Abstract
X-ray crystallography is a powerful method for obtaining the three-dimensional structures of biological macromolecules and macromolecular complexes. Improvements in protein production, crystallization, data collection, as well as structure solution and refinement methods have brought the field to the verge of rapid high-throughput genomic scale structure determination. The major bottle neck to this process remains protein production and crystallization. This chapter describes essential information on standard protein production and crystallization methods and ongoing efforts to perform this work using high-throughput robotics.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Venter, J. C., Adams, M. D., Myers, E. W., et al. (2001) The sequence of the human genome. Science 291, 1304–1351.
Lander, E. S., Linton, L. M., Birren, B. C., et al. (2001) International Human Genome Sequencing Consortium: initial sequencing and analysis of the human genome. Nature 409, 860–921.
Goffeau, A., Barrell, B. G., Bussey, H., et al. (1996) Life with 6000 genes. Science 274, 546, 563–567.
Adams, M. D., Celniker, S. E., Holt, R. A., et al. (2000) The genome sequence of Drosophila melanogaster. Science 287, 2185–2195.
Gibbs, R. A., Weinstock, G. M., Metzker, M. L., et al. (2004) Rat Genome Sequencing Project Consortium: genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature 428, 493–521.
Waterston, R. H., Lindblad-Toh, K., Birney, E., et al. (2002) Mouse Genome Sequencing Consortium: initial sequencing and comparative analysis of the mouse genome. Nature 420, 520–562.
Holt, R. A., Subramanian, G. M., Halpern, A., et al. (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298, 129–149.
Cole, S. T., Brosch, R., Parkhill, J., et al. (1998) Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature 393, 537–544.
Liu, J. and Rost, B. (2002) Target space for structural genomics revisited. Bioinformatics 18, 922–933.
Liu, J. and Rost, B. (2004) CHOP proteins into structural domain-like fragments. Proteins 55, 678–688.
Liu, J., Hegyi, H., Acton, T. B., Montelione, G. T., and Rost, B. (2004) Automatic target selection for structural genomics on eukaryotes. Proteins 56, 188–200.
Portugaly, E., Kifer, I., and Linial, M. (2002) Selecting targets for structural determination by navigating in a graph of protein families. Bioinformatics 18, 899–907.
Portugaly, E. and Linial, M. (2000) Estimating the probability for a protein to have a new fold: a statistical computational model. Proc. Natl. Acad. Sci. USA 97, 5161–5166.
Gilliland, G. L., Tung, M., and Ladner, J. (1996) The Biological Macromolecule Crystallization Database and NASA Protein Crystal Growth Archive. J. Res. Natl. Inst. Stand Technol. 101, 309–320.
Cudney, R. (1994) Screening and optimization strategies for macromolecular crystal growth. Acta Crystallogr. D. Biol. Crystallogr. 50, 414–423.
Jancarik, J. A. K. S. (1991) Sparse Matrix Sampling: a screening method for crystallization of proteins. J. Appl. Cryst. 24, 409.
Mancia, F., Patel, S. D., Rajala, M. W., et al. (2004) Optimization of protein production in mammalian cells with a coexpressed fluorescent marker. Structure (Camb) 12, 1355–1360.
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.
Lesley, S. A., Kuhn, P., Godzik, A., et al. (2002) Structural genomics of the Thermotoga maritima proteome implemented in a high-throughput structure determination pipeline. Proc. Natl. Acad. Sci. USA 99, 11,664–11,669.
Yee, A., Chang, X., Pineda-Lucena, A., et al. (2002) An NMR approach to structural proteomics. Proc. Natl. Acad. Sci. USA 99, 1825–1830.
Boettner, M., Prinz, B., Holz, C., Stahl, U., and Lang, C. (2002) High-throughput screening for expression of heterologous proteins in the yeast Pichia pastoris. J. Biotechnol. 99, 51–62.
