Skip to main content

Genetic Construct Design and Recombinant Protein Expression for Structural Biology

  • Protocol
  • First Online:
Structure-Based Drug Discovery

Part of the book series: Methods in Molecular Biology ((MIMB,volume 841))

Abstract

Obtaining diffraction quality crystals is frequently an iterative process which traditionally has involved screening large numbers of crystallization conditions. Due to advances in high-throughput gene engineering, recombinant expression, and purification, the protein of interest has now become one of the many variables routinely investigated during crystallization trials. As such, construct design is a critical step in the path toward successful crystallization. In this chapter will we address construct design strategies frequently employed to improve the solution and crystallization behavior of proteins. Topics covered include choosing a recombinant expression system and reducing disorder through truncations and surface mutagenesis. Also covered are strategies to reduce heterogeneity from posttranslational modifications, impurities, and aggregation.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 84.99
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 159.00
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 109.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Dale, G. E., Oefner, C., D’Arcy, A. (2003) The protein as a variable in protein crystallization. J. Struct. Biol. 142, 88–97.

    Article  PubMed  CAS  Google Scholar 

  2. Notredame C., Higgins D.G. and Heringa J. (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302, 205–217.

    Article  PubMed  CAS  Google Scholar 

  3. Edgar R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797.

    Article  PubMed  CAS  Google Scholar 

  4. Jacobson M. and Sali A. (2004) Comparative protein structure modeling and its applications to drug discovery. Ann. Reports Med. Chem. 39, 259–276.

    Article  CAS  Google Scholar 

  5. Mooij W.T.M., Mitsiki E. and Perrakis A. (2009) ProteinCCD: enabling the design of protein truncation constructs for expression and crystallization experiment. Nucleic Acids Research, 37, W402–W405.

    Article  PubMed  CAS  Google Scholar 

  6. Malawski, G. A., Hillig, R. C., Monteclaro, F., Eberspaecher, U., Schmitz, A. A. P., Crusius, K., Huber, M., Egner, U., Donner, P. and Mueller-Tiemann, B. (2006) Identifying protein construct variants with increased crystallization propensity-A case study. Prot. Sci. 15, 2718–2728.

    Article  CAS  Google Scholar 

  7. Pantazatos D., Kim J.S., Klock H.E., Stevens R.C., Wilson I.A., Lesley S.A., Woods V. L. Jr. (2004) Rapid refinement of crystallographic protein construct definition employing enhanced hydrogen/deuterium exchange MS. Proc. Natl. Acad. Sci. USA. 101, 751–756.

    Article  PubMed  CAS  Google Scholar 

  8. Spraggon, G., D. Pantazatos, D., Klock, H. E., Wilson, I. A., Woods, V. L. and Lesley, S. A. (2004) On the use of DXMS to produce more crystallizable proteins: structures of the T. maritima proteins TM0160 and TM1171. Prot. Sci. 13, 3187–3199.

    Google Scholar 

  9. Hamuro, Y., Coales, S. J., Southern, M. R. Nemeth-Cawley, J. F., Stranz, D. D. and Griffin, P. R. (2003) Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry. J. Biomol. Tech. 14, 171–182.

    PubMed  Google Scholar 

  10. Sharma, S., Zheng, H., Huang, Y. J., Hamuro, Y., Rossi, P., Tejero, R., Acton, T. B., Xiao, R., Jiang, M., Zhao, L., Ma, L. C., Swapna, G. V., Aramini, J. M. and Montelione, G. T. (2009) Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry Proteins. 76, 882–894.

    Article  PubMed  CAS  Google Scholar 

  11. Gray D. and Subramanian S. (2001) Choice of cellular protein expression system. Curr. Protocol. Prot. Sci. 5.16, 1–34.

    Google Scholar 

  12. Dvir, H. and Choe, S. (2009) Bacterial expression of a eukaryotic membrane protein in fusion to various Mistic orthologs. Prot. Expr. Purif. 68, 28–33.

    Article  CAS  Google Scholar 

  13. Leviatan, S., Sawada, K., Moriyama, Y. and Nelson, N. (2010). Combinatorial method for overexpression of membrane proteins in Escherichia coli. J. Biol. Chem. 285, 23548–23556.

    Article  PubMed  CAS  Google Scholar 

  14. Ponniah K., Loo T.S., Edwards P.J.B., Pascal S.M., Jameson G.B. and Norris G.E. (2010) Prot. Exp. Purif. 70, 283–289.

    Article  CAS  Google Scholar 

  15. Brusehaber E., Schwiebs A., Schmidt M., Bottcher D. and Bornscheuer U.T. (2010) App. Microbiol. Biotechnol. 86, 1337–1344.

