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Determination of Structures of Larger Proteins in Solution by Three- and Four-dimensional Heteronuclear Magnetic Resonance Spectroscopy

  • Chapter
NMR of Proteins

Part of the book series: Topics in Molecular and Structural Biology ((TMSB))

Abstract

A complete understanding of protein function and mechanism of action can only be accomplished with a knowledge of its three-dimensional structure at atomic resolution. At the present time there are two methods available for determining such structures. The first method, which has been established for many years, is X-ray diffraction of protein single crystals. The second method has only blossomed in the last 5–10 years and is based on the application of nuclear magnetic resonance (NMR†) spectroscopy of proteins in solution. The driving force for the development of an alternative to X-ray crystallography was threefold. First, many proteins do not crystallize; and even when they do, the crystals may diffract poorly or difficulties in solving the phase problem (e.g. finding suitable heavy atom derivatives) may be encountered. Second, there may be significant and possibly important functional differences between structures in the crystal state and in solution. Third, dynamic processes ranging from the picosecond to second time-scales are amenable to study by NMR. Despite these attractive features, it should be borne in mind that, just like crystallography, NMR also has a number of limitations. In particular, the protein under investigation must be soluble and should not aggregate up to a concentration of at least 1 mM.

Adapted from a review that appeared in Science, 252, 1390–1399 (1991).

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References

  • Archer, S. J., Ikura, M., Torchia, D. A. and Bax, A. (1991). An alternative 3D NMR technique for correlating backbone 15N with side chain Hβ resonances in larger proteins. J. Magn. Reson., 95, 636–641

    Google Scholar 

  • Aue, W. P., Bartholdi, E. and Ernst, R. R. (1976). Two-dimensional spectroscopy: application to nuclear magnetic resonance. J. Chem. Phys., 64, 2229–2246

    Article  Google Scholar 

  • Baldwin, E. T., Weber, I. T., St. Charles, R., Zuan, J. C., Appella, E., Matsushima, K., Edwards, B. F. P., Clore, G. M., Gronenborn, A. M. and Wlodower, A. (1991). Crystal structure of interleukin-8: symbiosis of NMR and crystallography. Proc. Natl Acad. Sci. USA, 88, 502–506

    Article  Google Scholar 

  • Bax, A., Clore, G. M., Driscoll, P. C., Gronenborn, A. M., Ikura, M. and Kay, L. E. (1990a). Practical aspects of proton-carbon-carbon-proton three-dimensional correlation spectroscopy of 15C-labeled proteins. J. Magn. Reson., 87, 620–627

    Google Scholar 

  • Bax, A., Clore, G. M. and Gronenborn, A. M. (1990b). 1H-1H correlation via isotropic mixing of 13C magnetization: a new three-dimensional approach for assigning 1H and 13C spectra of 13C-enriched proteins. J. Magn. Reson., 88, 425–431

    Google Scholar 

  • Bax, A. and Lerner, L. (1986). Two-dimensional NMR spectroscopy. Science, 232, 960–970

    Article  Google Scholar 

  • Billeter, M., Qian, Y., Otting, G., Müller, M., Gehring, W. J. and Wüthrich, K. (1990). Determination of the three-dimensional structure of the Antennapedia homeodomain from Drosophila in solution by 1H nuclear magnetic resonance spectroscopy. J. Mol. Biol., 214, 183–197

    Article  Google Scholar 

  • Braun, W. (1987). Distance geometry and related methods for protein structure determination of NMR data. Quart. Rev. Biophys., 19, 115–157

    Article  Google Scholar 

  • Braun, W. and Go, N. (1985). Calculation of protein conformation by proton-proton distance constraints: a new efficient algorithm. J. Mol. Biol., 186, 611–626

    Article  Google Scholar 

  • Brünger, A. T. (1992). Free-R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature, 355, 472–474

    Article  Google Scholar 

  • Brünger, A. T., Clore, G. M., Gronenborn, A. M. and Karplus, M. (1986). Three-dimensional structures of proteins determined by molecular dynamics with interproton distance restraints: application to crambin. Proc. Natl Acad. Sci. USA, 83, 3801–3805

    Article  Google Scholar 

  • Clore, G. M. and Gronenborn, A. M. (1987). Determination of three-dimensional structures of proteins in solution by nuclear magnetic resonance spectroscopy. Protein Eng., 1, 275–288

    Article  Google Scholar 

  • Clore, G. M. and Gronenborn, A. M. (1989). Determination of three-dimensional structures of proteins and nucleic acids in solution by nuclear magnetic resonance spectroscopy. CRC Crit. Rev. Biochem. Mol. Biol., 24, 479–564

