• Journal of the Korean Magnetic Resonance Society
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• v.13 no.2
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• pp.108-116
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• 2009

The HP0902, a homodimeric 22.1 kDa protein, has been suggested as a putative secretory protein from Helicobacter pylori, although the protein possesses no signal peptide for secretion. Since it may be associated with the virulence of the bacterium, NMR study has been initiated in terms of structural genomics. In our previous effort to assign the backbone NMR resonances, using 800MHz NMR machine at pH 7.8, the resonances from eight of the 99 residues could not be assined due to missing of the signals. In this work, to enhance the extent of assignments, a 900 MHz machine was employed and the sample pH was reduced down to 6.5. Finally, almost all signals, except for those from G9 and S24, could be clearly assigned. The determined secondary structure using the assined chemical shifts indicated that the HP0902 consists of 11 ${\beta}$-strands with no helices. In our database search result, HP0902 was predicted to interact with VacA (Vacuolating cytotoxin A), which is a representative virulence factor secreted from Helicobacter pylori. Thus, molecular interaction between HP0902 and VacA would be worthy of investigation, on the basis of the present results of NMR assignments.

• Journal of the Korean Magnetic Resonance Society
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• v.25 no.1
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• pp.8-11
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• 2021

Transthyretin (TTR) is an important transporter protein for thyroxine (T4) and a holo-retinol protein in human. In its native state, TTR forms a tetrameric complex to construct the hydrophobic binding pocket for T4. On the other hand, this protein is also infamous for its amyloidogenic propensity, which causes various human diseases, such as senile systemic amyloidosis and familial amyloid polyneuropathy/cardiomyopathy. In this work, to investigate various structural features of TTR with solution-state nuclear magnetic resonance (NMR) spectroscopy, we conducted backbone NMR signal assignments. Except the N-terminal two residues and prolines, backbone 1H-15N signals of all residues were successfully assigned with additional chemical shift information of 13CO, 13Cα, and 13Cβ for most residues. The chemical shift information reported here will become an important basis for subsequent structural and functional studies of TTR.

• Bulletin of the Korean Chemical Society
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• v.19 no.8
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• pp.847-851
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• 1998

13C, 15N, and 29Si NMR chemical shifts have been computed for selected X-substituted silatranes (X=Cl, F, H, CH3) using Gauge-Including Atomic Orbitals (GIAO) and Continuous Set of Gauge Transformations (CSGT) at the Hartree-Fock level of theory. The isotropic 13C chemical shifts are largely insensitive to substituent-induced structural changes. In this study, the isotropic 13C chemical shifts GIAO and CSGT calculations at the HF/6-31G and HF/6-31G* levels are sufficiently accurate to aid in experimental peak assignments. The isotropic 13C chemical shifts X-substituted silatranes at HF/6-31G* level are approximately 4 ppm different from the experimental values. In contrast, the isotropic 15N and 29Si chemical shifts and the chemical shielding tensors are quite sensitive to substituent-induced structural changes. These trends are consistent with those of the experiment. The 15N chemical shift parameters demonstrate a very clear correlation with Si-N distance, especially when we use the polarization function. Changes in anisotropy, 3a as well as in the 15N isotropic chemical shifts are due primarily to changes in the value of a.. But in case of "Si the correlations are not as clean as for the 15N chemical shift.

• Molecules and Cells
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• v.24 no.3
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• pp.437-440
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• 2007

$OGL-20P^T$-358 is a novel 66 amino acid residue protein from the hyperthermophile Thermococcus thioreducens sp. nov., strain $OGL-20P^T$, which was collected from the wall of the hydrothermal black smoker in the Rainbow Vent along the mid-Atlantic ridge. This protein, which has no detectable sequence homology with proteins or domains of known function, has a calculated pI of 4.76 and a molecular mass of 8.2 kDa. We report here the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of $OGL-20P^T$-358. Assignments are 97.5% (316/324) complete. Chemical shift index was used to determine the secondary structure of the protein, which appears to consist of primarily ${\alpha}$-helical regions. This work is the foundation for future studies to determine the three-dimensional solution structure of the protein.

• Journal of the Korean Magnetic Resonance Society
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• v.22 no.3
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• pp.64-70
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• 2018

Human Tid1, belonging to the family of the Hsp40/DnaJ, functions as a co-chaperone of cytosolic and mitochondrial Hsp70 proteins. In addition, the conserved J-domain and G/F-rich region of Tid1 has been suggested to interact with the p53 tumor suppressor protein, to translocate it to the mitochondria. Here, backbone NMR assignments were achieved for the putative p53-binding domain of Tid1. The obtained chemical shift information identified five ${\alpha}$-helices including four helices characteristic of J-domain, which are connected to a short ${\alpha}$-helix in the G/F-rich region via a flexible loop region. We expect that this structural information would contribute to our progressing studies to elucidate atomic structure and molecular interaction of the domain with p53.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.2
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• pp.50-54
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• 2017

