• Interdisciplinary Bio Central
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• v.3 no.2
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• pp.8.1-8.6
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• 2011

Background: Thanks to the development of the mathematical/statistical reverse engineering and the high-throughput measuring biotechnology, lots of biologically meaningful genegene interaction networks have been revealed. Steady-state analysis of these systems provides an important clue to understand and to predict the systematic behaviours of the biological system. However, modeling such a complex and large-scale system is one of the challenging difficulties in systems biology. Results: We introduce a new stochastic modeling approach that can describe gene regulatory mechanisms by dividing two (DNA and protein) layers. Simple queuing system is employed to explain the DNA layer and the protein layer is modeled using G-networks which enable us to account for the post-translational protein interactions. Our method is applied to a transcription repression system and an active protein degradation system. The steady-state results suggest that the active protein degradation system is more sensitive but the transcription repression system might be more reliable than the transcription repression system. Conclusions: Our two layer stochastic model successfully describes the long-run behaviour of gene regulatory networks which consist of various mRNA/protein processes. The analytic solution of the G-networks enables us to extend our model to a large-scale system. A more reliable modeling approach could be achieved by cooperating with a real experimental study in synthetic biology.

• BMB Reports
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• v.35 no.3
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• pp.343-347
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• 2002

The human protein tyrosine kinase-6 (PTK6) polypeptide that is deduced from the cDNA sequence contains a Src homology (SH) 3 domain, SH2 domain, and catalytic domain of tyrosine kinase. We initiated biochemical and NMR characterization of PTK6 SH3 domain in order to correlate the structural role of the PTK6 using circular dichroism and heteronuclear NMR techniques. The circular dichroism data suggested that the secondary structural elements of the SH3 domain are mainly composed of $\beta$-sheet conformations. It is most stable when the pH is neutral based on the pH titration data. In addition, a number of cross peaks at the low-field area of the proton chemical shift of the NMR spectra indicated that the PTK6 SH3 domain retains a unique and folded conformation at the neutral pH condition. For other pH conditions, the SH3 domain became unstable and aggregated during NMR measurements, indicating that the structural stability is very sensitive to pH environments. Both the NMR and circular dichroism data indicate that the PTK6 SH3 domain experiences a conformational instability, even in an aqueous solution.

• Journal of the Korean Society of Food Science and Nutrition
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• v.24 no.2
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• pp.336-340
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• 1995

Urinary excretion of total amino acids was measrued in normal and diabetic rats, streptozotocin-induced diabetic rats excreted increased amount of urinary total amino acids and nitrogen. This suggested increased degradation of body protein. Although excretion of total amino acids increased in the diabetic rats, the amino acid pattern of amino acids for both groups were very similar. The efficiency of dietary protein utilization was significantly lower in diabetic rats then that of normal rats. Streptozotocin injeciton affected the urinary excretion of 3-methylhistidine whereas diet did not. These findings suggest that the rate of urinary excretion of total amino acids can be empolyed as an index of protein metabolism, particulary as a simple index in the assesing the status of protein nutrition.

• Asian-Australasian Journal of Animal Sciences
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• v.15 no.6
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• pp.834-837
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• 2002

The effect of undecorticated sunflower cake (USFC) as critical protein supplement was assessed and compared with deoiled groundnut cake (DGNC) in adult goats and sheep. The animals were fed a basal diet of wheat straw ad libitum and supplemented with either USFC or DGNC to meet their protein requirement for maintenance. Total dry-matter intake by sheep and goats (g/kg $BW^{0.75}$) on USFC was similar to their counterparts on DGNC supplemented group. However, while intake of cake moiety was significantly (p<0.05) higher in USFC, the intake of wheat straw was significantly (p<0.05) higher by animals on DGNC. Digestibility of various nutrients, except lower crude protein digestibility by goats in USFC group, did not differ significantly between animals given DGNC or USFC. DCP and TDN concentration (% DM) was comparable in sheep and goats irrespective of dietary supplement. Similarly, the intake (g/kg $W^{0.75}$) of DCP, DDM, DOM, and TDN was similar between DGNC and USFC in both sheep and goats. It may be concluded that undecorticated sunflower cake is comparable to deoiled groundnut cake as a critical protein supplement to the roughage based diet of small ruminants.

• Korean Journal of Agricultural Science
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• v.24 no.2
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• pp.121-125
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• 1997

A total of 437 landraces of rice from Vietnam were analyzed for total seed protein by SDS-PAGE and phenol reaction. The different types of glutelin $\alpha$ subunits were detected. The level of wx protein with 60kDa molecular weight was divided into 3 groups, corresponding to non-glutinous, intermediate and glutinous starch types. Based on the variation in seed storage protein and wx protein, landraces were classified into 7 groups. Frequency distribution of types A and B of glutelin $\alpha$ subunits changed with the latitude at which rice landraces were collected. Geographical cline for phenol reaction was detected.

