Structural Proteomics pp 537-559

Part of the Methods in Molecular Biology™ book series (MIMB, volume 426)

Bacterial Structural Genomics Initiative: Overview of Methods and Technologies Applied to the Process of Structure Determination

  • Miroslaw Cygler
  • Ming-ni Hung
  • John Wagner
  • Allan Matte

The focus over the last several years on increasing the number of three-dimensional structures of macromolecules by implementation of high throughput methodology has led to the establishment of dedicated structural genomics programs around the world. These worldwide efforts have in turn led to development of novel, parallelized approaches to cloning, expression, purification, and crystallization of proteins. This chapter describes in some detail the approaches and protocols that have been implemented in the Bacterial Structural Genomics Initiative.

References

  1. 1.
    Rupp, B. (2003). High throughput crystallography at an affordable cost: the TB Structural Genomics Consortium Crystallization Facility. Acc. Chem. Res. 36, 173–181.CrossRefPubMedGoogle Scholar
  2. 2.
    Busso, D., Kim, R., and Kim, S. H. (2003). Expression of soluble recombinant proteins in a cell-free system using a 96-well format. J. Biochem. Biophys. Meth. 55, 233–240.CrossRefPubMedGoogle Scholar
  3. 3.
    Dieckman, L. J., Hanly, W. C., and Collart, E. R. (2006). Strategies for high throughput gene cloning and expression. Genet. Eng. (NY) 27, 179–190.CrossRefGoogle Scholar
  4. 4.
    Lesley, S. A. (2001). High throughput proteomics: protein expression and purifica tion in the postgenomic world. Protein Expr. Purif. 22, 159–164.CrossRefPubMedGoogle Scholar
  5. 5.
    Peti, W., Page, R., Moy, K., O'Neil-Johnson, M., Wilson, I. A., Stevens, R. C., and Wuthrich, K. (2005). Towards miniaturization of a structural genomics pipeline using micro-expression and microcoil NMR. J. Struct. Funct. Genom. 6, 259–267.CrossRefGoogle Scholar
  6. 6.
    Bhikhabhai, R., Sjoberg, A., Hedkvist, L., Galin, M., Liljedahl, P., Frigard, T., Pettersson, N., Nilsson, M., Sigrell-Simon, J. A., and Markeland-Johansson, C. (2005). Production of milligram quantities of affinity tagged-proteins using automated multistep chromatographic purification. J. Chromatogr. A 1080, 83–92.CrossRefPubMedGoogle Scholar
  7. 7.
    Scheich, C., Sievert, V., and Bussow, K. (2003). An automated method for high throughput protein purification applied to a comparison of His-tag and GST-tag affinity chromatography. BMC Biotechnol. 3, 12.CrossRefPubMedGoogle Scholar
  8. 8.
    Kim, Y., Dementieva, I., Zhou, M., Wu, R., Lezondra, L., Quartey, P., Joachimiak, G., Korolev, O., Li, H., and Joachimiak, A. (2004). Automation of protein purification for structural genomics. J. Struct. Funct. Genomics 5, 111–118.CrossRefPubMedGoogle Scholar
  9. 9.
    Page, R., and Stevens, R. C. (2004). Crystallization data mining in structural genomics: using positive and negative results to optimize protein crystallization screens. Methods 34, 373–389.CrossRefPubMedGoogle Scholar
  10. 10.
    Kimber, M. S., Vallee, F., Houston, S., Necakov, A., Skarina, T., Evdokimova, E., Beasley, S., Christendat, D., Savchenko, A., Arrowsmith, C. H., Vedadi, M., Gerstein, M., and Edwards, A. M. (2003). Data mining crystallization databases: knowledge-based approaches to optimize protein crystal screens. Proteins 51, 562–568.CrossRefPubMedGoogle Scholar
