Conformationally driven gas-phase H/D exchange of dinucleotide negative ions

[en] Gas-phase hydrogen/deuterium exchange of six deprotonated dinucleoticles with CD3OD was performed in the second hexapole of a Fourier transform ion-cyclotron resonance (FTICR) mass spectrometer. To complete these experiments, dynamic simulations were carried out to investigate the different conformations adopted by the dinucleotides. In the experimental conditions and in integrating the experimental and theoretical results, H/D exchange was shown to be controlled by hydrogen accessibility and not by the chemical nature of the heteroatom bearing the exchangeable hydrogen. A model including simultaneous H/D exchanges at the experimental time scale was used to reproduce the dinucleotide H/D exchange kinetic plots. The relay mechanism was not relevant for dinucleotides. This allowed the H/D exchange rates to be directly linked to conformations.

Disciplines :

Physics
Chemistry

Author, co-author :

Balbeur, Dorothée ; Université de Liège - ULiège > Chimie physique, spectrométrie de masse

Dehareng, Dominique ; Université de Liège - ULiège > Centre d'ingénierie des protéines

De Pauw, Edwin ; Université de Liège - ULiège > Chimie physique, spectrométrie de masse

Language :

English

Title :

Conformationally driven gas-phase H/D exchange of dinucleotide negative ions

Publication date :

October 2007

Journal title :

Journal of the American Society for Mass Spectrometry

ISSN :

1044-0305

eISSN :

1879-1123

Publisher :

Elsevier Science Inc, New York, United States - New York

Volume :

Issue :

Pages :

1827-1834

Peer reviewed :

Peer Reviewed verified by ORBi

Funders :

BELSPO - SPP Politique scientifique - Service Public Fédéral de Programmation Politique scientifique
F.R.S.-FNRS - Fonds de la Recherche Scientifique

Available on ORBi :

since 05 January 2009

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Bibliography

Gard E., Green 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
Campbell S.C., Rodgers M.T., Marzluff E.M., and Beauchamp J.L. Deuterium Exchange Reactions as a Probe of Biomolecule Structure. Fundamental Studies of Gas Phase H/D Exchange Reactions of Protonated Glycine Oligomers with D2O, CD3OD, CD3CO2D, and ND3. J. Am. Chem. Soc 117 (1995) 12840-12854
Freitas M.A., Shi S.D.H., Hendrickson C.L., and Marshall A.G. Gas-Phase RNA and DNA Ions. 1. H/D Exchange of the [M - H]- Anions of Nucleoside 5′ Monophosphates (GMP, dGMP, AMP, dAMP, CMP, dCMP, UMP, dTMP), Ribose 5-Monophosphate, and 2-Deoxyribose 5-Monophosphate with D2O and D2S. J. Am. Chem. Soc 120 (1998) 10187-10193
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
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
Wyttenbach T., and Bowers M.T. The Hydrogen/Deuterium Exchange Mechanism. J. Am. Soc. Mass Spectrom 10 (1999) 9-14
Gree-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
Crestoni M.E., and Fornarini S. Gas-Phase Hydrogen/Deuterium Exchange of Adenine Nucleotides. J. Mass Spectrom 38 (2003) 854-861
Wang F., Freitas M.A., Marshall A.G., and Skyes B.D. Gas-Phase Memory of Solution-Phase Protein Conformation: H/D Exchange and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry of the N-Terminal Domain of Cardiac Troponin C. Int. J. Mass Spectrom 192 (1999) 319-325
Herrmann K., Wysocki V., and Vorpagel E.R. Computational Investigation and Hydrogen/Deuterium Exchange of the Fixed Charge Derivative Tris(2,4,6-Trimethoxyphenyl) Phosphonium: Implication of the Aspartic Acid Cleavage Mechanism. J. Am. Soc. Mass Spectrom 16 (2005) 1067-1080
Herrmann K.A., Kuppannan K., and Wysocki V.H. Fragmentation of Doubly-Protonated Peptide Ion Populations Labeled by H/D Exchange with CD3OD. Int. J. Mass Spectrom 249/250 (2006) 93-105
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
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
Reyzer M.L., and Brodbelt J.S. Gas-Phase H/D Exchange Reactions of Polyamine Complexes: (M + H)+, (M + Alkali Metal+), and (M + 2H)2+. J. Am. Soc. Mass Spectrom 11 (2000) 711-721
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
Chipuk J.E., and Brodbelt J.S. Gas-Phase Hydrogen/Deuterium Exchange of 5′ and 3′ Mononucleotides in a Quadrupole ion Trap: Exploring the Role of Conformation and System Energy. J. Am. Soc. Mass Spectrom 18 (2007) 724-736
Gidden J., and Bowers M.T. Gas-Phase Conformational and Energetic Properties of Deprotonated Dinucleotides. Eur. Phys. J. D 20 (2002) 409-419
Goodner K.L., Milgram K.E., Williams K.R., Watson C.H., and Eyler J.R. Quantification of Ion Abundances in Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. J. Am. Soc. Mass Spectrom 9 (1998) 1204-1212
Marshall A.G., Comisarow M.B., and Parisod G. Relaxation and Spectral Line Shape in Fourier Transform Ion Resonance Spectroscopy. J. Chem. Phys 71 (1979) 4434-4444
Nir E., Imhof P., Kleinermanns K., and de Vries M.S. REMPI Spectroscopy of Laser Desorbed Guanosines. J. Am. Chem. Soc 122 (2000) 8091-8092
Rodgers M.T., Campbell S., Marzluff E.M., and Beauchamp J.L. Low-Energy Collision-Induced Dissociation of Deprotonated Dinucleotides: Determination of the Energetically Favored Dissociation Pathways and the Relative Acidities of Nucleic Acid Bases. Int. J. Mass Spectrom. Ion Processes 137 (1994) 121-149
Gidden J., and Bowers M.T. Gas-Phase Conformation of Deprotonated and Protonated Mononucleotides Determined by Ion Mobility and Theoretical Modeling. J. Phys. Chem 107 (2003) 12829-12837
Liu D., Wyttenbach T., and Bowers M.T. Hydration of Mononucleotides. J. Am. Chem. Soc 128 (2006) 15155-15163
Saenger W. Principles of Nucleic Acid Structure (1984), Springer-Verlag, New York 14-23
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., Baboul A.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
McDonnell L.A., Giannakopulos A.E., Derrick P.J., Tsybin Y.O., and Hakansson P.A. Theoretical Investigation of The Kinetic Energy of Ions Trapped in a Radio-Frequency Hexapole Ion Trap. Eur. J. Mass Spectrom 8 (2002) 181-189