Measuring the Conformational Stability of a Protein by Hydrogen Exchange

  • Beatrice M. P. Huyghues-Despointes
  • C. Nick Pace
  • S. Walter Englander
  • J. Martin Scholtz
Part of the Methods in Molecular Biology™ book series (MIMB, volume 168)


Measuring the conformational stability of a protein is one key to solving the protein folding problem. It is also of practical importance for answering questions such as these:

  1. 1.

    How stable is a protein under physiological conditions?

  2. 2.

    How does the stability depend on temperature, pH, and salt concentration?

  3. 3.

    Can the stability be increased by osmolytes?

  4. 4.

    Can the stability be increased by ligands that bind the native state?

  5. 5.

    Does an amino-acid substitution increase or decrease the stability?



Nuclear Magnetic Resonance Conformational Stability Amide Proton Hydrogen Exchange Nuclear Overhauser Effect 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. 1.
    Pace, C. N., Shirley, B. A., McNutt, M., and Gajiwala, K. (1996) Forces contributing to the conformational stability of proteins. FASEB J. 76, 75–83.Google Scholar
  2. 2.
    Pace, C. N. (1975) The stability of globular proteins. CRC Crit. Rev. Biochem. 3, 1–43.PubMedCrossRefGoogle Scholar
  3. 3.
    Freire, E. (1995) Thermal denaturation methods in the study of protein folding. Methods Enzymol. 259, 144–168.PubMedCrossRefGoogle Scholar
  4. 4.
    Pace, C. N. and Scholtz, J. M. (1997) Measuring the conformational stability of a protein, in Protein Structure. A Practical Approach, (Creighton, T. E., ed.), Oxford University Press Inc., New York, NY, pp.299–321.Google Scholar
  5. 5.
    Jaenicke, R. (1987) Folding and association of proteins. Prog. Biophys. Mol. Biol. 49, 117–237.PubMedCrossRefGoogle Scholar
  6. 6.
    Makhatadze, G. I. (1999) Thermodynamics of protein interactions with urea and guanidinium hydrochloride. J. Phys. Chem. 103, 4781–4785.Google Scholar
  7. 7.
    Chamberlain, A. K. and Marqusee, S. (1997) Touring the landscapes: partially folded proteins examined by hydrogen exchange. Structure 5, 859–863.PubMedCrossRefGoogle Scholar
  8. 8.
    Hvidt, A. and Neilson, S. O. (1966) Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287–386.PubMedCrossRefGoogle Scholar
  9. 9.
    Bai, Y., Milne, J. S., Mayre, L., and Englander, S. W. (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75–86.PubMedCrossRefGoogle Scholar
  10. 10.
    Loh, S. N., Rohl, C. A., Kiefhaber, T., and Baldwin, R. L. (1996) A general two-process model describes the hydrogen exchange behavior of RNase A in unfolding conditions. Proc. Natl. Acad. Sci. USA 93, 1982–1987.PubMedCrossRefGoogle Scholar
  11. 11.
    Qian, H. and Chan, S. I. (1999) Hydrogen exchange kinetics of proteins in denaturants: a generalized two-process model. J. Mol. Biol. 286, 607–616.PubMedCrossRefGoogle Scholar
  12. 12.
    Huyghes-Despointe, B. M. P., Scholtz, J. M., and Pace, C. N. (1999) Protein conformational stabilities can be determined from hydrogen-exchange rates. Nat. Struct. Biol. 6, 910–912.CrossRefGoogle Scholar
  13. 13.
    Connelly, G. P., Bai, Y., Jeng, M.-F. amd Englander, S. W. (1993) Isotope effect in peptide group hydrogen exchange. Proteins 17, 87–92.PubMedCrossRefGoogle Scholar
