• Proceedings of the Microbiological Society of Korea Conference
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• 2006.05a
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• pp.66-68
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• 2006

SUF machinery in Echerichia coli, responsible for the biosynthesis of iron-sulfur clusters, is composed of six protein components (SufABCDSE), among which SufB, SufC, and SufD associate in a complex. We have determined the structures of SufA, SufC, and SufD by X-ray crystallography. SufA is a dimer, in which C-terminal segments containing essential cysteine residues (Cys-Gly-Cys) are positioned to allow coordination of an Fe-S cluster and/or an Fe atom. SufC has the overall structure similar to that of ABC-ATPase but takes an inactive form. SufD has a ${\beta}-helix$ flanked with a-helical domains. We also studied the functional roles of the residues in SufD by mutagenesis and determined the crystal structure of SufCD complex. Molecular mechanism of Fe-S cluster biosynthesis is discussed on the basis of the structural and functional evidence.

• Natural Product Sciences
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• v.27 no.4
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• pp.228-233
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• 2021

Bioactivity-guided fractionation by preliminary screening using interleukin-1β production in lipopolysaccharides (LPS)-induced J774A.1 cell line led to the isolation of fourteen structures including chromone, isocoumarins, flavanoids, and triterpenes from the aerial part of Agrimonia pilosa Ledeb. All structures were determined by measuring their spectroscopic data and comparing their spectroscopic data with the literatures. All the isolates were tested for their inhibitory activities against interleukin-1β production in LPS-induced J774A.1 cell. Of the tested compounds, (S)-(+)-5,7-dihydroxy-2-(1-methylpropyl)chromone (1), agrimonolide-6-O-β-D-glucopyranoside (5), agrimonolide-6-O-α-L-arabinofuranosyl-(1→6)-β-D-glucopyranoside (6), and catechin (10) were found to be active. Furthermore, compound 1 suppressed the protein expressions of NLRP3 and NLRC4 in murine macrophage.

• Applied Biological Chemistry
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• v.46 no.4
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• pp.305-310
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• 2003

Hydrophobic core variant of ubiquitin appeared to have partially folded structure at pH around 2. The intrinsic tryptophan fluorescence emission maximum of this ubiquitin variant at pH 2 showed slight blue shift compare to that of unfolded state, suggesting that some residual tertiary structures remain in this solvent condition. At the same solvent condition, this ubiquitin variant binds with hydrophobic dye, 8-anilinonaphthalene-1-sulfonic acid(AMS), which is known to bind to exposed hydrophobic surface. Furthermore, far-UV circular dichroic spectrum of this ubiquitin variant in the diminished pH was remarkably different from the far-UV CD spectrum of the native state or unfolded state. Based on the molar ellipticity at 220 nm, this ubiquitin variant at pH 2 appeared to have significant amount of secondary structures. All these observations suggest that this ubiquitin variant in the diminished solvent pH has loosely folded hydrophobic core with some secondary structures, which are key features of molten globule conformation. Since molten globule has long been considered as a protein folding intermediate, it is considered that this hydrophobic core variant ubiquitin will serve as a valuable model to study protein folding process.

• Biotechnology and Bioprocess Engineering:BBE
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• v.6 no.5
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• pp.326-331
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• 2001

With the aim of developing of pH-sensitive controlled drug release system, a poly(Llysine) (PLL) based cationic semi-interpenetrating polymer network (semi-IPN) has been synthesized. This cationic hydrogel was designed to swell at lower pH and de-swell at higher pH and therefore be applicable for achieving regulated drug release at a specific pH range. In addition to the pH sensitivity, this hydrogel was anticipated to interact with an ionic drug, providing another means to regulate the release rate of ionic drugs. This semi-IPN hydrogel was prepared using a free-radical polymerization method and by crosslinking of the polyethylene glycol (PEG)-methacrylate polymer through the PLL network. The two polymers were penetrated with each other via interpolymer complexation to yield the semi-IPN structures. The PLL hydrogel thus prepared showed dynamic swelling/de-swelling behavior in response to pH change, and such a behavior was influenced by both the concentrations of PLL and PEG-methacrylate. Drug release from this semi-IPN hydrogel was also investigated using a model protein drug, streptokinase. Streptokinase release was found to be dependent on its ionic interaction with the PLL backbones as well as on the swelling of the semi-IPN hydrogel. These results suggest that a PLL semi-IPN hydrogel could potentially be used as a drug delivery platform to modulate drug release by pH-sensitivity and ionic interaction.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.3817-3825
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• 2015

