• Proceedings of the Korean Society of Applied Pharmacology
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• 1998.11a
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• pp.136-136
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• 1998

L-asparaginyl and L- aspartyl residues in proteins are subject to spontaneous degradation reactions generating isomerized and racemized aspartyl derivatives. Proteins containing L-isoaspartyl and D-aspartyl residues usually have altered structures and diminished biological activities. These residues can be recognized and be repaired to normal L-aspartyl residues by protein L-isoaspartyl methyltransferase(PIMT), which is present at high levels in testis. Although testicular PIMT have been shown to be involved in either sperm motility or sperm maturation, it may play an important role in the repair of damaged sperm proteins during the prolonged period of epididymal transport and storage. In the present study, as a initial step toward elucidating the function of protein carboxylmethylation in testis, we purified PIMT from porcine testicular cytosol as a momeric 27,000 Da species by ammonium sulfate precipitation, DEAE-sephacel chromatography, SAH-liganded affinity chromatography, and gel filtration chromatography. The optimum pH for the reaction was 6.0. $K_{m}$ values of the enzyme for the S-adenosyl-L-methionine (SAM), synthetic oligopeptide(VYP-L-isoD-HA) and histone type II-As were 1.0 ${\mu}$M, 33.2 ${\mu}$M and 276 ${\mu}$M respectively. Consequently, properties of the porcine testicular PIMT is similar to that of other mammalian PIMTs.

• Journal of Life Science
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• v.8 no.2
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• pp.226-226
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• 1998

Discovery of molecular chaperone has stimulate cell biologists and thus made it possible to re-examine the processes whereby proteins achieve and maintain their functional conformations within living cells. the term ‘Molecular chaperone’ was first coined to describe one particular protein involved in the assembly of nucleosomes, but the term has now been extended to describe the function of a wide variety of proteins that assist protein transport across membranes, folding of nascent polypeptide, the assembly and disassembly of oligomeric structures, and the recovery or removal of proteins damaged by various environmental stresses including heat shock. Progress of molecular chaperone research is still limited by the lack of 3-dimensional structural information and detailed interacts with taget proteins in the cell. However, several laboratories around the world are attempting to extend our knowledge on the functions of molecular chaperone, and such efforts seem justified to finally provide the answers to the most burning questions shortly.

• Journal of Ginseng Research
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• v.38 no.1
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• pp.28-33
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• 2014

Background: Panax notoginseng has been used as a general tonic agent to invigorate human body for millennia in China and continued to be used until present. Methods: Some chromatographic methods were performed to isolate pure triterpenoids, and their structures were determined by nuclear magnetic resonance (NMR) experiments. Anti-diabetes activities of isolated compounds were evaluated through their inhibitory activity of protein tyrosine phosphatase 1B (PTP1B) enzyme. Results and Conclusion: Three new dammarane-type triterpenoids, notoginsenoside-LX (1), notoginsenoside-LY (2), and notoginsenoside-FZ (3) together with eighteen known compounds were isolated from the Panax notoginseng leaves. The structure-activity relationship of the compounds with dammaranetype triterpenoids and their PTP1B inhibitory activity were also reported. Results showed that compounds 2, 15, 20, and 21 can significantly inhibit the enzyme activity of PTP1B in a dose-dependent manner, with inhibitory concentration 50 ($IC_{50}$) values of $29.08{\mu}M$, $21.27{\mu}M$, $28.12{\mu}M$, and $26.59{\mu}M$, respectively. The results suggested that Panax notoginseng leaves might have potential as a new therapeutic agent for the treatment of diabetes.

