Time-resolved pulsed hydrogen/deuterium exchange mass spectrometry probes gaseous proteins structural kinetics

Journal of the American Society for Mass Spectrometry

Volumn 26, Issue 1, 2014, Pages 71-82

  Rajabi, Khadijeh ^a,b  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^b UNIVERSITY OF LEEDS   (United Kingdom)

Author keywords

Continuum gas flow; Electrospray ionization (ESI) MS; Gas phase HDX kinetics; Ion molecule reactions; Isotopic labeling; Protein; Pulsed hydrogen deuterium exchange mass spectrometry (HDX MS); Time of flight mass spectrometry (TOF MS); Time resolved structural analysis

Indexed keywords

ELECTROSPRAY IONIZATION; FLOW OF GASES; GASES; HYDROGEN; ION EXCHANGE; IONIZATION OF GASES; IONS; KINETICS; MASS SPECTROMETRY;

ELECTROSPRAY IONIZATION (ESI); GASPHASE; HYDROGEN/DEUTERIUM EXCHANGE; ION-MOLECULE REACTION; ISOTOPIC LABELING; TIME OF FLIGHT MASS SPECTROMETRY; TIME-RESOLVED;

PROTEINS;

CYTOCHROME C; ION; PROTEIN; UBIQUITIN;

ACIDITY; ARTICLE; CHEMICAL REACTION; CONTROLLED STUDY; DEUTERIUM HYDROGEN EXCHANGE; ELECTROSPRAY; EVOLUTION; GAS; ION TRAP MASS SPECTROMETRY; KINETICS; MASS SPECTROMETRY; NONHUMAN; PROTEIN STRUCTURE; PROTON TRANSPORT; PULSE RATE; TIME; TIME OF FLIGHT MASS SPECTROMETRY; CHEMISTRY; PROCEDURES;

DEUTERIUM EXCHANGE MEASUREMENT; KINETICS; MASS SPECTROMETRY; PROTEINS;

EID: 84919950774     PISSN: 10440305     EISSN: 18791123     Source Type: Journal    
DOI: 10.1007/s13361-014-1004-y     Document Type: Article

References (58)

