• BMB Reports
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• v.42 no.3
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• pp.166-171
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• 2009

Hsp70s assist in the process of protein folding through nucleotide-controlled cycles of substrate binding and release by alternating from an ATP-bound state in which the affinity for substrate is low to an ADP-bound state in which the affinity for substrate is high. It has been long recognized that the two-domain structure of Hsp70 is critical for these regulated interactions. Therefore, it is important to obtain information about conformational changes in the relative positions of Hsp70 domains caused by nucleotide binding. In this study, analytical ultracentrifugation and dynamic light scattering were used to evaluate the effect of ADP and ATP binding on the conformation of the human stress-induced Hsp70.1 protein. The results of these experiments showed that ATP had a larger effect on the conformation of Hsp70 than ADP. In agreement with previous biochemical experiments, our results suggest that conformational changes caused by nucleotide binding are a consequence of the movement in position of both nucleotide- and substrate-binding domains.

• BMB Reports
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• v.40 no.5
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• pp.723-730
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• 2007

Kinesin is an ATP-driven microtubule motor protein that plays important roles in control of microtubule dynamics, intracellular transport, cell division and signal transduction. The kinesin superfamily is composed of numerous members that are classified into 14 subfamilies. Animal kinesins have been well characterized. In contrast, plant kinesins have not yet to be characterized adequately. Here, a novel plant-specific kinesin gene, GhKCH2, has been cloned from cotton (Gossypium hirsutum) fibers and biochemically identified by prokaryotic expression, affinity purification, ATPase activity assay and microtubule-binding analysis. The putative motor domain of GhKCH2, $M_{396-734}$ corresponding to amino acids Q396-N734 was fused with 6$\times$His-tag, soluble-expressed in E. coli and affinity-purified in a large amount. The biochemical analysis demonstrated that the basal ATPase activity of $M_{396-734}$ is not activated by $Ca^{2+}$, but stimulated 30-fold max by microtubules. The enzymatic activation is microtubule-concentration-dependent, and the concentration of microtubules that corresponds to half-maximum activation was about 11 ${\mu}M$, much higher than that of other kinesins reported. The cosedimentation assay indicated that $M_{396-734}$ could bind to microtubules in vitro whenever the nucleotide AMP-PNP is present or absent. As a plant-specific microtubule-dependent kinesin with a lower microtubule-affinity and a nucleotide-independent microtubule-binding ability, cotton GhKCH2 might be involved in the function of microtubules during the deposition of cellulose microfibrils in fibers or the formation of cell wall.

• Molecules and Cells
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• v.19 no.1
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• pp.39-45
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• 2005

RPK118 is a sphingosine kinase-1-binding protein that has been implicated in sphingosine 1 phosphate-mediated signaling. It contains a PX (phox homology) domain and two pseudo-kinase domains, and co-localizes with sphingosine kinase-1 on early endosomes. In this study we identified a novel RPK118-binding protein, PRDX3 (peroxiredoxin-3), by yeast two-hybrid screening. The interaction between these proteins was confirmed by pull-down assays and co-immunoprecipitation experiments. Deletion studies showed that RPK118 interacted with PRDX3 through its pseudokinase domains, and with early endosomes through its PX domain. Double immunofluorescence experiments demonstrated that PRDX3 co-localized with RPK118 on early endosomes in COS7 cells. PRDX3 is a member of the antioxidant family of proteins synthesized in the cytoplasm and functioning in mitochondria. Our findings indicate that RPK118 is a PRDX3-binding protein that may be involved in transporting PRDX3 from the cytoplasm to its mitochondrial site of function or to other membrane structures via endosome trafficking.

• Journal of Pharmaceutical Investigation
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• v.10 no.3
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• pp.27-32
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• 1980

This paper was to investigate the biovailability of antipyrine, ampicillin and protein binding in pathological rats and rabbits pretreated with typhoid vaccine. The results are as follows: The absorption of antipyrine and ampicillin respectively were reduced in rats pretreated with typhoid vaccine as compared with those of normal rats. Especially absorption of ampicillin was more decreased than those of antipyrine. The blood level of antipyrine in severe state was decreased but in mild state. Blood level of ampicillin was decreased in mild state as well as in severe state. Relative bioavailability of antipyrine and ampicillin were mostly decreased in rabbits pretreated with typhoid vaccine except that of antipyrine in mild state. Renal clearance of antipyrine was not affected, but that of ampicillin was apt to increase. Protein binding of antipyrine and ampicillin were decreased by high concentration of typhoid vaccine.

