Quantifying Protein-Carbohydrate Interactions Using Liquid Sample Desorption Electrospray Ionization Mass Spectrometry

  • Yuyu Yao
  • Km Shams-Ud-Doha
  • Rambod Daneshfar
  • Elena N. Kitova
  • John S. Klassen
Research Article

Abstract

The application of liquid sample desorption electrospray ionization mass spectrometry (liquid sample DESI-MS) for quantifying protein–carbohydrate interactions in vitro is described. Association constants for the interactions between lysozyme and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc and β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc, and between a single chain antibody and α-D-Galp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 and β-D-Glcp-(1 → 2)-[α-D-Abep-(1 → 3)]-α-D-Manp-OCH3 measured using liquid sample DESI-MS were found to be in good agreement with values measured by isothermal titration calorimetry and the direct ESI-MS assay. The reference protein method, which was originally developed to correct ESI mass spectra for the occurrence of nonspecific ligand-protein binding, was shown to reliably correct liquid sample DESI mass spectra for nonspecific binding. The suitability of liquid sample DESI-MS for quantitative binding measurements carried out using solutions containing high concentrations of the nonvolatile biological buffer phosphate buffered saline (PBS) was also explored. Binding of lysozyme to β-D-GlcNAc-(1 → 4)-β-D-GlcNAc-(1 → 4)-D-GlcNAc in aqueous solutions containing up to 1× PBS was successfully monitored using liquid sample DESI-MS; with ESI-MS the binding measurements were limited to concentrations less than 0.02 X PBS.

Graphical Abstract

Keywords

Protein Carbohydrate Affinity Liquid sample desorption electrospray ionization mass spectrometry 

Notes

Acknowledgments

The authors acknowledge the Alberta Glycomics Center and the Natural Sciences and Engineering Research Council of Canada for funding, and thank Professor D. Bundle (University of Alberta) for generously donating oligosaccharides used in this study.

Supplementary material

13361_2014_1008_MOESM1_ESM.docx (4.7 mb)
ESM 1(DOCX 4825 kb)

