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Elucidating Structure, Stability, and Conformational Distributions during Protein Aggregation with Hydrogen Exchange and Mass Spectrometry

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Abstract

Engineering processes and proteins to control aggregation behavior has been hindered by the lack of detailed information about the mechanisms of protein aggregation. In the studies described here, hydrogen-deuterium isotope exchange detected by mass spectrometry (HX-MS) has revealed kinetic, thermodynamic, and structural aspects of model and pharmaceutical protein unfolding under destabilizing, aggregation conditions. First, hen egg white lysozyme was studied during salt-induced precipitation. Bimodal mass distributions in the HX-MS-labeling experiments for precipitates indicated that lysozyme continues to exhibit two-state unfolding behavior under these conditions, with the denatured state being only partially unfolded, resembling molten globule states observed in other folding studies.

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References

  1. 1. K. A. Dill and H. S. Chan, From Levinthal to pathways to funnels, Nature Struct. Biol. 4(1), 10–9 (1997).

    Article  PubMed  CAS  Google Scholar 

  2. 2. H. S. Chan and K. A. Dill, Protein folding in the landscape perspective: chevron plots and non-Arrhenius kinetics, Proteins 30(1), 2–33 (1998).

    Article  PubMed  CAS  Google Scholar 

  3. 3. S. B. Ozkan, I. Bahar, and K. A. Dill, Transition states and the meaning of phi-values in protein folding kinetics, Nature Struct. Biol. 8(9), 765–769 (2001).

    Article  PubMed  CAS  Google Scholar 

  4. 4. S. B. Ozkan, K. A. Dill, and I. Bahar, Computing the transition state populations in simple protein models, Biopolymers 68(1), 35–46 (2003).

    Article  PubMed  CAS  Google Scholar 

  5. 5. A. Hvidt, and S. O. Nielsen, Hydrogen exchange in proteins, Adv. Protein Chem. 21, 287–386 (1966).

    Article  PubMed  CAS  Google Scholar 

  6. 6. G. Wagner, and K. Wuthrich, Amide protein exchange and surface conformation of the basic pancreatic trypsin inhibitor in solution. Studies with two-dimensional nuclear magnetic resonance, J. Mol. Biol. 160(2), 343–61 (1982).

    Article  PubMed  CAS  Google Scholar 

  7. 7. H. Roder and K. Wüthrich, Protein folding kinetics by combined use of rapid mixing techniques and NMR observation of individual amide protons, Proteins 1(1):34–42 (1986).

    Article  PubMed  CAS  Google Scholar 

  8. 8. K. Roder, G. A. Elöve, and S. W. Englander, Structural characterization of folding intermediates in cytochrome c by H-exchange labelling and proton NMR, Nature 335, 700–704 (1988).

    Article  PubMed  CAS  Google Scholar 

  9. 9. S. W. Englander, Protein folding intermediates and pathways studied by hydrogen exchange, Annu. Rev. Biophys. Biomol. Struct. 29, 213–38 (2000).

    Article  PubMed  CAS  Google Scholar 

  10. 10. A. Miranker, C. V. Robinson, S. E. Radford, R. T. Aplin, and C. M. Dobson, Detection of transient protein folding populations by mass spectrometry, Science 262(5135), 896–900 (1993).

    Article  PubMed  CAS  Google Scholar 

  11. 11. A. N. Hoofnagle, K. A. Resing, and N. G. Ahn, Protein analysis by hydrogen exchange mass spectrometry, Annu. Rev. Biophys. Biomol. Struct. (2003).

    Google Scholar 

  12. 12. S. A. Tobler, N. E. Sherman, and E. J. Fernandez, Tracking lysozyme unfolding during salt-induced precipitation with hydrogen exchange and mass spectrometry, Biotech. Bioeng. 71(3), 194–207 (2001).

    Article  CAS  Google Scholar 

  13. 13. S. A. Tobler and E. J. Fernandez, Structural features of interferon-gamma aggregation revealed by hydrogen exchange, Protein Sci. 11(6), 1340–1352 (2002).

    Article  PubMed  CAS  Google Scholar 

  14. 14. S. A. Tobler, B. H. Holmes, M. E. Cromwell, and E. J. Fernandez, Benzyl alcohol-induced aggregation of interferon-γ: A study by hydrogen-deuterium isotope exchange, J. Pharm. Sci. 93, 1605–1617 (2004).

    Article  PubMed  CAS  Google Scholar 

  15. 15. I. Kheterpal, S. Zhou, K. D. Cook, and R. Wetzel, A beta-amyloid fibrils possess a core structure highly resistant to hydrogen exchange, Proc. Natl. Acad. Sci. USA 97(25), 13597–13601 (2000).

