Abstract
It has been apparent for some years that the structures of proteins are dynamic rather than static. For some proteins, dynamics is essential to function (e.g., refs. 1–7). These structural changes have been detected for more than 30 yr by observing hydrogen exchange between peptide amide hydrogens and solvent containing the hydrogen isotopes tritium or deuterium (8–10). Although tritium is no longer used extensively for this purpose, deuterium is widely used in hydrogen exchange studies, especially in multidimensional nuclear magnetic resonance (NMR), in which amide hydrogen signals disappear on deuteration. Since deuterium weighs 1 Dalton more than protium, hydrogen exchange in proteins can also be detected by mass spectrometry. This approach is complementary to NMR in some respects and clearly advantageous in others.
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References
Nimmesgern E., Fox T., Fleming M. A., and Thomson J. A. (1996) Conformational changes and stabilization of inosine 5′-monophosphate dehydrogenase associated with ligand binding and inhibition by mycophenolic acid. J. Biol. Chem. 271, 19,421-19,427.
Creighton T. E. (1992) Protein Folding. W. H. Freeman, New York.
Wilson I. A. and Stanfield R. L. (1994) Antibody-antigen interactions: New structures and new conformational changes. Curr. Opin. Struct. Biol. 4, 857–867.
Spolar R. S. and Record M. T., Jr. (1994) Coupling of local folding to sitespecific binding of proteins to DNA. Science 263, 777–784.
Kriwacki R. W., Hengst L., Tennent L., Reed S. I., and Wright P. E. (1996) Structural studies of p21Waf1/Cip1/Sdi1 in the free and Cdk-2 bound state: conformational disorder mediates binding diversity. Proc. Natl. Acad. Sci. USA 93, 11,504-11,509.
Shen F., Triezenberg S. J., Hensley P., Porter D., and Knutson J. (1996) Transcriptional activation domain of the herpesvirus protein VP16 becomes conformationally constrained upon interaction with basal transcription factors. J. Biol. Chem. 271, 4827–4837.
Alexandrescu A. T., Abeygunawardana C., and Shortle D. (1994) Structure and dynamics of a denatured 131-residue fragment of Staphlococcal nuclease: a heteronuclear study. Biochemistry 33, 1063–1072.
Hvidt A. and Nielsen S. O. (1966) Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287–385.
Woodward C., Simon I., and Tuchsen E. (1982) Hydrogen exchange and the dynamic structure of proteins. Mol. Cell. Biochem. 48, 135–160.
Englander S. W. and Kallenbach N. R. (1984) Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16, 521–655.
Smith D. L., Deng Y., and Zhang Z. (1997) Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry. J. Mass Spectrom. 32, 135–146.
Katta V. and Chait B. T. (1991) Conformational changes in proteins probed by hydrogen-exchange electrospray-ionization mass spectrometry. Rapid Commun. Mass Spectrom. 5, 214–217.
Wang F. and Tang X.-J. (1996) Conformational heterogeneity and stability of apomyoglobin studied by hydrogen-deuterium exchange and electrospray ionization mass spectrometry. Biochemistry 35, 4069–4078.
Ramanathan R., Gross M. L., Zielinski W. L., and Layloff T. P. (1997) Monitoring recombinant protein drugs: a study of insulin by H/D exchange and electrospray ionization mass spectrometry.Anal. Chem. 69, 5142–5145.
Miranker A., Robinson C. V., Radford S. E., Aplin R. T., and Dobson C. M. (1993) Detection of transient protein folding populations by mass spectrometry. Science 262, 896–900.
Engen J. R., Smithgall T. E., Gmeiner W. H., and Smith D. L. (1997) Identification and localization of slow, natural, cooperative unfolding in the hematopoietic cell kinase SH3 domain by amide hydrogen exchange and mass spectrometry. Biochemistry 36, 14,384-14,391.
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.