    Article  Google Scholar 

  16. Yan W.K., Goette M., Hofmann G., Zaror I. and Sim J. (2010) Prot. Exp. Purif. 70, 270–276.

    Article  Google Scholar 

  17. Bachmair A., Finley D. and Varshavsky A. (1986) In vivo half-life of a protein is a function of its amino-terminal residue. Science. 234, 179–186.

    Article  PubMed  CAS  Google Scholar 

  18. Dalboge, H., Bayne, S. and Pedersen, J. (1990) In vivo processing of N-terminal methionine in E. coli. FEBS Lett. 266, 1–3.

    Article  PubMed  CAS  Google Scholar 

  19. Murphy, C. I., Piwnica-Worms, H., Grunwald, S., Romanow, W. G., Francis, N. and Fan, H. Y. (2004) Expression and purification of recombinant proteins using the baculovirus system. Curr. Prot. Mol. Biol. Chapter 16, Unit 16 11.

    Google Scholar 

  20. Ratnala, V. R. (2006) New tools for G-protein coupled receptor (GPCR) drug discovery: combination of baculoviral expression system and solid state NMR. Biotech. Lett. 28, 767–778.

    Article  CAS  Google Scholar 

  21. Taxis, C. and Knop, M. (2006) System of centromeric, episomal, and integrative vectors based on drug resistance markers for Saccharomyces cerevisiae. Biotechniques 40, 73–78.

    Article  PubMed  CAS  Google Scholar 

  22. Kyrieleis O.J.P., Huber R., Ong E., Oehler R., Hunter M., Madison E.L. and Jacob U. (2007) Crystal structure of the catalytic domain of DESC1, a new member of the type II transmembrane serine proteinase family. FEBS Journal. 274, 2148–2160.

    Article  PubMed  CAS  Google Scholar 

  23. Friedrich R., Fuentes-Prior P., Ong E., Coombs G., Oehler R., Hunter M., Pierson D., Gonzalez R., Huber R., Bode W. and Madison E.L. (2002) Catalytic domain structures of MT-SP1/Matriptase, a matrix-degrading transmembrane serine proteinase. J. Biol. Chem. 277, 2160–2168.

    Article  PubMed  CAS  Google Scholar 

  24. Katz, B. A., Mackman, R., Luong, C., Radika, K., Martelli, A., Sprengeler, P. A., Wang, J., Chan, H. and Wong, L. (2000) Structural basis for selectivity of a small molecule, S1-binding, submicromolar inhibitor of urokinase-type plasminogen activator. Chem. Biol. 7, 299–312.

    Article  PubMed  CAS  Google Scholar 

  25. Yoo H.Y., Kim S.S. and Rho H.M. (1999) Overexpression and simple purification of human superoxide dismutase (SOD1) in yeast and its resistance to oxidative stress. J. Biotechnol. 68, 29–35.

    Article  PubMed  CAS  Google Scholar 

  26. Barr P.J., Cousens L.S., Lee-Ng C.T., Medina-Selby A., Masiarz F.R., Hallewell R.A., Chamberlain S.H., Bradley J.D., Lee D., Steimer K.S., Poulter L., Burlingame A.L., Esch F. and Baird A. (1988) Antigenicity and immunogenicity of domains of the human immunodeficiency virus (HIV) envelope polypeptide expressed in the yeast Saccharomyces cerevisiae. J. Biol. Chem. 263,16471–16478.

    PubMed  CAS  Google Scholar 

  27. Cabezon T., de Wilde M., Herion P., Loriau, R. and Bollen A. (1984) Expression of human alpha 1-antitrypsin cDNA in the yeast Saccharomyces cerevisiae. Proc. Natl. Acad. Sci. 81, 6594–6598.

    Article  PubMed  CAS  Google Scholar 

  28. Lawson D.M., Artymiuk P.J., Yewdall S.J., Smith J.M.A., Livingstone J.C., Treffry A., Luzzago A., Levi S., Arosio P., Casareni G., Thomas C.D., Shaw W.V. and Harrison P.M. (1991) Solving the structure of human H ferritin by genetically engineering intermolecular crystal contacts. Nature. 349, 541–544.

    Article  PubMed  CAS  Google Scholar 

  29. D’Arcy A., Stihle M., Kostrewa D. and Dale, G. (1999) Crystal engineering: a case study using the 24 kDa fragment of the DNA gyrase B subunit from Escherichia coli. Acta. Cryst. D55,1623–1625.

    Google Scholar 

  30. Derewenda, Z.S. (2004) Rational protein crystallization by mutational surface engineering. Structure, 12, 529–535.

    Article  PubMed  CAS  Google Scholar 

  31. Doye J.P.K., Louis A.A. and Vendruscolo M. (2004) Inhibition of protein crystallization by evolutionary negative design. Phys. Biol. 1, P9–P13.

