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Why protein crystals favour some space-groups over others

Abstract

One of the most puzzling observations in protein crystallography is that the various space-group symmetries occur with striking non-uniformity. Molecular close-packing has been invoked to explain similar observations for crystals of small organic compounds, but does not appear to be the dominant factor for proteins. Instead, we find that the observed frequencies for both two and three-dimensional crystals can be explained by an entropic model. Under a requirement for connectivity, the favoured space groups are simply less restrictive than others in that they allow the molecules more rigid-body degrees of freedom and can therefore be realized in a greater number of ways. This result underscores the importance of the nucleation event in crystallization and leads to specific ideas for crystallizing water-soluble and membrane proteins.

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References

  1. Diffraction Methods for Biological Macromolecules (eds Wyckoff, H. W., Hirs, C.H.W. & Timasheff S.N.) Meths. Enzymol. 114 (Academic Press, Orlando, 1985).

  2. Ducruix, A. & Giege, R. Crystallization of Nucleic Acids and Proteins: A Practical Approach (IRL Press, Oxford, 1992).

    Google Scholar 

  3. Carter, C.W. Jr. & Carter, C.W. Protein crystallization using incomplete factorial experiments. J. biol. Chem. 254, 12219–12223 (1979).

    CAS  PubMed  Google Scholar 

  4. Zulauf, M. & D'Arcy, A. Light scattering of proteins as a criterion for crystallization. J. cryst. Growth 122, 102–106 (1992).

    Article  CAS  Google Scholar 

  5. Velikov, P.G., Ataka, M. & Katsura, T. Laser Michelson interferometry investigation of protein crystal growth. J. cryst. Growth 130, 317–320 (1993).

    Article  Google Scholar 

  6. Mezey, P.G. A global approach to molecular symmetry: theorems on symmetry relations between ground and excited-state configurations. J. Am. Chem. Soc. 112, 3791–3802 (1990).

    Article  CAS  Google Scholar 

  7. International Tables for Crystallography. Vol. A. 2nd ed.(ed. Hahn, T.) Space Group Symmetry. (Kluwer Academic Publishers, Dordrecht, 1989).

  8. Nowacki, W. Symmetrie und physikalisch-chemische eigenschaften krystallisierter verbindungen. II. Die allgemeiner bauprinzipien organischer verbindungen. Helv. chim. Acta 26, 459–462 (1943).

    Article  CAS  Google Scholar 

  9. Mighell, A.D. & Himes, V.L. Space-group frequencies for organic compounds. Acta crystallogr. A 39, 737–740 (1983).

    Article  Google Scholar 

  10. Donohue, J. Revised space–group frequencies for organic compounds. Acta crystallogr. A 41, 203–204 (1985).

    Article  Google Scholar 

  11. Padmaja, N., Ramakurar, S. & Viswamitra, M.A. Space-group frequencies of proteins and of organic compounds with more than one formula unit in the asymmetric unit. Acta crystallogr. A46, 725–730 (1990).

    Article  CAS  Google Scholar 

  12. Brock, C.P. & Dunitz, J.D. Towards a grammar of crystal packing. Chem. Mat. 6, 1118–1127 (1994).

    Article  CAS  Google Scholar 

  13. Kitaigorodskii, A.I. Organic chemical Crystallography (Consultants Bureau: New York, 1961) (Originally published in Russian by Press of the Academy of Sciences of the USSR, Moscow, 1955).

    Google Scholar 

  14. Wilson, A.J.C. Kitajgorodskij's categories. Acta crystallogr. A49, 210–212 (1993).

    Article  Google Scholar 

  15. Michel, H. Crystallization of membrane proteins. Trends biochem. Sci. 8, 56–59 (1983).

    Article  CAS  Google Scholar 

  16. Weiss, M.S., Abele, U., Weckesser, J., Welte, W., Schiltz, E. & Schultz, G.E. Molecular architecture and electrostatic properties of a bacterial porin. Science 254, 1627–1630 (1991).

    Article  CAS  Google Scholar 

  17. Allen, J.P., Feher, G., Yeates, T.O., Komiya, H. & Rees, D.C. Structure of the reaction center from Rhodobacter sphaeroides R-26: The protein subunits. Proc. natn. Acad. Sci. U.S.A. 84, 6162–6166 (1987).

    Article  CAS  Google Scholar 

  18. Chang, C.-H., El-Kabbani, O., Tiede, D., Norris, J. & Schiffer, M. Structure of the membrane-bound protein photosynthetic reaction center from Rhodobacter sphaeroides. Biochemistry 30, 5352–5360 (1991).

    Article  CAS  Google Scholar 

  19. Deisenhofer, J., Epp, O., Miki, K., Huber, R. & Michel, H. X-ray structure analysis of a membrane protein complex. J. molec. Biol. 180, 385–398 (1984).

    Article  CAS  Google Scholar 

  20. Zawadzke, L.E. & Berg, J.M. The structure of a centrosymmetric protein crystal. Proteins 16, 301–305 (1993).

    Article  CAS  Google Scholar 

  21. Henderson, R. et al. Model for the structure of bacteriorhodopsin based on high-resolution electron cryo-microscopy. J. molec. Biol. 213, 899–929 (1990).

    Article  CAS  Google Scholar 

  22. Kühlbrandt, W., Wang, D.N. & Fujiyoshi, Y. Atomic model of plant light-harvesting complex by electron crystallography. Nature 367, 614–621 (1994).

    Article  Google Scholar 

  23. Holser, W.T. Point groups and plane groups in a two-sided plane and their subgroups. Z. Kristallogr. 110, 266–281 (1958).

    Article  CAS  Google Scholar 

  24. Kühlbrandt, W. Two-dimensional crystallization of membrane proteins. Q. Rev. Biophys. 25, 1–49 (1992).

    Article  Google Scholar 

  25. Dekker, J.P., Betts, S.D., Yokum, C.F. & Boekema, E.J. Characterization by electron microscopy of isolated particles and two-dimensional crystals of the CP47-D1-D2-cytochrome b-559 complex of photosystem II. Biochem. 29, 3220–3225 (1990).

    Article  CAS  Google Scholar 

  26. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F. Jr. & Brice, M.D. The protein data bank: a computer-based archival file for macromolecular structures. J. molec. Biol. 112, 535–542 (1977).

    Article  CAS  Google Scholar 

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Wukovitz, S., Yeates, T. Why protein crystals favour some space-groups over others. Nat Struct Mol Biol 2, 1062–1067 (1995). https://doi.org/10.1038/nsb1295-1062

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