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Comparison of four independently determined structures of human recombinant interleukin–4

Abstract

Four independent structures of human interleukin–4, two determined by nuclear magnetic resonance techniques and two by X–ray diffraction, have been compared in detail. The core of this four helix bundle protein is very similar in all the structures but there are some differences in loop regions that are known to be mobile in solution. Careful comparison of the experimental data sets and the methods of analysis of the different laboratories has provided clues to the sources of most of the differences, and also answered some general questions about the accuracy of protein structure determination by these two techniques.

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References

  1. Billeter, M. Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals. Q. Rev. Biophys. 25, 325–377 (1992).

    Article  CAS  Google Scholar 

  2. Billeter, M., Kline, A.D., Braun, W., Huber, R. & Wüthrich, K. Comparison of the high-resolution structures of the α-amylase inhibitor tendamistat determined by nuclear magnetic resonance in solution and by X-ray diffraction in single crystals. J. molec. Biol. 206, 677–687 (1989).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  4. Berndt, K.D., Güntert, P., Orbons, L.P.M. & Wüthrich, K. Determination of a high-quality nuclear magnetic resonance solution structure of the bovine pancreatic trypsin inhibitor and comparison with three crystal structures. J. molec. Biol. 227, 757–775 (1992).

    Article  CAS  Google Scholar 

  5. Baldwin, E.T. et al. Crystal structure of interleukin-8: symbiosis of NMR and crystallography. Proc. natn. Acad. Sci. U.S.A. 88, 502–506 (1991).

    Article  CAS  Google Scholar 

  6. Clore, G.M. & Gronenborn, A.M. Comparison of the solution nuclear magnetic resonance and crystal structures of interleukin-8 Possible implications for the mechanism of receptor binding. J. molec. Biol. 217, 611–620 (1991).

    Article  CAS  Google Scholar 

  7. Furey, W.F. et al. Crystal structure of Cd, Zn metallothioneine. Science 231, 704–710 (1986).

    Article  CAS  Google Scholar 

  8. Schultze, P. et al. Conformation of [Cd7] metallothionein-2 from rat liver in aqueous solution determined by nuclear magnetic resonance spectroscopy. J. molec. Biol. 203, 251–268 (1988).

    Article  CAS  Google Scholar 

  9. Shaanan, B. et al. Combining experimental information from crystal and solution studies: joint X-ray and NMR refinement. Science, 257, 961–964 (1992).

    Article  CAS  Google Scholar 

  10. Smith, L.J. et al. Human interleukin 4: The solution structure of a four-helix bundle protein. J. molec. Biol. 224, 900–904 (1992).

    Article  Google Scholar 

  11. Powers, R. et al. Three-dimensional solution structure of human interleukin-4 by multidimensional heteronuclear magnetic resonance spectroscopy. Science 256, 1673–1677 (1992).

    Article  CAS  Google Scholar 

  12. Wlodawer, A., Pavlovsky, A. & Gustchina, A. Crystal structure of human recombinant interleukin-4 at 2.25 Å resolution. FEBS Lett. 309, 59–64 (1992).

    Article  CAS  Google Scholar 

  13. Walter, M.R. et al. Crystal structure of recombinant human interleukin-4. J. biol. Chem.. 267, 20371–20376 (1992).

    CAS  PubMed  Google Scholar 

  14. Redfield, C. et al. Secondary structure and topology of human interleukin 4 in solution. Biochemistry 30, 11029–11035 (1991).

    Article  CAS  Google Scholar 

  15. Garrett, D.S. et al. Determination of the secondary structure andfolding topology of human interleukin-4 using three-dimensionalheteronuclear magnetic resonance spectroscopy. Biochemistry 31, 4347–4353 (1992).

    Article  CAS  Google Scholar 

  16. Powers, R. et al. The high-resolution three-dimensional solutionstructure of human interleukin-4 determined by multi-dimensionalheteronuclear magnetic resonance spectroscopy. Biochemistry 32, 6744–6762 (1993).

    Article  CAS  Google Scholar 

  17. Redfield, C. et al. Loop mobility in a four-helix-bundle protein: 15N NMR relaxation measurements on human interleukin-4. Biochemistry 31, 10431–10437 (1992).

    Article  CAS  Google Scholar 

  18. Kabsch, W. & Sanders, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577–2637 (1983).

    Article  CAS  Google Scholar 

  19. Schulz, G.E. & Schirmer, R.H. Principles of Protein Structure. (Springer-Verlag, New York, 1979).

    Book  Google Scholar 

  20. Morris, A.L., MacArthur, M.W., Hutchinson, E.G. & Thornton, J.M. Stereochemical quality of protein structure coordinates. Proteins 12, 345–364 (1992).

    Article  CAS  Google Scholar 

  21. Brünger, A.T. X-plor version 3 1. A system for X-ray crystallography and NMR (Yale University Press, 1992).

    Google Scholar 

  22. Wüthrich, K. NMR of Protein and Nucleic Acids (Wiley, New York, 1986).

    Book  Google Scholar 

  23. Powers, R. et al. 1H, 15N, 13C and 13CO assignments of humaninterleukin-4 using three-dimensional double- and triple- resonance heteronuclear magnetic resonance spectroscopy. Biochemistry 32, 4334–4347 (1992).

    Article  Google Scholar 

  24. Nilges, M., Kuszewski, J. & Brünger, A.T. Sampling properties of simulated annealing and distance geometry. Proceedings of the NATO Advanced Research Workshop on Computational Aspects of the Study of Biological Macromolecules by NMR. (Il Ciocco, Italy, 1991) 451–455 (Plenum Press, New York).

    Google Scholar 

  25. Nilges, M., Gronenborn, A.M., Brünger, A.T. & Clore, G.M. 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. Prot. Engng. 2, 27–38 (1988).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  27. Brünger, A.T., Clore, G.M., Gronenborn, A.M. & Karplus, M. Application of molecular dynamics with interproton distance restraints: application to crambin. Proc. natn. Acad. Sci. U.S.A. 83, 3801–3805 (1986).

    Article  Google Scholar 

  28. Clore, G.M. et al. The three-dimensional structure of α1-purothionin in solution: combined use of nuclear magnetic resonance, distance geometry and restrained molecular dynamics. EMBO J. 5, 2729–2735 (1986).

    Article  CAS  Google Scholar 

  29. Satow, Y., Cohen, G.H., Padlan, E.A. & Davies, D.A. Phosphocholine binding immunoglobulin Fab McPC603. An X-ray diffraction study at 2.7 Å. J. molec. Biol. 190, 593–604 (1986).

    Article  CAS  Google Scholar 

  30. Kraulis, P. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. appl. Crystallogr. 24, 946–950 (1991).

    Article  Google Scholar 

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Smith, L., Redfield, C., Smith, R. et al. Comparison of four independently determined structures of human recombinant interleukin–4. Nat Struct Mol Biol 1, 301–310 (1994). https://doi.org/10.1038/nsb0594-301

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