  14. 14.
    Molday, R. S., Englander, S. W., and Kallen, R. G. (1972) Primary structure effects on peptide group hydrogen exchange. Biochemistry 11, 150–158.PubMedCrossRefGoogle Scholar
  15. 15.
    Bai, Y., Milne, J. S. Mayne, L., and Englander, S. W. (1994) Protein stability parameters measured by hydrogen exchange. Proteins 20, 4–14.PubMedCrossRefGoogle Scholar
  16. 16.
    Roder, H., Wagner, G., and Wüthrich, K. (1985) Amide proton exchange in proteins by EX1 kinetics: studies of the basic pancreatic trypsin inhibitor at variable pD and temperature. Biochemistry 24, 7396–7407.PubMedCrossRefGoogle Scholar
  17. 17.
    Tüchsen, E. and Woodward, C. (1987) Biochemistry 26, 8073–8078.PubMedCrossRefGoogle Scholar
  18. 18.
    Swint-Kruse, L. and Robertson, A. D. (1996) Temperature and pH dependences of hydrogen exchange and global stability for ovomu-coid third domain. Biochemistry 35, 171–180.PubMedCrossRefGoogle Scholar
  19. 19.
    Mayo, S. L. and Baldwin, R. L. (1993) Guanidinium chloride induction of partial unfolding in amide proton exchange in RNase A. Science 262, 873–876.Google Scholar
  20. 20.
    Bai, Y., Sosnick, T. R., Mayne, L., and Englander, S. W. (1995) Protein folding intermediates: native state hydrogen exchange. Science 269, 192–197.PubMedCrossRefGoogle Scholar
  21. 21.
    Chamberlain, A. K., Handel, T. M., and Marqusee, S. (1996) Detection of rare partially folded molecules in equilibrium with the native conformation of RNase H. Nat. Struct. Biol. 3, 782–787.PubMedCrossRefGoogle Scholar
  22. 22.
    Grantcharova, V. P. and Baker, D. (1997) Folding dynamics of the src SH3 domain. Biochemistry 36, 15,685–15,692.PubMedCrossRefGoogle Scholar
  23. 23.
    Yi, Q., Scalley, M. L., Simons, K. T., Gladwin, S. T., and Baker, D. (1997) Characterization of the free energy spectrum of peptostreptococcal protein L. Fold. Des. 2, 271–279.PubMedCrossRefGoogle Scholar
  24. 24.
    Bhuyan, A. K. and Udgaonkar, J. B. (1998) Two structural subdomains of barstar detected by rapid mixing NMR measurement of amide hydrogen exchange. Proteins 30, 295–308.PubMedCrossRefGoogle Scholar
  25. 25.
    Fuentes, E. J. and Wand, A. J. (1998) Dynamics and stability of apocytochrome b562 examined by hydrogen exchange. Biochemistry 37, 3687–3698.PubMedCrossRefGoogle Scholar
  26. 26.
    Fuentes, E. J. and Wand, A. J. (1998) Local stability and dynamics of apocytochrome B562 examined by the dependence of hydrogen exchange on hydrostatic Pressure. Biochemistry 37, 9877–9883.PubMedCrossRefGoogle Scholar
  27. 27.
    Huyghes-Despointe, B. M. P., Langhoest, U., Steyaert, J., Pace, C. N., and Scholtz, J. M. (1999) Hydrogen-exchange stabilities of RNase T1 and variants with buried and solvent-exposed Ala→Gly mutations in the helix. Biochemistry Google Scholar
  28. 28.
    Pace, C. N., Laurents, D. V., and Thomson, J. A. (1990) pH dependence of the urea and guanidine hydrochloride denaturation of ribo-nuclease A and ribonuclease T1. Biochemistry 29, 2564–2572.PubMedCrossRefGoogle Scholar
  29. 29.
    Glasoe, P. F. and Long, F. A. (1960) Use of glass electrodes to measure acidities in deuterium oxide. J. Phys. Chem. 64, 188–193.CrossRefGoogle Scholar
  30. 30.
