• Korean Journal of Veterinary Research
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• v.33 no.2
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• pp.199-209
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• 1993

The effects of ${\alpha}_1$-adrenergic stimulation on membrane potential, intracellular sodium activity $(a_N{^i{_a}})$, and contractility were investigated in the isolated papillary muscle of euthyroid, hyperthyroid, and hypothyroid guinea pigs. Cardiac alterations in the thyroid state have been shown to induce marked changes in action potential characteristics, the most pronounced shortening of action potential duration by hyperthyroidism and an increase in duration by hypothyroidism. $10^{-5}M$ Phenylephrine produced a decrease in $(a_N{^i{_a}})$ in euthyroid and hypothyroid preparations, but an increase in $(a_N{^i{_a}})$ in hyperthyroid ones. The major findings were that phenylephrine produced a stronger positive inotropic effect(PIE) without initial negative inotropic effect(NIE) in hyperthyroid preparations, while phenylephrine produced markedly NIE in hypothyroid ones. The alterations in membrane potential, $(a_N{^i{_a}})$, and contractility were abolished by $3{\times}10^{-5}M$ prazosin in hypothyroidism. In hypothyroid ventricular muscle, the decrease in $(a_N{^i{_a}})$ caused by phenylephrine were not abolished or reduced by $10^{-5}M$ strophanthidin, $10^{-5}M$ TTX, $3{\times}10^{-4}M$ lidocaine, or $100^{-5}M$ verapamil. These results indicate that the ${\alpha}_1$-adrenoceptor-mediated decrease in $(a_N{^i{_a}})$ is not associated with a stimulation of the $Na^+$-$K^+$ pump, inhibition of the $Na^+$ or $Ca^+$ channel in hypothyroid ventricular muscle. $10^{-5}M$ Phenylephrine decreased $(a_N{^i{_a}})$ but increased $(a_N{^i{_a}})$ in the presence of a PKC activator phorbol dibutyrate$(PDB_u)$. In conclusion, it is suggested that the following sequence of events in response to phenyleplhane occur in guinea pig ventricular muscle. First, changes in thyroid state may contribute to the ventacular electrophysiological propeties or ion transport system. Second, the adrenoceptor-mediated initial transient NIE may be associated with the decrease in $(a_N{^i{_a}})$ by PKC activation.

• Molecular & Cellular Toxicology
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• v.4 no.4
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• pp.307-310
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• 2008

AAD16034 is an alginate lyase from Pseudoalteromonas sp. IAM14594. A very close homologue with known 3D structure exists (marine bacterium Pseudoalteromonas sp. strain no. 272). A three-dimensional structure of AAD16034 was generated based on this template (PDB code: 1J1T) by comparative modeling. The modeled enzyme exhibited a jelly-roll like structure very similar to its template structure. Both enzymes possess the characteristic alginate sequence YFKhG+Y-Q. Since AAD16034 displays enzymatic activity for poly-M alginate, docking of a tri-mannuronate into the modeled structure was performed. Two separate and adjacent binding sites were found. The ligand was accommodated inside each binding site. By considering both binding sites, a plausible binding pose for the poly-M alginate polymer could be deduced. From the modeled docking pose (i.e., the most important factor that attracts alginate polymer into this lyase) the most likely interaction was electrostatic. In accordance with a previous report, the hydroxyl group of Y345 was positioned close to the ${\alpha}$-hydrogen of ${\beta}$-mannuronate, which was suitable to initiate a ${\beta}$-elimination reaction. K347 was also very near to the carboxylatemoiety of the ligand, which might stabilize the dianion intermediate during the ${\beta}$-elimination reaction. This implies that the characteristic alginate sequence is absolutely crucial for the catalysis. These results may be exploited in the design of novel enzymes with desired properties.

• Journal of Integrative Natural Science
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• v.3 no.2
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• pp.72-77
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• 2010

Alginate lyases, also known as alginases or alginate depolymerases, catalyze the degradation of alginate by a ${\beta}$-elimination mechanism that has yet to be fully elucidated. Alginate is a copolymer of ${\alpha}$-L-guluronate (G) and its C5 epimer ${\beta}$-D-mannuronate (M), arranged as homopolymeric G blocks, M blocks, alternating GM or random heteropolymeric G/M stretches. Almost all alginate lyases depolymerize alginate in an endolytical fashion via a ${\beta}$-elimination reaction. The alginate lyase Atu3025 from Agrobacterium tumefaciens strain C58, consisting of 776 amino-acid residues, is a novel exotype alginate lyase classified into polysaccharide lyase family 15. Till now there is no crystal structure available for this class of proteins. Since there is no template with high sequence identity, three-dimensional coordinates for exotype alginate lyase (PL 15 family) were determined using modeling methods (Comparitive modeling and Fold recognition). The structures were modeled using the X-ray coordinates from Heparinase protein family (PDB code: 3E7J). This enzyme (Atu3025) displays enzymatic activity for both poly-M and poly-G alginate. Since poly-M is widespread; docking of a tri-mannuronate against the modeled structure was performed. We identified some of those residues which are crucial for lyase activity. The results from this study should guide future mutagenesis studies and also provides a starting point for further proceedings.

