Gas-Phase Hydrogen/Deuterium Exchange of 5′- and 3′-Mononucleotides in a Quadrupole Ion Trap: Exploring the Role of Conformation and System Energy

Journal of the American Society for Mass Spectrometry

Volumn 18, Issue 4, 2007, Pages 724-736

  Chipuk, Joseph E ^a   Brodbelt, Jennifer S ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DEUTERIUM EXCHANGE; GAS-PHASE CONFORMATIONS; NUCLEOBASE; PHOSPHATE MOIETY;

CONFORMATIONS; DEUTERIUM; HYDROGEN; ION EXCHANGE; MASS SPECTROMETRY;

NUCLEOTIDES;

2' DEOXYADENOSINE 3' PHOSPHATE; 2' DEOXYCYTIDINE 3' PHOSPHATE; 2' DEOXYGUANOSINE 3' PHOSPHATE; 2' DEOXYTHYMIDINE 3' PHOSPHATE; 2' DEOXYTHYMIDINE 5' PHOSPHATE; ANION; DEOXYADENOSINE PHOSPHATE; DEOXYCYTIDINE PHOSPHATE; DEOXYGUANOSINE PHOSPHATE; DEOXYRIBONUCLEOTIDE; DEUTERIUM OXIDE; HYDROGEN; NUCLEIC ACID BASE; UNCLASSIFIED DRUG;

ACIDITY; ARTICLE; CONFORMATION; DEUTERIUM HYDROGEN EXCHANGE; ENERGY; GAS; ION TRAP MASS SPECTROMETRY; ISOMER; MOLECULAR MODEL; THEORETICAL STUDY;

DEUTERIUM; GASES; MODELS, MOLECULAR; NUCLEOTIDES; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION;

EID: 33947313681     PISSN: 10440305     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jasms.2006.12.007     Document Type: Article

References (53)

