Advertisement

Biochemistry (Moscow)

, Volume 83, Issue 6, pp 708–716 | Cite as

Construction of Artificial TNF-Binding Proteins Based on the 10th Human Fibronectin Type III Domain Using Bacterial Display

  • L. N. Shingarova
  • L. E. Petrovskaya
  • A. V. Zlobinov
  • S. Sh. Gapizov
  • E. A. Kryukova
  • K. R. Birikh
  • E. F. Boldyreva
  • S. A. Yakimov
  • D. A. Dolgikh
  • M. P. Kirpichnikov
Article
  • 1 Downloads

Abstract

Construction of antibody mimetics on the base of alternative scaffold proteins is a promising strategy for obtaining new products for medicine and biotechnology. The aim of our work was to optimize the cell display system for the 10th human fibronectin type III domain (10Fn3) scaffold protein based on the AT877 autotransporter from Psychrobacter cryohalolentis K5T and to construct new artificial TNF-binding proteins. We obtained a 10Fn3 gene combinatorial library and screened it using the bacterial display method. After expression of the selected 10Fn3 variants in Escherichia coli cells and analysis of their TNF-binding activity, we identified proteins that display high affinity for TNF and characterized their properties.

Keywords

tumor necrosis factor TNF-binding proteins 10th human fibronectin type III domain bacterial display autotransporter from Psychrobacter cryohalolentis K5T 

