Determination of DNA and Protein Structures in Solution via Complete Relaxation Matrix Analysis of 2D NOE Spectra

  • Thomas L. James
  • Brandan A. Borgias
  • Anna Maria Bianucci
  • Ning Zhou
Part of the Basic Life Sciences book series (BLSC, volume 56)


A major objective of scientists for years has been the determination of molecular structures in non-crystalline environments. In general, researchers were forced to accept limited structural information due to the techniques available; certainly high-resolution structures such as those derived from x-ray diffraction (XRD) on crystals could not be remotely attained. However, recent developments provide us with the means to obtain considerable insight into solution structures (with resolution approaching, but not equaling, that of XRD on crystals).


Internuclear Distance Spin Diffusion Distance Geometry Bovine Pancreatic Trypsin Inhibitor Interproton Distance 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Altona, C., and Sundaralingam, M., 1972, J. Amer. Chem. Soc., 94:8205.CrossRefGoogle Scholar
  2. Borgias, B. A., and James, T. L., 1988, “COMATOSE: A Method for Constrained Refinement of Macromolecular Structure Based on Two-Dimensional Nuclear Overhauser Effect Spectra,” J. Magn. Reson., 79:493–512.Google Scholar
  3. Braun, W., and Go, N., 1985, “Calculation of Protein Conformations by Proton-Proton Distance Constraints. A New Efficient Algorithm,” J. Mol. Biol., 186:611–626.PubMedCrossRefGoogle Scholar
  4. Broido, M. S., James, T. L., Zon, G., and Keepers, J. W., 1985, “Investigation of the Solution Structure of a DNA Octamer [d-(GGAATTCC)J2 Using Two-Dimensional Nuclear Overhauser Effect Spectroscopy,” Eur. J. Biochem., 150:117–128.PubMedCrossRefGoogle Scholar
  5. Bull, T. E., 1987, “Cross-Correlation and 2D NOE Spectra,” J. Magn. Reson., 72:397–413.Google Scholar
  6. 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,” ed., Sutcliffe, L. H., Pergamon Press, Oxford, pp. 1–32.Google Scholar
  7. Havel, T. F., Kuntz, I. D., and Crippen, G. M., 1983, “The Theory and Practice of Distance Geometry,” Bull. Math. Biol., 45:665–720.Google Scholar
  8. Havel, T. F., and Wüthrich, K., 1985, “An Evaluation of the Combined Use of Nuclear Magnetic Resonance and Distance Geometry for the Determination of Protein Conformations in Solution,” J. Mol. Biol., 182:281–294.PubMedCrossRefGoogle Scholar
  9. Jamin, N., James, T. L., and Zon, G., 1985, “Two-Dimensional Nuclear Overhauser Effect Investigation of the Solution Structure and Dynamics of the DNA Octamer [d-(GGTATACC)]2,” Eur. J. Biochem., 152:157–166.PubMedCrossRefGoogle Scholar
  10. Jeener, J., 1971, AMPERE International Summer School, Basko Polje, Yugoslavia.Google Scholar
  11. Jeener, J., Meier, B. H., Bachmann, P., and Ernst, R. R., 1979, “Investigation of Exchange Processes by 2D NMR Spectroscopy,” J. Chem. Phys., 371:4546–4553.CrossRefGoogle Scholar
  12. Karplus, M., and McCammon, J. A., 1979, “Protein structural fluctuations during a period of 100 ps,” Nature, 277:578.PubMedCrossRefGoogle Scholar
  13. Kay, L. E., Scarsdale, J. N., Hare, D. R., and Prestegard, J. H., 1986a, “Simulation of Two-Dimensional Cross-Relaxation Spectra in Strongly Coupled Spin Systems,” J. Magn. Reson., 68:515–525.Google Scholar