References

  1. 1.
    Bewley, C.A.: Protein–Carbohydrate Interactions in Infectious Diseases. RSC Publishing, Cambridge, UK (2006)CrossRefGoogle Scholar
  2. 2.
    Disney, M.D., Seeberger, P.H.: The use of carbohydrate microarrays to study carbohydrate-cell interactions and to detect pathogens. Chem. Biol. 11, 1701–1707 (2004)CrossRefGoogle Scholar
  3. 3.
    Leavitt, S., Freire, E.: Direct measurement of protein binding energetics by isothermal titration calorimetry. Curr. Opin. Struct. Biol. 11, 560–566 (2001)CrossRefGoogle Scholar
  4. 4.
    Frostell, Å., Vinterbäck, L., Sjöbom, H.: Protein–Ligand Interactions Using SPR Systems. In: Protein–Ligand Interactions, Williams, M.A., Daviter, T., Eds. Humana Press: 1008, 139–165 (2013)Google Scholar
  5. 5.
    Zech, S.G., Olejniczak, E., Hajduk, P., Mack, J., McDermott, A.E.: Characterization of protein − ligand interactions by high-resolution solid-state NMR spectroscopy. J. Am. Soc. Mass Spectrom. 126, 13948–13953 (2004)Google Scholar
  6. 6.
    Orosz, F., Ovadi, J.: A simple method for the determination of dissociation constants by displacement ELISA. J. Immunol. Methods 270, 155–162 (2002)CrossRefGoogle Scholar
  7. 7.
    El-Hawiet, A., Kitova, E.N., Klassen, J.S.: Quantifying protein interactions with isomeric carbohydrate ligands using a catch and release electrospray ionization-mass spectrometry assay. Anal. Chem. 85, 7637–7644 (2013)CrossRefGoogle Scholar
  8. 8.
    Lin, H., Kitova, E.N., Klassen, J.S.: Measuring positive cooperativity using the direct ESI-MS assay. Cholera toxin B subunit homopentamer binding to GM1 pentasaccharide. J. Am. Soc. Mass Spectrom. 25, 104–110 (2014)CrossRefGoogle Scholar
  9. 9.
    Han, L., Kitov, P.I., Kitova, E.N., Tan, M., Wang, L., Xia, M., Jiang, X., Klassen, J.S.: Affinities of recombinant norovirus P dimers for human blood group antigens. Glycobiology 23, 276–285 (2013)CrossRefGoogle Scholar
  10. 10.
    El-Hawiet, A., Kitova, E.N., Arutyunov, D., Szymanski, C.M., Klassen, J.S.: Quantifying ligand binding to large protein complexes using electrospray ionization mass spectrometry. Anal. Chem. 84, 3867–3870 (2012)CrossRefGoogle Scholar
  11. 11.
    El-Hawiet, A., Kitova, E.N., Klassen, J.S.: Quantifying carbohydrate–protein interactions by electrospray ionization mass spectrometry analysis. Biochemistry 51, 4244–4253 (2012)CrossRefGoogle Scholar
  12. 12.
    Daniel, J.M., Friess, S.D., Rajagopalan, S., Wendt, S., Zenobi, R.: Quantitative determination of noncovalent binding interactions using soft ionization mass spectrometry. Int. J. Mass Spectrom. 216, 1–27 (2002)CrossRefGoogle Scholar
  13. 13.
    Kitova, E.N., El-Hawiet, A., Schnier, P.D., Klassen, J.S.: Reliable determinations of protein–ligand interactions by direct ESI-MS measurements. Are we there yet? J. Am. Soc. Mass Spectrom. 23, 431–441 (2012)CrossRefGoogle Scholar
  14. 14.
    El-Hawiet, A., Kitova, E.N., Liu, L., Klassen, J.S.: Quantifying labile protein–ligand interactions using electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 21, 1893–1899 (2010)Google Scholar
  15. 15.
    Deng, L., Sun, N., Kitova, E.N., Klassen, J.S.: Direct quantification of protein-metal ion affinities by electrospray ionization mass spectrometry. Anal. Chem. 82, 2170–2174 (2010)CrossRefGoogle Scholar
  16. 16.
    El-Hawiet, A., Shoemaker, G.K., Daneshfar, R., Kitova, E.N., Klassen, J.S.: Applications of a catch and release electrospray ionization mass spectrometry assay for carbohydrate library screening. Anal. Chem. 84, 50–58 (2011)CrossRefGoogle Scholar
  17. 17.
    Loo, J.A.: Studying noncovalent protein complexes by electrospray ionization mass spectrometry. Mass Spectrom. Rev. 16, 1–23 (1997)CrossRefGoogle Scholar
  18. 18.
    Wang, W., Kitova, E.N., Klassen, J.S.: Influence of solution and gas phase processes on protein − carbohydrate binding affinities determined by nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 75, 4945–4955 (2003)CrossRefGoogle Scholar
  19. 19.
    Kebarle, P.: A brief overview of the present status of the mechanisms involved in electrospray mass spectrometry. J. Mass Spectrom. 35, 804–817 (2000)CrossRefGoogle Scholar
  20. 20.
    Banerjee S., Mazumdar S.: Electrospray ionization mass spectrometry: a technique to access the information beyond the molecular weight of the analyte. Int. J. Anal. Chem. 2012, 1–40 (2012)Google Scholar
  21. 21.
    Sterling, H., Batchelor, J., Wemmer, D., Williams, E.: Effects of buffer loading for electrospray ionization mass spectrometry of a noncovalent protein complex that requires high concentrations of essential salts. J. Am. Soc. Mass Spectrom. 21, 1045–1049 (2010)CrossRefGoogle Scholar
  22. 22.
    Yang, P., Cooks, R.G., Ouyang, Z.: Gentle protein ionization assisted by high-velocity gas flow. Anal. Chem. 77, 6174–6183 (2005)CrossRefGoogle Scholar
  23. 23.
    Takáts, Z., Wiseman, J.M., Gologan, B., Cooks, R.G.: Mass spectrometry sampling under ambient conditions with desorption electrospray ionization. Science 306, 471–473 (2004)CrossRefGoogle Scholar
  24. 24.
    Shin, Y.-S., Drolet, B., Mayer, R., Dolence, K., Basile, F.: Desorption electrospray ionization-mass spectrometry of proteins. Anal. Chem. 79, 3514–3518 (2007)CrossRefGoogle Scholar
  25. 25.
    Lu, X., Ning, B., He, D., Huang, L., Yue, X., Zhang, Q., Huang, H., Liu, Y., He, L., Ouyang, J.: High throughput screening of high-affinity ligands for proteins with anion-binding sites using desorption electrospray ionization (DESI) mass spectrometry. J. Am. Soc. Mass Spectrom. 25, 454–463 (2014)CrossRefGoogle Scholar