Abbreviations

ASP

alternative scaffold protein

AT

autotransporter

bioTNF

biotinylated TNF

CDR

complementarity-determining region

10Fn3

10th human fibronectin type III domain

IPTG

isopropyl β-D-1-thiogalactopyranoside

MTT

3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide

PBS

phosphate buffered saline

PMSF

phenyl-methylsulfonyl fluoride

TMB

3,3′,5,5′-tetramethylbenzidine

TNF

tumor necrosis factor

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Kalliolias, G. D., and Ivashkiv, L. B. (2016) TNF biology, pathogenic mechanisms and emerging therapeutic strate-gies, Nat. Rev. Rheumatol., 12, 49–62.CrossRefPubMedGoogle Scholar
  2. 2.
    Efimov, G. A., Kruglov, A. A., Shavarev, D. S., Drutskaya, M. S., and Nedospasov, S. A. (2014) New trends in anticy-tokine therapy, Russ. Zh. Immunol., 8, 706–710.Google Scholar
  3. 3.
    Korneev, K. V., Atretkhany, K.-S. N., Drutskaya, M. S., Grivennikov, S. I., Kuprash, D. V., and Nedospasov, S. A. (2017) TLR-signaling and proinflammatory cytokines as drivers of tumorigenesis, Cytokine, 89, 127–135.CrossRefPubMedGoogle Scholar
  4. 4.
    Kruglov, A. A., Kuchmiy, A., Grivennikov, S. I., Tumanov, A. V., Kuprash, D. V., and Nedospasov, S. A. (2008) Physiological functions of tumor necrosis factor and the consequences of its pathologic overexpression or blockade: mouse models, Cytokine Growth Factor Rev., 19, 231–244.CrossRefPubMedGoogle Scholar
  5. 5.
    Zelova, H., and Hosek, J. (2013) TNF-alpha signalling and inflammation: interactions between old acquaintances, J. Inflamm. Res., 62, 641–651.CrossRefGoogle Scholar
  6. 6.
    Astrakhantseva, I. V., Efimov, G. A., Drutskaya, M. S., Kruglov, A. A., and Nedospasov, S. A. (2014) Modern anti-cytokine therapy of autoimmune diseases, Biochemistry (Moscow), 79, 1308–1321.CrossRefGoogle Scholar
  7. 7.
    Steed, P. M., Tansey, M. G., Zalevsky, J., Zhukovsky, E. A., Desjarlais, J. R., Szymkowski, D. E., Abbott, C., Carmichael, D., Chan, C., Cherry, L., Cheung, P., Chirino, A. J., Chung, H. H., Doberstein, S. K., Eivazi, A., Filikov, A. V., Gao, S. X., Hubert, R. S., Hwang, M., Hyun, L., Kashi, S., Kim, A., Kim, E., Kung, J., Martinez, S. P., Muchhal, U. S., Nguyen, D.-H. T., O’Brien, C., O’Keefe, D., Singer, K., Vafa, O., Vielmetter, J., Yoder, S. C., and Dahiyat, B. I. (2003) Inactivation of TNF signaling by rationally designed dominant-negative TNF variants, Science, 301, 1895–1898.CrossRefPubMedGoogle Scholar
  8. 8.
    Coppieters, K., Dreier, T., Silence, K., Haard, H. D., Lauwereys, M., Casteels, P., Beirnaert, E., Jonckheere, H., Wiele, C. V. D., and Staelens, L. (2006) Formatted anti-tumor necrosis factor α VHH proteins derived from camelids show superior potency and targeting to inflamed joints in a murine model of collagen-induced arthritis, Arthritis Rheum., 54, 1856–1866.CrossRefPubMedGoogle Scholar
  9. 9.
    Tregubchak, T. V., Shekhovtsov, S. V., Nepomnyashchikh, T. S., Peltek, S. E., Kolchanov, N. A., and Shchelkunov, S. N. (2015) TNF-binding domain of the variola virus CrmB pro-tein synthesized in Escherichia coli cells effectively interacts with human TNF, Dokl. Biochem. Biophys., 462, 176–180.CrossRefPubMedGoogle Scholar
  10. 10.
    Shchelkunova, G. A., and Shchelkunov, S. N. (2016) Immunomodulating drugs based on poxviral proteins, BioDrugs, 30, 9–16.CrossRefPubMedGoogle Scholar
  11. 11.
    Vazquez-Lombardi, R., Phan, T. G., Zimmermann, C., Lowe, D., Jermutus, L., and Christ, D. (2015) Challenges and opportunities for non-antibody scaffold drugs, Drug Discov. Today, 20, 1271–1283.CrossRefPubMedGoogle Scholar
  12. 12.
    Kariolis, M. S., Kapur, S., and Cochran, J. R. (2013) Beyond antibodies: using biological principles to guide the development of next-generation protein therapeutics, Curr. Opin. Biotechnol., 24, 1072–1077.CrossRefPubMedGoogle Scholar
  13. 13.