    Article  PubMed  CAS  Google Scholar 

  32. Longnecker K.L., Garrard S.M., Sheffield P.J. and Derewenda Z.S. (2001) Protein crystallization by rational mutagenesis of surface residues: Lys to Ala mutations promote crystallization of RhoGDI. Acta Cryst. D57, 679–688.

    Google Scholar 

  33. Derewenda Z.S. (2004) The use of recombinant methods and molecular engineering in protein crystallization. Methods, 34, 354–363.

    Article  PubMed  CAS  Google Scholar 

  34. Czepas J., Devedjiev Y., Krowarsch D., Derewenda U., Otlewski J. and Derewenda Z.S. (2004) The impact of Lys→Arg surface mutations on the crystallization of the globular domain of RhoGDI. Acta Cryst., D60, 275–280.

    CAS  Google Scholar 

  35. Baud F. and Karlin S. (1999) Measures of residue density in protein structures. Proc. Natl. Acad. Sci. 96, 12494–12499.

    Article  PubMed  CAS  Google Scholar 

  36. Mateja, A., Devedjiev, Y., Krowarsch, D., Longenecker, K., Dauter,. Z., Otlewski, J. and Derewenda, Z. S. (2002) Entropy and surface engineering in protein crystallization. Acta Cryst. D58, 1983–1991.

    CAS  Google Scholar 

  37. Price, W. N. II, Chen, Y., Handelman, S. K., Neely, H., Manor, P. et al. (2009) Understanding the physical properties controlling protein crystallization based on analysis of large-scale experimental data. Nat. Biotechnol. 27, 51–57.

    Article  PubMed  CAS  Google Scholar 

  38. Rosenbaum D. M., Cherezov V., Hanson M. A., Rasmussen S. G. F., Thian F. S., Kobilka T. S., Choi H. -J., Yao X. -J., Weis W. I., Stevens R. C. and Kobilka B. K. (2007) High-Resolution Crystal Structure of an Engineered Human beta 2-Adrenergic G Protein–Coupled Receptor. Science, 318, 1266–1273.

    Article  PubMed  CAS  Google Scholar 

  39. Proteau, A., Shi, R. and Cygler M. (2010). Curr. Prot. Prot. Sci. Chapter 17, Unit 17 10.

    Google Scholar 

  40. Davis S. J., Puklavec M. J., Ashford D. A., Harlos K., Jones E. Y., Stuart D. I., and Williams A. F. (1993) Expression of soluble recombinant glycoproteins with predefined glycosylation: application to the crystallization of the T-cell glycoprotein CD2. Prot. Eng. 6, 229–232.

    Article  CAS  Google Scholar 

  41. Chrencik, J. E., Patny, A., Leung, I. K., Korniski, B., Emmons T. L. et al. (2010) Structural and thermodynamic characterization of the TYK2 and JAK3 kinase domains in complex with CP-690550 and CMP-6. J Mol Biol 400, 413–433.

    Article  PubMed  CAS  Google Scholar 

  42. Panneerselvam, S., Marx, A., Mandelkow, E. M., and Mandelkow, E. (2006) Structure of the catalytic and ubiquitin-associated domains of the protein kinase MARK/Par-1. Structure 14, 173–183.

    Article  PubMed  CAS  Google Scholar 

  43. Marx, A., Nugoor, C., Panneerselvam, S. and Mandelkow, E. (2010) Structure and function of polarity-inducing kinase family MARK/Par-1 within the branch of AMPK/Snf1-related kinases. FASEB J. 24, 1637–1648.

    Article  PubMed  CAS  Google Scholar 

  44. Sallach, R. E., Conticello, V. P. and Chalkof, E. L. (2009) Expression of a recombinant elastin-like protein in Pichia pastoris . Biotechnol. Prog. 25, 1810–1818.

    PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Ronald V. Swanson .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media, LLC

About this protocol

Cite this protocol

Edavettal, S.C., Hunter, M.J., Swanson, R.V. (2012). Genetic Construct Design and Recombinant Protein Expression for Structural Biology. In: Tari, L. (eds) Structure-Based Drug Discovery. Methods in Molecular Biology, vol 841. Humana Press. https://doi.org/10.1007/978-1-61779-520-6_2

Download citation

  • DOI: https://doi.org/10.1007/978-1-61779-520-6_2

  • Published:

  • Publisher Name: Humana Press

  • Print ISBN: 978-1-61779-519-0

  • Online ISBN: 978-1-61779-520-6

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics