• Molecules and Cells
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• v.44 no.2
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• pp.79-87
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• 2021

Chromatin dynamics is essential for maintaining genomic integrity and regulating gene expression. Conserved bromodomain-containing AAA+ ATPases play important roles in nucleosome organization as histone chaperones. Recently, the high-resolution cryo-electron microscopy structures of Schizosaccharomyces pombe Abo1 revealed that it forms a hexameric ring and undergoes a conformational change upon ATP hydrolysis. In addition, single-molecule imaging demonstrated that Abo1 loads H3-H4 histones onto DNA in an ATP hydrolysis-dependent manner. However, the molecular mechanism by which Abo1 loads histones remains unknown. Here, we investigated the details concerning Abo1-mediated histone loading onto DNA and the Abo1-DNA interaction using single-molecule imaging techniques and biochemical assays. We show that Abo1 does not load H2A-H2B histones. Interestingly, Abo1 deposits multiple copies of H3-H4 histones as the DNA length increases and requires at least 80 bp DNA. Unexpectedly, Abo1 weakly binds DNA regardless of ATP, and neither histone nor DNA stimulates the ATP hydrolysis activity of Abo1. Based on our results, we propose an allosteric communication model in which the ATP hydrolysis of Abo1 changes the configuration of histones to facilitate their deposition onto DNA.

• Molecules and Cells
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• v.45 no.8
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• pp.575-587
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• 2022

Human ABCB6 is an ATP-binding cassette transporter that regulates heme biosynthesis by translocating various porphyrins from the cytoplasm into the mitochondria. Here we report the cryo-electron microscopy (cryo-EM) structures of human ABCB6 with its substrates, coproporphyrin III (CPIII) and hemin, at 3.5 and 3.7 Å resolution, respectively. Metal-free porphyrin CPIII binds to ABCB6 within the central cavity, where its propionic acids form hydrogen bonds with the highly conserved Y550. The resulting structure has an overall fold similar to the inward-facing apo structure, but the two nucleotide-binding domains (NBDs) are slightly closer to each other. In contrast, when ABCB6 binds a metal-centered porphyrin hemin in complex with two glutathione molecules (1 hemin: 2 glutathione), the two NBDs end up much closer together, aligning them to bind and hydrolyze ATP more efficiently. In our structures, a glycine-rich and highly flexible "bulge" loop on TM helix 7 undergoes significant conformational changes associated with substrate binding. Our findings suggest that ABCB6 utilizes at least two distinct mechanisms to fine-tune substrate specificity and transport efficiency.

• Journal of Microbiology and Biotechnology
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• v.22 no.2
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• pp.176-183
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• 2012

Eukaryotic translation termination is governed by eRF1 and eRF3. eRF1 recognizes the stop codons and then hydrolyzes peptidyl-tRNA. eRF3, which facilitates the termination process, belongs to the GTPase superfamily. In this study, the effect of the MC domain of eRF1a (eRF1aMC) on the GTPase activity of eRF3 was analyzed using fluorescence spectra and high-performance liquid chromatography. The results indicated eRF1aMC promotes the GTPase activity of eRF3, which is similar to the role of eRF1a. Furthermore, the increased affinity of eRF3 for GTP induced by eRF1aMC was dependent on the concentration of $Mg^{2+}$. Changes in the secondary structure of eRF3C after binding GTP/GDP were detected by CD spectroscopy. The results revealed changes of conformation during formation of the eRF3C GTP complex that were detected in the presence of eRF1a or eRF1aMC. The conformations of the eRF3C eRF1a GTP and eRF3C eRF1aMC GTP complexes were further altered upon the addition of $Mg^{2+}$. By contrast, there was no change in the conformation of GTP bound to free eRF3C or the eRF3C eRF1aN complex. These results suggest that alterations in the conformation of GTP bound to eRF3 is dependent on eRF1a and $Mg^{2+}$, whereas the MC domain of eRF1a is responsible for the change in the conformation of GTP bound to eRF3 in Euplotes octocarinatus.

