• Bulletin of the Korean Chemical Society
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• v.35 no.3
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• pp.749-752
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• 2014

New software was developed for the assignment of elemental formulae based on high-resolution mass spectra and subsequent hydrogen/deuterium exchange data. Entire peaks in high-resolution mass spectra were grouped by their Kendrick mass defect values, and the weighted RMS deviations between theoretical and experimental values were used to determine elemental formulae. After this initial assignment, formulae containing deuterium atoms were sorted in order to interpret hydrogen/deuterium exchange spectra. The software was successfully applied to hydrogen/deuterium exchange spectra of resins and aromatic fractions from heavy crude oil.

• Bulletin of the Korean Chemical Society
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• v.28 no.10
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• pp.1643-1644
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• 2007

• BMB Reports
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• v.41 no.1
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• pp.35-40
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• 2008

The molten globular conformation of V26A ubiquitin (valine to alanine mutation at residue 26) was studied by nuclear magnetic resonance spectroscopy in conjunction with amide hydrogen/deuterium exchange. Most of the amide protons that are involved in the native secondary structures were observed to be protected in the molten globule state with the protection factors from 1.2 to 6.7. These protection factors are about 2 to 6 orders of magnitude smaller than those of the native state. These observations indicate that V26A molten globule has native-like backbone structure with marginal stability. The comparison of amide protection factors of V26A ubiquitin molten globule state with those of initial collapsed state of the wild type ubiquitin suggests that V26A ubiquitin molten globule state is located close to unfolded state in the folding reaction coordinate. It is considered that V26A ubiquitin molten globule is useful model to study early events in protein folding reaction.

• Mass Spectrometry Letters
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• v.12 no.4
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• pp.146-151
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• 2021

In this study, the hydrogen/deuterium (HDX) exchange mechanism of active hydrogen, nitrogen, and sulfur-containing polycyclic aromatic hydrocarbon (PAH) dissolved in toluene and deuterated methanol by atmospheric pressure photoionization (APPI) is investigated. The comparison of the data obtained using APPI suggests that aniline and benzene-1,2-dithiol contain two exchanging hydrogens. The APPI HDX that best explains the experimental findings was investigated with the use of quantum mechanical calculations. The HDX mechanism is composed of a two-step reaction: in the first step, analyte radical ion gets deuterated, and in the second step, the hydrogen transfer occurs from deuterated analyte to de-deuterated methanol to complete the exchange reaction. The suggested mechanism provides fundamentals for the HDX technique that is important for structural identification with mass spectrometry. This paper is dedicated to Professor Seung Koo Shin for his outstanding contributions in chemistry and mass spectrometry.

• Bulletin of the Korean Chemical Society
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• v.6 no.5
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• pp.270-272
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• 1985

The rate constants of the hydrogen-deuterium exchange of 8-CH groups in 5'-rAMP and 5'-GMP were measured by laser Raman spectroscopy. The Arrhenius activation energies calculated from the rate constants measured as a function of temperature were similar for both compounds. However, the effects of pD on exchange rate constants were different for the two compounds. Our kinetic data support the exchange reaction mechanism involving an ylide type intermediate.

• Bulletin of the Korean Chemical Society
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• v.34 no.5
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• pp.1401-1406
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• 2013

This study tested the feasibility of observing H/D exchange of intact protein by top-down electron capture dissociation (ECD) mass spectrometry for the investigation of protein structure. Ubiquitin is selected as a model system. Local structural information was obtained from the deuteration levels of c and $z^{\cdot}$ ions generated from ECD. Our results showed that ${\alpha}$-helix region has the lowest deuteration level and the C-terminal fraction containing a highly mobile tail has the highest deuteration level, which correlates well with previous X-Ray and HDX/NMR analyses. We studied site-specific H/D exchange kinetics by monitoring H/D exchange rate of several structural motives of ubiquitin. Two hydrogen bonded ${\beta}$-strands showed similar HDX rates. However, the outer ${\beta}$-strand always has higher deuteration level than the inner ${\beta}$-strand. The HDX rate of the turn structure (residues 8-11) is lower than that of ${\beta}$-strands (residues 1-7 and residues 12-17) it connects. Although isotopic distribution gets broader after H/D exchange which results in a limited number of backbone cleavage sites detected, our results demonstrate that this method can provide valuable detailed structural information of proteins. This approach should also be suitable for the structural investigation of other unknown proteins, protein conformational changes, as well as protein-protein interactions and dynamics.

• Bulletin of the Korean Chemical Society
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• v.34 no.10
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• pp.2959-2962
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• 2013

As the concentration of aqueous $CD_3OH$ solutions was decreased, the OD peaks in $^2H$ NMR spectra grew relative to the $CD_3$ peaks. Isotope impurity for OH groups of $CD_3OH$ and deuterium naturally present in water contributed to the OD peaks. Using these peak area data, the site-specific isotope populations of isotope enriched chemicals were measured. In addition, the method using both $^1H$ and $^2H$ NMR spectroscopy was demonstrated with neat $CD_3OH$ to measure the site-specific isotope populations. The results indicate that although it represents only ~0.015% of hydrogen isotopes, the deuterium naturally present in solvents cannot be ignored, especially when the concentration of deuterium-enriched solutes is varied. Proton/deuteron exchange between methyl and methyl/hydroxyl groups was confirmed to be negligible, while that among hydroxyl groups was detectable.

• Journal of Photoscience
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• v.9 no.2
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• pp.299-301
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• 2002

Recent denaturation experiments of bacteriorhodopsin (bR) in the dark and under illumination at high temperatures revealed that irreversible thermal bleaching occurs above ~ 70°C and the preceding reversible structural changes in the dark above 60°C are closely related to irreversible photobleaching observed in the same temperature range (Yokoyama et al. (2002). J Biochem. 131,785). In this study, structural properties of bacteriorhodopsin (bR) at high temperatures were extensively probed by hydroxylamine reactivity with the Schiff base in the dark and hydrogen-deuterium (H-D) exchange in the peptide groups. In the Arrhenius plot from kinetics measurements of the hydroxylamine reaction, a good linear relationship between the reaction time constant and the inverse of the absolute temperature was observed below 60°C, while significant increase started above 60°C, suggesting that remarkable increase in water accessibility of the Schiff base in the temperature region. FT-IR spectroscopic studies on the H-D exchange suggested increase in the deuterium exchanges rate of the peptide hydrogen in the same temperature region.

• Proceedings of the Korean Nuclear Society Conference
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• 1998.10a
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• pp.340-340
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• 1998

• Nuclear Engineering and Technology
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• v.53 no.8
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• pp.2570-2575
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• 2021

The exchange behaviors of hydrogen isotopes between protonated lithium metal compounds and deuterated water or tritiated water were investigated. The various protonated lithium metal compounds were prepared by acid treatment of lithium metal compounds with different crystal structures and metal compositions. The protonated lithium metal compounds could more effectively reduce the deuterium concentration in water compared with the corresponding pristine lithium metal compounds. The H⁺ in the protonated lithium metal compounds was speculated to be more readily exchangeable with hydrons in the aqueous solution compared with Li⁺ in the pristine lithium metal compounds, and the exchanged heavier isotopes were speculated to be more stably retained in the crystal structure compared with the light protons. When the tritiated water (157.7 kBq/kg) was reacted with the protonated lithium metal compounds, the protonated lithium manganese nickel cobalt oxide was found to adsorb and retain twice as much tritium (163.9 Bq/g) as the protonated lithium manganese oxide (69.9 Bq/g) and the protonated lithium cobalt oxide (75.1 Bq/g) in the equilibrium state.