Structure Determination via Complete Relaxation Matrix Analysis (CORMA) of Two-Dimensional Nuclear Overhauser Effect Spectra

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Biological Magnetic Resonance

Part of the book series: Biological Magnetic Resonance ((BIMR,volume 9))

Abstract

Methods for the complete high-resolution determination of molecular structure in solution have been a goal of scientists since the development of X-ray diffraction techniques in the early part of this century. Methods that yield at least a part of the structural picture include hydrodynamic techniques, electron diffraction and other scattering techniques, circular dichroism, fluorescence decay, extended X-ray absorption fine structure, and magnetic resonance. The information obtainable from these methods ranges from rough estimates of the overall shape and dimension of a molecule to a gauge of the extent of secondary structure (local conformational properties such as α-helix and β-sheet). At best it is possible to obtain a measure of some of the distances within the molecule. However, with the possible exception of nuclear magnetic resonance, a high-resolution structural model is not yet attainable with any of these methods.

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References

  • Abel, E. W., Coston, T. P. J., Orrell, K. G., Sik, V., and Stephenson, D., 1986, J. Mag. Res. 70: 34.

    CAS  Google Scholar 

  • Altona, C., and Sundaralingam, M., 1972, J. Am. Chem. Soc. 94: 8205.

    PubMed  CAS  Google Scholar 

  • Arnott, S., and Hukins, D. W. L., 1972, Biochem. Biophys. Res. Commun. 47: 1504.

    PubMed  CAS  Google Scholar 

  • Arnott, S., and Hukins, D. W. L., 1973, J. Mol. Biol. 81: 93.

    PubMed  CAS  Google Scholar 

  • Arnott, S., and Seising, E., 1974, J. Mol. Biol. 88: 509.

    PubMed  CAS  Google Scholar 

  • Arnott, S., Chandrasekaran, R., Puigjaner, L. C., Walker, J. K., Hall, I. H., Birdsall, D.L., and Ratliff, R. L., 1983, Nucleic Acids Res. 11: 1457.

    PubMed  CAS  Google Scholar 

  • Assa-Munt, N., and Kearns, D. R., 1984, Biochemistry 23: 791.

    PubMed  CAS  Google Scholar 

  • Becker, E. D., Ferretti, J. A., and Gambhir, P. N., 1979, Anal. Chem. 51: 1413.

    CAS  Google Scholar 

  • Boelens, R., Scheek, R. M., Dijkstra, K., and Kaptein, R., 1985, J. Mag. Res. 62: 378.

    CAS  Google Scholar 

  • Boelens, R., Koning, T. M. G., and Kaptein, R., 1988, J. Mol. Struct. 173, 299–311.

    CAS  Google Scholar 

  • Boelens, R., Koning, T. M. G., van der Marel, G. A., van Boom, J. H., and Kaptein, R., 1989, J. Magn. Reson. 82, 290–308.

    CAS  Google Scholar 

  • Borah, B., Cohen, J. S., and Bax, A., 1985, Biopolymers 24: 747.

    PubMed  CAS  Google Scholar 

  • Borgias, B. A., Thomas, P. D., and James, T. L., 1987, Complete Relaxation Matrix Analysis (Corma), University of California, San Francisco.

    Google Scholar 

  • Borgias, B. A., Thomas, P. D., and James, T. L., 1989, Complete Relaxation Matrix Analysis (Corma), University of California, San Francisco.

    Google Scholar 

  • Borgias, B. A., and James, T. L., 1988, J. Magn. Reson. 79, 493–512.

    CAS  Google Scholar 

  • Borgias, B. A., and James, T. L., 1989a, Two-dimensional nuclear Overhauser effect: complete relaxation matrix analysis, in Methods in Enzymology (Oppenheimer, N. J., and James, T. L., eds.), vol. 176, Academic Press, San Diego.

    Google Scholar 

  • Borgias, B. A., and James, T. L., 1989b, J. Magn. Reson. (to be published).

