• Journal of the Korean Magnetic Resonance Society
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• v.24 no.3
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• pp.70-76
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• 2020

The CRISPR-Cas system provides an adaptive immunity for bacteria and archaea against invading phages or foreign plasmids. In the type II CRISPR-Cas system, a single effector protein Cas9 and a guide RNA form an RNA-guided endonuclease complex that can degrade DNA targets of foreign origin. To avoid the Cas9-mediated destruction, phages evolved anti-CRISPR (Acr) proteins that neutralize the host bacterial immunity by inactivating the CRISPR-Cas system. Here we report the backbone ¹H, ¹⁵N, and ¹³C resonance assignments of AcrIIA5 that inhibits the endonuclease activity of type II-A Streptococcus thermophilus Cas9 and also Streptococcus pyogenesis Cas9 using triple resonance nuclear magnetic resonance spectroscopy. The backbone chemical shifts of AcrIIA5 predict a disordered region at the N-terminus, followed by an αββββαβββ fold.

• Journal of the Korean Magnetic Resonance Society
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• v.23 no.4
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• pp.104-107
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• 2019

Many proteins are expressed as an insoluble form during the production using Escherichia coli (E. coli) system. Although various methods are applied to increase their amounts of soluble expression, refolding is the only feasible way to obtain a target protein in some cases. Moreover, protein NMR experiments require ¹³C/¹⁵N-labeled proteins that can only be obtained from E. coli systems in terms of cost and technical difficulty. The finding of appropriate refolding conditions for a target protein is a time-consuming process. In particular, it is very difficult to determine whether the refolded protein has a native structure, when a target protein has no enzymatic activity and its refolding yield is very low. Here, we showed that 1-dimensional ¹H-¹⁵N heteronuclear single quantum correlation (1D ¹H-¹⁵N HSQC) experiment can be efficiently used to screen an optimal condition for the refolding of a target protein by monitoring both the structure and concentration of the refolded protein.

• Molecules and Cells
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• v.20 no.3
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• pp.442-445
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• 2005

HP0894 (SwissProt/TrEMBL ID O25554) is an 88-residue conserved hypothetical protein from Helicobacter pylori strain 26695 with a calculated pI of 8.5 and a molecular weight of 10.38 kDa. Proteins with sequence similarity to HP0894 exist in Vibrio choierae, Enterococcus faecalis, Campylobacter jejuni, Streptococcus pneumoniae, Haemophilus influenzae, Escherichia coli O157, etc. Here we report the sequence-specific backbone resonance assignments of HP0894. About 97.5% (418/429) of the HN, N, CO, $C{\alpha}$, $C{\beta}$ resonances of the 88 residues of HP0894 were assigned. On the basis of these assignments, three helical regions and four strand regions were identified using the CSI program. This study is a prerequisite for calculating the solution structure of HP0894, and studying its interaction with its substrates, if any, and/or with other proteins.

• BMB Reports
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• v.40 no.5
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• pp.839-843
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• 2007

HP0495 (Swiss-Prot ID; Y495_HELPY) is an 86-residue hypothetical protein from Helicobacter pylori strain 26695. The function of HP0495 cannot be identified based on sequence homology, and HP0495 is included in a fairly unique sequence family. Here, we report the sequencespecific backbone resonance assignments of HP0495. About 97% of all the $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances were assigned unambiguously. We could predict the secondary structure of HP0495, by analyzing the deviation of the $^{13}C{\alpha}$ and $^{13}C{\beta}$ shemical shifts from their respective random coil values. Secondary structure prediction shows that HP0495 consists of two $\alpha$-helices and four $\beta$-strands. This study is a prerequisite for determining the solution structure of HP0495 and investigating the protein-protein interaction between HP0495 and other Helicobacter pylori proteins.

• Journal of the Korean Magnetic Resonance Society
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• v.12 no.2
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• pp.65-73
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• 2008

HP1298 (Swiss-Prot ID ; P65108) is an 72-residue protein from Helicobacter pylori strain 26695. The function of HP1298 was identified as Translation initiation factor IF-l based on sequence homology, and HP1298 is included in IF-l family. Here, we report the sequence-specific backbone resonance assignments of HP1298. About 97% of all the $^{1}HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$, and $^{13}CO$ resonances could be assigned unambiguously. We could predict the secondary structure of HP1298, by analyzing the deviation of the $^{13}C{\alpha}$ and $^{13}C{\beta}$ shemical shifts from their respective random coil values. Secondary structure prediction shows that HP1298 consists of six $\beta$-strands. This study is a prerequisite for determining the solution structure of HP1298 and investigating the structure-function relationship of HP1298. Assigned chemical shift can be used for the study on interaction between HP1298 and other Helicobacter pylori proteins.

• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2535-2541
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• 2009

Prebiotic isomaltooligosaccharide preparations contain $\alpha$-D-glucooligosaccharides comprising isomaltooligosaccharides (IMOs) and non-prebiotic maltooligosaccharides (MOs). They are both glucose oligosaccharides characterized by their degree of polymerization (DP) value (from 2 to $\sim$10), linkages types and positions (IMOs: $\alpha$-(1$\rightarrow$2, 3, 6 and in a lower proportion internal 1$\rightarrow$4) linkages, MOs: α-(1$\rightarrow$4) linkages). Their structure is the key factor for their prebiotic potential. In order to determine and elucidate the exact structure of unknown IMOs and MOs, unambiguous assignments of $^{13}C$ and $^1H$ chemical shifts of commercial standards, representative of IMOs and MOs diversity, have been determined using optimized standard one and two-dimensional experiments such as $^1H$ NMR, $^{13}C$ NMR, APT and ${^1}H-{^1}H$ COSY, TOCSY, NOESY and <$^1H-{^{13}}C$ heteronuclear HSQC, HSQC-TOCSY, and HMBC. Here we point out the differential effect of substitution by a glucose residue at different positions on chemical shifts of anomeric as well as ring carbons together with the effect of the reducing end configuration for low DP oligosaccharides and diasteroisotopic effect for H-6 protons. From this study, structural $^{13}C$ specific spectral features can be identified as tools for structural analysis of isomaltooligosaccharides.

• Bulletin of the Korean Chemical Society
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• v.26 no.1
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• pp.131-135
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• 2005

Gallium nitride (GaN) powders and nanowires were prepared by using tris(N,N-dimethyldithiocarbamato)gallium(III) (Ga(DmDTC)$_3$) and tris(N,N-diethyldithiocarbamato)gallium(III) (Ga(DeDTC)$_3$) as new precursors. The GaN powders were obtained by reaction of the complexes with ammonia in the temperature ranging from 500 to 1100 ${^{\circ}C}$. The process of conversion of the complexes to GaN was monitored by their weight loss, XRD, and $^{71}$Ga magic-angle spinning (MAS) NMR spectroscopy. Most likely the complexes decompose to $\gamma$ -Ga$_2$S$_3$ and then turn into GaN via amorphous gallium thionitrides (GaS$_x$N$_y$). The reactivity of Ga(DmDTC)$_3$ with ammonia was a little higher than that of Ga(DeDTC)$_3$. Room-temperature photoluminescence spectra of asprepared GaN powders exhibited the band-edge emission of GaN at 363 nm. GaN nanowires were obtained by nitridation of as-ground $\gamma$ -Ga$_2$S$_3$ powders to GaN powders, followed by sublimation without using templates or catalysts.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.3
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• pp.71-75
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• 2018

The CRISPR-Cas system is the adaptive immune system in bacteria and archaea against invading phages or foreign plasmids. In the type II CRISPR-Cas system, an endonuclease Cas9 cleaves DNA targets of phages as directed by guide RNA comprising crRNA and tracrRNA. To avoid targeting and destruction by Cas9, phages employ anti-CRISPR (Acr) proteins that act against host bacterial immunity by inactivating the CRISPR-Cas system. Here we report the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of AcrIIA4 that inhibits endonuclease activity of type II-A Listeria monocytogenes Cas9 and also Streptococcus pyogenesis Cas9 using triple resonance nuclear magnetic resonance spectroscopy. The secondary structures of AcrIIA4 predicted by the backbone chemical shifts show an ${\alpha}{\beta}{\beta}{\beta}{\alpha}{\alpha}$ fold, which is used to determine the solution structure.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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• pp.42-48
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• 2015

The mannitol transporter Enzyme $II^{Mtl}$ of the bacterial phosphotransferase system has two cytoplasmic phosphoryl transfer domains $IIA^{Mtl}$ and $IIB^{Mtl}$. The two domains are linked by a flexible peptide linker in mesophilic bacterial strains, whereas they are expressed as separated domains in thermophilic strains. Here, we carried out backbone assignment of $IIA^{Mtl}$ from thermophilic Thermoanaerobacter Tencongensis using a suite of heteronuclear triple resonance NMR spectroscopy. We have completed 94% of the backbone assignment, and obtained secondary structural information based on torsion angles derived from the chemical shifts. $IIA^{Mtl}$ of Thermoanaerobacter Tencongensis is predicted to have six ${\beta}$ strands and six ${\alpha}$ helices, which is analogous to $IIA^{Mtl}$ of Escherichia coli.

• Mass Spectrometry Letters
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• v.14 no.3
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• pp.110-115
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• 2023

The reaction of (COD)PdCl₂ with new C₃-symmetric tridentate L (COD = 1,5-cyclooctadien; L = 1,3,5-tris(picolinoyloxyethyl)cyanurate) in a mixture of acetone and dichloromethane produces single crystals consisting of unprecedented monometallacyclic [PdCl₂(L)]. This cyclic compound arises from trans-chelation of two of three donating pyridyl groups of L, while the third pyridyl group remains uncoordinated. Electrospray ionization mass spectrometry (ESI-MS) data on L exhibited the major peak corresponding to [C₂₇H₂₄N₆O₉ + H⁺]⁺. Fast atom bombardment mass spectrometry (FABMS) data on [PdCl₂(L)], however, showed the mass peak corresponding to the L instead of the present palladium(II) compound species, due to the insolubility and dissociation in solution. The physicochemical properties of the present palladium(II) compound were fully characterized by means of infrared (IR) and nuclear magnetic resonance (NMR) spectroscopy, thermal analysis, single-crystal X-ray diffraction (SC-XRD) measurement.