  11. 11.
    Newman, J., Egan, D., Walter, T. S., Meged, R., Berry, I., Ben, J. M., Sussman, J. L., Stuart, D. I., and Perrakis, A. (2005). Towards rationalization of crystallization screening for small- to medium-sized academic laboratories: the PACT/JCSG+ strategy. Acta Crystallogr. D. Biol. Crystallogr. 61, 1426–1431.CrossRefPubMedGoogle Scholar
  12. 12.
    Matte, A., Sivaraman, J., Ekiel, I., Gehring, K., Jia, Z., and Cygler, M. (2003). Contribution of structural genomics to understanding the biology of Escherichia coli. J. Bacteriol. 185, 3994–4002.CrossRefPubMedGoogle Scholar
  13. 13.
    Blattner, F. R., Plunkett, G., Bloch, C. A., Perna, N. T., Burland, V., Riley, M., Collado-Vides, J., Glasner, J. D., Rode, C. K., Mayhew, G. F., Gregor, J., Davis, N. W., Kirkpatrick, H. A., Goeden, M. A., Rose, D. J., Mau, B., and Shao, Y. (1997). The complete genome sequence of Escherichia coli K-12. Science 277, 1453–1474.CrossRefPubMedGoogle Scholar
  14. 14.
    Perna, N. T., Plunkett, G. I., Blattner, F. R., Mau, B., and Blattner, F. R. (2001). Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature 409, 529–533.CrossRefPubMedGoogle Scholar
  15. 15.
    Welch, R. A., Burland, V., Plunkett, G., III, Redford, P., Roesch, P., Rasko, D., Buckles, E. L., Liou, S. R., Boutin, A., Hackett, J., Stroud, D., Mayhew, G. F., Rose, D. J., Zhou, S., Schwartz, D. C., Perna, N. T., Mobley, H. L., Donnenberg, M. S., and Blattner, F. R. (2002). Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc. Natl. Acad. Sci. USA 99, 17020–17024.CrossRefPubMedGoogle Scholar
  16. 16.
    Keseler, I. M., Collado-Vides, J., Gama-Castro, S., Ingraham, J., Paley, S., Paulsen, I. T., Peralta-Gil, M., and Karp, P. D. (2005). EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res. 33, D334–D337.CrossRefPubMedGoogle Scholar
  17. 17.
    Kanehisa, M., Goto, S., Hattori, M., Oki-Kinoshita, K. F., Itoh, M., Kawashima, S., Katayama, T., Araki, M., and Hirakawa, M. (2006). From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res. 34, D354–D357.CrossRefPubMedGoogle Scholar
  18. 18.
    Misra, R. V., Horler, R. S., Reindl, W., Goryanin, I. I., and Thomas, G. H. (2005). EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res. 33, D329–D333.CrossRefPubMedGoogle Scholar
  19. 19.
    Teichmann, S. A., Rison, S. C., Thornton, J. M., Riley, M., Gough, J., and Chothia, C. (2001). The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. J. Mol. Biol. 311, 693–708.CrossRefPubMedGoogle Scholar
  20. 20.
    Riley, M., Abe, T., Arnaud, M. B., Berlyn, M. K., Blattner, F. R., Chaudhuri, R. R., Glasner, J. D., Horiuchi, T., Keseler, I. M., Kosuge, T., Mori, H., Perna, N. T., Plunkett, G., III, Rudd, K. E., Serres, M. H., Thomas, G. H., Thomson, N. R., Wishart, D., and Wanner, B. L. (2006). Escherichia coli K-12: a cooperatively developed annotation snapshot—2005. Nucleic Acids Res. 34, 1–9.CrossRefPubMedGoogle Scholar
  21. 21.
    Riley, M., and Serres, M. H. (2000). Interim report on genomics of Escherichia coli. Annu. Rev. Microbiol. 54, 341–411.CrossRefPubMedGoogle Scholar
  22. 22.
