Gas-phase structures of solution-phase zwitterions: Charge solvation or salt bridge?

Drayss, Miriam K.; Blunk, Dirk; Polfer, Nick C.; Schmuck, Carsten; Gao, Bing; Wyttenbach, Thomas; Bowers, Michael T.; Schäfer, Matthias

doi:10.1016/j.ijms.2008.12.011

Cited by 17 publications

(19 citation statements)

References 16 publications

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“…The properties of the three lowest‐energy protonation states are considered (below 40 kJ/mol) which all have the titrable site of the rhodamine dye protonated (see Table S1, supporting information). It is interesting to note that it is not the charge‐solvated but a zwitterionic type of structure that has a good chance to be the lowest in energy, a finding that is in line with earlier studies . Upon explicit collision trajectory calculations, we can estimate the CCS for each structural prototype (predicted CCS values in Table ).…”

Section: Resultssupporting

confidence: 80%

“…The hierarchical structuration of biomolecules nevertheless renders the problem of structure determination particularly tricky to solve, thus justifying the combination of putatively complementary techniques. An appealing approach is to use a measure of the global shape of a molecule, like the collision cross sections measured by IMS, with more local information on the molecular arrangement that can be obtained from IRMPD, or other spectroscopic techniques . Such attempts have nevertheless been limited to relatively small systems in general.…”

Section: Introductionmentioning

confidence: 99%

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Ion mobility resolved photo‐fragmentation to discriminate protomers

Choi

Kulesza

Daly

et al. 2018

Rapid Comm Mass Spectrometry

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Section: Resultssupporting

confidence: 80%

Section: Introductionmentioning

confidence: 99%

Ion mobility resolved photo‐fragmentation to discriminate protomers

Choi

Kulesza

Daly

et al. 2018

Rapid Comm Mass Spectrometry

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“…In [m 7 GuoþNa] þ , bidentate (N1,O6) sodium cation binding is stabilized by shielding the partial negative character of the m 7 Guo zwitterion through the formation of a Na þ Á Á ÁO6 -Á Á ÁC7H 3 þ salt-bridge structure similar to those observed in metal cationized amino acids. [84][85][86][87][88][89][90][91] Guanine orientation and sugar puckering of the calculated conformers…”

Section: Cation Binding Sites Of the Calculated Conformersmentioning

confidence: 99%

Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating

Devereaux

Zhu

Rodgers

2018

Eur J Mass Spectrom (Chichester)

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The frequency and diversity of posttranscriptional modifications add an additional layer of chemical complexity beyond canonical nucleic acid sequence. Methylations are particularly frequently occurring and often highly conserved throughout the kingdoms of life. However, the intricate functions of these modified nucleic acid constituents are often not fully understood. Systematic foundational research that reduces systems to their minimum constituents may aid in unraveling the complexities of nucleic acid biochemistry. Here, we examine the relative intrinsic N-glycosidic bond stabilities of guanosine and five naturally occurring methylguanosines (O2'-, 1-, 7-, N2,N2-di-, and N2,N2,O2'-trimethylguanosine) probed by energy-resolved collision-induced dissociation tandem mass spectrometry and complemented with quantum chemical calculations. Apparent glycosidic bond stability is generally found to increase with increasing methyl substitution (canonical < mono- < di- < trimethylated). Many biochemical transformations, including base excision repair mechanisms, involve protonation and/or noncovalent interactions to increase nucleobase leaving-group ability. The protonated gas-phase methylguanosines require less activation energy for glycosidic bond cleavage than their sodium cationized forms. However, methylation at the N7 position intrinsically weakens the glycosidic bond of 7-methylguanosine more significantly than subsequent cationization, and thus 7-methylguanosine is suggested to be under perpetually activated conditions. N7 methylation also alters the nucleoside geometric preferences relative to the other systems, including the nucleobase orientation in the neutral form, sugar puckering in the protonated form, and the preferred protonation and sodium cation binding sites. All of the methylated guanosines examined here are predicted to have proton affinities and gas-phase basicities that exceed that of canonical guanosine. Additionally, the proton affinity and gas-phase basicity trends exhibit a roughly inverse correlation with the apparent glycosidic bond stabilities.

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“…In the former, the net charge is determined by Coulomb repulsion and distribution of individual residues across the surface area of the protein ion, whilst in the latter charge is determined by a combination of the p K a of each ionizable functional group and the solution pH. Ionic interactions are dominant in the gas‐phase, and may be the principal driving force for structural stabilisation [8–11] . While kinetically trapped, partially collapsed gas‐phase protein ions can remain unperturbed for many milliseconds, [12] which is typically longer than the time from desolvation to detection in a nMS measurement.…”

Section: Introductionmentioning

confidence: 99%

Decoding Protein Gas‐Phase Stability with Alanine Scanning and Collision‐Induced Unfolding Ion Mobility Mass Spectrometry

et al. 2020

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Native mass spectrometry is a widely used tool in structural biology, providing information on protein structure and interactions through preservation of complexes in the gas phase. Herein, the importance of intramolecular non‐covalent interactions in the gas phase has been studied by alanine scanning and collision‐induced unfolding (CIU) ion mobility‐mass spectrometry. Mutation of specific polar and ionic residues on the surface of an acyl carrier protein (ACP) were found to destabilise the compact gas‐phase structure with mutants E31A, D32A, D41A and D65A being particularly destabilised. Molecular dynamics simulations of the ACP 7+ and 8+ ions showed extended intramolecular interactions, resulting from sidechain collapse of polar surface residues, which were confined to the gas phase and consistent with the CIU data. These findings provide evidence for the importance of specific ionic residues, and their interactions, in the maintenance of compact protein gas‐phase structure.

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Gas-phase structures of solution-phase zwitterions: Charge solvation or salt bridge?

Cited by 17 publications

References 16 publications

Ion mobility resolved photo‐fragmentation to discriminate protomers

Ion mobility resolved photo‐fragmentation to discriminate protomers

Relative glycosidic bond stabilities of naturally occurring methylguanosines: 7-methylation is intrinsically activating

Decoding Protein Gas‐Phase Stability with Alanine Scanning and Collision‐Induced Unfolding Ion Mobility Mass Spectrometry

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