• KSBB Journal
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• v.15 no.5
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• pp.525-528
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• 2000

Time course monitoring of FCW/DCW ratio, production of intra and extracellular protein, and peroxidase activity were performed during suspension culture of Taxus chinensis cells. The observed FCW/DCW ratio was 12 at day 14, which was the lowest value during cultivation, and the specific protein production, based on dry cell weight, was also the lowest at day 14, which showed 4.3 mg/g DCW. The pattern of POD activity was similar to that of protein production. The results in this report were obtained using actively growing cells in flasks, therefore it is possible to use those results to control the process and indicate the stresses imposed on cells during large-scale cultivation.

• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.62-66
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• 2016

Tumor suppressor protein p53 loses its function upon binding with the HDM2 protein, and inhibiting the p53-HDM2 interaction is critical to suppress tumor cell growth. Recently, the cyclized helix-loop-helix peptide (cHLH) mimicking the ${\alpha}-helix$ part of the p53 protein has been designed and found to exhibit high binding affinity with HDM2. Here, we report the structural and thermodynamic characteristics of the bound complex of the cHLH peptide with the HDM2 protein. We performed molecular dynamics simulations to investigate the structural features of the cHLH peptide as well as its complex with the HDM2. The binding free energy calculation based on the integral equation theory was also executed to quantify the binding affinity for the cHLH/HDM2 complex and to understand the factors contributing to the binding affinity. We found a variety of factors for the helix stability of the cHLH peptide as well as in the complexation with the HDM2, which may provide an insight into the development of anti-cancer drug designs.

• Journal of Microbiology and Biotechnology
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• v.22 no.2
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• pp.226-229
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• 2012

Bacterial hemoglobin from Vitreoscilla (VHb) is recognized as a good fusion protein for the soluble expression of foreign protein. In this study, we generated a monoclonal antibody (MAb) against VHb for its detection. For the rapid screening of MAb, a protein chip technology based on the Alexa-488 (A488) dye labeling method was introduced. In order to fabricate the chip, the VHb protein was chemically coupled to the chip surface and then the culture supernatants of 84 hybridoma cell lines were spotted onto the VHb chip. The bound MAbs were measured by A488-modified anti-mouse IgG. A single spot (MAb A10) exhibited significantly high signal intensity. The immunoblot analysis evidenced that the MAb A10 can detect VHb-fused proteins with high specificity.

• Journal of Animal Science and Technology
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• v.63 no.2
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• pp.405-416
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• 2021

The aim of the study was to determine the effect of whole milk powder (WMP) as heterologous proteins on chicken breast emulsion-type sausages. The quality properties of WMP on such chicken breast emulsion-type sausages were investigated by measuring the proximate composition, pH, color, cooking yield, protein solubility, and by applying other methods, such as texture profile analysis (TPA), microphotograph, sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), and electronic nose. The crude fat, protein, and ash contents of 15% WMP samples were significantly higher than the control samples (p < 0.05). The redness of the cooked samples significantly increased with an increase in the WMP contents (p < 0.05). The cooking yield of WMP treated samples was significantly higher than the control sample (p < 0.05). Additionally, the hardness, gumminess, and chewiness of WMP treated samples were significantly higher than the control sample (p < 0.05). The sarcoplasmic and myofibrillar proteins of samples containing 15% WMP were significantly higher than the control samples (p < 0.05). The result of SDS-PAGE showed that the C protein, sarcoplasmic protein, actin, and tropomyosin increased with an increase in the WMP contents. The principal component analysis plot of WMP-treated samples was clearly different from that of the control samples. Based on these results, it was predicted that WMP could be useful as heterologous protein on emulsion-type sausage.

• Journal of the Korean Magnetic Resonance Society
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• v.6 no.2
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• pp.94-102
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• 2002

An interesting recent application of intermolecular NOE experiment is the saturation transfer difference NMR(STD-NMR) method that is useful in screening compound libraries to identify bio-active ligands. This technique also identifies the group epitopes of the bound ligand in a reversibly forming protein-ligand complex. We present here a complete relaxation and conformational exchange matrix (CORCEMA) theory (Moseley et al., J. Magn. Reson. B, 108, 243-261 (1995)) applicable for the STD-NMR experiment. Using some ideal model systems we have analyzed the factors that influence the STD intensity changes in the ligand proton NMR spectrum when the resonances from some protons on the receptor protein are saturated. These factors will be discussed and some examples of its application in some model systems will be presented. This CORCEMA theory for STD-NMR and the associated algorithm are useful in a quantitative interpretation of the STD-NMR effects, and are likely to be useful in structure-based drug design efforts. They are also useful in a quantitative characterization of protein-protein (or protein-nucleic acid) contact surfaces from an intermolecular cross-saturation NMR experiment.