    Google Scholar 

  • Borgias, B. A., Gochin, M., Kerwood, D. J., and James, T. L., 1990, Relaxation matrix analysis of 2D NMR data, in Progress in Nuclear Magnetic Resonance Spectroscopy (Emsley, J. W., Feeney, J., and Sutcliffe, L. H., eds.), vol. XX, Pergamon, Oxford (to be published).

    Google Scholar 

  • Braun, W., and Gó, N., 1985, J. Mol. Biot 186: 611.

    CAS  Google Scholar 

  • Braun, W., Wagner, G., Wörgötter, E., Vasak, M., Kägi, J. H. R., and Wüthrich, K., 1986, J. Mol. Biol. 187: 125.

    Google Scholar 

  • Bremer, J., Mendz, G. L., and Moore, W. J., 1984, J. Am. Chem. Soc. 106: 4691.

    CAS  Google Scholar 

  • Broido, M. S., Zon, G., and James, T. L., 1984, Biochem. Biophys. Res. Commun. 19: 663.

    Google Scholar 

  • Broido, M. S., James, T. L., Zon, G., and Keepers, J. W., 1985, Eur. J. Biochem. 150: 117.

    PubMed  CAS  Google Scholar 

  • Bull, T. E., 1987, J. Mag. Res. 72: 397.

    CAS  Google Scholar 

  • Chary, K. V. R., Hosur, R. V., Govil, G., Zu-kun, T., and Miles, H. T., 1987, Biochemistry 26: 1315.

    PubMed  CAS  Google Scholar 

  • Chazin, W. J., Wüthrich, K., Hyberts, S., Rance, M., Denny, W. A., and Werner, L., 1986, J. Mol. Biol. 190: 439.

    PubMed  CAS  Google Scholar 

  • Clore, G. M., and Gronenborn, A. M., 1984, FEBS Lett. 175: 117.

    PubMed  CAS  Google Scholar 

  • Clore, G. M., Gronenborn, A. M., Piper, E. A., McLaughlin, L. W., Graeser, E., and Van Boom, J. H., 1984, Biochem. J. 221: 737.

    PubMed  CAS  Google Scholar 

  • Clore, G. M., Gronenborn, A. M., and McLaughlin, L. W., 1985a, Eur. J. Biochem. 151: 153.

    PubMed  CAS  Google Scholar 

  • Clore, G. M., Gronenborn, A. M., Moss, D. S., and Tickle, I. J., 1985b, J. Mol. Biot 185: 219.

    CAS  Google Scholar 

  • Clore, G. M., Sukumaran, D. K., Nilges, M., and Gronenborn, A. M., 1987a, Biochemistry 26: 1732.

    CAS  Google Scholar 

  • Clore, G. M., Sukumaran, D. K., Nilges, M. Zarbock, J., and Gronenborn, A. M., 19876, EMBO J. 6: 529.

    Google Scholar 

  • Cremer, D., and Pople, J. A., 1975, J. Am. Chem. Soc. 97: 1354.

    CAS  Google Scholar 

  • Crippen, G. M., 1984, J. Comp. Chem. 5: 548.

    CAS  Google Scholar 

  • Davies, D. R., and Baldwin, R. L., 1963, J. Mol. Biol. 6: 251.

    PubMed  CAS  Google Scholar 

  • Denk, W., Wagner, G., Rance, M., and Wüthrich, K., 1985, J. Mag. Res. 62: 350.

    CAS  Google Scholar 

  • Dickerson, R. E., and Drew, H. R., 1981, J. Mol. Biol. 149: 761.

    PubMed  CAS  Google Scholar 

  • Drew, H. R., and Dickerson, R. E., 1982, EMBO J. 1: 663.

    PubMed  CAS  Google Scholar 

  • Ernst, R. R., 1966, Advan. Magn. Res. 2: 1.

    CAS  Google Scholar 

  • Feigon, J., Wang, A. H.-J., van der Marel, G. A., van Boom, J. H., and Rich, A., 1984, Nucl. Acids Res. 12: 1243.

