Investigating solution-phase protein structure and dynamics by hydrogen exchange mass spectrometry

Current Protocols in Protein Science

Volumn , Issue SUPPL.58, 2009, Pages

  Morgan, Christopher R ^a   Engen, John R ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

Author keywords

Hydrogen exchange; Mass spectrometry; Proteins

Indexed keywords

DEUTERIUM; WATER; HYDROGEN;

CHEMICAL LABELING; DEUTERIUM HYDROGEN EXCHANGE; HYDROGEN EXCHANGE MASS SPECTROMETRY; LIGAND BINDING; MASS SPECTROMETRY; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; METHODOLOGY; MOLECULAR DYNAMICS; MOLECULAR SIZE; PH; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; REVIEW; STRUCTURE ANALYSIS; ARTICLE; BIOTECHNOLOGY; CATALYSIS; CLINICAL PROTOCOL; DATA ANALYSIS; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; NITROGEN DYNAMICS; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN FUNCTION; PROTEIN INTERACTION; SOLUTION PHASE PROTEIN STRUCTURE;

ALGORITHMS; AMINO ACID SEQUENCE; DEUTERIUM; DEUTERIUM EXCHANGE MEASUREMENT; HYDROGEN; KINETICS; MASS SPECTROMETRY; PROTEIN CONFORMATION; PROTEINS; SOLUTIONS;

EID: 75749148378     PISSN: 19343655     EISSN: 19343663     Source Type: Journal    
DOI: 10.1002/0471140864.ps1706s58     Document Type: Review

References (59)