Bailey, C. G., Tait, A. S., and Sunstrom, N. A. (2002) High-throughput clonal selection of recombinant CHO cells using a dominant selectable and amplifiable metallothionein-GFP fusion protein. Biotechnol. Bioeng. 80, 670–676.
Berger, I., Fitzgerald, D. J., and Richmond, T. J. (2004) Baculovirus expression system for heterologous multiprotein complexes. Nat. Biotechnol. 22, 1583–1587.
Terpe, K. (2003) Overview of tag protein fusions: from molecular and biochemical fundamentals to commercial systems. Appl. Microbiol. Biotechnol. 60, 523–533.
Song, J. J., Liu, J., Tolia, N. H., et al. (2003) The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10, 1026–1032.
Smyth, D. R., Mrozkiewicz, M. K., McGrath, W. J., Listwan, P., and Kobe, B. (2003) Crystal structures of fusion proteins with large-affinity tags. Protein Sci. 12, 1313–1322.
Jenny, R. J., Mann, K. G., and Lundblad, R. L. (2003) A critical review of the methods for cleavage of fusion proteins with thrombin and factor Xa. Protein Expr. Purif. 31, 1–11.
Kapust, R. B. and Waugh, D. S. (1999) Escherichia coli maltose-binding protein is uncommonly effective at promoting the solubility of polypeptides to which it is fused. Protein Sci. 8, 1668–1674.
Routzahn, K. M. and Waugh, D. S. (2002) Differential effects of supplementary affinity tags on the solubility of MBP fusion proteins. J. Struct. Funct. Genomics 2, 83–92.
Knaust, R. K. and Nordlund, P. (2001) Screening for soluble expression of recombinant proteins in a 96-well format. Anal. Biochem. 297, 79–85.
Braun, P., Hu, Y., Shen, B., et al. (2002) Proteome-scale purification of human proteins from bacteria. Proc. Natl. Acad. Sci. USA 99, 2654–2659.
Chance, M. R., Bresnick, A. R., Burley, S. K., et al. (2002) Structural genomics: a pipeline for providing structures for the biologist. Protein Sci. 11, 723–738.
Page, R., Moy, K., Sims, E. C., et al. (2004) Scalable high-throughput micro-expression device for recombinant proteins. Biotechniques 37, 364, 366, 368 passim.
Lesley, S. A. (2001) High-throughput proteomics: protein expression and purification in the postgenomic world. Protein Expr. Purif. 22, 153–160.
Choi, K. H., Groarke, J. M., Young, D. C., et al. (2004) Design, expression, and purification of a Flaviviridae polymerase using a high-throughput approach to facilitate crystal structure determination. Protein Sci. 13, 2685–2692.
Cohen, S. L. and Chait, B. T. (2001) Mass spectrometry as a tool for protein crystallography. Annu. Rev. Biophys. Biomol. Struct. 30, 67–85.
Stura, E. A., Nermerow, G. R., and Wilson, I. A. (1992) Strategies in the crystallization of glycoproteins and protein complexes. J. Cryst. Growth. 122, 273–285.
Xu, T., Logsdon, N. J., and Walter, M. R. (2004) Crystallization and X-ray diffraction analysis of insect cell derived IL-22. Acta Crystallogr. D. Biol. Crystallogr. D60, 1295–1298.
Josephson, K., McPherson, D. T., and Walter, M. R. (2001) Purification, crystallization and preliminary X-ray diffraction of a complex between IL-10 and soluble IL-10R1. Acta Crystallogr. D. Biol. Crystallogr. 57, 1908–1911.
Strelkov, S. V., Herrmann, H., and Geisler, N. (2001) Divide-and-conquer crystallographic approach towards an atomic structure of intermediate filaments. J. Mol. Biol. 306, 773–781.
Barwell, J. A., Bochkarev, A., Pfuetzner, R. A., et al. (1995) Overexpression, purification, and crystallization of the DNA binding and dimerization domains of the Epstein-Barr virus nuclear antigen 1. J. Biol. Chem. 270, 20,556–20,559.