    Article  Google Scholar 

  • Clore, G. M. and Gronenborn, A. M. (1991a). Two, three and four dimensional NMR methods for obtaining larger and more precise three-dimensional structures of proteins in solution. Ann. Rev. Biophys. Biophys. Chem., 21, 29–63

    Article  Google Scholar 

  • Clore, G. M. and Gronenborn, A. M. (1991b). Comparison of the solution nuclear magnetic resonance and X-ray structures of human recombinant interleukin-1β. J. Mol. Biol., 221, 47–53

    Article  Google Scholar 

  • Clore, G. M. and Gronenborn, A. M. (1991c). Applications of three- and four-dimensional heteronuclear NMR spectroscopy to protein structure determination. Prog. NMR Spectrosc., 23, 43–92

    Article  Google Scholar 

  • Clore, G. M., Appella, E., Yamada, M., Matsushima, K. and Gronenborn, A. M. (1990a). The three-dimensional structure of interleukin-8 in solution. Biochemistry, 29, 1689–1696

    Article  Google Scholar 

  • Clore, G. M., Bax, A., Driscoll, P. C., Wingfield, P. T. and Gronenborn, A. M. (1990b). Assignment of side chain 1H and 13C resonances of interleukin-1β using double and triple resonance heteronuclear three-dimensional NMR spectroscopy. Biochemistry, 29, 8172–8184

    Article  Google Scholar 

  • Clore, G. M., Bax, A. and Gronenborn, A. M. (1991a). Stereospecific assignment of β-methylene protons in larger proteins using three-dimensional 15N-separated Hartmann-Hahn and 13 C-separated rotating frame Overhauser spectroscopy. J. Biomol. NMR, 1, 13–22

    Article  Google Scholar 

  • Clore, G. M., Bax, A., Wingfield, P. T. and Gronenborn, A. M. (1990c). Identification and localization 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, 29, 5671–5676

    Article  Google Scholar 

  • Clore, G. M., Brünger, A. T., Karplus, M. and Gronenborn, A. M. (1986a). Application of molecular dynamics with interproton distance restraints to three-dimensional protein structure determination: a model study of crambin. J. Mol. Biol., 191, 523–551

    Article  Google Scholar 

  • Clore, G. M., Driscoll, P. C., Wingfield, P. T. and Gronenborn, A. M. (1990d). Low resolution structure of interleukin-1β in solution derived from 1H-15N heteronuclear three-dimensional NMR spectroscopy. J. Mol. Biol., 214, 811–817

    Article  Google Scholar 

  • Clore, G. M., Gronenborn, A. M., Brünger, A. T. and Karplus, M. (1985). The solution conformation of a heptadecapeptide comprising the DNA binding helix F of the cyclic AMP receptor protein of Escherichia coli: combined use of 1N-nuclear magnetic resonance and restrained molecular dynamics. J. Mol. Biol., 186, 435–455

    Article  Google Scholar 

  • Clore, G. M., Kay, L. E., Bax, A. and Gronenborn, A. M. (1991b). Four dimensional 13C/13C-edited nuclear Overhauser enhancement spectroscopy of a protein in solution: application to interleukin-1β. Biochemistry, 30, 12–18

    Article  Google Scholar 

  • Clore, G. M., Nilges, M., Sukuraman, D. K., Brünger, A. T., Karplus, M. and Gronenborn, A. M. (1986b). The three-dimensional structure of a1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO Jl, 5, 2728–2735

    Google Scholar 

  • Clore, G. M., Wingfield, P. T. and Gronenborn, A. M. (1991c). High resolution three dimensional structure of interleukin-1β in solution by three and four dimensional nuclear magnetic resonance spectroscopy. Biochemistry, 30, 2315–2323

    Article  Google Scholar 

  • Crippen, G. M. and Havel, T. F. (1988). Distance Geometry and Molecular Conformation. Wiley, New York

    Google Scholar 

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

    Article  Google Scholar 

  • Driscoll, P. C., Gronenborn, A. M., Beress, L. and Clore, G. M. (1989a). Determination of the three-dimensional structure of the anti-hypertensive and anti-viral protein BDS-I from the sea anemone Anemonia sulcata: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. Biochemistry, 28, 2188–2198

    Article  Google Scholar 

  • Driscoll, P. C., Gronenborn, A. M. and Clore, G. M. (1989b). The influence of stereospecific assignments on the determination of three-dimensional structures of proteins by nuclear magnetic resonance spectroscopy: application to the sea anemone protein BDS-1. FEBS Lett., 243, 223–233

