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Structure Determination Using Isomorphous Replacement

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Book cover Crystallographic Methods and Protocols

Part of the book series: Methods in Molecular Biology™ ((MIMB,volume 56))

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Abstract

The determination of the three-dimensional structure of molecules using single crystal X-ray diffraction techniques requires the measurement of amplitudes and the calculation of phases for each diffraction point (maximum). Although amplitudes can be directly measured from diffracting crystals, phases are indirectly determined, because there are no lenses that can bend and focus X-rays. Thus, methods were developed to calculate phases from the intensities of the diffracted waves. Isomorphous replacement is the most widely used method for ab initio phase determination of macromolecules. Its first successful application to large biological molecules was undertaken in 1954 by Perutz and coworkers (1) while studying hemoglobin. Since then, this method has played a central role in the determination of almost all unique protein and nucleic acid structures, and it is likely to retain such a role in the foreseeable future.

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References

  1. Green, D W, Ingram, V M., and Perutz, M F (1954) The structure determination of heamoglobin IV Sign determination by the isomorphous replacement method. Proc R Soc London A225, 287–307

    Google Scholar 

  2. Wang, B. C. (1985) Resolution of phase ambiguity in macromolecular crystallography, in Methods in Enzymology, vol 115 (Wyckoff, H W, Hirs, C. H W, and Timasheff, S N, eds), Academic, New York, pp 90–112

    Google Scholar 

  3. McPherson, A (1982) Preparation and Analysis of Protein Crystals John Wiley & Sons, New York

    Google Scholar 

  4. Wyckoff, H W, Hirs, C H. W., and Timasheff, S N, eds. (1985) Methods in Enzymology, vol 114. Diffraction Methods for Biological Macromolecules Academic, New York

    Google Scholar 

  5. Blundell, T L and Johnson, L. N (1976) Protein Crystallography Academic, London

    Google Scholar 

  6. Petsko, G A. (1985) Preparation of isomorphous heavy-atom derivatives, in Methods in Enzymology, vol 114 (Wyckoff, H. W, Hirs, C. H W., and Timasheff, S N, eds), Academic, New York, pp 147–156

    Google Scholar 

  7. Kim, S.-H., Shin, W. C, and Warrant, R W (1985) Heavy metal ion-nucleic acid Interaction, in Methods in Enzymology, vol. 114 (Wyckoff, H. W., Hirs, C. H W, and Timasheff, S N, eds), Academic, New York, pp 156–167

    Google Scholar 

  8. Holbrook, S R and Kim, S-H (1985) Crystallization and heavy-atom derivatives of polynucleotides, in Methods in Enzymology, vol 114 (Wyckoff, H. W, Hirs, C H W, and Timasheff, S N, eds.), Academic, New York, pp 167–176

    Google Scholar 

  9. Ringe, D, Petsko, G A, Yanahura, F, Suzuki, K, and Ohmori, D (1983) Structure of iron superoxide dismutase from Pseudomonas ovalis at 2 9 Å resolution. Proc Natl Acad Sci USA 80, 3879–3883

    Article  CAS  Google Scholar 

  10. Drew, H, Takano, T, Takana, S, Itakura, K, and Dickerson, R. E. (1980) High-salt d(CpGpCpG), a left-handed Z′ DNA double helix. Nature (London) 286, 567–573

    Article  CAS  Google Scholar 

  11. Abdel-Meguid, S S., Grindley, N. D. F., Templeton, N. S., and Steitz, T A (1984) Cleavage of the site-specific recombination protein ψδ resolvase. the smaller of the two fragments binds DNA specifically. Proc Nat1 Acad Sci USA 81, 2001–2005

    Article  CAS  Google Scholar 

  12. Hatfull, G F., Sanderson, M R., Freemont, P S., Raccuia, P R, Grindley, N D F., and Steitz, T A (1989) Preparation of heavy-atom derivatives using site-directed mutagenesis introduction of cysteine residues into ψδ resolvase. J Mol Biol 208, 661–667.

    Article  CAS  Google Scholar 

  13. Petsko, G A, Phillips, D C., Williams, R. J. P., and Wilson, I A (1978) On the protein crystal chemistry of chloroplatinite ions general principles and interactions with triose phosphate isomerase. J. Mol. Biol. 120, 345–359.

    Article  CAS  Google Scholar 

  14. Buerger, M. J. (1964) The Precession Method Wiley, New York

    Google Scholar 

  15. Patterson, A. L. (1934) A Fourier serves method for the determination of the components of interatomic distances in crystals. Phys Rev 46, 372–376

    Article  CAS  Google Scholar 

  16. Abdel-Meguld, S. S, Shieh, H.-S., Smith, W. W., Dayringer, H E., Violand, B N, and Bentle, L A (1987) Three-dimensional structure of a genetically engineered variant of porcine growth hormone. Proc Nat1 Acad Sci USA 84, 6434–6437

    Article  Google Scholar 

  17. Abdel-Meguid, S.S, Smith, W W., Violand, B N, and Bentle, L.A (1986) Crystallization of methionyl porcine somatotropin, a genetically engineered variant of porcine growth hormone. J Mol Biol 192, 159,160.

    Article  CAS  Google Scholar 

  18. Watenphaugh, K D. (1985) Overview of phasing by isomorphous replacement, in Methods in Enzymology, vol 115 (Wyckoff, H W, Hirs, C H W., and Timasheff, S N, eds), Academic, New York, pp 3–15

    Google Scholar 

  19. Cullis, A F, Muirhead, H, Perutz, M F, Rossmann, M G, and North, A C T (1962) The structure of haemoglobin VIII. A three-dimensional Fourier synthesis at 5.5 Å resolution: determination of phase angles. Proc R Soc London A265, 15–38

    Google Scholar 

  20. Abdel-Meguid, S. S., Moore, P B, and Steitz, T. A (1983) Crystallization of a ribonuclease-resistant fragment of Escherichia coli 5 S ribosomal RNA and its complex with protein L25. J Mol Biol 171, 207–215

    Article  CAS  Google Scholar 

  21. Stettz, T A. (1968) A new method of locating heavy atoms bound to protein crystals. Acta Cryst B24, 504–507

    Google Scholar 

  22. Kretsmger, R H. (1968) A crystallographic study of iodinated sperm whale metmyoglobin. J Mol Biol 31, 315–318.

    Article  Google Scholar 

  23. Wright, C S, Alden, R A, and Kraut, J. (1969) Structure of subtilisin BPN′ at 2 5 Å resolution. Nature 221, 235–242

    Article  CAS  Google Scholar 

  24. McPherson, A., Jurnak, F A., Wang, A. H. J., Molineux, I., and Rich, A. (1979) Structure at 2.3 Å resolution of the gene 5 product of bacteriophage fd. a DNA unwiding protein. J Mol. Biol 134, 379–400

    Article  CAS  Google Scholar 

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© 1996 Humana Press Inc.

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Abdel-Meguid, S.S. (1996). Structure Determination Using Isomorphous Replacement. In: Jones, C., Mulloy, B., Sanderson, M.R. (eds) Crystallographic Methods and Protocols. Methods in Molecular Biology™, vol 56. Humana Press. https://doi.org/10.1385/0-89603-259-0:153

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  • DOI: https://doi.org/10.1385/0-89603-259-0:153

  • Publisher Name: Humana Press

  • Print ISBN: 978-0-89603-259-0

  • Online ISBN: 978-1-59259-543-3

  • eBook Packages: Springer Protocols

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