Cupin-superfamily proteins represent the most functionally diverse groups of proteins and include a huge number of functionally uncharacterized proteins. Recently, YaiE, a cupin protein from Escherichia coli has been suggested to be involved in a novel activity of pyrimidine/purine nucleoside phosphorylase (PPNP). In the present study, we achieved a complete backbone NMR assignments of YaiE, by a series of heteronuclear multidimensional NMR experiments on its [$^{13}C/^{15}N$]-enriched sample. Subsequently, secondary structure analysis using the assigned chemical shift values identified 10 obvious ${\beta}-strands$ and a tentative $3_{10}-helix$. Taken all together, the results constitute the first structural characterization of a putative PPNP cupin protein.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.1
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• pp.20-25
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• 2017

The cytoplasmic domains A and B of the mannitol transporter enzyme $II^{Mtl}$ are covalently linked in Escherichia coli, but separately expressed in Thermoanaerobacter Tengcongensis. The phosphorylation of domain B ($TtIIB^{Mtl}$) substantially increases the binding affinity to the domain A ($TtIIA^{Mtl}$) in T. Tengcongensis. To understand the structural basis of the enhanced domain-domain interaction by protein phosphorylation, we obtained NMR backbone assignments of the phospho-$TtIIB^{Mtl}$ using a standard suite of triple resonance experiments. Our results will be useful to monitor chemical shift changes at the active site of phosphorylation and the binding interfaces.

• Journal of the Korean Magnetic Resonance Society
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• v.27 no.2
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• pp.5-9
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• 2023

t ENOD40B, a plant peptide hormone, was doubly labeled with C-13 and N-15 by recombinant production in Escherichia coli. The peptide was prepared by affinity chromatography followed by protease cleavage and reverse-phase chromatography. To elucidate the mode of action against its receptor, sucrose synthase, we proceeded to assign the backbone and side-chain resonances using a set of double and triple resonance experiments. This result will be used to determine the three-dimensional structure of the peptide at its bound state as well as to observe the chemical shift changes upon binding.

• Proceedings of the Korean Society of Applied Pharmacology
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• 1996.04a
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• pp.183-183
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• 1996

Bacteriophage T4 endonuclease V initiates the repair of ultraviolet (UV)-induced pyrimidine dimer photoproducts in duplex DNA. The mechanism of DNA strand cleavage involves four sequential stens: linear diffusion along dsDNA, pyrimidine dimer-specific binding,l pyrimidine dimer-DNA glycosylase activity, and Af lyase activity. Although crystal structure is known for this enzyme, solution structure has not been yet known. In order to elucidate the solution structure of this enzyme NMR spectroscopy was used. As a basis for the NMR peak assignment of the protein, HSQC spectrum was obtained on the uniformly $\^$15/N-labeled T4 endonuclease V. Each amide peak of the spectrum were classified according to amino acid spin systems by interpreting the spectrum of $\^$15/N amino acid-specific labeled T4 endonuclease V. The assignment was mainly obtained from three-dimensional NMR spectra such as 3D NOESY-HMQC, 3D TOCSY-HMQC. These experiments were carried out will uniformly $\^$15/N-labeled sample. In order to assign tile resonance of backbon atom, triple-resonance theree-dimensional NMR experiments were also performed using double labeled($\^$15/N$\^$13/C) sample. 3D HNCA, HN(CO)CA, HNCO, HN(CA)HA spectra were recorded for this purpose. The results of assignments were used to interpret the interaction of this enzyme with DNA. HSQC spectrum was obtained for T4 endonuclease V with specific $\^$15/N-labeled amino acids that have been known for important residue in catalysis. By comparing the spectrum of enzyme*DNA complex with that of the enzyme, we could confirm the important role of some residues of Thr, Arg, Tyr in activity. The results of assignments were also used to predict the secondary structure by chemical shift index (CSI).

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.2
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• pp.56-60
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• 2016

Adenylate kinase (AK) enzyme which acts as the catalyst of reversible high energy phosphorylation reaction between ATP and AMP which associate with energetic metabolism and nucleic acid synthesis and signal transmission. This enzyme has three distinct domains: Core, AMP binding domain (AMPbd) and Lid domain (LID). The primary role of AMPbd and LID is associated with conformational changes due to flexibility of two domains. Three dimensional structure of human AK1 has not been confirmed and various mutation experiments have been done to determine the active sites. In this study, AK1R138A which is changed arginine[138] of LID domain with alanine[138] was made and conducted with NMR experiments, backbone dynamics analysis and mo-lecular docking dynamic simulation to find the cause of structural change and substrate binding site. Synthetic human muscle type adenylate kinase 1 (hAK1) and its mutant (AK1R138A) were re-combinded with E. coli and expressed in M9 cell. Expressed proteins were purified and finally gained at 0.520 mM hAK1 and 0.252 mM AK1R138A. Multinuclear multidimensional NMR experiments including HNCA, HN(CO)CA, were conducted for amino acid sequence analysis and signal assignments of $^1H-^{15}N$ HSQC spectrum. Our chemical shift perturbation data is shown LID domain residues and around alanine[138] and per-turbation value(0.22ppm) of valine[179] is consid-ered as inter-communication effect with LID domain and the structural change between hAK1 and AK1R138A.