    Stahl, S., Kronqvist, N., Jonsson, A., and Lofblom, J. (2013) Affinity proteins and their generation, J. Chem. Technol. Biotechnol., 88, 25–38.CrossRefGoogle Scholar
  14. 14.
    Deyev, S., Lebedenko, E., Petrovskaya, L., Dolgikh, D., Gabibov, A., and Kirpichnikov, M. (2015) Man-made anti-bodies and immunoconjugates with desired properties: function optimization using structural engineering, Russ. Chem. Rev., 84, 1–26.CrossRefGoogle Scholar
  15. 15.
    Skrlec, K., Strukelj, B., and Berlec, A. (2015) Non-immunoglobulin scaffolds: a focus on their targets, Trends Biotechnol., 33, 408–418.CrossRefPubMedGoogle Scholar
  16. 16.
    Koide, S., Koide, A., and Lipovsek, D. (2012) Target-bind-ing proteins based on the 10th human fibronectin type III domain (10Fn3), Methods Enzymol., 503, 135–156.CrossRefPubMedGoogle Scholar
  17. 17.
    Lipovsek, D. (2011) Adnectins: engineered target-binding protein therapeutics, Protein Eng. Des. Sel., 24, 3–9.CrossRefPubMedGoogle Scholar
  18. 18.
    Petrovskaya, L., Novototskaya-Vlasova, K., Kryukova, E., Rivkina, E., Dolgikh, D., and Kirpichnikov, M. (2015) Cell surface display of cold-active esterase EstPc with the use of a new autotransporter from Psychrobacter cryohalolentis K5T, Extremophiles, 19, 161–170.CrossRefPubMedGoogle Scholar
  19. 19.
    Petrovskaya, L. E., Zlobinov, A. V., Shingarova, L. N., Boldyreva, E. F., Gapizov, S. Sh., Novototskaya-Vlasova, K. A., Rivkina, E. M., Dolgikh, D. A., and Kirpichnikov, M. P. (2018) Fusion with the cold-active esterase facilitates autotransporter-based surface display of the 10th human fibronectin domain in Escherichia coli, Extremophiles, 22, 141–150.CrossRefPubMedGoogle Scholar
  20. 20.
    Shingarova, L., Sagaidak, L., Turetskaia, R., Nedospasov, S., Esipov, D., and Korobko, V. (1996) Human tumor necrosis factor mutants: preparation and some properties, Bioorg. Khim., 22, 243–251.PubMedGoogle Scholar
  21. 21.
    Petrovskaya, L. E., Shingarova, L. N., Kryukova, E. A., Boldyreva, E. F., Yakimov, S. A., Guryanova, S. V., Novoseletsky, V. N., Dolgikh, D. A., and Kirpichnikov, M. P. (2012) Construction of TNF-binding proteins by grafting hypervariable regions of F10 antibody on human fibronectin domain scaffold, Biochemistry (Moscow), 77, 62–70.CrossRefGoogle Scholar
  22. 22.
    Studier, F. W. (2005) Protein production by auto-induction in high-density shaking cultures, Protein Expr. Purif., 41, 207–234.CrossRefPubMedGoogle Scholar
  23. 23.
    Martineau, P. (2010) Affinity measurements by competition ELISA, in Antibody Engineering (Kontermann, R., and Dubel, S., eds.) Springer-Verlag, Berlin-Heidelberg, pp. 657-665.Google Scholar
  24. 24.
    Brockmann, E. C., Akter, S., Savukoski, T., Huovinen, T., Lehmusvuori, A., Leivo, J., Saavalainen, O., Azhayev, A., Lovgren, T., Hellman, J., and Lamminmaki, U. (2011) Synthetic single-framework antibody library integrated with rapid affinity maturation by VL shuffling, Protein Eng. Des. Sel., 24, 691–700.CrossRefPubMedGoogle Scholar
  25. 25.
    Fellouse, F. A., Esaki, K., Birtalan, S., Raptis, D., Cancasci, V. J., Koide, A., Jhurani, P., Vasser, M., Wiesmann, C., Kossiakoff, A. A., Koide, S., and Sidhu, S. S. (2007) High-throughput generation of synthetic anti-bodies from highly functional minimalist phage-displayed libraries, J. Mol. Biol., 373, 924–940.CrossRefPubMedGoogle Scholar
  26. 26.
    Hackel, B. J., Kapila, A., and Wittrup, K. D. (2008) Picomolar affinity fibronectin domains engineered utilizing loop length diversity, recursive mutagenesis, and loop shuf-fling, J. Mol. Biol., 381, 1238–1252.Google Scholar
  27. 27.
    Main, A. L., Harvey, T. S., Baron, M., Boyd, J., and Campbell, I. D. (1992) The three-dimensional structure of the tenth type III module of fibronectin: an insight into RGD-mediated interactions, Cell, 71, 671–678.CrossRefPubMedGoogle Scholar
  28. 28.