1. Wales, T.E.; Engen, J.R.: Hydrogen exchange mass spectrometry for the analysis of protein dynamics. Mass Spectrom. Rev. 25, 158-170 (2006)
2. Iacob, R.E.; Engen, J.R.: Hydrogen exchange mass spectrometry: are we out of the quicksand? J. Am. Soc. Mass Spectrom. 23, 1003-1010 (2012)
3. Rob, T.; Wilson, D.J.: Time-resolved mass spectrometry for monitoring millisecond time-scale solution-phase processes. Eur. J. Mass Spectrom. 18, 205-214 (2012)
4. Smith, D.L.: Local structure and dynamics in proteins characterized by hydrogen exchange and mass spectrometry. Biokhimiia 63, 285-293 (1998)
5. Suckau, D.; Shi, Y.; Beu, S.C.; Senko, M.W.; Quinn, J.P.; Wampler, F.M.; McLafferty, F.W.: Coexisting stable conformations of gaseous protein ions. Proc. Natl. Acad. Sci. U. S. A. 90, 790-793 (1993)
6. Mo, J.; Todd, G.C.; Håkansson, K.J.: Characterization of nucleic acid higher order structure by gas-phase H/D exchange in a quadrupole-FT-ICR mass spectrometer. Biopolymers 91, 256-264 (2009)
7. Hofstadler, S.A.; Sannes-Lowery, K.A.; Griffey, R.H.: Enhanced gas-phase hydrogen-deuterium exchange of oligonucleotide and protein ions stored in an external multipole ion reservoir. J. Mass Spectrom. 35, 62-70 (2000)
8. n ions. Int. J. Mass Spectrom. 316/318, 164-173 (2012)
9. Mao, D.; Douglas, D.J.: H/D exchange of gas phase bradykinin ions in a linear quadrupole ion trap. J. Am. Soc. Mass Spectrom. 14, 85-94 (2003)
10. Kaltashov, I.A.; Doroshenko, V.M.; Cotter, R.J.: Gas phase hydrogen/deuterium exchange reactions of peptide ions in a quadrupole ion trap mass spectrometer. Proteins 28, 53-58 (1997)
11. 2+. J. Am. Soc. Mass Spectrom. 11, 711-721 (2000)
12. Winkler, H.D.F.; Dzyuba, E.V.; Schalley, C.A.: Gas-phase H/D-exchange experiments in supramolecular chemistry. New J. Chem. 35, 529-541 (2011)
13. Badman, E.R.; Myung, S.; Clemmer, D.E.: Evidence for unfolding and refolding of gas-phase cytochrome c ions in a Paul trap. J. Am. Soc. Mass Spectrom. 16, 1493-1497 (2005)
14. Badman, E.R.; Hoaglund-Hyzer, C.S.; Clemmer, D.E.: Monitoring structural changes of proteins in an ion trap over ~10-200 ms: unfolding transitions in cytochrome c ions. Anal. Chem. 73, 6000-6007 (2001)
15. 2 s. Proc. Natl. Acad. Sci. U. S. A. 105, 18145-18152 (2008)
16. Steinberg, M.Z.; Elber, R.; McLafferty, F.W.; Gerber, R.B.; Breuker, K.: Early structural evolution of native cytochrome c after solvent removal. Chem. Biochem. 9, 2417-2423 (2008)
17. Konermann, L.; Collings, B.A.; Douglas, D.J.: Cytochrome c folding kinetics studied by time-resolved electrospray ionization mass spectrometry. Biochemistry 36, 5554-5559 (1997)
18. Konermann, L.; Rosell, F.I.; Mauk, A.G.; Douglas, D.J.: Acid-induced denaturation of myoglobin studied by time-resolved electrospray ionization mass spectrometry. Biochemistry 36, 6448-6454 (1997)
19. 3: exchange kinetics do not reflect parent ion structures. J. Am. Chem. Soc. 126, 6485-6490 (2004)
20. Myung, S.; Badman, E.R.; Lee, Y.J.; Clemmer, D.E.: Structural transitions of electrosprayed ubiquitin ions stored in an ion trap over ~10 ms to 30 s. J. Phys. Chem. A 106, 9976-9982 (2002)
21. Freitas, M.; Marshall, A.G.: Gas-phase bovine ubiquitin cation conformations resolved by gas-phase hydrogen/deuterium exchange rate and extent. Int. J. Mass Spectrom. 185/186/187, 565-575 (1999)
22. Rand, K.D.; Pringle, S.D.; Murphy III, J.P.; Fadgen, K.E.; Brown, J.; Engen, J.R.: Gas-phase hydrogen/deuterium exchange in a traveling wave ion guide for the examination of protein conformations. Anal. Chem. 81, 10019-10028 (2009)
23. Rand, K.D.; Pringle, S.D.; Morris, M.; Brown, J.M.: Site-specific analysis of gas-phase hydrogen/deuterium exchange of peptides and proteins by electron transfer dissociation. Anal. Chem. 84, 1931-1940 (2012)
24. Valentine, S.J.; Counterman, A.E.; Clemmer, D.E.: Conformer-dependent proton-transfer reactions of ubiquitin ions. J. Am. Soc. Mass Spectrom. 8, 954-961 (1997)
25. l2+ ions produced by electrospray ionization mass spectrometry. J. Mass Spectrom. 31, 247-254 (1996)
26. 11+ enhance hydrogen/deuterium exchange. J. Phys. Chem. B 115, 4509-4515 (2011)
27. Robinson, E.W.; Williams, E.R.: Multidimensional separations of ubiquitin conformers in the gas phase: relating ion cross sections to H/D exchange measurements. J. Am. Soc. Mass Spectrom. 16, 1427-1437 (2005)
28. Wright, P.J.; Zhang, J.; Douglas, D.J.: Conformations of gas-phase ions of ubiquitin, cytochrome c, apomyoglobin, and β-lactoglobulin produced from two different solution conformations. J. Am. Soc. Mass Spectrom. 19, 1906-1913 (2008)
29. 3. J. Am. Chem. Soc. 117, 12840-12854 (1995)