• Computers and Concrete
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• v.11 no.4
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• pp.305-316
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• 2013

This paper aims to study the effect of measurement methods and cracking on chloride transport of concrete materials. Three kinds of measurement methods were carried out, including immersion test, rapid migration test and steady-state migration test. All of these measurements of chloride transport show that chloride ion diffusion coefficient decreased with the reduction of water to cement ratio. Results of the immersion test were less than that of rapid migration test and steady-state migration test. For the specimen of lower water to cement ratio, the external electrical field has little effect on chloride binding relatively. Compared with the results obtained by these different measurement methods, the lower water to cement ratio may cause smaller differences among these different methods. The external voltage can reduce chloride binding of concrete, and the higher electrical field made a strong impact on the chloride binding. Considering the effect of high voltage on the specimen, results indicate that results based on the steady-state migration test should be more reasonable. For cracked concrete, cracking can accelerate the chloride ion diffusion.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.770-774
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• 2012

Protein loops are often involved in diverse biological functions, and some functional loops show conformational changes upon ligand binding. Since this conformational change is directly related to ligand binding pose and protein function, there have been numerous attempts to predict this change accurately. In this study, we show that it is plausible to obtain meaningful ensembles of loop conformations for flexible, ligand-binding protein loops efficiently by applying a loop modeling method. The loop modeling method employs triaxial loop closure algorithm for trial conformation generation and conformational space annealing for global energy optimization. When loop modeling was performed on the framework of ligand-free structure, loop structures within $3\AA$ RMSD from the crystal loop structure for the ligand-bound state were sampled in 4 out of 6 cases. This result is encouraging considering that no information on the ligand-bound state was used during the loop modeling process. We therefore expect that the present loop modeling method will be useful for future developments of flexible protein-ligand docking methods.

• Bulletin of the Korean Chemical Society
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• v.21 no.12
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• pp.1207-1212
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• 2000

The free energy simulation technique is used to evaluate the relative binding affinity of a set of hydroxyethylene isostere inhibitors of the HIV-1 protease. The binding reactions and an alchemical mutation construct the thermodynamic cycle, which reduces the free energy difference of the binding interactions into that of the alchemical processes. In the alchemical process, a methyl group is mutated into a hydrogen atom. Albeit the change is a small perturbation to the inhibitor-protease complex, it results in 25 fold difference in the binding constants. The simulation reproduces the experimentally measured binding affinities within 2% of the free energy difference. The protonation state of the catalytic aspartic acid residues is also investigated through the free energy simulations.

• BMB Reports
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• v.45 no.11
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• pp.665-670
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• 2012

The insect midgut epithelium is generally lined with a unique chitin and protein structure, the peritrophic membrane (PM), which facilitates food digestion and protects the gut epithelium. We used gel electrophoresis and mass spectrometry to identify the extracted proteins from the silkworm PM to obtain an in-depth understanding of the biological function of the silkworm PM components. A total of 305 proteins, with molecular weights ranging from 8.02 kDa to 788.52 kDa and the isoelectric points ranging from 3.39 to 12.91, were successfully identified. We also found several major classes of PM proteins, i.e. PM chitin-binding protein, invertebrate intestinal mucin, and chitin deacetylase. The protein profile provides a basis for further study of the physiological events in the PM of Bombyx mori.

• Proceedings of the IEEK Conference
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• 2004.06a
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• pp.261-264
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• 2004

We propose a location management with adaptive binding idle lifetime scheme for IP-based wireless network. In our proposed scheme, the binding idle lifetime value is adaptively varied according to user characteristics. The main idea is that the mobile node (MN) does location update (LU) even in idle state. Furthermore a sequential paging scheme is used to reduce the paging cost. The proposed scheme can be used in both cellular network and IP-based network.

• Archives of Pharmacal Research
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• v.28 no.1
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• pp.115-119
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• 2005

The clearance of ICG, a known hepatic blood flow marker was investigated in rats in order to examine whether DDB-S influences hepatic blood flow. The effect of DDB-S on the protein binding and blood-to-plasma partition of ICG was measured. The steady-state plasma concentration of ICG was monitored before and after co-administration of various concentration of DDB-S, and ICG clearance was estimated from the steady-state concentration and the infusion rate of ICG. There was no significant difference in protein binding and blood-to-plasma partition of ICG with and without addition of DDB-S (10, 20, and 40 ${\mu}g/mL)$. When ICG was infused into DDB-S pretreated rats, the steady-state concentrations of ICG decreased and the calculated ICG clearance increased. However, no dose-dependency of ICG Css on DDB-S Css was observed. Since DDB-S did not affect the protein binding and blood-to-plasma partition of ICG, the increased clearance of ICG with co-administration of DDB-S seems to be due to the increased hepatic blood flow by DDB-S.