• Animal cells and systems
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• 제9권3호
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• pp.139-144
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• 2005

The attractant (orange light) or repellent (white light) signal is transmitted from SRI (Sensory Rhodopsin I) via protein-protein interaction with its transducer Htrl (Halobacterial Transducer for Sensory Rhodopsin I) which in turn controls a cytoplasmic phospho-transfer pathway that modulates flagella motor switching in Halobacterium salinarum. Some mutations in both SRI and Htrl showed an unusual mutant phenotype called inverted signaling, in which the cell produces a repellent response to normally attractant light. Twelve mutations at the Glutamate 56 (E56) position in the second transmembrane helix of Htrl were introduced by site-specific random mutagenesis. Almost all E56 mutants showed orange-light inverted responses in pH and temperature-dependent manners except E56D and E56Y. Except for these two mutants, all mutants accelerated the $S_{373}$ decay compared to wild-type at $18^{\circ}C$. This supported that there is an interaction between SRI and the second transmembrane of Htrl. Also a structural model of Htrl based on the Tar crystal structure and the secondary structure prediction program proposed the E56 residue to be in the middle of the proton channel. The most important observation is that the E56 mutant provides the evidence that this residue is very sensitive for signal relay, which can be explained by the open and closed conformations of the channel (A and R conformations) in SRI, as was postulated by the unified conformational shuttling model for transport and signaling.

• 한국정보처리학회:학술대회논문집
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• 한국정보처리학회 2008년도 추계학술발표대회
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• pp.785-787
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• 2008

생명체의 생명현상을 주관하는 각종 화학반응들은 단백질이 관여하고 있다. 단백질은 일정한 질서에 따라 서로 조립되기도 하고, 기능적으로 연관돼 네트워크를 이루고 있다. 이 네트워크를 구성하는 단백질-단백질 상호작용은 단백질의 기능과 밀접하게 관련되어 있다. 즉, 상호작용하는 단백질은 같은 기능을 수행할 가능성이 크다. 이러한 사실은 단백질-단백질 상호작용을 통해 기능이 알려지지 않은 미지 단백질의 기능을 예측할 수 있게 한다. 대표적인 연구로는 이웃 노드에 존재하는 기능분포를 이용하는 이웃노드 카운트(Neighborhood Counting)방식과 특정 기능의 나타날 빈도를 계산하여 기능을 예측하는 카이-제곱(Chi-Square)방식 등이 있다. 본 논문에서는 단백질 기능 예측의 정확성을 높이기 위해 이들 두 방식의 장점을 취합한 보완된 카이-제곱 방식을 제안한다. 그리고 다양한 단백질 상호작용 네트워크 데이터를 비교 분석하여 보완된 카이-제곱 방식이 기능 예측의 정확성이 높음을 증명한다.

• Genomics & Informatics
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• 제13권2호
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• pp.53-59
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• 2015

In developing countries threat of cholera is a significant health concern whenever water purification and sewage disposal systems are inadequate. Vibrio cholerae is one of the responsible bacteria involved in cholera disease. The complete genome sequence of V. cholerae deciphers the presence of various genes and hypothetical proteins whose function are not yet understood. Hence analyzing and annotating the structure and function of hypothetical proteins is important for understanding the V. cholerae. V. cholerae O139 is the most common and pathogenic bacterial strain among various V. cholerae strains. In this study sequence of six hypothetical proteins of V. cholerae O139 has been annotated from NCBI. Various computational tools and databases have been used to determine domain family, protein-protein interaction, solubility of protein, ligand binding sites etc. The three dimensional structure of two proteins were modeled and their ligand binding sites were identified. We have found domains and families of only one protein. The analysis revealed that these proteins might have antibiotic resistance activity, DNA breaking-rejoining activity, integrase enzyme activity, restriction endonuclease, etc. Structural prediction of these proteins and detection of binding sites from this study would indicate a potential target aiding docking studies for therapeutic designing against cholera.

• BMB Reports
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• 제52권7호
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• pp.445-450
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• 2019

TTYH2 is a calcium-activated, inwardly rectifying anion channel that has been shown to be related to renal cancer and colon cancer. Based on the topological prediction, TTYH2 protein has five transmembrane domains with the extracellular N-terminus and the cytoplasmic C-terminus. In the present study, we identified a vesicle transport protein, ${\beta}$-COP, as a novel specific binding partner of TTYH2 by yeast two-hybrid screening using a human brain cDNA library with the C-terminal region of TTYH2 (TTYH2-C) as a bait. Using in vitro and in vivo binding assays, we confirmed the protein-protein interactions between TTYH2 and ${\beta}$-COP. We also found that the surface expression and activity of TTYH2 were decreased by co-expression with ${\beta}$-COP in the heterologous expression system. In addition, ${\beta}$-COP associated with TTYH2 in a native condition at a human colon cancer cell line, LoVo cells. The over-expression of ${\beta}$-COP in the LoVo cells led to a dramatic decrease in the surface expression and activity of endogenous TTYH2. Collectively, these data suggested that ${\beta}$-COP plays a critical role in the trafficking of the TTYH2 channel to the plasma membrane.