30. Wood, T.D.; Chorush, R.A.; Wampler III, F.M.; Little, D.P.; O'Connor, P.B.; McLafferty, F.W.: Gas-phase folding and unfolding of cytochrome c cations. Proc. Natl. Acad. Sci. U. S. A. 92, 2451-2454 (1995)
31. Campbell, J.M.; Collings, B.A.; Douglas, D.J.: A new linear ion trap time-of-flight system with tandem mass spectrometry capabilities. Rapid Commun. Mass Spectrom. 12, 1463-1474 (1998)
32. n capabilities. Rapid Commun. Mass Spectrom. 15, 1777-1795 (2001)
33. French, J.B.: Planetary atmospheric simulation using molecular beams. CASI Trans. 3, 77-83 (1970)
34. Douglas, D.J.; French, J.B.: Gas dynamics of the inductively coupled plasma mass spectrometry interface. J. Anal. At. Spectrom. 3, 743-747 (1988)
35. Siegmund, O.H.W.; Vallerga, J.; Wargelin, B.: Background events in microchannel plates. IEEE Trans. Nucl. Sci. 35, 524-528 (1988)
36. Geller, O.; Lifshitz, C.: A fast flow tube study of gas phase H/D exchange of multiply protonated ubiquitin. J. Phys. Chem. A 109, 2217-2222 (2005)
37. Skinner, O.S.; McLafferty, F.W.; Breuker, K.: How ubiquitin unfolds after transfer into the gas phase. J. Am. Soc. Mass Spectrom. 23, 1011-1014 (2012)
38. Reuben, B.G.; Ritov, Y.; Geller, O.; McFarland, M.A.; Marshall, A.G.; Lifshitz, C.: Applying a new algorithm for obtaining site specific rate constants for H/D exchange of the gas phase proton-bound arginine dimer. Chem. Phys. Lett. 380, 88-94 (2003)
39. Mazurek, U.; Geller, O.; Lifshitz, C.: Protonated serine octamer cluster: structure elucidation by gas-phase H/D exchange reactions. 109, 2107-2112 (2005)
40. Squires, R.R.; Bierbaum, V.M.; Grabowski, J.J.; DePuy, C.H.: Multiple proton transfers within long-lived ion-molecule complexes. J. Am. Chem. Soc. 105, 5185-5192 (1983)
41. Meot-Ner, M.: Molecular Structures and Energetics. VCH, New York (1986)
42. Bohme, D.K.: Interactions between Ions and Molecules. Plenum, New York (1975)
43. Farneth, W.E.; Brauman, J.I.: Dynamics of proton transfer involving delocalized negative ions in the gas phase. J. Am. Chem. Soc. 98, 7891-7898 (1976)
44. Kharlamova, A.; Fisher, C.M.; McLuckey, S.A.: Hydrogen/deuterium exchange in parallel with acid/base induced protein conformational change in electrospray droplets. J. Mass Spectrom. 49, 437-444 (2014)
45. Lias, S.G.; Liebman, J.F.; Levin, R.D.: Evaluated gas phase basicities and proton affinities of molecules; heats of formation of protonated molecules. J. Phys. Chem. Ref. Data 13, 695-808 (1984)
46. Hoaglund-Hyzer, C.S.; Counterman, A.E.; Clemmer, D.E.: Anhydrous protein ions. Chem. Rev. 99, 3037-3079 (1999)
47. Winger, B.E.; Light-Wahl, K.J.; Smith, R.D.: Gas-phase proton transfer reactions involving multiply charged cytochrome c ions and water under thermal conditions. J. Am. Soc. Mass Spectrom. 3, 624-630 (1992)
48. Koppenol, W.H.; Margoliash, E.: The asymmetric distribution of charges on the surface of horse cytochrome c. Functional implications. J. Biol. Chem. 257, 4426-4437 (1982)
49. Dickerson, R.E.; Timkovich, R.: In Boyer, P.D. (Ed.) The Enzymes, vol. XIA, Academic: New York, (1975)
50. Meyer, Y.P.; Saturno, A.F.: Horse heart ferri-cytochrome c: conformation and heme configuration of low ionic strength acidic forms. J. Protein Chem. 9, 379-387 (1990)
51. Shelimov, K.B.; Clemmer, D.E.; Hudgins, R.R.; Jarrold, M.F.: Protein structure in vacuo: gas-phase conformations of BPTI and cytochrome c. J. Am. Chem. Soc. 119, 2240-2248 (1997)
52. Shelimov, K.B.; Jarrold, M.F.: "Denaturation" and refolding of cytochrome c in vacuo. J. Am. Chem. Soc. 118, 10313-10314 (1996)
53. Oomens, J.; Polfer, N.; Moore, D.T.; van der Meer, L.; Marshall, A.G.; Eyler, J.R.; Meijer, G.; von Helden, G.: Charge-state resolved mid-infrared spectroscopy of a gas-phase protein. Phys. Chem. Chem. Phys. 7, 1345-1348 (2005)
54. Winger, B.E.; Light-Wahl, K.J.; Ogorzalek Loo, R.R.; Udseth, H.R.; Smith, R.D.: Observation and implications of high mass-to-charge ratio ions from electrospray ionization mass spectrometry. J. Am. Soc. Mass Spectrom. 4, 536-545 (1993)
55. Covey, T.; Douglas, D.J.: Collision cross sections for protein ions. J. Am. Soc. Mass Spectrom. 4, 616-623 (1993)
56. McLafferty, F.W.; Guan, Z.; Haupts, U.; Wood, T.D.; Kelleher, N.L.: Gaseous conformational structures of cytochrome c. J. Am. Chem. Soc. 120, 4732-4740 (1998)
57. Oh, H.; Breuker, K.; Sze, S.K.; Ge, Y.; Carpenter, B.K.; McLafferty, F.W.: Secondary and tertiary structures of gaseous protein ions characterized by ECD mass spectrometry and photofragment spectroscopy. Proc. Natl. Acad. Sci. U. S. A. 99, 15863-15868 (2002)
58. Steinberg, M.Z.; Breuker, K.; Elber, R.; Gerber, R.B.: The dynamics of water evaporation from partially solvated cytochrome c in the gas phase. Phys. Chem. Chem. Phys. 9, 4690-4697 (2007)