1. Kaltashov I.A., Doroshenko V.M., and Cotter R.J. Gas Phase Hydrogen/Deuterium Exchange Reactions of Peptide Ions in a Quadrupole Ion Trap Mass Spectrometer. Proteins: Struct. Funct. Genet. 28 (1997) 53-58
2. Reid G.E., O'Hair R.A.J., Styles M.L., McFadyen W.D., and Simpson R.J. Gas Phase Ion-Molecule Reactions in a Modified Ion Trap: H/D Exchange of Noncovalent Complexes and Coordinatively Unsaturated Platinum Complexes. Rapid Commun. Mass Spectrom. 12 (1998) 1701-1708
3. Reid G.E., Simpson R.J., and O'Hair R.A.J. Probing the Fragmentation Reactions of Protonated Glycine Oligomers Via Multistage Mass Spectrometry and Gas-Phase Ion-Molecule Hydrogen/Deuterium Exchange. Int. J. Mass Spectrom. 191 (1999) 209-230
4. Felix T., Reyzer M., and Brodbelt J. Hydrogen/Deuterium Exchange of Nucleoside Analogs in a Quadrupole Ion Trap Mass Spectrometer. Int. J. Mass Spectrom. 191 (1999) 161-170
5. Hofstadler S.A., Sannes-Lowery K.A., and Griffey R.H. Enhanced Gas-Phase Hydrogen-Deuterium Exchange of Oligonucleotide and Protein Ions Stored in an External Multipole Reservoir. J. Mass Spectrom. 35 (2000) 62-70
6. 2+. J. Am. Soc. Mass Spectrom. 11 (2000) 711-721
7. 2O. J. Am. Soc. Mass Spectrom. 11 (2000) 167-171
8. Wyttenbach T., Paizs B., Barran P., Breci L., Liu D., Suhai S., Wysocki V.H., and Bowers M.T. The Effect of the Initial Water of Hydration on the Energetics, Structures, and H/D Exchange Mechanism of a Family of Pentapeptides: An Experimental and Theoretical Study. J. Am. Chem. Soc. 125 (2003) 13768-13775
9. Mao D., Babu K.R., Chen Y.L., and Douglas D.J. Conformations of Gas-Phase Lysozyme Ions Produced from Two Different Solution Conformations. Anal. Chem. 75 (2003) 1325-1330
10. Zhang J., and Brodbelt J.S. Gas-Phase Hydrogen/Deuterium Exchange and Conformations of Deprotonated Flavonoids and Gas-Phase Acidities of Flavonoids. J. Am. Chem. Soc. 126 (2004) 5906-5919
11. Hermann K., Wysocki V., and Vorpagel E.R. Computational Investigation and Hydrogen/Deuterium Exchange of the Fixed Charge Derivative Tris(2,4,6-Trimethoxyphenyl) Phosphonium: Implications of the Aspartic Acid Cleavage Mechanism. J. Am. Soc. Mass Spectrom. 16 (2005) 1067-1080
12. 3OD. Int. J. Mass Spectrom. 249-250 (2006) 93-105
13. - Ions of Nucleotides and Their Non-Covalent Homo- and Heterodimer Complexes. Aust. J. Chem. 56 (2003) 389-399
14. Gard E., Grenn M.K., Bregar J., and Lebrilla C.B. Gas-Phase Hydrogen/Deuterium Exchange as a Molecular Probe for the Interaction of Methanol and Protonated Peptides. J. Am. Soc. Mass Spectrom. 5 (1994) 623-631
15. 3. J. Am. Chem. Soc. 117 (1995) 12840-12854
16. Wood T.D., Chorush R.A., Wampler III F.M., Little D.P., O'Conner P.B., and McLafferty F.W. Gas-Phase Folding and Unfolding of Cytochrome c Cations. Proc. Natl. Acad. Sci. U.S.A. 92 (1995) 2451-2454
17. McLafferty F.W., Guan Z., Haupts U., Wood T.D., and Kelleher N.L. Gaseous Conformational Structures of Cytochrome c. J. Am. Chem. Soc. 120 (1998) 4732-4740
18. Robinson J.M., Greig M.J., Griffey R.H., Venkantraman M., and Laude D.A. Hydrogen/Deuterium Exchange of Nucleotides in the Gas Phase. Anal. Chem. 70 (1998) 3566-3571
19. 2S. J. Am. Chem. Soc. 120 (1998) 10187-10193
20. Wyttenbach T., and Bowers M.T. Gas-Phase Conformations of Biological Molecules: The Hydrogen/Deuterium Exchange Mechanism. J. Am. Soc. Mass Spectrom. 10 (1999) 9-14