    Finn, R. D., Mistry, J., Schuster-Bockler, B., Griffiths-Jones, S., Hollich, V., Lassmann, T., Moxon, S., Marshall, M., Khanna, A., Durbin, R., Eddy, S. R., Sonnhammer, E. L., and Bateman, A. (2006). Pfam: clans, web tools and services. Nucleic Acids Res. 34, D247–D251.CrossRefPubMedGoogle Scholar
  23. 23.
    Bairoch, A., Apweiler, R., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., Martin, M. J., Natale, D. A., O'Donovan, C., Redaschi, N., and Yeh, L. S. (2005). The Universal Protein Resource (UniProt). Nucleic Acids Res. 33, D154–D159.CrossRefPubMedGoogle Scholar
  24. 24.
    Gasteiger, E., Gattiker, A., Hoogland, C., Ivanyi, I., Appel, R. D., and Bairoch, A. (2003). ExPASy: the proteomics server for in-depth protein knowledge and analy sis. Nucleic Acids Res. 31, 3784–3788.CrossRefPubMedGoogle Scholar
  25. 25.
    Raymond, S., O'Toole, N., and Cygler, M. (2004). A data management system for structural genomics. Proteome. Sci. 2, 4.CrossRefPubMedGoogle Scholar
  26. 26.
    Bendtsen, J. D., Nielsen, H., Von, H. G., and Brunak, S. (2004). Improved predic tion of signal peptides: SignalP 3.0. J. Mol. Biol. 340, 783–795.CrossRefPubMedGoogle Scholar
  27. 27.
    Kall, L., Krogh, A., and Sonnhammer, E. L. (2004). A combined transmembrane topology and signal peptide prediction method. J. Mol. Biol. 338, 1027–1036.CrossRefPubMedGoogle Scholar
  28. 28.
    Kapust, R. B., Tozser, J., Fox, J. D., Anderson, D. E., Cherry, S., Copeland, T. D., and Waugh, D. S. (2001). Tobacco etch virus protease: mechanism of autolysis and rational design of stable mutants with wild-type catalytic proficiency. Protein Eng. 14, 993–1000.CrossRefPubMedGoogle Scholar
  29. 29.
    Dougherty, W. G., Carrington, J. C., Cary, S. M., and Parks, T. D. (1988). Biochemical and mutational analysis of a plant virus polyprotein cleavage site. EMBO J. 7, 1281–1287.PubMedGoogle Scholar
  30. 30.
    Carrington, J. C., and Dougherty, W. G. (1988). A viral cleavage cassette: Identification of amino acid sequences required for tobacco etch virus polyprotein processing. Proc. Natl. Acad. Sci. USA 85, 3391–3395.CrossRefPubMedGoogle Scholar
  31. 31.
    Bradford, M. M. (1976). A rapid and sensitive method for the quantitation of micro-gram quantities of protein-dye binding. Anal. Biochem. 72, 248–254.CrossRefPubMedGoogle Scholar
  32. 32.
    Studier, F. W. (2005). Protein production by auto-induction in high density shaking cultures. Protein Expr. Purif. 41, 207–234.CrossRefPubMedGoogle Scholar
  33. 33.
    Hendrickson, W. A., Horton, J. R., and LeMaster, D. M. (1990). Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J. 9, 1665–1672.PubMedGoogle Scholar
  34. 34.
    Doublie, S. (1997). Preparation of selenomethionyl proteins for phase determina tion. Meth. Enzymol. 276, 523–530.CrossRefPubMedGoogle Scholar
  35. 35.
    Koth, C. M., Orlicky, S. M., Larson, S. M., and Edwards, A. M. (2003). Use of lim ited proteolysis to identify protein domains suitable for structural analysis. Meth. Enzymol. 368, 77–84.CrossRefPubMedGoogle Scholar
  36. 36.
    Heras, B., and Martin, J. L. (2005). Post-crystallization treatments for improving diffrac tion quality of protein crystals. Acta Crystallogr. D. Biol. Crystallogr. 61, 1173–1180.CrossRefPubMedGoogle Scholar
  37. 37.
    Terwilliger, T. C. (2002). Automated structure solution, density modification and model building. Acta Crystallogr. D Biol. Crystallogr. 58, 1937–1940.CrossRefPubMedGoogle Scholar