    PubMed  CAS  Google Scholar 

  • Frechet, D., Clem, D. M., Kan, L.-S., and Ts’o, P. O. P., 1983, Biochemistry 22: 5194.

    PubMed  CAS  Google Scholar 

  • Frederick, C. A., Grable, J., Melia, M., Samudzi, C., Jen-Jacobsen, L., Wang, B.-C., Greene, P., Boyer, H. W., and Rosenberg, J. M., 1984, Nature 309: 327.

    PubMed  CAS  Google Scholar 

  • Gronenborn, A. M., and Clore, G. M., 1985, Investigation of the solution structures of short nucleic acid fragments by means of NOE measurements, in Progress in Nuclear Magnetic Resonance Spectroscopy (Emsley, J. W., Feeney, J., and Sutcliffe, L. H., eds.), vol. 17, Pergamon, Oxford, pp. 1–32.

    Google Scholar 

  • Gronenborn, A. M., Clore, G. M., Jones, M. B., and Jiricny, J., 1984a, FEBS Lett. 165: 216.

    PubMed  CAS  Google Scholar 

  • Gronenborn, A. M., Clore, G. M., and Kimber, B. J., 1984b, Biochem. J. 221: 723.

    PubMed  CAS  Google Scholar 

  • Gupta, G., Sarma, M. H., Dhingra, M. M., Sarma, R. H., Rajagopalan, M., and Sasisekharan, V., 1983, J. Biomol. Struct. Dyn. 1: 395.

    PubMed  CAS  Google Scholar 

  • Haasnoot, C. A. G., Westerink, H. P., van der Marel, G. A., and van Boom, J. H., 1984, J. Biomol. Struct. Dynam. 2: 345.

    CAS  Google Scholar 

  • Harbison, G. S., Feigon, J., Ruben, D. J., Herzfeld, J., and Griffin, R. G., 1985, J. Am. Chem. Soc. 107: 5567.

    CAS  Google Scholar 

  • Hare, D. R., Wemmer, D. E., Chou, S.-H., Drobny, B., and Reid, B. R., 1983, J. Mol. Biol. 171: 319.

    PubMed  CAS  Google Scholar 

  • Havel, T. F., and Wüthrich, K., 1985, J. Mol. Biol. 182: 281.

    PubMed  CAS  Google Scholar 

  • Hertz, H. G., 1983, The problem of intramolecular rotation in liquids and NMR, in Progress in Nuclear Magnetic Resonance Spectroscopy (Emsley, J. W., Feeney, J., and Sutcliffe, L. H., eds.), vol. 16, Pergamon, Oxford, pp. 115–162.

    Google Scholar 

  • Jamin, N., James, T. L., and Zon, G., 1985, Eur. J. Biochem. 152: 157.

    PubMed  CAS  Google Scholar 

  • Jeener, J., 1971, lecture given at Ampere International Summer School I I, Basko Polje, Yugoslavia.

    Google Scholar 

  • Jeener, J., Meier, B. H., Bachmann, P., and Ernst, R. R., 1979, J. Chem. Phys. 71: 4546.

    CAS  Google Scholar 

  • Kay, L. E., Scarsdale, J. W., Hare, D. R., and Prestegard, J. H., 1986a, J. Mag. Res. 68: 515.

    CAS  Google Scholar 

  • Kay, L. E., Holak, T. A., Johnson, B. A., Armitage, I. M., and Prestegard, J. H., 1986b, J. Am. Chem. Soc. 108: 4242.

    CAS  Google Scholar 

  • Keepers, J. W., and James, T. L., 1982, J. Am. Chem. Soc. 104: 929.

    CAS  Google Scholar 

  • Keepers, J. W., and James, T. L., 1984, J. Mag. Res. 57: 404.

    CAS  Google Scholar 

  • King, G. C., and Coleman, J. E., 1987, Biochemistry 26: 2929.

    PubMed  CAS  Google Scholar 

  • Kitimura, K., Wakahara, A., Mizuno, H., Baba, H., and Tomita, K., 1981, J. Am. Chem. Soc. 103: 3899.

