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Large-scale evaluation of protein reductive methylation for improving protein crystallization

Nature Methods volume 5, pages 853–854 (2008)Cite this article

To the editor:

Obtaining diffraction-quality crystals is a major bottleneck in protein X-ray crystallography. For example, the current success rate for protein structure solution at the Midwest Center for Structural Genomics (starting from purified protein) is ∼10%. Protein crystallization is influenced by many factors, and many methods have been developed to enhance crystallization. In particular, reductive methylation of proteins has been successfully applied to obtain high-quality crystals1,2,3,4. Several studies3,5,6 have indicated that methylating the solvent-exposed ɛ-amino group of lysines changes protein properties (pI, solubility and hydropathy)7,8, which may promote crystallization via improving crystal packing. Reductive methylation of proteins is a simple, generic method; it is fast, specific and requires few steps under relatively mild buffer and chemical conditions and can be executed for several proteins in parallel. Native and methylated proteins have very similar structures, and, in most cases, methylated proteins maintain their biochemical function2,5,9. Some proteins can only be crystallized after methylation3,10, and crystals of modified proteins often diffract to higher resolution3,9. The efficacy of the method has been previously tested on 10 proteins, with a 30% success rate3.

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Figure 1: Plots of isotropic B factors calculated for protein structures solved in both the native and methylated states.

References

  1. D'Arcy, A., Stihle, M., Kostrewa, D. & Dale, G. Acta Crystallogr. D Biol. Crystallogr. 55, 1623–1625 (1999).

    Article  CAS  Google Scholar 

  2. Rypniewski, W.R., Holden, H.M. & Rayment, I. Biochemistry 32, 9851–9858 (1993).

    Article  CAS  Google Scholar 

  3. Walter, T.S. et al. Structure 14, 1617–1622 (2006).

    Article  CAS  Google Scholar 

  4. Shaw, N. et al. BMC Struct. Biol. 7, 46 (2007).

    Article  Google Scholar 

  5. Means, G.E. Methods Enzymol. 47, 469–478 (1977).

    Article  CAS  Google Scholar 

  6. Means, G.E. & Feeney, R.E. Anal. Biochem. 224, 1–16 (1995).

    Article  CAS  Google Scholar 

  7. Canaves, J.M., Pagea, R., Wilson, I.A. & Stevens, R.C. J. Mol. Biol. 344, 977–991 (2004).

    Article  CAS  Google Scholar 

  8. Kyte, J. & Doolittle, R.F. J. Mol. Biol. 157, 105–132 (1982).

    Article  CAS  Google Scholar 

  9. Kobayashi, M., Kubota, M. & Matsuura, Y. Acta Crystallogr. D Biol. Crystallogr. 55, 931–933 (1999).

    Article  CAS  Google Scholar 

  10. Schubot, F.D. & Waugh, D.S. Acta Crystallogr. D Biol. Crystallogr. 60, 1981–1986 (2004).

    Article  Google Scholar 

  11. Means, G.E. & Feeney, R.E. Bioconjug. Chem. 1, 2–12 (1990).

    Article  CAS  Google Scholar 

  12. Kim, Y. et al. J. Struct. Funct. Genomics 5, 111–118 (2004).

    Article  CAS  Google Scholar 

  13. Magalhaes, A. et al. J. Protein Chem. 13, 195–215 (1994).

    Article  CAS  Google Scholar 

  14. Anashkina, A., Kuznetso, E., Esipova, N. & Tumanyan, V. Proteins 67, 1060–1077 (2007).

    Article  CAS  Google Scholar 

  15. Glaser, F., Steinberg, D.M., Vakser, I.A. & Ben-Tal, N. Proteins 43, 89–102 (2001).

    Article  CAS  Google Scholar 

  16. Juers, D.H. & Matthews, B.W. J. Mol. Biol. 311, 851–862 (2001).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

We thank all members of the Structural Biology Center and Midwest Center for Structural Genomics at Argonne National Laboratory for their help in conducting these experiments, S. Li, C.B. Lindberg and C. Giometti for running mass spectrometry experiments, A. Edwards for reading and commenting on the drafts, and L. Butler for preparing the manuscript. This work was supported by US National Institutes of Health (GM62414, GM074942) and by the US Department of Energy, Office of Biological and Environmental Research, under contract DE-AC02-06CH11357.

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Authors and Affiliations

  1. Biosciences Division, Midwest Center for Structural Genomics, Argonne National Laboratory, 9700 S. Cass Ave., Argonne, 60439, Illinois, USA

    Youngchang Kim, Pearl Quartey, Hui Li, Lour Volkart, Catherine Hatzos, Changsoo Chang, Boguslaw Nocek, Marianne Cuff, Jerzy Osipiuk, Kemin Tan, Yao Fan, Natalia Maltseva, Ruiying Wu, Min Zhou, T Andrew Binkowski, Rong-guang Zhang & Andrzej Joachimiak

  2. Midwest Center for Structural Genomics, On Assignment, Labsupport Services, 9450 W. Bryn Mawr Avenue, Rosemont, 60018, Illinois, USA

    Lance Bigelow, Maria Borovilos & Erika Duggan

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Supplementary Figures 1–5, Supplementary Tables 1–2, Supplementary Methods (PDF 602 kb)

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Kim, Y., Quartey, P., Li, H. et al. Large-scale evaluation of protein reductive methylation for improving protein crystallization. Nat Methods 5, 853–854 (2008). https://doi.org/10.1038/nmeth1008-853

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