Summary
Amide hydrogen/deuterium (H/D) exchange of proteins monitored by mass spectrometry has established itself as a powerful method for probing protein conformational dynamics and protein interactions. The method uses isotope labeling to probe the rate at which protein backbone amide hydrogens undergo exchange. Backbone amide hydrogen exchange rates are particularly sensitive to hydrogen bonding; hydrogen bonding slows the exchange rates dramatically. Exchange rates reflect on the conformational mobility, hydrogen bonding strength, and solvent accessibility in protein structure. Mass spectrometric techniques are used to monitor the exchange events as mass shifts that arise through the incorporation of deuterium into the protein. Global conformational information can be deduced by monitoring the exchange profiles over time. Combining the labeling experiment with proteolysis under conditions that preserve the exchange information allows for localizing exchange events to distinct regions of the protein backbone and thus, the study of protein conformation with medium spatial resolution. Over the past decade, H/D exchange mass spectrometry has evolved into a versatile technique for investigating conformational dynamics and interactions in proteins, protein–ligand and protein–protein complexes.
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References
Katta, V., Chait, B. T. Conformational changes in proteins probed by hydrogen-exchange electrospray ionization mass spec-trometry. Rapid Commun. Mass Spectrom. 5, 214–217 (1991).
Englander, S. W., Kallenbach, N. Hydrogen exchange and structural dyamics of proteins and nucleic acids. Q. Rev. Biophys. 16, 521–655 (1984).
Englander, S. W., Sosnick, T. R., Englan-der, J. J., Mayne, L. Mechanisms and uses of hydrogen exchange. Curr. Opin. Struct. Biol. 6, 18–23 (1996).
Mandell, J. G., BaergaOrtiz, A., Akashi, S., Takio, K., Komives, E. A. Solvent accessibility of the thrombin–thrombomodulin interface. J. Mol. Biol. 306, 575–589 (2001).
Mandell, J. G., Falick, A. M. & Komives, E. A. Identification of protein–protein interfaces by decreased amide proton solvent accessibility. Proc. Natl Acad. Sci. USA 95, 14705–14710 (1998).
Zhang, Z., Smith, D. L. Determination of amide hydrogen exchange by mass spectrom-etry: A new tool for protein structure elucidation. Protein Sci. 2, 522–531 (1993).
Smith, D. L., Deng, Y., Zhang, Z. Probing the non-covalent structure of proteins by amide hydrogen exchange and mass spectrometry. J. Mass Spectrom. 32, 135–146 (1997).
Eigen, M 1964 Proton transfer, acid-base catalysis, and enzymatic hydrolysis Angew. Chem 3 1–19
Eriksson, M. A. L., Haerd, T., Nilsson, L. On the pH dependance of amide proton exchange rates in proteins. Biophys. J.69, 329–339 (1995).
Bai, Y., Milne, J. S., Mayne, L., Englander, S. W. Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75–86 (1993).
Englander, J. J., Rogero, J. R., Englander, S. W. Protein hydrogen exchange studied by the fragment separation method. Anal. Biochem. 147, 234–244 (1985).
Miranker, A., Robinson, C. V., Radford, S. E., Aplin, R. T., Dobson, C. M. Detection of transient protein folding populations by mass spectrometry. Science 262, 896–899 (1993).
Demmers, J. A., Rijkers, D. T., Haverkamp, J., Killian, J. A., Heck, A. J. Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination. J. Am. Chem. Soc. 124, 11191–11198 (2002).
Kim, M. Y., Maier, C. S., Reed, D. J., Deinzer, M. L. Site-specific amide hydrogen/deuterium exchange in E. coli thiore-doxins measured by electrospray ionization mass spectrometry. J. Am. Chem. Soc. 123, 9860–9866 (2001).
Kaltashov, I. A., Eyles, S. J. Crossing the phase boundary to study protein dynamics and function: Combination of amide hydrogen exchange in solution and ion fragmentation in the gas phase. J. Mass Spectrom. 37, 557–565 (2002).