• Molecules and Cells
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• v.43 no.8
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• pp.694-704
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• 2020

HslUV is a bacterial heat shock protein complex consisting of the AAA+ ATPase component HslU and the protease component HslV. HslV is a threonine (Thr) protease employing the N-terminal Thr residue in the mature protein as the catalytic residue. To date, HslUV from Gram-negative bacteria has been extensively studied. However, the mechanisms of action and activation of HslUV from Gram-positive bacteria, which have an additional N-terminal sequence before the catalytic Thr residue, remain to be revealed. In this study, we determined the crystal structures of HslV from the Gram-positive bacterium Staphylococcus aureus with and without HslU in the crystallization conditions. The structural comparison suggested that a structural transition to the symmetric form of HslV was triggered by ATP-bound HslU. More importantly, the additional N-terminal sequence was cleaved in the presence of HslU and ATP, exposing the Thr9 residue at the N-terminus and activating the ATP-dependent protease activity. Further biochemical studies demonstrated that the exposed N-terminal Thr residue is critical for catalysis with binding to the symmetric HslU hexamer. Since eukaryotic proteasomes have a similar additional N-terminal sequence, our results will improve our understanding of the common molecular mechanisms for the activation of proteasomes.

• BMB Reports
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• v.40 no.1
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• pp.58-64
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• 2007

Similar to the other known structures of Bacillus thuringiensis Cry $\delta$-endotoxins, the crystal structure of the 65-kDa activated Cry4Ba toxin comprises three domains which are, from the N- to C-terminus, a bundle of $\alpha$-helices, a three-$\beta$-sheet domain, and a $\beta$-sandwich. To investigate the properties of the C-terminal domain III in isolation from the rest of the toxin, the cloned Cry4Ba-domain III was over-expressed as a 21-kDa soluble protein in Escherichia coli, which cross-reacted with anti-Cry4Ba domain III monoclonal antibody. A highly-purified domain III was obtained in a monomeric form by ion-exchange and size-exclusion FPLC. Circular dichroism spectroscopy indicated that the isolated domain III fragment distinctly exists as a $\beta$-sheet structure, corresponding to the domain III structure embodied in the Cry4Ba crystal structure. In vitro binding analysis via immuno-histochemical assay revealed that the Cry4Ba-domain III protein was able to bind to the apical microvilli of the susceptible Stegomyia aegypti larval midguts, albeit at lower-binding activity when compared with the full-length active toxin. These results demonstrate for the first time that the C-terminal domain III of the Cry4Ba mosquito-larvicidal protein, which can be isolated as a native folded monomer, conceivably participates in toxin-receptor recognition.

• Molecules and Cells
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• v.38 no.12
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• pp.1086-1095
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• 2015

The psychrophilic organism Colwellia psychrerythraea strain 34H produces extracellular polysaccharide substances to tolerate cold environments. Sedoheptulose 7-phosphate isomerase (GmhA) is essential for producing $\small{D}$-glycero-$\small{D}$-mannoheptose 7-phosphate, a key mediator in the lipopolysaccharide biosynthetic pathway. We determined the crystal structure of GmhA from C. psychrerythraea strain 34H (CpsGmhA, UniProtKB code: Q47VU0) at a resolution of $2.8{\AA}$. The tetrameric structure is similar to that of homologous GmhA structures. Interestingly, one of the catalytic residues, glutamate, which has been reported to be critical for the activity of other homologous GmhA enzymes, is replaced by a glutamine residue in the CpsGmhA protein. We also found differences in the conformations of several other catalytic residues. Extensive structural and sequence analyses reveal that CpsGmhA shows high similarity to Escherichia coli DnaA initiatorassociating protein A (DiaA). Therefore, the CpsGmhA structure reported here may provide insight into the structural and functional correlations between GmhA and DiaA among specific microorganisms.

• Molecules and Cells
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• v.21 no.1
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• pp.63-75
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• 2006

The 5′-region of Potato virus X (PVX) RNA, which contains an AC-rich, single-stranded region and stem-loop structure 1 (SL1), affects RNA replication and assembly. Using Systemic Evolution of Ligands by EXponential enrichment (SELEX) and the electrophoretic mobility shift assay, we demonstrate that SL1 interacts specifically with tobacco protoplast protein extracts (S100). The 36 nucleotides that correspond to the top region of SL1, which comprises stem C, loop C, stem D, and the tetra loop (TL), were randomized and bound to the S100. Remarkably, the wild-type (wt) sequence was selected in the second round, and the number of wt sequences increased as selection proceeded. All of the selected clones from the fifth round contained the wt sequence. Secondary structure predictions (mFOLD) of the recovered sequences revealed relatively stable stem-loop structures that resembled SL1, although the nucleotide sequences therein were different. Moreover, many of the clones selected in the fourth round conserved the TL and C-C mismatch, which suggests the importance of these elements in host protein binding. The SELEX clone that closely resembled the wt SL1 structure with the TL and C-C mismatch was able to replicate and cause systemic symptoms in plants, while most of the other winners replicated poorly only on inoculated leaves. The RNA replication level on protoplasts was also similarly affected. Taken together, these results indicate that the SL1 of PVX interacts with host protein(s) that play important roles related to virus replication.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.2
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• pp.67-75
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• 2013