Background: The human protein methyl-transferase DOT1L catalyzes the methylation of histone H3 on lysine 79 (H3K79) at homeobox genes and is also involved in a number of significant processes ranging from gene expression to DNA-damage response and cell cycle progression. Inhibition of DOT1L activity by shRNA or small-molecule inhibitors has been established to prevent proliferation of various MLL-rearranged leukemia cells in vitro, establishing DOT1L an attractive therapeutic target for mixed lineage leukemia (MLL). Most of the drugs currently in use for the MLL treatment are reported to have low efficacy, hence this study focused on various natural compounds which exhibit minimal toxic effects and high efficacy for the target receptor. Materials and Methods: Structures of human protein methyl-transferase DOT1L and natural compound databases were downloaded from various sources. Virtual screening, molecular docking, dynamics simulation and drug likeness studies were performed for those natural compounds to evaluate and analyze their anti-cancer activity. Results: The top five screened compounds possessing good binding affinity were identified as potential high affinity inhibitors against DOT1L's active site. The top ranking molecule amongst the screened ligands had a Glide g-score of -10.940 kcal/mol and Glide e-model score of -86.011 with 5 hydrogen bonds and 12 hydrophobic contacts. This ligand's behaviour also showed consistency during the simulation of protein-ligand complex for 20000 ps, which is indicative of its stability in the receptor pocket. Conclusions: The ligand obtained out of this screening study can be considered as a potential inhibitor for DOT1L and further can be treated as a lead for the drug designing pipeline.

• Korean Journal of Veterinary Research
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• v.55 no.2
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• pp.89-95
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• 2015

Johne's disease, caused by Mycobacterium avium subsp. paratuberculosis (MAP), is one of the most widespread and economically important diseases in cattle. Current diagnostic methods are based on the detection of anti-MAP antibodies in serum or isolation of the causative agent. However, these techniques are often not applicable for cases of subclinical infection due to relatively low sensitivity. Therefore, finding new antigen candidates that strongly react with the host immune system had been attempted. To effectively detect infection during the subclinical stage, several antigen candidates were selected based on previous researches. Characteristics of the selected antigen candidates were analyzed using bioinformatics-based prediction tools. A total of nine antigens were selected (MAP0862, MAP3817c, MAP2077c, MAP0860c, MAP3954, MAP3155c, MAP1204, MAP1087, and MAP2963c) that have MAP-specific and/or high immune responses to infected animals. Using a transmembrane prediction tool, five of the nine antigen candidates were predicted to be membrane protein (MAP3817c, MAP3954, MAP3155c, MAP1087, and MAP1204). Some of the predicted protein structures identified using the I-TASSER server shared similarities with known proteins found in the Protein Data Bank database (MAP0862, MAP1204, and MAP2077c). In future studies, the characteristics and diagnostic efficiency of the selected antigen candidates will be evaluated.

• BMB Reports
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• v.36 no.6
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• pp.603-607
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• 2003

Abstract Plant lipid transfer proteins (LTPs) are a class of proteins whose functions are still unknown. Some are proposed to have antimicrobial activities. To understand whether LTP110, a rice LTP that we previously identified from rice leaves, plays a role in the protection function against some serious rice pathogens, we investigated the antifungal and antibacterial properties of LTP110. A cDNA sequence, encoding the mature peptide of LTP110, was cloned into the Impact-CN prokaryotic expression system. The purified protein was used for an in vitro inhibition test against rice pathogens, Pyricularia oryzae and Xanthomonas oryzae. The results showed that LTP110 inhibited the germination of Pyricularia oryzae spores, and its inhibitory activity decreased in the presence of a divalent cation. This suggests that the antifungal activity is affected by ions in the media; LTP110 only slightly inhibited the growth of Xanthomonas oryzae. However, the addition of LTP110 to cultured Chinese hamster ovarian cells did not retard growth, suggesting that the toxicity of LTP110 is only restricted to some cell types. Its antimicrobial activity is potentially due to interactions between LTP and microbe-specific structures.