21. Freitas M.A., and Marshall A.G. Gas-Phase RNA and DNA Ions. 2. Conformational Dependence of the Gas-Phase H/D Exchange of Nucleotide-5′-Monophosphates. J. Am. Soc. Mass Spectrom. 12 (2001) 780-785
22. Green-Church K.B., Limbach P.A., Freitas M.A., and Marshall A.G. Gas-Phase Hydrogen/Deuterium Exchange of Positively Charged Mononucleotides by Use of Fourier-Transform Ion Cyclotron Resonance Mass Spectrometry. J. Am. Soc. Mass Spectrom. 12 (2001) 268-277
23. Reed D., and Kass S. Hydrogen-Deuterium Exchange at Nonlabile Sites: A New Reaction Facet with Broad Implications for Structural and Dynamic Determinations. J. Am. Soc. Mass Spectrom. 12 (2001) 1163-1168
24. Jurchen J.C., Cooper R.E., and Williams E.R. The Role of Acidic Residues and of Sodium Ion Adduction on the Gas-Phase H/D Exchange of Peptides and Peptide Dimers. J. Am. Soc. Mass Spectrom. 14 (2003) 1477-1487
25. Crestoni M.E., and Fornarini S. Gas-Phase Hydrogen/Deuterium Exchange of Adenine Nucleotides. J. Mass Spectrom. 38 (2003) 854-861
26. 3: Exchange Kinetics Do Not Reflect Parent Ion Structures. J Am. Chem. Soc. 126 (2004) 6485-6490
27. Roǐzman M., Bertoǐsa B., Klasinc L., and Srzic D. Gas Phase H/D Exchange of Sodiated Amino Acids: Why Do We See Zwitterions?. J. Am. Soc. Mass Spectrom. 17 (2006) 29-36
28. Grabowski J.J., DePuy C.H., Van Doren J.M., and Bierbaum V.M. Gas-Phase Hydrogen-Deuterium Exchange Reactions of Anions: Kinetics and Detailed Mechanism. J. Am. Chem. Soc. 107 (1985) 7384-7389
29. Valentine S.J., and Clemmer D.E. H/D Exchange Levels of Shape-Resolved Cytochrome c Conformers in the Gas Phase. J. Am. Chem. Soc. 119 (1997) 3558-3566
30. Kato S., DePuy C.H., Gronert S., and Bierbaum V.M. Gas-Phase Hydrogen/Deuterium Exchange Reactions of Fluorophenyl Anions. J. Am. Soc. Mass Spectrom. 10 (1999) 840-847
31. Ausloos P., and Lias S.G. Thermoneutral Isotope Exchange Reactions of Cations in the Gas Phase. J. Am. Chem. Soc. 103 (1981) 3641-3647
32. Ranasinghe A., Cooks R.G., and Sethi S.K. Selective Isotopic Exchange of Polyfunctional Ions in Tandem Mass Spectrometry: Methodology, Applications, and Mechanism. Org. Mass Spectrom. 27 (1992) 77
33. Gidden J., and Bowers M.T. Gas-Phase Conformations of Deprotonated and Protonated Mononucleotides Determined by Ion Mobility and Theoretical Modeling. J. Phys. Chem. 107 (2003) 12829-12837
34. Dearden,, D. V. KINFIT: Kinetics Fitting for Coupled Ordinary Differential Equations, version 2.0 http://chemwww.byu.edu/people/dvdearden/kinfit.htm (posted April 2003).
35. Frisch M.J., Trucks G.W., Schlegel H.B., Scuseria G.E., Robb M.A., Cheeseman J.R., Montgomery Jr. J.A., Vreven T., Kudin K.N., Burant J.C., Millam J.M., Iyengar S.S., Tomasi J., Barone V., Mennucci B., Cossi M., Scalmani G., Rega N., Petersson G.A., Nakatsuji H., Hada M., Ehara M., Toyota K., Fukuda R., Hasegawa J., Ishida M., Nakajima T., Honda Y., Kitao O., Nakai H., Klene M., Li X., Knox J.E., Hratchian H.P., Cross J.B., Adamo C., Jaramillo J., Gomperts R., Stratmann R.E., Yazyev O., Austin A.J., Cammi R., Pomelli C., Ochterski J.W., Ayala P.Y., Morokuma K., Voth G.A., Salvador P., Dannenberg J.J., Zakrzewski V.G., Dapprich S., Daniels A.D., Strain M.C., Farkas O., Malick D.K., Rabuck A.D., Raghavachari K., Foresman J.B., Ortiz J.V., Cui Q.A., Baboul G., Clifford S., Cioslowski J., Stefanov B.B., Liu G., Liashenko A., Piskorz P., Komaromi I., Martin R.L., Fox D.J., Keith T., Al-Laham M.A., Peng C.Y., Nanayakkara A., Challacombe M., Gill P.M.W., Johnson B., Chen W., Wong M.W., Gonzalez C., and Pople J.A. Gaussian 03, revision C. 02 (2004), Gaussian, Inc, Wallingford, CT