Jorgensen, T. J., Gardsvoll, H., Ploug, M., Roepstorff, P. Intramolecular migration of amide hydrogens in protonated peptides upon collisional activation. J. Am. Chem. Soc. 127, 2785–2793 (2005).
de Mol, N. J. et-al.., Changes in structural dynamics of the Grb2 adaptor protein upon binding of phosphotyrosine ligand to its SH2 domain. Biochim. Biophys. Acta 1700, 53–64 (2004).
Guilloteau, J. P. et-al.., Purification, stabilization, and crystallization of a modular protein: Grb2. Proteins 25, 112–119 (1996).
Kim, M. Y., Maier, C. S., Ho, S., Deinzer, M. L. Intramolecular interactions in chemically modified Escherichia coli thioredoxin monitored by hydrogen/deuterium exchange and electrospray ionization mass spectrometry. Biochemistry 40, 14413–14421 (2001).
Kim, M. Y., Maier, C. S., Reed, D. J., Deinzer, M. L. Conformational changes in chemically modified Escherichia coli thioredoxin monitored by H/D exchange and electrospray ionization mass spectrometry. Protein Sci. 11, 1320–1329 (2002).
Egea, P. F. et-al.., Ef fects of ligand binding on the association properties and conformation in solution of retinoic acid receptors RXR and RAR. J. Mol. Biol. 307, 557–576 (2001).
Maier, C. S., Schimerlik, M. I., Deinzer, M. L. Thermal denaturation of Escherichia coli thioredoxin studied by hydrogen/deuterium exchange and electrospary ionization mass spectrometry: Monitoring a two-state protein unfolding transition. Biochemistry 38, 1136–1143 (1999).
Matagne, A. et-al.., Thermal unfolding of an intermediate is associated with non-Arrhen-ius kinetics in the folding of hen lysozyme. J. Mol. Biol. 297, 193–210 (2000).
Yan, X., Broderick, D., Leid, M. E., Schimerlik, M. I., Deinzer, M. L. Dynamics and ligand-induced solvent accessibility changes in human retinoid X receptor homodimer determined by hydrogen deuterium exchange and mass spec-trometry. Biochemistry 43, 909–917 (2004).
Yan, X., Zhang, H., Watson, J., Schimerlik, M. I., Deinzer, M. L. Hydrogen/deuterium exchange and mass spectrometric analysis of a protein containing multiple disulfide bonds: Solution structure of recombinant macrophage colony stimulating factor-beta (rhM-CSFbeta). Protein Sci. 11, 2113–2124 (2002).
Zhang, Z., Marshall, A. G. A universal algorithm for fast and automated charge state deconvolution of electrospray mass-to-charge ratio spectra. J. Am. Soc. Mass Spectrom. 9, 225–233 (1998).
Wang, L., Smith, D. L. Downsizing improves sensitivity 100-fold for hydrogen exchange- mass spectrometry. Anal. Biochem. 314, 46–53 (2003).
Wu, Y., Kaveti, S., Engen, J. R. Extensive deuterium back-exchange in certain immobilized pepsin columns used for H/D exchange mass spectrometry. Anal. Chem. 78, 1719–1723 (2006).
Hvidt, A., Nielsen, S. O. Hydrogen exchange in proteins. Adv. Protein Chem. 21, 287–386 (1966).
Zhang, Y. H., Yan, X., Maier, C. S., Schimerlik, M. I., Deinzer, M. L. Structural comparison of recombinant human macrophage colony stimulating factor beta and a partially reduced derivative using hydrogen deuterium exchange and electrospray ionization mass spectrometry. Protein Sci. 10, 2336–2345 (2001).
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Yan, X., Maier, C.S. (2009). Hydrogen/Deuterium Exchange Mass Spectrometry. In: Lipton, M.S., Paša-Tolic, L. (eds) Mass Spectrometry of Proteins and Peptides. Methods In Molecular Biology, vol 492. Humana Press. https://doi.org/10.1007/978-1-59745-493-3_15
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DOI: https://doi.org/10.1007/978-1-59745-493-3_15
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