    Article  Google Scholar 

  • Driscoll, P. C., Gronenborn, A. M., Wingfield, P. T. and Clore, G. M. (1990b). Determination of the secondary structure and molecular topology of interleukin-1β using two- and three-dimensional heteronuclear 15N-1H NMR spectroscopy. Biochemistry, 29, 4468–4682

    Google Scholar 

  • Dyson, H. J., Gippert, G. P., Case, D. A., Holmgren, A. and Wright, P. E. (1990). Three dimensional structure of reduced thioredoxin from Escherichia coli determined by nuclear magnetic resonance spectroscopy. Biochemistry, 29, 4129–4136

    Article  Google Scholar 

  • Ernst, R. R., Bodenhausen, G. and Wokaun, A. (1987). Principles of Nuclear Magnetic Resonance in One and Two Dimensions. Clarendon Press, Oxford

    Google Scholar 

  • Fesik, S. W., Eaton, H. L., Olejniczak, E. T., Zuiderweg, E. R. P., McIntosh, L. P. and Dahlquist, F. W. (1990). 2D and 3D NMR spectroscopy employing 13C-13C magnetization transfer by isotropic mixing: spin system identification in large proteins. J. Am. Chem. Soc., 112, 886–887

    Article  Google Scholar 

  • Fesik, S. W. and Zuiderweg, E. R. P. (1988). Heteronuclear three dimensional NMR spectroscopy: a strategy for the simplification of homonuclear two dimensional NMR spectra. J. Magn. Reson., 78, 588–593

    Google Scholar 

  • Finzel, B. C., Clancy, L. L., Holland, D. R., Muchmore, S. W., Watenpaugh, K. D. and Einspahr, H. M. (1989). Crystal structure of recombinant human interleukin-1β at 2.0 Å resolution. J. Mol. Biol., 209, 779–791

    Article  Google Scholar 

  • Folkers, P. J. M., Clore, G. M., Driscoll, P. C., Dodt, J., Køohler, S. and Gronenborn, A. M. (1989). The solution structure of recombinant hirudin and the Lys-47→Glu mutant: a nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing study. Biochemistry, 28, 2601–2617

    Article  Google Scholar 

  • Forman-Kay, J. D., Clore, G. M., Wingfield, P. T. and Gronenborn, A. M. (1991). The high resolution three-dimensional structure of reduced recombinant human thioredoxin in solution. Biochemistry, 30, 2685–2698

    Article  Google Scholar 

  • Forman-Kay, J. D., Gronenborn, A. M., Kay, L. E., Wingfield, P. T. and Clore, G. M. (1990). Studies on the solution conformation of human thioredoxin using heteronuclear 15N-1N nuclear magnetic resonance spectroscopy. Biochemistry, 29, 1566–1572

    Article  Google Scholar 

  • Gronenborn, A. M., Filpula, D. R., Essig, N. Z., Achari, A., Whitlow, M., Wiungfield, P. T. and Clore, G. M. (1991). A novel highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science, 253, 657–661

    Article  Google Scholar 

  • Grzesiek, S., Ikura, M., Clore, G. M., Gronenborn, A. M. and Bax, A. (1992). A 3D triple resonance NMR technique for qualitative measurement of carbonyl-Hβ couplings in isotopically enriched proteins. J. Magn. Reson., 96, 215–221

    Google Scholar 

  • Güntert, P., Braun, W., Wider, W. and Wüthrich, K. (1989). Automated stereospecific 1H NMR assignments and their impact on the precision of protein structure determinations in solution. J. Am. Chem. Soc., 111, 3997–4004

    Article  Google Scholar 

  • Haruyama, H. and Wüthrich, K. (1989). Conformation of recombinant desulfato-hirudin in aqueous solution determined by nuclear magnetic resonance. Biochemistry, 28, 4301–4312

    Article  Google Scholar 

  • Havel, T. F., Kurtz, I. D. and Crippen, G. M. (1983). Theory and practice of distance geometry. Bull. Math. Biol., 45, 665–720

    Article  Google Scholar 

  • Ikura, M., Clore, G. M., Gronenborn, A. M., Zhu, G., Klee, C. B. and Bax, A. (1992). Solution structure of a calmodulin-target peptide complex by multi-dimensional NMR. Science, 256, 632–638

    Article  Google Scholar 

  • Ikura, M., Kay, L. E. and Bax, A. (1990). A novel approach for sequential assignment of 1H, 13C and 15N spectra of larger proteins: heteronuclear triple-resonance NMR spectroscopy. Application to calmodulin. Biochemistry, 29, 4659–4667