    Google Scholar 

  • Klevit, R., 1985, J. Mag. Res. 62: 551.

    CAS  Google Scholar 

  • Kline, A. D., Braun, W., and Wüthrich, K., 1986, J. Mol. Biol. 189: 377.

    PubMed  CAS  Google Scholar 

  • Klug, A., Jack, A., Viswamitra, M. A., Kennard, O., Shakked, Z., and Steitz, T. A., 1979, J. Mol. Biol. 131: 669.

    PubMed  CAS  Google Scholar 

  • Kumar, A., Ernet, R. R., and Wüthrich, K., 1980, Biochem. Biophys. Res. Commun. 95: 1.

    PubMed  CAS  Google Scholar 

  • Kumar, A., Hosur, R. V., Chandrasekhar, K., and Murali, N., 1985, J. Mag. Res. 63: 107.

    CAS  Google Scholar 

  • Kuntz, I. D., Crippen, G. M., and Kollman, P. A., 1979, Biopolymers 18: 939.

    CAS  Google Scholar 

  • Lavery, R., Sklenar, H., Zakrzewska, K., and Pullman, B., 1986a, J. Biomol. Struct. Dynam. 3: 989.

    CAS  Google Scholar 

  • Lavery, R., Sklenar, H., and Pullman, B., 1986b, J. Biomol. Struct. Dynam. 3: 1015.

    CAS  Google Scholar 

  • Levitt, M., and Warshel, A., 1978, J. Am. Chem. Soc. 100: 2607.

    CAS  Google Scholar 

  • Levy, G. C., Marchetti, P. S., Ejchart, A., Levy, L. F., Kumar, A., Hilliard, P. R., and Rill, R. L., 1983, J. Biomol. Struct. Dynam. 1: 795.

    CAS  Google Scholar 

  • Macura, S., and Ernst, R. R., 1980, Mol. Phys. 41: 95.

    CAS  Google Scholar 

  • Macura, S., Huang, Y., Suter, D., and Ernst, R. R., 1981, J. Mag. Res. 43: 259.

    CAS  Google Scholar 

  • Macura, S., Wüthrich, K., and Ernst, R. R., 1982, J. Mag. Res. 46: 269.

    CAS  Google Scholar 

  • Macura, S., Farmer, II, B. T., and Brown, L. R., 1986, J. Mag. Res. 70: 493.

    CAS  Google Scholar 

  • Marvin, D. A., Spencer, M., Wilkins, M. H. F., and Hamilton, L. D., 1961, Mol. Biol. 3: 547.

    CAS  Google Scholar 

  • Massefski, W., Jr., and Bolton, P. H., 1985, J. Mag. Res. 65: 526.

    CAS  Google Scholar 

  • Mehlkopf, A. F., Korbee, D., Tiggelman, T. A., and Freeman, R., 1984, J. Mag. Res. 56: 315.

    Google Scholar 

  • Mirau, P. A., 1988, J. Mag. Res. 80: 439.

    CAS  Google Scholar 

  • Ohkubo, T., Kobayashi, Y., Shimonishi, Y., and Kyoguku, Y., 1986, Biopolymers 25: S123.

    PubMed  CAS  Google Scholar 

  • Ohuchi, M., Hosono, M., Furihata, K., and Seto, H., 1987, J. Mag. Res. 72: 279.

    CAS  Google Scholar 

  • Olejniczak, E. T., Gampe, R. T., Jr., and Fesik, S. W., 1986, J. Mag. Res. 67: 28.

    CAS  Google Scholar 

  • Otting, G., Widmer, H., Wagner, G., and Wüthrich, K., 1986, J. Mag. Res. 66: 187.

    CAS  Google Scholar 

  • Rance, M., Bodenhausen, G., Wagner, G., Wüthrich, K., and Ernst, R. R., 1985, J. Mag. Res. 62: 497.

    CAS  Google Scholar 

  • Rinkel, L. J., and Altona, C., 1987, J. Biomol. Struct. Dynam. 4: 621.