  14. Kay, L. E., Holak, T. A., Johnson, B. A., Armitage, I. M., and Prestegard, J. H., 1986b, “Second Order Effects in Two Dimensional Cross-Relaxation Spectra of Proteins: Investigation of Glycine Spin Systems,” J. Am. Chem. Soc., 108:4242.CrossRefGoogle Scholar
  15. Keepers, J. W., and James, T. L., 1984, “A Theoretical Study of Distance Determinations from NMR. Two-Dimensional Nuclear Overhauser Effect Spectra,” J. Magn. Reson., 57:404–426.Google Scholar
  16. Lefevre, J. -F., Lane, A. N., and Jardetzky, O., 1987, “Solution Structure of the Trp Operator of Escherichia coli Determined by NMR,” Biochemistry, 26:5076–5090.PubMedCrossRefGoogle Scholar
  17. Macura, S., and Ernst, R. R., 1980, “Elucidation of Cross Relaxation in Liquids by 2D NMR Spectroscopy,” Mol. Phys., 41:95–117.CrossRefGoogle Scholar
  18. Macura, S., Farmer, B. T., and Brown, L. R., 1986, “An Improved Method for the Determination of Cross-Relaxation Rates From NOE Data,” J. Magn. Reson., 70:493–499.Google Scholar
  19. Massefski, Jr., W., and Bolton, P. H., 1985, “Quantitative Analysis of Nuclear Overhauser Effects,” J. Magn. Reson., 65:526–530.Google Scholar
  20. Olejniczak, E. T., Gampe, Jr., R. T., and Fesik, S. W., 1986, “Accounting for Spin Diffusion in the Analysis of 2D NOE Data,” J. Magn. Reson., 67:28–41.Google Scholar
  21. Singh, U. C, Weiner, P. K., Caldwell, J., and Kollman, P. A., 1986, AMBER 3.0, University of California, San Francisco.Google Scholar
  22. Solomon, I., 1955, “Relaxation Processes in a System of Two Spins,” Phys. Rev., 99:559.CrossRefGoogle Scholar
  23. Suzuki, E. -I., Pattabiraman, N., Zon, G., and James, T. L., 1986, “Solution Structure of [d-(AT),-]o via Complete Relaxation Matrix Analysis of 2D NOE Spectra and Molecular Mechanics Calculati ons,” Biochemistry, 25:6854–6865.PubMedCrossRefGoogle Scholar
  24. van Gunsteren, W. F., Boelens, R., Kaptein, R., and Zuiderweg, E. R. P., 1983, “Nuclear Acid Conformation and Dynamics, Report of NAT0/CECAM Workshop,” ed., Olson, W. K.Google Scholar
  25. Weiner, P. K., and Kollman, P. A., 1981, “AMBER: Assisted Model Building with Energy Refinement. A General Program for Modeling Molecules and Their Interactions,” J. Comp. Chem., 2:287–303.CrossRefGoogle Scholar
  26. Werbelow, L., and Grant, D. M., 1978, Adv. Magn. Reson., 9:189.Google Scholar
  27. Widmer, H., and Wuthrich, K., 1987, “Simulated Two-Dimensional NMR Cross-Peak Fine Structures for H Spin Systems in Polypeptides and Polydeoxynucleotides,” J. Magn. Reson., 74:316–336.Google Scholar
  28. Young, G. B., and James, T. L., 1984, “Determination of Molecular Structure in Solution via Two-Dimensional Nuclear Overhauser Effect Experiments: Proflavine as a Rigid Molecular Test Case,” J. Am. Chem. Soc., 106:7986–7988.CrossRefGoogle Scholar
  29. Zhou, N., Bianucci, A. M., Pattabiraman, N., and James, T. L., 1987, “Solution Structure of [d-(GGTATACC)]2: Wrinkled D Structure of the TATA Moiety,” Biochemistry, 26:7905–7913.PubMedCrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1990

Authors and Affiliations

  • Thomas L. James
    • 1
  • Brandan A. Borgias
    • 1
  • Anna Maria Bianucci
    • 2
  • Ning Zhou
    • 3
  1. 1.Departments of Pharmaceutical Chemistry and RadiologyUniversity of CaliforniaSan FranciscoUSA
  2. 2.Istituto di Chimica Farmaceutica e TossicologicaDell’Universita di PisaPisaItaly
  3. 3.Biological Sciences DepartmentUniversity of CalgaryCalgaryCanada

Personalised recommendations