    Article  Google Scholar 

  • Jeener, J. (1971). Unpublished lecture, Ampere International Summer School, BaskoPolj, Yugoslavia

    Google Scholar 

  • Jeener, J., Meier, B. H., Bachmann, P. and Ernst, R. R. (1979). Investigation of exchange processes by two-dimensional NMR spectroscopy. J. Chem. Phys., 71, 4546–4553

    Article  Google Scholar 

  • Kaptein, R., Zuiderweg, E. R. P., Scheek, R. M., Boelens, R. and van Gunsteren, W. F. (1985). A protein structure from nuclear magnetic resonance data: lac repressor headpiece. J. Mol. Biol., 182, 179–182

    Article  Google Scholar 

  • Kay, L. E. and Bax, A. (1990). New methods for the measurement of NH-CαH J couplings in 15N labeled proteins. J. Magn. Reson., 86, 110–126

    Google Scholar 

  • Kay, L. E., Clore, G. M., Bax, A. and Gronenborn, A. M. (1990). Four-dimensional heteronuclear triple resonance NMR spectroscopy of interleukin-1β in solution. Science, 249, 411–414

    Article  Google Scholar 

  • Kline, A. D., Braun, W. and Wüthrich, K. (1988). Determination of the complete three-dimensional structure of the α-amylase inhibitor tendamistat in aqueous solution by nuclear magnetic resonance and distance geometry. J. Mol. Biol., 204, 675–724

    Article  Google Scholar 

  • Kraulis, P. J., Clore, G. M., Nilges, M., Jones, A. T., Petterson, G., Knowles, J. and Gronenborn, A. M. (1989). Determination of the three-dimensional solution structure of the C-terminal domain of cellobiohydrolase I from Trichoderma ressei: a study using nuclear magnetic resonance and hybrid distance geometry-dynamical simulated annealing. Biochemistry, 28, 7241–7257

    Article  Google Scholar 

  • Marion, D., Driscoll, P. C., Kay, L. E., Wingfield, P. T., Bax, A., Gronenborn, A. M. and Clore, G. M. (1989). Overcoming the overlap problem in the assignment of 1H-NMR spectra of larger proteins using three-dimensional heteronuclear 1H-15N Hartmann-Hahn and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin-1β. Biochemistry, 29, 6150–6156

    Article  Google Scholar 

  • Moore, J. M., Lepre, C., Gippert, G. P., Chazin, W. J., Case, D. A. and Wright, P. E. (1991). High resolution solution structure of reduced French bean plasticyanin and comparison with the crystal structure of popular plastocyanin. J. Mol. Biol., 221, 533–555

    Article  Google Scholar 

  • Müller, L. (1987). PE.COSY: a simple alternative to E.COSY. J. Magn. Reson., 72, 191–196

    Google Scholar 

  • Nilges, M., Clore, G. M. and Gronenborn, A. M. (1988a). Determination of three-dimensional structures of proteins from interproton distance data by dynamical simulated annealing from a random array of atoms. FEBS Lett., 239, 129–136

    Article  Google Scholar 

  • Nilges, M., Clore, G. M. and Gronenborn, A. M. (1990). 1H-NMR stereospecific assignments by conformation database searches. Biopolymers, 29, 813–822f

    Article  Google Scholar 

  • Nilges, M., Gronenborn, A. M., Brünger, A. T. and Clore, G. M. (1988b). Determination of three-dimensional structures of proteins by simulated annealing with interproton distance restraints: application to crambin, potato-carboxypeptidase inhibitor and barley serine proteinase inhibitor 2. Protein Eng., 2, 27–38

    Article  Google Scholar 

  • Nilges, M., Gronenborn, A. M. and Clore, G. M. (1988c). Determination of three-dimensional structures of proteins from interproton distance data by hybrid distance geometry-dynamical simulated annealing calculations. FEBS Lett., 229, 317–324

    Article  Google Scholar 

  • Noggle, J. H. and Schirmer, R. E. (1971). The Nuclear Overhauser Effect—Chemical Applications. Academic Press, New York

    Google Scholar 

  • Omichinski, J. G., Clore, G. M., Appella, E., Sakaguchi, K. and Gronenborn, A. M. (1990). High resolution three-dimensional solution structure of a single zinc finger from a human enhancer binding protein in solution. Biochemistry, 29, 9324–9334