    Dickinson, C. D., Veerapandian, B., Dai, X.-P., Hamlin, R. C., Xuong, N.-h., Ruoslahti, E., and Ely, K. R. (1994) Crystal structure of the tenth type III cell adhesion module of human fibronectin, J. Mol. Biol., 236, 1079–1092.CrossRefPubMedGoogle Scholar
  29. 29.
    Gilbreth, R. N., Esaki, K., Koide, A., Sidhu, S. S., and Koide, S. (2008) A dominant conformational role for amino acid diversity in minimalist protein–protein inter-faces, J. Mol. Biol., 381, 407–418.CrossRefPubMedPubMedCentralGoogle Scholar
  30. 30.
    Lofblom, J. (2011) Bacterial display in combinatorial pro-tein engineering, Biotechnol. J., 6, 1115–1129.CrossRefPubMedGoogle Scholar
  31. 31.
    Chen, T. F., de Picciotto, S., Hackel, B. J., and Wittrup, K. D. (2013) Engineering fibronectin-based binding proteins by yeast surface display, Methods Enzymol., 523, 303–326.CrossRefPubMedGoogle Scholar
  32. 32.
    Van Bloois, E., Winter, R. T., Kolmar, H., and Fraaije, M. W. (2011) Decorating microbes: surface display of proteins on Escherichia coli, Trends Biotechnol., 29, 79–86.CrossRefPubMedGoogle Scholar
  33. 33.
    Leo, J. C., Grin, I., and Linke, D. (2012) Type V secretion: mechanism(s) of autotransport through the bacterial outer membrane, Philos. Trans. R. Soc. Lond. B. Biol. Sci., 367, 1088–1101.CrossRefPubMedPubMedCentralGoogle Scholar
  34. 34.
    Leyton, D. L., Rossiter, A. E., and Henderson, I. R. (2012) From self sufficiency to dependence: mechanisms and fac-tors important for autotransporter biogenesis, Nat. Rev. Microbiol., 10, 213–225.CrossRefPubMedGoogle Scholar
  35. 35.
    Nicolay, T., Vanderleyden, J., and Spaepen, S. (2015) Autotransporter-based cell surface display in Gram-nega-tive bacteria, Crit. Rev. Microbiol., 41, 109–123.CrossRefPubMedGoogle Scholar
  36. 36.
    Noinaj, N., Kuszak, A. J., Gumbart, J. C., Lukacik, P., Chang, H., Easley, N. C., Lithgow, T., and Buchanan, S. K. (2013) Structural insight into the biogenesis of β-barrel membrane proteins, Nature, 501, 385–390.CrossRefPubMedPubMedCentralGoogle Scholar
  37. 37.
    Junker, M., Besingi, R. N., and Clark, P. L. (2009) Vectorial transport and folding of an autotransporter viru-lence protein during outer membrane secretion, Mol. Microbiol., 71, 1323–1332.CrossRefPubMedGoogle Scholar
  38. 38.
    Braselmann, E., and Clark, P. L. (2012) Autotransporters: the cellular environment reshapes a folding mechanism to promote protein transport, J. Phys. Chem. Lett., 3, 1063–1071.CrossRefPubMedPubMedCentralGoogle Scholar
  39. 39.
    Plaxco, K. W., Spitzfaden, C., Campbell, I. D., and Dobson, C. M. (1997) A comparison of the folding kinetics and thermodynamics of two homologous fibronectin type III modules, J. Mol. Biol., 270, 763–770.CrossRefPubMedGoogle Scholar
  40. 40.
    Novototskaya-Vlasova, K., Petrovskaya, L., Yakimov, S., and Gilichinsky, D. (2012) Cloning, purification, and char-acterization of a cold adapted esterase produced by Psychrobacter cryohalolentis K5T from Siberian cryopeg, FEMS Microbiol. Ecol., 82, 367–375.Google Scholar
  41. 41.
    Xu, L., Aha, P., Gu, K., Kuimelis, R. G., Kurz, M., Lam, T., Lim, A. C., Liu, H., Lohse, P. A., and Sun, L. (2002) Directed evolution of high-affinity antibody mimics using mRNA display, Chem. Biol., 9, 933–942.CrossRefPubMedGoogle Scholar

Copyright information

© Pleiades Publishing, Ltd. 2018

Authors and Affiliations

  • L. N. Shingarova
    • 1
  • L. E. Petrovskaya
    • 1
  • A. V. Zlobinov
    • 1
    • 2
  • S. Sh. Gapizov
    • 1
    • 2
  • E. A. Kryukova
    • 1
  • K. R. Birikh
    • 1
  • E. F. Boldyreva
    • 1
  • S. A. Yakimov
    • 1
  • D. A. Dolgikh
    • 1
    • 2
  • M. P. Kirpichnikov
    • 1
    • 2
  1. 1.Shemyakin−Ovchinnikov Institute of Bioorganic ChemistryRussian Academy of SciencesMoscowRussia
  2. 2.Lomonosov Moscow State UniversityFaculty of BiologyMoscowRussia

Personalised recommendations