    Article  PubMed  CAS  Google Scholar 

  16. 16. J. H. Ippel, A. Olofsson, J. Schleucher, E. Lundgren, and S. S. Wijmenga, Probing solvent accessibility of amyloid fibrils by solution NMR spectroscopy, Proc. Natl. Acad. Sci. USA 99(13), 8648–8653 (2002).

    Article  PubMed  CAS  Google Scholar 

  17. 17. S. S. Wang, S. A. Tobler, T. A. Good, and E. J. Fernandez, Hydrogen exchange-mass spectrometry analysis of beta-amyloid peptide structure, Biochemistry 42(31), 9507–9514 (2003).

    Article  PubMed  CAS  Google Scholar 

  18. 18. M. Kraus, M. Bienert, and E. Krause, Hydrogen exchange studies on Alzheimer's amyloid-beta peptides by mass spectrometry using matrix-assisted laser desorption/ionization and electrospray ionization, Rapid Commun. Mass Spectrom. 17(3), 222–228 (2003).

    Article  PubMed  CAS  Google Scholar 

  19. 19. Y. S. Kim, J. S. Wall, J. Meyer, C. Murphy, T. W. Randolph, M. C. Manning, A. Solomon, and J. F. Carpenter, Thermodynamic modulation of light chain amyloid fibril formation, J. Biol. Chem. 275(3), 1570–1574 (2000).

    Article  PubMed  CAS  Google Scholar 

  20. 20. S. E. Radford, M. Buck, K. D. Topping, C. M. Dobson, and P. A. Evans, Hydrogen exchange in native and denatured states of hen egg-white lysozyme, Proteins 14(2), 237–248 (1992).

    Article  PubMed  CAS  Google Scholar 

  21. 21. L. Pershina and A. Hvidt, A study by the hydrogen-exchange method of the complex formed between the basic pancreatic trypsin inhibitor and trypsin, Eur. J. Biochem. 48(2), 339–344 (1974).

    Article  PubMed  CAS  Google Scholar 

  22. 22. Y. Paterson, S. W. Englander, and H. Roder, An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR, Science 249, 755–759 (1990).

    Article  PubMed  CAS  Google Scholar 

  23. 23. K. Linderstrøm-Lang, Deterium exchange between peptides and water, Chem. Soc. (London) Spec. Publ. 2, 1–20 (1955).

    Google Scholar 

  24. 24. R. S. Molday, S. W. Englander, and R. G. Kallen, Primary structure effects on peptide group hydrogen exchange, Biochemistry 11(2), 150–158 (1972).

    Article  PubMed  CAS  Google Scholar 

  25. 25. Y. Bai, J. S. Milne, L. Mayne, and S. W. Englander, Primary structure effects on peptide group hydrogen exchange. Proteins: Struct. Funct. Genet. 1993;17:75–86.

    Article  CAS  Google Scholar 

  26. 26. S. Ghaemmaghami, M. C. Fitzgerald, and T. G. Oas, A quantitative, high-throughput screen for protein stability, Proc. Natl. Acad. Sci. USA 97(15), 8296–8301 (2000).

    Article  PubMed  CAS  Google Scholar 

  27. 27. Y. Hamuro, S. J. Coales, M. R. Southern, J. F. Nemeth-Cawley, D. D. Stranz, and P. R. Griffin, Rapid analysis of protein structure and dynamics by hydrogen/deuterium exchange mass spectrometry. J. Biomol. Tech. 14(3), 171–182 (2003).

    PubMed  Google Scholar 

  28. 28. K. Wüthrich and G. Wagner, Nuclear magnetic resonance of labile protons in basic pancreatic trypsin inhibitor. J. Mol. Biol. 130, 1–18 (1979).

    Article  PubMed  Google Scholar 

  29. 29. S. T. Chang and E. J. Fernandez, Probing residue-level unfolding during lysozyme precipitation, Biotech. Bioeng. 59(2), 144–155 (1998).

    Article  CAS  Google Scholar 

  30. 30. J. L. McNay and E. J. Fernandez, How does a protein unfold on a reversed-phase liquid chromatography surface? J. Chromatogr. A 849(1), 135–148 (1999).

    Article  CAS  Google Scholar 

  31. 31. Z. Zhang and D. L. Smith, Determination of amide hydrogen exchange by mass spectrometry: A new tool for protein structure elucidation, Protein Sci. 2(4), 522–531 (1993).