    Oas, T. G. and Toone, E. J. (1997) Thermodynamic solvent isotope effects and molecular hydrophobicity, in Adv. Biophys. Chem. (Bush, C., ed.), JAI Press, Inc., Greenwich, CT pp. 1–52.Google Scholar
  31. 31.
    Makhatadze, G. I., Clore, G. M., and Gronenborn, A. M. (1995) Solvent isotope effect of protein stability. Nat. Struct. Biol. 2, 852–855.PubMedCrossRefGoogle Scholar
  32. 32.
    Jabs, A., Weiss, M. S., and Hilgenfeld, R. (1999) Non-proline cis peptide bonds in proteins. J. Mol. Biol. 286, 291–304.PubMedCrossRefGoogle Scholar
  33. 33.
    Reimer, U., Scherer, G., Drewello, M., Kruber, S., Schutkowski, M., and Fischer, G. (1998) Side-chain effects of peptidyl-prolyl cis/trans isomer-ization. J. Mol. Biol. 279, 449–460.PubMedCrossRefGoogle Scholar
  34. 34.
    Sharp, K. A. and Englander, S. W. (1994) How much is a stabilizing bond worth? Trends Biochem. Sci. 19, 526–529.CrossRefGoogle Scholar
  35. 35.
    Kragelund, B. B., Knudsen, J., and Poulsen, F. M. (1995) Local perturbations by ligand binding of hydrogen deuterium exchange kinetics in a four-helix bundle protein, acyl coenzyme A binding protein (ACBP). J. Mol. Biol. 250, 695–706.PubMedCrossRefGoogle Scholar
  36. 36.
    Li, R. and Woodward, C. (1999) Hydrogen exchange and protein folding. Protein Sci. 8, 1571–1591.PubMedCrossRefGoogle Scholar
  37. 37.
    Neira, J. L., Sevilla, P., Menéndez, M., Bruix, M., and Rico, M. (1999) Hydrogen exchange in ribonuclease A and ribonuclease S: evidence for residual structure in the unfolded state under native conditions. J. Mol. Biol. 285, 627–643.PubMedCrossRefGoogle Scholar
  38. 38.
    Sivaraman, T., Kumar, T. K. S., and Yu, C. (1999) Investigation of the structural stability of cardiotoxin analogue III from the taiwan cobra by hydrogen-deuterium exchange kinetics. Biochemistry 38, 9899–9905.PubMedCrossRefGoogle Scholar
  39. 39.
    Chakshusmathi, G., Ratnaparkhi, G. S., Madhu, P. K., and Vara-darajan, R. (1999) Native-state hydrogen-exchange studies of a fragment complex can provide structural information about the isolated fragments. Proc. Natl. Acad. Sci. USA 96, 7899–7904.PubMedCrossRefGoogle Scholar
  40. 40.
    Llinás, M., et al. (1999) The energetics of T4 lysozyme reveal a hier-archy of conformations. Nat. Struct. Biol. 6, 1072–1076.PubMedCrossRefGoogle Scholar
  41. 41.
    Loh, S. N., Prehoda, K. E., Wang, J., and Markley, J. L. (1993) Hydrogen exchange in unligated and ligated staphylococcal nuclease. Biochemistry 32, 11,022–11,028.PubMedCrossRefGoogle Scholar
  42. 42.
    Wrabl, J. and Shortle, D. (1999) A model of the changes in denatured state structure underlying m value effects in staphylococcal nuclease. Nat. Struct. Biol. 6, 876–883.PubMedCrossRefGoogle Scholar
  43. 43.
    Brandts, J. F., Halvorson, H. R., and Brennan, M. (1975) Consideration of the possibility that the slow step in protein denaturation reactions is due to cis-trans isomerization of proline residues. Biochemistry 14, 4953–4963.PubMedCrossRefGoogle Scholar

Copyright information

© Humana Press Inc. 2001

Authors and Affiliations

  • Beatrice M. P. Huyghues-Despointes
  • C. Nick Pace
  • S. Walter Englander
  • J. Martin Scholtz

There are no affiliations available

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