ATP synthase produces ATP, a major energy source for metabolic processes in organisms, from ADP and inorganic phosphate in cellular membranes. ATP synthase is known as a rotary motor, in which the c-subunit ring functions as a rotor. In this work, we have tried to develop a more general preparation procedure of thermophilic $F_oc$-ring ($TF_oc$-ring) for NMR measurements. The expression of $TF_oF_1$ is easily affected by various experimental conditions such as temperature, shape and size of a flask, a volume of medium, and shaking rate of an incubator. Accordingly, we have tried to optimize the expression conditions of $TF_oF_1$. $TF_oc$-rings were purified from $TF_oF_1$ according to a reported method. We modified purification procedures to improve purity and yield of $TF_oc$. On top of them, we found a new combination of detergents for the purification at anion-exchange column chromatography. To examine the effect of lipid environments on the structure, the $TF_oc$-rings were reconstituted into two kinds of lipid bilayers, namely, saturated and unsaturated lipid ones. Then, we have compared characteristics of the $TF_oc$-ring structures in these membranes with solid-state NMR.

• Advances in nano research
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• v.7 no.6
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• pp.443-457
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• 2019

In this investigation, dynamic and bending behaviors of isolated protein microtubules are analyzed. Microtubules (MTs) can be considered as bio-composite structures that are elements of the cytoskeleton in eukaryotic cells and posses considerable roles in cellular activities. They have higher mechanical characteristics such as superior flexibility and stiffness. In the modeling purpose of microtubules according to a hollow beam element, a novel single variable sinusoidal beam model is proposed with the conjunction of modified strain gradient theory. The advantage of this model is found in its new displacement field involving only one unknown as the Euler-Bernoulli beam theory, which is even less than the Timoshenko beam theory. The equations of motion are constructed by considering Hamilton's principle. The obtained results are validated by comparing them with those given based on higher shear deformation beam theory containing a higher number of variables. A parametric investigation is established to examine the impacts of shear deformation, length scale coefficient, aspect ratio and shear modulus ratio on dynamic and bending behaviors of microtubules. It is remarked that when length scale coefficients are almost identical of the outer diameter of MTs, microstructure-dependent behavior becomes more important.

• Molecules and Cells
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• v.42 no.1
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• pp.56-66
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• 2019

Histidine triad nucleotide-binding protein (HINT) is a member of the histidine triad (HIT) superfamily, which has hydrolase activity owing to a histidine triad motif. The HIT superfamily can be divided to five classes with functions in galactose metabolism, DNA repair, and tumor suppression. HINTs are highly conserved from archaea to humans and function as tumor suppressors, translation regulators, and neuropathy inhibitors. Although the structures of HINT proteins from various species have been reported, limited structural information is available for fungal species. Here, to elucidate the structural features and functional diversity of HINTs, we determined the crystal structure of HINT from the pathogenic fungus Candida albicans (CaHINT) in complex with zinc ions at a resolution of $2.5{\AA}$. Based on structural comparisons, the monomer of CaHINT overlaid best with HINT protein from the protozoal species Leishmania major. Additionally, structural comparisons with human HINT revealed an additional helix at the C-terminus of CaHINT. Interestingly, the extended C-terminal helix interacted with the N-terminal loop (${\alpha}1-{\beta}1$) and with the ${\alpha}3$ helix, which appeared to stabilize the dimerization of CaHINT. In the C-terminal region, structural and sequence comparisons showed strong relationships among 19 diverse species from archea to humans, suggesting early separation in the course of evolution. Further studies are required to address the functional significance of variations in the C-terminal region. This structural analysis of CaHINT provided important insights into the molecular aspects of evolution within the HIT superfamily.