    Article  PubMed  CAS  Google Scholar 

  32. 32. Y. Z. Deng, H. Pan, and D. L. Smith, Selective isotope labeling demonstrates that hydrogen exchange at individual peptide amide linkages can be determined by collision-induced dissociation mass spectrometry, J. Am. Chem. Soc. 121(9), 1966–1967 (1999).

    Article  CAS  Google Scholar 

  33. 33. L. Wang and D. L. Smith, Down sizing improves sensitivity 100-fold for hydrogen exchange-mass spectrometry, Anal. Biochem. 314(1), 46–53 (2003).

    Article  PubMed  CAS  Google Scholar 

  34. 34. J. G. Mandell, A. M. Falick, and E. A. Komives, Measurement of amide hydrogen exchange by MALDI-TOF mass spectrometry, Anal. Chem. 70(19), 3987–3995 (1998).

    Article  PubMed  CAS  Google Scholar 

  35. 35. Y. Z. Deng, Z. Q. Zhang, and D. L. Smith, Comparison of continuous and pulsed labeling amide hydrogen exchange/mass spectrometry for studies of protein dynamics. J. Am. Soc. Mass Spec. 10(8), 675–684 (1999).

    Article  CAS  Google Scholar 

  36. 36. S. W. Englander, T. R. Sosnick, J. J. Englander, and L. Mayne, Mechanisms and uses of hydrogen exchange, Curr. Opin. Struct. Biol. 6(1), 18–23 (1996).

    Article  PubMed  CAS  Google Scholar 

  37. 37. J. Clarke and L. S. Itzhaki, Hydrogen exchange and protein folding, Curr. Opin. Struct. Biol. 8(1), 112–118 (1998).

    Article  PubMed  CAS  Google Scholar 

  38. 38. J. G. Mandell, A. M. Falick, and E. A. Komives, Identification of protein-protein interfaces by decreased amide proton solvent accessibility. Proc. Natl. Acad. Sci. USA 95(25), 14705–14710 (1998).

    Article  PubMed  CAS  Google Scholar 

  39. 39. H. Ehring, Hydrogen exchange/electrospray ionization mass spectrometry studies of structural features of proteins and protein/protein interactions, Anal. Biochem. 267(2), 252–259 (1999).

    Article  PubMed  CAS  Google Scholar 

  40. 40. Y. R. Hsu and T. Arakawa, Structural studies on acid unfolding and refolding of recombinant human interferon gamma, Biochemistry 24(27), 7959–7963 (1985).

    Article  PubMed  CAS  Google Scholar 

  41. 41. M. G. Mulkerrin and R. Wetzel, pH dependence of the reversible and irreversible thermal denaturation of gamma interferons, Biochemistry 28(16), 6556–6561 (1989).

    Article  PubMed  CAS  Google Scholar 

  42. 42. X. M. Lam, T. W. Patapoff, and T. H. Nguyen, The effect of benzyl alcohol on recombinant human interferon-gamma, Pharm. Res. 14(6), 725–729 (1997).

    Article  PubMed  CAS  Google Scholar 

  43. 43. B. S. Kendrick, J. L. Cleland, X. Lam, T. Nguyen, T. W. Randolph, M. C. Manning, and J. F. Carpenter, Aggregation of recombinant human interferon gamma: Kinetics and structural transitions, J. Pharm. Sci. 87(9), 1069–1076 (1998).

    Article  PubMed  CAS  Google Scholar 

  44. 44. S. E. Ealick, W. J. Cook, S. Vijay-Kumar, M. Carson, T. L. Nagabhushan, P. P. Trotta, and C. E. Bugg, Three-dimensional structure of recombinant human interferon-gamma, Science 252(5006), 698–702 (1991).

    Article  PubMed  CAS  Google Scholar 

  45. 45. S. Grzesiek, H. Dobeli, R. Gentz, G. Garotta, A. M. Labhardt, and A. Bax, 1H, 13C, and 15N NMR backbone assignments and secondary structure of human interferon-gamma, Biochemistry 31(35), 8180–8190 (1992).

    Article  PubMed  CAS  Google Scholar 

  46. 46. G. Waschutza, V. Li, T. Schafer, D. Schomburg, C. Villmann, H. Zakaria, and B. Otto, Engineered disulfide bonds in recombinant human interferon-gamma: The impact of the N-terminal helix A and the AB-loop on protein stability, Protein Eng. 9(10), 905–912 (1996).

    Article  PubMed  CAS  Google Scholar 

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Fernandez, E.J., Tobler, S.A. (2006). Elucidating Structure, Stability, and Conformational Distributions during Protein Aggregation with Hydrogen Exchange and Mass Spectrometry. In: Misbehaving Proteins. Springer, New York, NY. https://doi.org/10.1007/978-0-387-36063-8_4

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