• Parasites, Hosts and Diseases
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• v.36 no.3
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• pp.191-198
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• 1998

The responses to antifolales of ToxopLasmc Bondii were investigated by measuring the dihydrorolate redLlctase (DHFR) activity. quantity of DHFR mRNA, and single-strand conformational polymorphism (SSCP) pattern. Pyrimethamine (PYM) and methotrexate (MTX) were tested ds anlifolates. When T. gondii was treated wish PYM, the viability was decreased by the increasing concentration of PYM. DHFR activity tended to increase as the passage proceeded. and the quantity of mRNA expressed was also increased according to passages. The viability of 7. gonnii was decreased by the increasing concentration of MTX, but it was maintained over 40% up to $100{\;}{\mu\textrm{m}}$ MTX. DHFR activity was 77.4% in the 1st passage ($1{\;}{\mu\textrm{m}}$). 82.2% in the 4th passage ($10{\;}{\mu\textrm{m}}$), and 141.3% in the 7th passage ($100{\;}{\mu\textrm{m}}$) But no changes were detected in SSCP pattern of T gondii rxposvd to FYM and MTX. both. These results suggested that the response of T gondii to FYN was rofulalcd by transrriptional level and that, in MTX. the viability of T. gonnii was derived from increasing DHFK activity.

• Journal of the Korean Society of Food Science and Nutrition
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• v.33 no.8
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• pp.1359-1366
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• 2004

Ultra high temperature treated (UHT) skim milk and colloidal calcium phosphate-free skim milk were treated with microbial transglutaminase (TGase), ultracentrifuged at various rates, lyophilized, and observed for morphological properties with a scanning electron microscope (SEM). UHT skim milk showed small holes of associated micelles at lower centrifugal rates, and became thick and irregular, and fine particles were associated regularly at higher centrifugal rates. When UHT skim milk with TGase was incubated for 1 hour, casein micelles aggregated and broadened as centrifugation rate increased. When UHT skim milk with TGase was incubated for 8 hours, casein micelles were associated irregularly to large aggregates and widened. Colloidal calcium phosphate-free skim milk with TGase incubated for 1 hour and separated by two-step centrifugation showed aggregated lump, while the milk incubated for 8 hours with TGase was associated with broadened, compact, and regular layers as the centrifugation rate increased. Such phenomena were caused by heat treatment, protein crosslinking reaction catalyzed by TGase and conformational changes of casein molecules, and could be dependent on reaction time, temperature and ultracentrifugation rate.

• Interdisciplinary Bio Central
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• v.1 no.1
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• pp.1.1-1.5
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• 2009

Many organisms control their physiology and behavior in response to the local light environment, which is first perceived by photoreceptors that undergo light-dependent conformational changes. Phytochromes are one of the major photoreceptors in plants, controlling wide aspects of plant physiology by recognizing the light in red (R) and far-red (FR) spectra. Higher plants have two types of phytochromes; the photo-labile type I (phyA in Arabidopsis) and photo-stable type II (phyB-E in Arabidopsis). Phytochrome B (phyB), a member of the type II phytochromes in Arabidopsis, shows classical R and FR reversibility between the inter-convertible photoisomers, Pr and Pfr. Interestingly, the Pr and Pfr isomers show partitioning in the cytosol and nucleus, respectively. In the over 50 years since its discovery, it has been thought that the type II phytochromes only function to mediate R light. As described in the text, we have now discovered phyB has an active function in FR light. Even striking is that the R and FR light exert an opposite effect. Thus, FR light is not simply nullifying the R effect but has an opposing effect to R light. What is more interesting is that the phyB-mediated actions of FR and R light occur at different cellular compartment of the plant cell, cytosol and nucleus, respectively, which was proven through utilization of the cytosolic and nuclear-localized mutant versions of phyB. Our observations thus shoot down a major dogma in plant physiology and will be considered highly provocative in phytochrome function. We argue that it would make much more sense that plants utilize the two isoforms rather than only one form, to effectively monitor the changing environmental light information and to incorporate the information into their developmental programs.

