• Bulletin of the Korean Chemical Society
• /
• v.17 no.9
• /
• pp.808-813
• /
• 1996

To explore protein folding mechanism, we simulated a folding pathway in a simplified 3×3×3 cubic lattice. In the lattice folding Monte Carlo simulations, each of the 28 possible native packing pairs that exist in the native conformation was used as a conformational restraint. The native packing restraints in the lattice model could be considered as a disulfide linkage restraint in a real protein. The results suggest that proteins denatured with a small disulfide loop can, but not always, fold faster than proteins without any disulfide linkage and than proteins with a larger disulfide loop. The results also suggest that there is a rough correlation between loop size of the native packing restraint and folding time. That is, the order of native residue-residue packing interaction in protein folding is likely dependent on the residue-residue distance in primary sequence. The strength of monomer-monomer pairwise interaction is not important in the determination of the packing order in lattice folding. From the folding simulations of five strong folding lattice sequences, it was also found that the context encoded in the primary sequence, which we do not yet clearly understand, plays more crucial role in the determination of detailed folding kinetics. Our restrained lattice model approach would provide a useful strategy to the future protein folding experiments by suggesting a protein engineering for the fast or slow folding research.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.8
• /
• pp.2722-2726
• /
• 2011

Plasticized poly(vinyl chloride), PVCs, with different membrane compositions tested for use in the construction of an ion-selective sensor for the determination dibucaine. A prepared membrane with dioctyl phthalate-PVC and ion-pair of N-(1-naphthyl)ethylenediamine dihydrochloride-tetraphenyl borate had a good potential to acts as a potentiometric sensor for the analysis of dibucaine. A linear relationship was obtained between potential and logC varying between $1.0{\times}10^{-6}$ and $1.0{\times}10^{-2}$ M dibucaine with a good repeatability and reproducibility. The sensor was applied for the determination of the drug in pharmaceuticals and biological fluids such as plasma and urine samples with satisfactory results. The drug electrode has also been used to study the interaction of bovine serum albumin (BSA) with dibucaine. The saturated quantities of dibucaine binding were 13.04, 5.30 and 9.70 mol/mol in 0.01, 0.02 and 0.1% of protein, respectively.

• The Korean Journal of Zoology
• /
• v.3 no.1
• /
• pp.19-23
• /
• 1960

A method for determination of thyroid secretion rate in rabbit by means of radioactive iodine presented. After injection of radioactive iodine, in vivo determination so f radioactivity in thyroid gland were made during a 19 day-experimental period. In the same period blood samples were drawn and analyzed for protein-bound iodine (PBI) and for protein-bound radioactive iodine(PBI181). A rate constant for secretion of thyroid hormone was calculated from the disappearance rate of radioactive iodine in thyroid gland. The secretion rate of radioactive hormone iodine was calculated by multiplying this rate constant by the amount of radioactive iodine present in thyroid gland. Assuming that the specific radioactiveness of the circulating thyroid hormone and of the hormone just secreted were identical , thyroid secretion rate was calculated by the equation. {{{{ { Secreted hormone-iodine , gamma /hr} over { Secreted hormone-I^131, % dose/hr }= { PBI, ${\gamma}$/ml.Serum} over { PBI^131 , % dose/ml . Serum } }} The method presented consisted of measurements for series of independent criteria on thyroid function, and the resulting thyroid secretion rate was calculated by combination of those.

• Toxicological Research
• /
• v.21 no.3
• /
• pp.195-208
• /
• 2005

Diabetes is a major cause of morbidity and mortality, and associated with a high risk of atherosclerosis, and liver, kidney, nerve and tissue damage. Defective insulin secretion in pancreas and/or insulin resistance in peripheral tissues is a central component of diabetes. It is well established that, regardless of the degree of muscle insulin resistance, glucose levels in diabetic and non-diabetic individuals are determined by the rate of hepatic glucose production. Moreover recently studies using liver-specific insulin receptor knockout mice show the paramount role of the liver in insulin resistance and diabetes. Insulin exerts a multifaceted and highly integrated series of actions via its intracellular signaling systems. The first major section of this review defines the major insulin-mediated signaling pathways including phosphatidylinositol 3-kinase and mitogen activated protein kinases. The second major section of the review presents a summary and evaluation of methods for determination of the role and function of signaling pathways, including methods for determination of kinase phosphorylation, the use of pharmacological inhibitors of kinase and dominant-negative kinase constructs, and the application of new RNA interference methods.

• Journal of the Korean Magnetic Resonance Society
• /
• v.26 no.4
• /
• pp.66-70
• /
• 2022

Protein structure determination using NMR spectroscopy requires a suite of heteronuclear 3-D NMR experiments that can take a couple of weeks for completion. During the experiments, protein samples may suffer from slow degradation due to co-purifying proteases, which complicates and slows down the assignment procedure. Here we describe a practical protocol to avoid unwanted proteolysis during the experiment.