Anderegg R. J. and Wagner D. S. (1995) Mass spectrometric characterization of a protein ligand interaction. J. Am. Chem. Soc. 117, 1374–1377.
Gross M., Robinson C. V., Mayhew H., Hartl F. U., and Radford S. E. (1996) Significant hydrogen exchange protection in GroEL-bound DHFR is maintained during iterative rounds of substrate cycling. Protein Sci. 5, 2506–2513.
Robinson C. V., Gross M., Eyles S. J., Ewbank J. J., Mayhew M., Hartl F. U., et al. (1994) Conformation of GroEL-bound alpha-lactalbumin probed by mass spectrometry. Nature 372, 646–651.
Zhang Z. and Smith D. L. (1993) Determination of amide hydrogen exchange by mass spectrometry: a new tool for protein structure elucidation. Protein Sci. 2, 522–531.
Rosa J. J. and Richards F. M. (1979) An experimental procedure for increasing the structural resolution of chemical hydrogen-exchange measurements on proteins: application to ribonuclease S peptide. J. Mol. Biol. 133, 399–416.
Rosa J. J. and Richards F. M. (1981) Hydrogen exchange from identified regions of the S-protein component of ribonuclease as a function of temperature, pH, and the binding of S-peptide. J. Mol. Biol. 145, 835–851.
Englander J. J., Rogero J. R., and Englander S. W. (1985) Protein hydrogen exchange studied by the fragment separation method. Anal. Biochem. 147, 234–244.
Dharmasiri K. and Smith D. L. (1997) Regional stability changes in oxidized and reduced cytochrome c located by hydrogen exchange and mass spectrometry. J. Am. Soc. Mass. Spectrom. 8, 1039–1045.
Remigy H., Jaquinod M., Petillot Y., Gagnon J., Cheng H., Xia B., et al. (1997) Probing the influence of mutation on the stability of a ferredoxin by mass spectrometry. J. Protein Chem. 16, 527–532.
Jaquinod M., Guy P., Halgand F., Caffrey M., Fitch J., Cusanovich M., et al. (1996) Stability of Rhodobacter capsulatus ferrocytochrome c2 wild-type and site-directed mutants using hydrogen/deuterium exchange monitored by electrospray ionization mass spectrometry. FEBS Lett. 380, 44–48.
Guy P., Remigy H., Jaquinod M., Bersch B., Blanchard L., Dolla A., et al. (1996) Study of the new stability properties induced by amino acid replacement of tyrosine 64 in cytochrome C553 from Desulfobibrio vulgaris Hildenborough using electrospray ionization mass spectrometry. Biochem. Biophys. Res. Commun. 218, 97–103.
Guy P., Jaquinod M., Remigy H., Andrieu J. P., Gagnon J., Bersch B., et al. (1996) New conformational properties induced by the replacement of Tyr-64 in Desulfovibrio vulgaris Hildenborough ferricytochrome d553 using isotopic] exchange monitored by mass spectrometry. FEBS Lett. 395, 53–57.
Wang F., Scapin G., Blanchard J. S., and Angeletti R. H. (1998) Substrate binding and conformational changes of Clostridium glutamicum diaminopimelate dehydrogenase revealed by hydrogen/deuterium, exchange and electrospray mass spectrometry. Protein Sci. 7, 293–299.
Wang F., Blanchard J. S., and Tang X. J. (1997) Hydrogen exchange/electrospray ionization mass spectrometry studies of substrate and inhibitor binding and conformational changes of Escherichia coli dihydrodipicolinate reductase. Biochemistry 36, 3755–3759.
Ohguro H., Palczewski K., Walsh K. A., and Johnson R. S. (1994) Topographic study of arrestin using differential chemical modifications and hydrogen/deuterium exchange. Protein Sci. 3, 2428–2434.
Johnson R. S. and Walsh K. A. (1994) Mass spectrometric measurement of protein amide hydrogen exchange rates of apo-and holo-myoglobin. Protein Sci. 3, 2411–2418.