    Article  Google Scholar 

  • Oschkinat, H., Griesinger, C., Kraulis, P. J., Sørensen, O. W., Ernst, R. R., Gronenborn, A. M. and Clore, G. M. (1988). Three-dimensional NMR spectroscopy of a protein in solution. Nature, 332, 374–376

    Article  Google Scholar 

  • Pardi, A., Billetter, M. and Wüthrich, K. (1984). Calibration of the angular dependence of the amide proton-Cα proton coupling constants, 3 J HNα, in a globular protein. J. Mol. Biol., 180, 741–751

    Article  Google Scholar 

  • Priestle, J. P., Scär, H. P. and Grütter, M. G. (1989). Crystallographic refinement of interleukin-1β at 2.0 Å resolution. Proc. Natl Acad. Sci. USA, 86, 9667–9671

    Article  Google Scholar 

  • Powers, R., Garrett, D. S., March, C. J., Frieden, E. A., Gronenborn, A. M. and Clore, G. M. (1992a). 1H, 15N, 13C and 13CO assignments of interleukin-4 using three-dimensional double and triple resonance heteronuclear magnetic resonance spectroscopy. Biochemistry, 31, 4334–4347

    Article  Google Scholar 

  • Powers, R., Garrett, D. S., March, C. J., Frieden, E. A., Gronenborn, A. M. and Clore, G. M. (1992b). Three-dimensional structure of interleukin-4 by multi-dimensional heteronuclear magnetic resonance spectroscopy. Science, 256, 1673–1677

    Article  Google Scholar 

  • Powers, R., Gronenborn, A. M., Clore, G. M. and Bax, A. (1991). Three dimensional triple resonance NMR of 13C/15N enriched proteins using constant-time evolution. J. Magn. Reson., 94, 209–213

    Google Scholar 

  • Shaanan, B., Gronenborn, A. M., Cohen, G. H., Gilliland, G. L., Veerapandian, B., Davies, D. R. and Clore, G. M. (1992). Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Science, 257, 961–964

    Article  Google Scholar 

  • Smith, L. J., Redfied, C., Boyd, J., Lawrence, G. M. P., Edwards, R. G., Smith, R. A. G. and Dobson, C. M. (1992). Human interleukin-4. The solution structure of a four-helix bundle protein. J. Mol. Biol., 224, 899–904

    Article  Google Scholar 

  • Veerapandian, B., Gilliland, G. L., Raag, R., Svensson, A. L., Masui, Y., Hirai, Y. and Poulos, T. L. (1992). Functional implications of interleukin-1b based on the three dimensional structure. Protein Struct. Funct. Genet., 12, 10–21

    Article  Google Scholar 

  • Wagner, G., Braun, W., Havel, T. F., Schaumann, T., Go, N. and Wüthrich, K. (1987). Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. J. Mol. Biol., 196, 611–639

    Article  Google Scholar 

  • Williamson, M. P., Havel, T. F. and Wüthrich, K. (1985). Solution conformation of proteinase inhibitor IIA from bull seminal plasma by 1H nuclear magnetic resonance and distance geometry. J. Mol. Biol., 182, 295–315

    Article  Google Scholar 

  • Wüthrich, K. (1986). NMR of Proteins. Wiley, New York

    Google Scholar 

  • Wüthrich, K. (1989). Protein structure determination in solution by nuclear magnetic resonance spectroscopy. Science, 243, 45–50

    Article  Google Scholar 

  • Wüthrich, K. (1990). Protein structure determination in solution by NMR spectroscopy. J. Biol. Chem., 265, 22059–22062

    Google Scholar 

  • Zuiderweg, E. R. P., Petros, A. M., Fesik, S. W. and Olejniczak, E. T. (1991). Four dimensional [13C, 1H, 13C, 1H] HNQC-NOE-HMQC NMR spectroscopy: resolving tertiary NOE distance constraints in the spectra of larger proteins. J. Am. Chem. Soc., 113, 370–371

    Article  Google Scholar 

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Authors
  1. G. M. Clore
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  2. A. M. Gronenborn
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Editors and Affiliations

  1. Laboratory of Chemical Physics, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, 20892, USA

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Clore, G.M., Gronenborn, A.M. (1993). Determination of Structures of Larger Proteins in Solution by Three- and Four-dimensional Heteronuclear Magnetic Resonance Spectroscopy. In: Clore, G.M., Gronenborn, A.M. (eds) NMR of Proteins. Topics in Molecular and Structural Biology. Palgrave, London. https://doi.org/10.1007/978-1-349-12749-8_1

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  • DOI: https://doi.org/10.1007/978-1-349-12749-8_1

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