36. Allinger N.L., Yuh Y.H., and Lii J.-H. Molecular Mechanics. The MM3 Force Field for Hydrocarbons. J. Am. Chem. Soc. 111 (1989) 8551-8566
37. Dewar J.S., Zoebisch E.G., Healy E.F., and Stewart J.P.A.M. 1: A New General Purpose Quantum Mechanical Molecular Model. J. Am. Chem. Soc. 107 (1985) 3902-3909
38. Foresman J.B., and Frisch M.J. Exploring Chemistry with Electronic Structure Methods (1996), Gaussian, Inc, Pittsburgh, PA
39. Pople J.A., Krishnan R., Schlegel H.B., DeFrees D., Binkley J.S., Frisch M.J., Whiteside R.F., Hout R.F., and Hehre W.J. Int. J. Quantum. Chem. Symp. (1981) 15269
40. Liu D., Wyttenbach T., and Bowers M.T. Hydration of Mononucleotides. J. Am. Chem. Soc. 128 (2006) 15155-15163
41. McLucky S.A., Glish G.L., Asano K.G., and Bartmess J.E. Protonated Water and Protonated Methanol Cluster Decompositions in a Quadrupole Ion Trap. . Int. J. Mass Spectrom. 109 (1991) 171-186
42. Gronert S. Estimation of Effective Ion Temperatures in a Quadrupole Ion Trap. J. Am. Soc. Mass Spectrom. 9 (1998) 845-848
43. Wyttenbach T., and Bowers M.T. Gas-Phase Conformations: The Ion Mobility/Ion Chromatography Method. Top. Curr. Chem. 225 (2003) 207-232
44. Nir E., Imhoff P., Kleinermanns K., and de Vries M.S. REMPI Spectra of Laser Desorbed Guanosines. J. Am. Chem. Soc. 122 (2000) 8091-8092
45. Habibi-Goudarzi S., and McLuckey S. Ion Trap Collisional Activation of the Deprotonated Deoxymononucleoside and Deoxydinucleoside Monophosphates. J. Am. Soc. Mass Spectrom. 6 (1995) 102-113
46. Yang X., Wang X., Vorpagel E.R., and Wang L. Direct Experimental Observation of the Low Ionization Potentials of Guanine in Free Oligonucleotides by Using Photoelectron Spectroscopy. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 17588-17592
47. Englander S.W. Hydrogen Exchange and Mass Spectrometry: A Historical Perspective. J. Am. Soc. Mass Spectrom. 17 (2006) 1481-1489
48. Salter E.A., Wierzbicki A., Sperl G., and Thompson W.J. Quantum Mechanical Study of the Syn and Anti-Conformations of Solvated Cyclic GMP. Struct. Chem. 14 (2003) 527-533
49. Kirschner K.N., and Shields G.C. Quantum Mechanical Investigation of Cyclic 3′,5′-Adenosine Monophosphate, the Second Hormonal Messenger. J. Mol. Struct. (Theochem.) 362 (1996) 297-304
50. Huang Y., and Kenttamaa H. Theoretical Estimations of the 298 K Gas-Phase Acidities of the Purine-Based Nucleobases Adenine and Guanine. J. Phys. Chem. A 108 (2004) 4485-4490
51. Rejnek J., Hanus M., Kabeláč M., Ryjáček F., and Hobza P. Correlated ab Initio Study of Nucleic Acid Bases and Their Tautomers in the Gas Phase, in a Microhydrated Environment, and in Aqueous Solution. Part 4. Uracil and Thymine P. Phys. Chem., Chem. Phys. 7 (2005) 2006-2017
52. Close D., Hernández C., Gorb L., and Leszczynski. Influence of Microhydration on the Ionization Energy Thresholds of Thymine: Comparisons of Theoretical and Experimental Values. J. Phys. Chem. A (2006) Published on Web 5/19/2006
53. Leszczynski J. Tautomeric Properties of Nucleic Acid Bases: Ab Initio Study. Encyclopedia of Computational Chemistry (1998), J. Wiley, New York