• BMB Reports
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• v.44 no.11
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• pp.719-724
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• 2011

The $Sec61{\alpha}$ subunit is the core subunit of the protein conducting channel which is required for protein translocation in eukaryotes and prokaryotes. In this study, we cloned a $Sec61{\alpha}$ subunit from Penicillium ochrochloron ($PoSec61{\alpha}$). Sequence and 3D structural model analysis showed that $PoSec61{\alpha}$ conserved the typical characteristics of eukaryotic and prokaryotic $Sec61{\alpha}$ subunit homologues. The pore ring known as the constriction point of the channel is formed by seven hydrophobic amino acids. Two methionine residues from transmembrane ${\alpha}$-helice 7 (TM7) contribute to the pore ring formation and projected notably to the pore area and narrowed the pore compared with the superposed residues at the corresponding positions in the crystal structures or the 3D models of the $Sec61{\alpha}$ subunit homologues in archaea or other eukaryotes, respectively. Results reported herein indicate that the pore ring residues differ among $Sec61{\alpha}$ subunit homologues and two hydrophobic residues in the TM7 contribute to the pore ring formation.

• Parasites, Hosts and Diseases
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• v.53 no.4
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• pp.455-463
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• 2015

The present study was performed to compare the mitochondrial genomes between 2 Spirometra tapeworms, Spirometra erinaceieuropaei and Spirometra decipiens (Cestoidea: Diphyllobothriidae), which larval stages are important etiological agents of sparganosis in humans. For each species, the full mitochondrial genome was amplified in 8 overlapping fragments using total genomic DNA purified from a single worm as the template. The mitochondrial genomes were 13,643 bp (S. erinaceieuropaei) and 13,641 bp (S. decipiens) in length and contained 36 genes; 12 protein-coding genes, 2 ribosomal RNA (rRNA, small and large subunits), and 22 transfer RNAs (tRNAs). The 12 protein-coding genes constituted 10,083 bp (S. erinaceieuropaei) and 10,086 bp (S. decipiens) of their respective mitochondrial genomes. The tRNA genes, ranging in length from 56 to 70 bp, were identified based on putative secondary structures such as the typical cloverleaf shape. A total of 23 intergenic sequences, varying from 1 to 204 bp in size, were interspersed in S. erinaceieuropaei (total, 504 bp) and S. decipiens (total, 496 bp) mtDNA. The 12 protein-coding genes of S. erinaceieuropaei and S. decipiens differed by 12.4%, whereas the overall difference in mtDNA sequence between S. erinaceieuropaei and S. decipiens was 12.9%. Thus, from the standpoint of the mitochondrial genome, S. decipiens represents a valid species that can be distinguished from S. erinaceieuropaei.

• Journal of Sericultural and Entomological Science
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• v.36 no.1
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• pp.30-36
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• 1994

choChorion(egg-shell) morphology of the F1 hybrid between Bombyx mori and Bombyx mandarina has been observed by scanning electrom microscope and chorion protein was analyzed by electrophoresis. The chorion surface structure of F1 hybrids in the lateral(flat) region was similar to that of maternal line. The F1 hybrids chorion was found to have basically a three layer structure. The middle and inner layer were very much like those of the Bombyx mandarina and Bombyx mori. There were many conic pillar structures in the outer layer of the F1 hybrid, which was similar to Bombyx mandarina. This conic pillar structure had a thin cover layer was more clear in the dorsal and ventral side of the F1 hybrid chorion. The conic pillar structure of Bombyx mandarina was found to be dominant in F1 hybrid chorion irrespective of their maternal line. Major components of chorion protein were analyzed by two-dimensional electrophoresis and found to have isoelectric points in the range of pH 4.0-6.5 and molecular weight 10 to 50 kd. F1 hybrid chorion protein components related directly to those of the maternal line. The conic pillar structure was dominat characteristic and it was present in all F1 hybrid.