1. Bai,Y., Milne, J.S., Mayne, L., and Englander, S.W. 1993. Primary structure effects on peptide group hydrogen exchange. Proteins 17:75-86. (Pubitemid 23261059)
2. Bai,Y., Milne, J.S., Mayne, L., and Englander, S.W. 1994. Protein stability parameters measured by hydrogen exchange. Proteins 20:4-14.
3. Bohak, Z. 1969. Purification and characterization of chicken pepsinogen and chicken pepsin. J. Biol. Chem. 244:4638-4648.
4. Brier, S. and Engen, J.R. 2008. Hydrogen exchange mass spectrometry: Principles and capabilities. In Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics (M. Chance, ed.) pp. 11-43. Wiley-Blackwell, New York.
5. Brier, S., Maria, G., Carginale, V., Capasso, A.,Wu, Y., Taylor, R.M.,Borotto,N.B., Capasso,C., and Engen, J.R. 2007. Purification and characterization of pepsins A1 and A2 from the Antarctic rock cod Trematomus bernacchii. FEBS J. 274:6152-6166.
6. Chowdhury, S.K., Katta, V., and Chait, B.T. 1990. Probing conformational changes in proteins by mass spectrometry. J. Am.Chem. Soc. 112:9012-9013
7. Cravello, L., Lascoux, D., and Forest, E. 2003. Use of different proteases working in acidic conditions to improve sequence coverage and resolution in hydrogen/deuterium exchange of large proteins. Rapid Commun. Mass Spectrom. 17:2387-2393.
8. Demmers, J.A., Haverkamp, J.,Heck,A.J.,Koeppe, R.E. 2nd, and Killian, J.A. 2000. Electrospray ionization mass spectrometry as a tool to analyze hydrogen/deuterium exchange kinetics of transmembrane peptides in lipid bilayers. Proc. Natl. Acad. Sci. U.S.A. 97:3189-3194.
9. Demmers, J.A., Rijkers, D.T., Haverkamp, J., Killian, J.A., and Heck, A.J. 2002. Factors affecting gas-phase deuterium scrambling in peptide ions and their implications for protein structure determination. J. Am. Chem. Soc. 124:11191-11198.
10. Deng, Y. and Smith, D.L. 1998. Identification of unfolding domains in large proteins by their unfolding rates. Biochemistry 37:6256-6262.
11. Deng, Y. and Smith, D.L. 1999. Rate and equilibrium constants for protein unfolding and refolding determined by hydrogen exchange-mass spectrometry. Anal. Biochem. 276:150-160.
12. Deng, Y., Pan, H., and Smith, D.L. 1999a. Selective isotope labeling demonstrates that hydrogen exchange at individual peptide amide linkages can be determined by collision-induced dissocation mass spectrometry. J. Am.Chem. Soc. 121:1966-1967.
13. Deng, Y., Zhang, Z., and Smith, D.L. 1999b. Comparison of continuous and pulsed labeling amide hydrogen exchange/mass spectrometry for studies of protein dynamics. J. Am. Soc. Mass Spectrom. 10:675-684.
14. 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.
15. Engen, J.R. and Smith, D.L. 2000. Investigating the higher order structure of proteins: Hydrogen exchange, proteolytic fragmentation, and mass spectrometry. Methods Mol. Biol. 146:95-112.
16. 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 36:14384-14391.
17. Englander, J.J., Rogero, J.R., and Englander, S.W. 1985. Protein hydrogen exchange studied by the fragment separationmethod. Anal. Biochem. 147:234-244.
18. Englander, S.W. and Poulsen, A. 1969. Hydrogentritium exchange of the random chain polypeptide. Biopolymers 7:379-393.
19. Englander, S.W. and Kallenbach, N.R. 1983. Hydrogen exchange and structural dynamics of proteins and nucleic acids. Q. Rev. Biophys. 16:521-655.
20. Garcia, R.A., Pantazatos, D., and Villarreal, F.J. 2004. Hydrogen/deuterium exchange mass spectrometry for investigating protein-ligand interactions. Assay Drug Dev. Technol. 2:81-91.
21. Hamuro, Y., Coales, S.J., Molnar, K.S., Tuske, S.J., and Morrow, J.A. 2008. Specificity of immobilized porcine pepsin in H/D exchange compatible conditions. Rapid Commun. Mass Spectrom. 22:1041-1046.
22. Hoerner, J.K., Xiao, H., Dobo, A., and Kaltashov, I.A. 2004. Is there hydrogen scrambling in the gas phase? Energetic and structural determinants of proton mobility within protein ions. J. Am. Chem. Soc. 126:7709-7717.
23. Hoofnagle, A.N., Resing, K.A., and Ahn, N.G. 2003. Protein analysis by hydrogen exchange mass spectrometry. Annu. Rev. Biophys. Biomol. Struct. 32:1-25.
24. Hoofnagle, A.N., Resing, K.A., and Ahn, N.G. 2004. Practical methods for deuterium exchange/mass spectrometry. Meth. Mol. Biol. 250:283-298.
25. Hvidt, A. and Linderstrom-Lang, K. 1954. Exchange of hydrogen atoms in insulin with deuterium atoms in aqueous solutions. Biochim. Biophys. Acta 14:574-575.
26. Hvidt, A. and Nielsen, S.O. 1966. Hydrogen exchange in proteins. Adv. Protein Chem. 21:287-386.
27. Jeng, M.-F., Englander, S.W., Elove, G.A., Wand, A.J., and Roder, H. 1990. Structural description of acid-denatured cytochrome c by hydrogen exchange and 2D NMR. Biochemistry 29:10433-10437.
28. Jorgensen, T.J., Gardsvoll, H., Ploug, M., and Roepstorff, P. 2005. Intramolecular migration of amide hydrogens in protonated peptides upon collisional activation. J. Am. Chem. Soc. 127:2785-2793.
29. 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.