  38. 38.
    Schneider, T. R., and Sheldrick, G. M. (2002). Substructure solution with SHELXD. Acta Crystallogr. D. Biol. Crystallogr. 58, 1772–1779.CrossRefPubMedGoogle Scholar
  39. 39.
    Weeks, C. M., and Miller, R. (1999). Optimizing Shake-and-Bake for proteins. Acta Crystallogr. D55, 492–500.Google Scholar
  40. 40.
    Bricogne, G., Vonrhein, C., Flensburg, C., Schiltz, M., and Paciorek, W. (2003). Generation, representation and flow of phase information in structure determina tion: recent developments in and around SHARP 2.0. Acta Crystallogr. D. Biol. Crystallogr. 59, 2023–2030.CrossRefPubMedGoogle Scholar
  41. 41.
    Sheldrick, G. M. (2002). Macromolecular phasing with SHELXE. Z. Kristallogr. 217, 644–650.CrossRefGoogle Scholar
  42. 42.
    Terwilliger, T. C. (2000). Maximum-likelihood density modification. Acta Crystallogr. D56, 965–972.Google Scholar
  43. 43.
    Perrakis, A., Morris, R., and Lamzin, V. S. (1999). Automated protein model build ing combined with iterative structure refinement. Nat. Struct. Biol. 6, 458–463.CrossRefPubMedGoogle Scholar
  44. 44.
    Dauter, Z., Li, M., and Wlodawer, A. (2000). Practical experience with the use of halides for phasing macromolecular structures: a powerful tool for structural genomics. Acta Crystallogr. D57, 239–249.Google Scholar
  45. 45.
    Rangarajan, E. S., Proteau, A., Wagner, J., Hung, M. N., Matte, A., and Cygler, M. (2006). E. coli histidinol phosphate phosphatase: Structural snapshots along the reaction pathway. J. Biol. Chem. 281, 37930–37941.CrossRefPubMedGoogle Scholar
  46. 46.
    Hung, M. N., Rangarajan, E., Munger, C., Nadeau, G., Sulea, T., and Matte, A. (2006). Crystal structure of TDP-fucosamine acetyltransferase (WecD) from Escherichia coli, an enzyme required for enterobacterial common antigen synthe sis. J. Bacteriol. 188, 5606–5617.CrossRefPubMedGoogle Scholar
  47. 47.
    Sivaraman, J., Myers, R. S., Boju, L., Sulea, T., Cygler, M., Jo Davisson, V., and Schrag, J. D. (2005). Crystal structure of Methanobacterium thermoautotrophicum phosphoribosyl-AMP cyclohydrolase HisI. Biochemistry 44, 10071–10080.CrossRefPubMedGoogle Scholar
  48. 48.
    Barbosa, J. A., Sivaraman, J., Li, Y., Larocque, R., Matte, A., Schrag, J. D., and Cygler, M. (2002). Mechanism of action and NAD+-binding mode revealed by the crystal structure of L-histidinol dehydrogenase. Proc. Natl. Acad. Sci. USA. 99, 1859–1864.CrossRefPubMedGoogle Scholar
  49. 49.
    Tocilj, A., Schrag, J. D., Li, Y., Schneider, B. L., Reitzer, L., Matte, A., and Cygler, M. (2005). Crystal structure of N-succinylarginine dihydrolase AstB, bound to sub strate and product, an enzyme from the arginine catabolic pathway of Escherichia coli. J. Biol. Chem. 280, 15800–15808.CrossRefPubMedGoogle Scholar
  50. 50.
    Michel, G., Sauvé, V., Larocque, R., Li, Y., Matte, A., and Cygler, M. (2002). The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot. Structure 10, 1303–1315.CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Miroslaw Cygler
    • 1
  • Ming-ni Hung
    • 1
  • John Wagner
    • 1
  • Allan Matte
    • 1
  1. 1.Biotechnology Research InstituteNational Research Council CanadaMontrealCanada

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