• Journal of Life Science
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• v.14 no.5
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• pp.752-760
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• 2004

The function of the [4Fe-4S] cluster containing iron (Fe-) protein in nitrogenase catalysis is to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. The MgADP-bound (or off) conformational state of the nitrogenase Fe protein structure described reveals mechanisms for long-range communication from the nucleotide-binding sites to control affinity of association with the MoFe protein component. Two pathways, termed switches I and II, appear to be integral to this nucleotide signal transduction mechanism. In addition, the structure of the MgADP bound Fe protein provides the basis for the changes in the biophysical properties of the [4Fe-4S] observed when Fe protein binds nucleotides. The structures of the nitrogenase Fe protein with defined amino acid substitutions in the nucleotide dependent signal transduction pathways of the Switch I and Switch II have been determined by X-ray diffraction methods. These two pathways have been also implicated by site directed mutagenesis studies, structural analysis and analogies to other proteins that utilize similar nucleotide dependent signal transduction pathways. We have examined the validity of the assignment of these pathways in linking the signals generated by MgATP binding and hydrolysis to macromolecular complex formation and intermolecular electron transfer. The results provide a structural basis for the observed biophysical and biochemical properties of the Fe protein variants and interactions within the nitrogenase Fe protein-MoFe protein complex.

• Journal of Korean Society of Environmental Engineers
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• v.32 no.11
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• pp.1054-1062
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• 2010

Oxidative coupling reactions of humic substances (HS) can be catalyzed by a variety of natural extracellular enzymes and metal oxides. In this study, property changes of HS induced by a natural enzyme, horseradish peroxidase (HRP), and the effect of it to microfiltration (MF) were investigated. PAHA was transformed by oxidative coupling reaction with HRP and hydrogen peroxide ($H_2O_2$), verifying the catalytic effects of the HRP. Size exclusion chromatography (SEC) revealed that weight-average molecular weight (MWw) of PAHA was proportionally increased with the dosages of HRP and $H_2O_2$, indicating the transform action of HS into larger and complex molecules. An increase in the conformational stability of HS was achieved through the promotion of intermolecular covalent bondings between heterogeneous humic molecules. Spectroscopic analysis (fluorescence and infrared spectroscopy) proved that functional groups were transformed by the reaction. Additionally, HS and transformed products were undergone microfiltration (MF) to examine the treatment potential of them in a water treatment facility. Original HS could not be removed by MF but larger molecules of transformed products could be removed. Meanwhile, transformed products caused more fouling on the filtration than original HS. This results proved that natural organic matter (NOM) can be removed by MF after its increase in molecular size by oxidative coupling reaction.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.38 no.3
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• pp.143-147
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• 2005

Relationship between structure and biological activity was performed using the five substance P-related peptides (SPRPs) [mammalian-SP (M-SP), cod-SP (C-SP), trout-SP (T-SP), lungfish-SP (L-SP) and Ranakinin] and four SP analogs [[$His^5$]-SP (5H-SP), [$Gly^5$]-SP (5G-SP), ($Ile^8$)-SP (8I-SP) and ($Trp^8$)-Ranakinin (8W-Ranakinin)]. The circular dichroism (CD) spectra showed that all of the peptides took an unordered structure in buffer solution and artificial liposomes. However, 8W-Ranakinin undergoes conformational changes by being transferred into neutral and acidic liposomes from an unordered structure to more ordered structure. The arterial relaxing effect of the peptides was also studied with guinea-pig aorta (GPA), As a result of the studies, L-SP was about 14-fold more potant than M-SP. The order of potency compared to $EC_{50}$ value was $L-SP{\gg}M-SP>5G-SP{\ge}8I-SP>5H-SP>T-SP$, C-SP, Ranakinin, 8W-Ranakinin.

• Korean Journal of Materials Research
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• v.8 no.2
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• pp.135-140
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• 1998

Drag reduction produced by dilute solution of water soluble ionic polymer-surfactant complex under turbulent flow in a rotating disk apparatus(RDA) was investigated in this study. Three different molecular weights of polyacrylic acid(PAA) were adopted as drag reducing additives, and distilled water was used as a solvent. Experiments were undertaken to observe the dependence of drag reduction on various factors such as polymer molecular weight, molecular expansions and flexibility, rotating speed of the disk and polymer concentration. Specific considerations were put on conformational difference between surfactant and polymer, and effect of pH on ionic polymer possessing various molecular conformation through pH. The complex of ionic polymer and surfactant(Sodium Dodecyl Sulfate) behaves like a large polyelectrolyte. Surfactant changes the polymer conformation and then increases the dimension of the polymer. The radius of gyration, hydrodynamic volume and relative viscosity of the polymer-surfactant system are observed to be greater than those of polymer itself. Such surfactant-polymer complex has enhanced drag reduction properties.