30. Kim, K.-S. and Woodward, C. 1993. Protein internal βexibility and global stability: Effect of urea on hydrogen exchange rates of bovine pancreatic trypsin inhibitor. Biochemistry 32:9609-9613.
31. Kim, M.Y., Maier, C.S., Reed, D.J., and Deinzer, M.L. 2001. Site-specific amide hydrogen/deuterium exchange in E. coli thioredoxins measured by electrospray ionization mass spectrometry. J. Am. Chem. Soc. 123:9860-9866.
32. Konermann, L. and Simmons, D.A. 2003. Protein-folding kinetics and mechanisms studied by pulsed-labeling and mass spectrometry. Mass Spectrom. Rev. 22:1-26.
33. Li, R. and Woodward, C. 1999. The hydrogen exchange core and protein folding. Protein Sci 8:1571-1590.
34. Mandell, J.G., Falick, A.M., and Komives, E.A. 1998. Measurement of amide hydrogen exchange by MALDI-TOF mass spectrometry. Anal. Chem. 70:3987-3995.
35. Mazon, H., Marcillat, O., Forest, E., Smith, D.L., and Vial, C. 2004. Conformational dynamics of the GdmHCl-induced molten globule state of creatine kinase monitored by hydrogen exchange and mass spectrometry. Biochemistry 43:5045-5054.
36. 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.
37. Molday, R.S., Englander, S.W., and Kallen, R.G. 1972. Primary structure effects on peptide group hydrogen exchange. Biochemistry 11:150-158.
38. Nikamanon, P., Pun, E., Chou, W., Koter, M.D., and Gershon, P.D. 2008. .TOF2H.: A precision toolbox for rapid, high density/high coverage hydrogen-deuterium exchange mass spectrometry via an LC-MALDI approach, covering the data pipeline from spectral acquisition to HDX rate analysis. BMC Bioinformatics 9:387.
39. Pan, H., Raza, A.S., and Smith, D.L. 2004. Equilibrium and kinetic folding of rabbit muscle triosephosphate isomerase by hydrogen exchange mass spectrometry. J. Mol. Biol. 336:1251-1263.
40. Pascal, B.D., Chalmers, M.J., Busby, S.A., and Griffin, P.R. 2009. HD desktop: An integrated platform for the analysis and visualization of H/D exchange data. J. Am. Soc. Mass Spectrom. 20:601-610.
41. 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.
42. 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.
43. Tello-Solis, S.R. and Hernandez-Arana, A. 1995. Effect of irreversibility on the thermodynamic characterization of the thermal denaturation of Aspergillus saitoi acid proteinase. Biochem. J. 311:969-974.
44. Tsutsui, Y. and Wintrode, P.L. 2007. Hydrogen/deuterium exchange-mass spectrometry: A powerful tool for probing protein structure, dynamics and interactions. Curr. Med. Chem. 14:2344-2358.
45. Wales, T.E. and Engen, J.R. 2006a. Partial unfolding of diverse SH3 domains on a wide timescale. J. Mol. Biol. 357:1592-1604.
46. Wales, T.E. and Engen, J.R. 2006b. Hydrogen ex-change mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 25:158-170.
47. Wales, T.E., Fadgen, K.E., Gerhardt, G.C., and Engen, J.R. 2008. High-speed and high-resolution UPLC separation at zero degrees celsius. Anal. Chem. 80:6815-6820.
48. Wang, L. and Smith, D.L. 2005. Capsid structure and dynamics of a human rhinovirus probed by hydrogen exchange mass spectrometry. Protein Sci. 14:1661-1672.
49. Wang, L., Pan, H., and Smith, D.L. 2002. Hydrogen exchange-mass spectrometry: Optimization of digestion conditions. Mol. Cell Proteomics 1:132-138.
50. Weis, D.D., Engen, J.R., and Kass, I.J. 2006a. Semi-automated data processing of hydrogen exchange mass spectra using HX-express. J. Am. Soc. Mass Spectrom. 17:1700-1703.
51. Weis, D.D., Wales, T.E., Engen, J.R., Hotchko, M., and Ten Eyck, L.F. 2006b. Identification and characterization of EX1 kinetics in H/D exchange mass spectrometry by peak width analysis. J. Am. Soc. Mass Spectrom. 17:1498-1509.
52. Woodard, S.L., Mayor, J.M., Bailey, M.R., Barker, D.K., Love, R.T., Lane, J.R., Delaney, D.E., McComas-Wagner, J.M., Mallubhotla, H.D., Hood, E.E., Dangott, L.J., Tichy, S.E., and Howard, J.A. 2003. Maize (Zea mays).derived bovine trypsin: Characterization of the first large-scale, commercial protein product from transgenic plants. Biotechnol. Appl. Biochem. 38:123-130.
53. Woodward, C., Simon, I., and Tuchsen, E. 1982. Hydrogen exchange and the dynamic structure of proteins. Mol. Cell Biochem. 48:135-160.
54. Wu, Y., Engen, J.R. and Hobbins, W.B. 2006a. Ultra performance liquid chromatography (UPLC) further improves hydrogen/deuterium exchange mass spectrometry. J. Am. Soc. Mass Spectrom. 17:163-167.
55. Wu, Y., Kaveti, S., and Engen, J.R. 2006b. Exten- sive deuterium back-exchange in certain immobilized pepsin columns used for H/D exchange mass spectrometry. Anal. Chem. 78:1719-1723.
56. Yang, H. and Smith, D.L. 1997. Kinetics of cytochrome c folding examined by hydrogen exchange and mass spectrometry. Biochemistry 36:14992-14999.
57. Zehl,M., Rand, K.D., Jensen, O.N., and Jorgensen, T.J. 2008. Electron transfer dissociation facilitates the measurement of deuterium incorporation into selectively labeled peptides with single residue resolution. J. Am. Chem. Soc. 130:17453-17459.
58. 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.
59. 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. (Pubitemid 26034562)