Resing K. A. and Ahn N. G. (1998) Deuterium exchange mass spectrometry as a probe of protein kinase activation. Analysis of wild-type and constitutively active mutants of MAP kinase kinase-1. Biochemistry 37, 463–475.
Dharmasiri K. and Smith D. L. (1996) Mass spectrometric determination of isotopic exchange rates of amide hydrogens located on the surfaces of proteins. Anal. Chem. 68, 2340–2344.
Yang H., and Smith D. L. (1997) Kinetics of cytochrome c folding examined by hydrogen exchange and mass spectrometry. Biochemistry 36, 14,992–14,999.
Zhang Z., Post C. B., and Smith D. L. (1996) Amide hydrogen exchange determined by mass spectrometry: application to rabbit muscle aldolase. Biochemistry 35, 779–791.
Liu Y. and Smith D. L. (1994) Probing high order structure of proteins by fastatom bombardment mass spectrometry. J. Am. Soc. Mass Spectrom. 5, 19–28.
Deng Y. and Smith D. L. (1998) Identification of unfolding domains in large proteins by their unfolding rates. Biochemistry 37, 6256–6262.
Zhang Z. and Smith D. L. (1996) Thermal-induced unfolding domains in aldolase by amide hydrogen exchange and mass spectrometry. Protein Sci. 5, 1282–1289.
Maier C. S., Kim O. H., andDeinzer M. L. (1997) Conformationalproperties of the A-state of cytochrome s studied by hydrogen/deuterium exchange and electrospray mass spectrometry. Anal. Biochem. 252, 127–135.
Zhang Z., Li W., Logan T. M., Li M., and Marshall A. G. (1997) Human recombinant [C22A] FK506-binding protein amide hydrogen exchange rates from mass spectrometry match and extend those from NMR. Protein Sci. 6, 2203–2217.
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.
Bai Y., Sosnick T. R., Mayne L., and Englander S. W. (1995) Protein folding intermediates: native-state hydrogen exchange. Science 269, 192–197.
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.
Kim K.-S. and Woodward C. (1993) Protein internal flexibility and global stability: effect of urea on hydrogen exchange rates of bovine pancreatic trypsin inhibitor. Biochemistry 32, 9609–9613.
Bai Y., Milne J. S., Mayne L., and Englander S. W. (1993) Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75–86.
Swint-Kruse L. and Robertson A. D. (1996) Temperature and pH dependence of hydrogen exchange and global stability for ovomucoid third domain. Biochemistry 35, 171–180.
Zhou Z. and Smith D. L. (1990) Assignment of disulfide bonds in proteins by partial acid hydrolysis and mass spectrometry. J. Protein Chem. 9, 523–532.
Biemann K. (1990) Sequencing of peptides by tandem mass spectrometry and high-energy collision-induced dissociation. Methods Enzymol. 193, 455–479.
Caprioli R. M. and Fan T. (1986) Peptide sequence analysis using exopeptidases with molecular analysis of the truncated polypeptides by mass spectrometry. Anal. Biochem. 154, 596–603.
Smith J. B., Sun Y., Smith D. L., and Green B. (1992) Identification of the posttranslational modifications of bovine lens alpha-B-crystallins by mass spectrometry. Protein Sci. 1, 601–608.
Zhang Z. (1995) Protein hydrogen exchange determined by mass spectrometry: a new tool for probing protein high-order structure and structural changes. Doctoral Dissertation, Purdue University.
Deng Y., Zhang Z., and Smith D. L. (1998) 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.
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Engen, J.R., Smith, D.L. (2000). Investigating the Higher Order Structure of Proteins. In: Chapman, J.R. (eds) Mass Spectrometry of Proteins and Peptides. Methods in Molecular Biology™, vol 146. Humana Press, Totowa, NJ. https://doi.org/10.1385/1-59259-045-4:95
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DOI: https://doi.org/10.1385/1-59259-045-4:95
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