Pantazatos, D., Kim, J. S., Klock, H. E., et al. (2004) Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc. Natl. Acad. Sci. USA 101, 751–756.
Harris, L. J., Larson, S. B., Hasel, K. W., Day, J., Greenwood, A., and McPherson, A. (1992) The three-dimensional structure of an intact monoclonal antibody for canine lymphoma. Nature 360, 369–372.
Harris, L. J., Skaletsky, E., and McPherson, A. (1998) Crystallographic structure of an intact IgG1 monoclonal antibody. J. Mol. Biol. 275, 861–872.
Kwong, P. D., Wyatt, R., Desjardins, E., et al. (1999) Probability analysis of variational crystallization and its application to gp120, the exterior envelope glycoprotein of type 1 human immunodeficiency virus (HIV-1). J. Biol. Chem. 274, 4115–4123.
Grimm, C., Klebe, G., Ficner, R., and Reuter, K. (2000) Screening orthologs as an important variable in crystallization: preliminary X-ray diffraction studies of the tRNA-modifying enzyme S-adenosyl-methionine:tRNA ribosyl transferase/isomerase. Acta Crystallogr. D. Biol. Crystallogr. 56, 484–488.
Ruf, W., Stura, E. A., LaPolla, R. J., Syed, T., Edgington, T. S., and Wilson I. A. (1992) Purification, sequence and crystallization of an anti-tissue factor Fab and its use for the crystallization of tissue factor. J. Cryst. Growth 122, 253–264.
Stura, E. A., Graille, M. J., and Charbonnier, J. B. (2001) Crystallization of macromolecular complexes: combinatorial complex crystallization. J. Cryst. Growth 232, 573–579.
Josephson, K., Jones, B. C., Walter, L. J., DiGiacomo, R., Indelicato, S. R., and Walter, M. R. (2002) Non-competitive antibody neutralization of IL-10 revealed by protein engineering and X-ray crystallography. Structure 10, 981–987.
Kwong, P. D., Wyatt, R., Robinson, J., Sweet, R. W., Sodroski, J., and Hendrickson, W. A. (1998) Structure of an HIV gp120 envelope glycoprotein in complex with the CD4 receptor and a neutralizing human antibody. Nature 393, 648–659.
Xiang, S. H., Kwong, P. D., Gupta, R., et al. (2002) Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein. J. Virol. 76, 9699–9888.
Ferre-D’Amare, A. R. and Burley, S. K. (1994) Use of dynamic light scattering to assess crystallizability of macromolecules and macromolecular assemblies. Structure 2, 357–359.
Bard, J., Ercolani, K., Svenson, K., Olland, A., and Somers, W. (2004) Automated systems for protein crystallization. Methods 34, 329–347.
Weselak, M., Patch, M. G., Selby, T. L., Knebel, G., and Stevens, R. C. (2003) Robotics for automated crystal formation and analysis. Methods Enzymol. 368, 45–76.
Cumbaa, C. A., Lauricella, A., Fehrman, N., et al. (2003) Automatic classification of sub-microlitre protein-crystallization trials in 1536-well plates. Acta Crystallogr. D. Biol. Crystallogr. 59, 1619–1627.
DeLucas, L. J., Bray, T. L., Nagy, L., et al. (2003) Efficient protein crystallization. J. Struct. Biol. 142, 188–206.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press Inc., Totowa, NJ
About this protocol
Cite this protocol
Deivanayagam, C., Cook, W.J., Walter, M.R. (2007). Protein Crystallization. In: Fisher, P.B. (eds) Cancer Genomics and Proteomics. Methods in Molecularbiologyâ„¢, vol 383. Humana Press. https://doi.org/10.1007/978-1-59745-335-6_22
Download citation
DOI: https://doi.org/10.1007/978-1-59745-335-6_22
Publisher Name: Humana Press
Print ISBN: 978-1-58829-504-0
Online ISBN: 978-1-59745-335-6
eBook Packages: Springer Protocols