhang, O. W., Formankay, J. D., and Kay, L. E. (1994) A heteronuclear correlation experiment for simultaneous determination of 15N longitudinal decay and chemical-exchange rates of systems in slow equilibrium. J. Biomol. NMR 4, 727–734.

    Article  PubMed  CAS  Google Scholar 

  31. Vold, R. R. and Vold, R. L. (1976) Transverse relaxation in heteronuclear coupled spin systems: AX, AX2, AX3, and AXY. J. Chem. Phys. 64, 320–332.

    Article  CAS  Google Scholar 

  32. Boyd, J., Hommel, U., and Campbell, I. D. (1990) Influence of cross-correlation between dipolar and anisotropic chemical-shift relaxation mechanisms upon longitudinal relaxation rates of 15N in macromolecules. Chem. Phys. Lett. 175, 477–482.

    Article  CAS  Google Scholar 

  33. Kay, L. E., Nicholson, L. K., Delaglio, F., Bax, A., and Torchia, D. A. (1992) Pulse sequences for removal of the effects of cross-correlation between dipolar and chemical-shift anisotropy relaxation mechanism on the measurement of heteronuclear T1 and T2 values in proteins. J. Magn. Reson. 97, 359–375.

    CAS  Google Scholar 

  34. Barbato, G., Ikura, M., Kay, L. E., Pastor, R. W., and Bax, A. (1992) Backbone dynamics of calmodulin studied by 15N relaxation using inverse detected 2-dimensional NMR-spectroscopy—the central helix is flexible. Biochemistry 31, 5269–5278.

    Article  PubMed  CAS  Google Scholar 

  35. Andrec, M., Inman, K. G., Weber, D. J., Levy, R. M., and Montelione, G. T. (2000) A Bayesian statistical method for the detection and quantification of rotational diffusion anisotropy from NMR relaxation data. J. Magn. Reson. 146, 66–80.

    Article  PubMed  CAS  Google Scholar 

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© 2004 Humana Press Inc., Totowa, NJ

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Rooney, L.M., Sachchidanand, Werner, J.M. (2004). Characterizing Domain Interfaces by NMR. In: Downing, A.K. (eds) Protein NMR Techniques. Methods in Molecular Biology™, vol 278. Humana Press. https://doi.org/10.1385/1-59259-809-9:123

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  • DOI: https://doi.org/10.1385/1-59259-809-9:123

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-58829-246-9

  • Online ISBN: 978-1-59259-809-0

  • eBook Packages: Springer Protocols

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