• The KIPS Transactions:PartD
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• v.11D no.3
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• pp.519-532
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• 2004

With the explosion of bioinformatics data such proteins and genes, biologists need a integrated system to analyze and organize large datasets that interact with heterogeneous types of biological data. In this paper, we propose a integration system based on a mediated data warehouse architecture using a XML model in order to combine protein related data at biology laboratories. A fact constellation model in this system is used at a common model for integration and an integrated schema it translated to a XML schema. In addition, to track source changes and provenance of data in an integrated database employ incremental update and management of sequence version. This paper shows modeling of integration for protein structures, sequences and classification of structures using the proposed system.

• Genomics & Informatics
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• v.6 no.3
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• pp.142-146
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• 2008

In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and disease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within $20\;{\AA}$ (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.

• Genomics & Informatics
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• v.14 no.3
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• pp.112-124
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• 2016

Solid tumor is generally observed in tissues of epithelial or endothelial cells of lung, breast, prostate, pancreases, colorectal, stomach, and bladder, where several genes transcription is regulated by the microRNAs (miRNAs). Argonaute (AGO) protein is a family of protein which assists in miRNAs to bind with mRNAs of the target genes. Hence, study of the binding mechanism between AGO protein and miRNAs, and also with miRNAs-mRNAs duplex is crucial for understanding the RNA silencing mechanism. In the current work, 64 genes and 23 miRNAs have been selected from literatures, whose deregulation is well established in seven types of solid cancer like lung, breast, prostate, pancreases, colorectal, stomach, and bladder cancer. In silico study reveals, miRNAs namely, miR-106a, miR-21, and miR-29b-2 have a strong binding affinity towards PTEN, TGFBR2, and VEGFA genes, respectively, suggested as important factors in RNA silencing mechanism. Furthermore, interaction between AGO protein (PDB ID-3F73, chain A) with selected miRNAs and with miRNAs-mRNAs duplex were studied computationally to understand their binding at molecular level. The residual interaction and hydrogen bonding are inspected in Discovery Studio 3.5 suites. The current investigation throws light on understanding miRNAs based gene silencing mechanism in solid cancer.

• Journal of Mushroom
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• v.3 no.1
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• pp.24-30
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• 2005

To study the cultural characteristics and wood rotting ability of the secondary mycellia of Armillaria mellea, it was cultivated on the various media. The optimal mycelial growth condition was 20~27 and pH 5.0~6.5 on PDB. A. mellea grew well on MEA, PDA and GP. Lactose and mannitol as carbon sources and glutamic acid as nitrogen sources were found to be effective as additives. A. mellea employed in this study have the characteristics of white rot types. Pine and oak wood were selected as candidates for sawdust substrate.

• Journal of Mushroom
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• v.7 no.3
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• pp.110-114
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• 2009

Sawdust bag cultivation of Shiitake mushroom (Lentinula edodes) is getting increase. The mycelia browning on the substrate surface is important for the stable production. The development of methods for the rapid mycelia browning is quite required. In this study changes in intracellular enzyme during the mycelial browning were investigated to find the rapid mycelia browning. Mycelia of L. edodes was changed into brown color while it grew in agar and liquid media like sawdust substrates. Mycelia of L. edodes was started to change color at 25 days after inoculation and browning was occurred in whole mycelia colony at 30 days and browning was completed at 40 days. The activities of enzymes was evaluated in these periodically color changing mycelia. Laccase activity was highest at 15 days after inoculation on PDB, but it gradually decreased from 15 days. Tyrosinase activity drastically increased in period between 30 days and 40 days while mycelia browning was progressed. The kinds of phosphotase identified by electrophoresis were esterase, acid phosphotase, and alkaline phosphotase. Activities of phosphotase were increased before the initiation of mycelial browning but they were decreased after browning.

• Molecules and Cells
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• v.41 no.8
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• pp.771-780
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• 2018

Angiogenesis must be precisely controlled because uncontrolled angiogenesis is involved in aggravation of disease symptoms. Vascular endothelial growth factor (VEGF)/VEGF receptor 2 (VEGFR-2) signaling is a key pathway leading to angiogenic responses in vascular endothelial cells (ECs). Therefore, targeting VEGF/VEGFR-2 signaling may be effective at modulating angiogenesis to alleviate various disease symptoms. Oleanolic acid was verified as a VEGFR-2 binding chemical from anticancer herbs with similar binding affinity as a reference drug in the Protein Data Bank (PDB) entry 3CJG of model A coordination. Oleanolic acid effectively inhibited VEGF-induced VEGFR-2 activation and angiogenesis in HUVECs without cytotoxicity. We also verified that oleanolic acid inhibits in vivo angiogenesis during the development and the course of the retinopathy of prematurity (ROP) model in the mouse retina. Taken together, our results suggest a potential therapeutic benefit of oleanolic acid for inhibiting angiogenesis in proangiogenic diseases, including retinopathy.

• The Korean Journal of Mycology
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• v.26 no.1 s.84
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• pp.20-24
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• 1998

The effects of liquid spawn to sawdust substrate on the growth of Flammulina velutipes were conducted for two years. The duration of optimal incubation for preculture and main culture of liquid spawn was 4 days and 6 days, respectively. When using liquid spawn, the application time for the first pinhead formation was similar with sawdust spawn, and incubation time of sawdust substrate was variable with liquid spawn and inoculum quantity. But, the overall yield of mushroom fruitbody was increased by using liquid spawn, excepting sesame hull extract medium.