  26. 26.
    Miao, Z., Chen, H.: Direct analysis of liquid samples by desorption electrospray ionization-mass spectrometry (DESI-MS). J. Am. Soc. Mass Spectrom. 20, 10–19 (2009)CrossRefGoogle Scholar
  27. 27.
    Liu, P., Zhang, J., Ferguson, C.N., Chen, H., Loo, J.A.: Measuring protein–ligand interactions using liquid sample desorption electrospray ionization mass spectrometry. Anal. Chem. 85, 11966–11972 (2013)CrossRefGoogle Scholar
  28. 28.
    Ferguson, C.N., Benchaar, S., Miao, Z., Loo, J.A., Chen, H.: Direct ionization of large proteins and protein complexes by desorption electrospray ionization-mass spectrometry. Anal. Chem. 83, 6468–6473 (2011)CrossRefGoogle Scholar
  29. 29.
    Moore, B.N., Hamdy, O., Julian, R.R.: Protein structure evolution in liquid DESI as revealed by selective noncovalent adduct protein probing. Int. J. Mass Spectrom. 330/332, 220–225 (2012)CrossRefGoogle Scholar
  30. 30.
    Takáts, Z., Wiseman, J.M., Cooks, R.G.: Ambient mass spectrometry using desorption electrospray ionization (DESI): Instrumentation, Mechanisms, and Applications in Forensics, Chemistry, and Biology. J. Mass Spectrom. 40, 1261–1275 (2005)CrossRefGoogle Scholar
  31. 31.
    Veros, C.T., Oldham, N.J.: Quantitative determination of lysozyme-ligand binding in the solution and gas phases by electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom. 21, 3505–3510 (2007)CrossRefGoogle Scholar
  32. 32.
    Sun, N., Soya, N., Kitova, E., Klassen, J.: Nonspecific interactions between proteins and charged biomolecules in electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 21, 472–481 (2010)CrossRefGoogle Scholar
  33. 33.
    Jecklin, M., Touboul, D., Bovet, C., Wortmann, A., Zenobi, R.: Which electrospray-based ionization method best reflects protein–ligand interactions found in solution? A comparison of ESI, nanoESI, and ESSI for the determination of dissociation constants with mass spectrometry. J. Am. Soc. Mass Spectrom. 19, 332–343 (2008)CrossRefGoogle Scholar
  34. 34.
    Zdanov, A., Li, Y., Bundle, D.R., Deng, S.J., MacKenzie, C.R., Narang, S.A., Young, N.M., Cygler, M.: Structure of a single-chain antibody variable domain (Fv) fragment complexed with a carbohydrate antigen at 1.7-A resolution. Proc. Natl. Acad. Sci. U. S. A. 91, 6423–6427 (1994)CrossRefGoogle Scholar
  35. 35.
    Rademacher, C., Shoemaker, G.K., Kim, H.-S., Zheng, R.B., Taha, H., Liu, C., Nacario, R.C., Schriemer, D.C., Klassen, J.S., Peters, T., Lowary, T.L.: Ligand specificity of CS-35, a monoclonal antibody that recognizes mycobacterial lipoarabinomannan: a model system for oligofuranoside-protein recognition. J. Am. Chem. Soc. 129, 10489–10502 (2007)CrossRefGoogle Scholar
  36. 36.
    Wang, W., Kitova, E.N., Klassen, J.S.: Nonspecific protein − carbohydrate complexes produced by nanoelectrospray ionization. Factors influencing their formation and stability. Anal. Chem. 77, 3060–3071 (2005)CrossRefGoogle Scholar
  37. 37.
    Sun, J., Kitova, E.N., Wang, W., Klassen, J.S.: Method for distinguishing specific from nonspecific protein − ligand complexes in nanoelectrospray ionization mass spectrometry. Anal. Chem. 78, 3010–3018 (2006)CrossRefGoogle Scholar
  38. 38.
    Daneshfar, R., Kitova, E.N., Klassen, J.S.: Determination of protein–ligand association thermochemistry using variable-temperature nanoelectrospray mass spectrometry. J. Am. Chem. Soc. 126, 4786–4787 (2004)CrossRefGoogle Scholar
  39. 39.
    Kitova, E.N., El-Hawiet, A., Klassen, J.S.: Screening carbohydrate libraries for protein interactions using the direct ESI-MS assay. Applications to libraries of unknown concentration. J. Am. Soc. Mass Spectrom. (2014). doi:10.1007/s13361-014-0964-2
  40. 40.
    Schindler, M., Assaf, Y., Sharon, N., Chipman, D.M.: Mechanism of lysozyme catalysis: role of ground-state strain in subsite D in hen egg-white and human lysozymes. Biochemistry 16, 423–431 (1977)CrossRefGoogle Scholar
  41. 41.
    Hunter, E.P., Lias, S.G.: Evaluated gas phase basicities and proton affinities of molecules: an update. J. Phys. Chem. Ref. Data 27, 413–656 (1998)CrossRefGoogle Scholar
  42. 42.
    Hopper, J.T.S., Sokratous, K., Oldham, N.J.: Charge state and adduct reduction in electrospray ionization-mass spectrometry using solvent vapor exposure. Anal. Biochem. 421, 788–790 (2012)CrossRefGoogle Scholar
  43. 43.
    Hopper, J.T.S., Oldham, N.J.: Alkali metal cation-induced destabilization of gas-phase protein–ligand complexes: consequences and prevention. Anal. Chem. 83, 7472–7479 (2011)CrossRefGoogle Scholar
  44. 44.
    Venter, A., Sojka, P.E., Cooks, R.G.: Droplet dynamics and ionization mechanisms in desorption electrospray ionization mass spectrometry. Anal. Chem. 78, 8549–8555 (2006)CrossRefGoogle Scholar
  45. 45.
    Miao, Z., Wu, S., Chen, H.: The study of protein conformation in solution via direct sampling by desorption electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 21, 1730–1736 (2010)CrossRefGoogle Scholar

Copyright information

© American Society for Mass Spectrometry 2014

Authors and Affiliations

  • Yuyu Yao
    • 1
  • Km Shams-Ud-Doha
    • 1
  • Rambod Daneshfar
    • 1
  • Elena N. Kitova
    • 1
  • John S. Klassen
    • 1
  1. 1.Alberta Glycomics Center and Department of ChemistryUniversity of AlbertaEdmontonCanada

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