    CAS  Google Scholar 

  • Sarma, R. H., 1980, in Nucleic Acid Geometry and Dynamics (Sarma, R. H., ed.), Pergamon Press, Elmsford, N.Y., pp. 143–155.

    Google Scholar 

  • Scheek, R. M., Boelens, R., Russo, N., Kaptein, R., and van Boom, J. H., 1983, J. Am. Chem. Soc. 105: 2914.

    CAS  Google Scholar 

  • Scheek, R. M., Boelens, R., Russo, N., van Boom, J. H., and Kaptein, R., 1984, Biochemistry 23: 1371.

    PubMed  CAS  Google Scholar 

  • Shakked, Z., Rabinovich, D., Kennard, O., Cruse, W. B. T., Salisbury, S. A., and Viswamitra, M. A., 1983, J. Mol. Biol. 166: 183.

    PubMed  CAS  Google Scholar 

  • Sklenar, H., Lavery, R., and Pullman, B., 1986, J. Biomol. Struct. Dynam. 3: 967.

    CAS  Google Scholar 

  • Solomon, I., 1955, Phys. Rev. 99: 559.

    CAS  Google Scholar 

  • States, D. J., Haberkorn, R. A., and Ruben, D. J., 1982, J. Mag. Res. 48: 286.

    CAS  Google Scholar 

  • Suzuki, E., Pattabiraman, N., Zon, G., and James, T. L., 1986, Biochemistry 25: 6854.

    PubMed  CAS  Google Scholar 

  • Tran-Dinh, S., Neumann, J. M., Huynh-Dinh, T., Igolen, J., and Kan, S. K., 1982, Org. Mag. Res. 18 (3): 148.

    CAS  Google Scholar 

  • Wagner, G., Wüthrich, W., and Tshesche, H., 1978, Eur. J. Biochem. 86: 67.

    PubMed  CAS  Google Scholar 

  • Wang, A. H.-J., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van der Marel, G., and Rich, A., 1979, Nature 282: 680.

    PubMed  CAS  Google Scholar 

  • Weiner, P. K., and Kollman, P. A., 1981, J. Comput. Chem. 2: 287.

    CAS  Google Scholar 

  • Weiner, P. K., Singh, U. C., Kollman, P. A., Caldwell, J., and Case, P. A., 1984, AMBER: A Molecular Mechanics and Dynamics Program, University of California, San Francisco.

    Google Scholar 

  • Weiss, G. H., Ferretti, J. A., 1983, J. Mag. Res. 55: 397.

    CAS  Google Scholar 

  • Werbelow, L., and Grant, D. M., 1978, Adv. Mag. Res. 9: 189.

    Google Scholar 

  • Wider, G., Macura, S., Kumar, A., Ernst, R. R., and Wüthrich, K., 1984, J. Mag. Res. 56: 207.

    CAS  Google Scholar 

  • Williamson, M. P., Havel, T. F., and Wüthrich, K., 1985, J. Mol. Biol. 182: 295.

    PubMed  CAS  Google Scholar 

  • Young, G. B., and James, T. L., 1984, J. Am. Chem. Soc. 106: 7986.

    CAS  Google Scholar 

  • Zhou, N., Bianucci, A. M., Pattabiraman, N., and James, T. L., 1987, Biochemistry 26: 7905.

    PubMed  CAS  Google Scholar 

  • Zhou, N., Manogoran, M., Zon, G., James, T. L., 1988, Biochemistry 27: 6013.

    PubMed  CAS  Google Scholar 

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Borgias, B.A., James, T.L. (1990). Structure Determination via Complete Relaxation Matrix Analysis (CORMA) of Two-Dimensional Nuclear Overhauser Effect Spectra. In: Berliner, L.J., Reuben, J. (eds) Biological Magnetic Resonance. Biological Magnetic Resonance, vol 9. Springer, Boston, MA. https://doi.org/10.1007/978-1-4615-6549-9_3

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