• Genomics & Informatics
• /
• v.7 no.4
• /
• pp.217-219
• /
• 2009

The primary clue for locating protein-coding regions is the open reading frame and the determination of ORFs (Open Reading Frames) is the first step toward the gene prediction, especially for prokaryotes. In this respect, we have developed a web-based ORF search tool called ORF Miner. The ORF Miner is a graphical analysis utility which determines all possible open reading frames of a selectable minimum size in an input sequence. This tool identifies all open reading frames using alternative genetic codes as well as the standard one and reports a list of ORFs with corresponding deduced amino acid sequences. The ORF Miner can be employed for sequence annotation and give a crucial clue to determination of actual protein-coding regions.

• Journal of the Korean Magnetic Resonance Society
• /
• v.18 no.2
• /
• pp.58-62
• /
• 2014

Human transmembrane proteins (hTMPs) are closely related to transport, channel formation, signaling, cell to cell interaction, so they are the crucial target of modern medicinal drugs. In order to study the structure and function of these hTMPs, it is important to prepare reasonable amounts of proteins. However, their preparation is seriously difficult and time-consuming due to insufficient yields and low solubility of hTMPs. We tried to produce large amounts of Syndecan-4 transmembrane domain (Syd4-TM) that is related to the healing wounds and tumor for a long time. In this study, we performed the structure determination of Syd4-TM combining the Polarity Index at Slanted Angle (PISA) wheel pattern analysis based on $^{15}N-^1H$ 2D SAMPI-4 solid-state NMR of expressed Syd4-TM and Molecular Dynamics (MD) simulation using Discovery Studio 3.1.

• Preventive Nutrition and Food Science
• /
• v.12 no.2
• /
• pp.103-110
• /
• 2007

The protein profiles among Korean rice cultivars were assessed by total protein determination, solubility fractionation, SDS-PAGE analysis and scanning densitometry. In the extraction of protein, the SDS/urea system at a neutral pH was more efficient than that at alkaline pH. The determination of total protein showed that the protein content was similar among cultivars, ranging from 87.9 to 92.7 mg/g dry weight. Additionally, the water/NaCl-soluble protein fraction, containing 14${\sim}$16 kDa albumin and 22 kDa globulin ${\alpha}$-globulin, was also similar among cultivars, with a range of 9.94 to 11.98 mg/g dry weight. The SDS-PAGE/densitometry of total protein showed that there was no discernable difference in proteins of higher molecular weights among various cultivars, whereas the amount of lower molecular weight proteins (14${\sim}$16 kDa) is somewhat variable among cultivars. Furthermore, SDS-PAGE analysis of water/NaCl-soluble and propanol-soluble fractions indicates that there is a discernible change in the content of albumin, globulin or prolamin among cultivars. Thus, the PAGE/densitometry method, preceded by solubility fractionation, is useful for examining differences in protein profiles of rice cultivars.

• KOREAN JOURNAL OF CROP SCIENCE
• /
• v.46 no.5
• /
• pp.401-406
• /
• 2001

The applicability of non-destructive near infrared reflectance spectroscopic (NIRS) method was tested to determine the protein and oil contents of intact soybean [Glycine max (L.) Merr.] seeds. A total of 198 soybean calibration samples and 101 validation samples were used for NIRS equation development and validation, respectively. In the developed non-destructive NIRS equation for analysis of protein and oil contents, the most accurate equation was obtained at 2, 8, 6, 1(2nd derivative, 8 nm gap, 6 points smoothing, and 1 point second smoothing) and 2, 1, 20, 10 math treatment conditions with Standard Normal Variate and Detrend (SNVD) scatter correction method and entire spectrum (400-2500 nm) by using Modified Partial Least Squares (MPLS) regression, respectively. Validation of these non-destructive NIRS equations showed very low bias (protein: 0.060%, oil: -0.017%) and standard error of prediction (SEP, protein: 0.568 %, oil : 0.451 %) as well as high coefficient of determination ($R^2$, protein: 0.927, oil: 0.906). Therefore, these non-destructive NIRS equations can be applicable and reliable for determination of protein and oil content of intact soybean seeds, and non-destructive NIRS method could be used as a mass screening technique for selection of high protein and oil soybean in breeding programs.

• Korean Journal of Food Science and Technology
• /
• v.11 no.2
• /
• pp.81-85
• /
• 1979

A Neotec infrared instrument was evaluated for determination of protein contents of wheat and barley. Correlation coefficients between protein content determined on the instrument and by the Kjeldahl method were highly significant (0.97 to 0.98). Accuracy of analyses, measured by the standard error of a single test was 0.07 to 0.16, giving a coefficient of variability of 0.6 to 1. 1%. Method of grinding samples affected particle size and type. Particle size did not directly influence protein values; however, greater accuracy and reproducibility were achieved with smaller particle sizes. Packing density inside the loading tell also influenced the analytical results.