• 한국해양바이오학회지
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• 제6권2호
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• pp.102-109
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• 2014

Cetaceans (whales, dolphins, and porpoises) are aquatic mammals that experienced drastic changes during the transition from terrestrial to aquatic environment. Morphological changes include streamlined body, alterations in the face, transformation of the forelimbs into flippers, disappearance of the hindlimbs and the acquisition of flukes on the tail. For a prolonged diving, cetaceans acquired hypoxia-resistance by developing various anatomical and physiological changes. However, molecular mechanisms underlying these adaptations are still limited. CREB-binding protein (CREBBP) is a transcriptional co-activator critical for embryonic development, growth control, metabolic homeostasis and responses to hypoxia. Natural selection analysis of five cetacean CREBBPs compared with those from 15 terrestrial relatives revealed strong purifying selection, supporting the importance of its role in mammals. However, prediction for amino acid changes that elicit functional difference of CREBBP identified three cetacean specific changes localized within a region required for interaction with SRCAP and in proximal regions to KIX domain of CREBBP. Mutations in CREBBP or SRCAP are known to cause craniofacial and skeletal defects in human, and KIX domain of CREBBP serves as a docking site for transcription factors including c-Myb, an essential regulator of haematopoiesis. In these respects, our study provides interesting insights into the functional adaptation of cetacean CREBBP for aquatic lifestyle.

• 한국근적외분광분석학회:학술대회논문집
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• 한국근적외분광분석학회 2001년도 NIR-2001
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• pp.1251-1251
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• 2001

The routine analysis of milk chemical components is of major importance both for the management of animals in dairy farms and for quality control in dairy industries. NIRS technology is an analytical technique which greatly simplifies this routine. One of the most critical aspects in NIRS analysis of milk is sample preparation and analysis modes which should be fast and straightforward. An important difficulty when obtaining NIR spectra of milk is the high water content (80 to 90%) of this product, since water absorbs most of the infrared radiation, and, therefore, limits the accuracy of calibrating for other constituents. To avoid this problem, the DESIR system was set up. Other ways of radiation-sample interaction adapted for liquids or semi-liquids exist, which are practically instantaneous and with limited or null necessity of sample preparation: Transmission and Folded Transmission or Transflectance. The objective of the present work is to compare the precision and accuracy of milk calibration equations in two analysis modes: Reflectance (dry milk) and Folded Transmission (liquid milk). A FOSS-NIR Systems 6500 I spectrophotometer (400-2500 nm) provided with a spinning module was used. Two NIR spectroscopic methods for milk analysis were compared: a) folded transmission: liquid milk samples in a 0.1 pathlength sample cell (ref. IH-0345) and b) reflectance: dried milk samples in glass fibre filters placed in a standard ring cell. A set of 101 milk samples was used to develop the calibration equations, for the two NIR analysis modes, to predict casein, protein, fat and dry matter contents, and 48 milk samples to predict Somatic Cell Count (SCC). The calibrations obtained for protein, fat and dry matter have an excellent quantitative prediction power, since they present $r^2$ values higher than 0.9. The $r^2$ values are slightly lower for casein and SCC (0.88 and 0.89 respectively), but they still are sufficiently high. The accuracy of casein, protein and SCC equations is not affected by the analysis modes, since their ETVC values are very similar in reflectance and folded transmission (0.19% vs 0.21%; 0.16% vs 0.19% and 55.57% vs 53.11% respectively), Lower SECV values were obtained for the prediction of fat and dry matter with the folded transmission equations (0.14% and 0.25% respectively) compared to the results with the reflectance ones (0.43% and 0.34% respectively). In terms of accuracy and speed of analytical response, NIRS analysis of liquid milk is recommended (folded transmission), since the drying procedure takes 24 hours. However, both analysis modes offer satisfactory results.

• Natural Product Sciences
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• 제25권3호
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• pp.215-221
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• 2019

Inflammation is the crucial biological process of immune system which acts as body's defense and protective response against the injuries or infection. However, the systemic inflammation devotes the adverse effects such as multiple inflammation associated diseases. One of the best ways to treat this entity is by blocking the tumor necrosis factor alpha ($TNF-{\alpha}$) and TNF-related apoptosis-inducing ligand (TRAIL) to avoid the proinflammation cytokines production. Thus, this study aims to evaluate the potency of Sambucus bioactive compounds as anti-inflammation through in silico approach. In order to assess that, molecular docking was performed to evaluate the interaction properties between the $TNF-{\alpha}$ or TRAIL with the ligands. The 2D structure of ligands were retrieved online via PubChem and the 3D protein modeling was done by using SWISS Model. The prediction results of the study showed that caffeic acid (-6.4 kcal/mol) and homovanillic acid (-6.6 kcal/mol) have the greatest binding affinity against the $TNF-{\alpha}$ and TRAIL respectively. This evidence suggests that caffeic acid and homovanillic acid may potent as anti-inflammatory agent against the inflammation associated diseases. Finally, this study needs further examination and evaluation to validate the potency of Sambucus bioactive compounds.

• Asian-Australasian Journal of Animal Sciences
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• 제16권5호
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• pp.693-701
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• 2003

In order to evaluate the nutritive value of the forage plants in South Sulawesi, Indonesia, 266 samples (61 grasses and 65 legumes grown in the dry season, 60 grasses and 80 legumes grown in the rainy season) were collected from the highland and lowland in 1998 to 2000, and were subjected to the determination of chemical composition and digestibility. The least-squares analysis of variance demonstrated that the in vitro dry matter digestibility (IVDMD) of grasses was not significantly affected by season or altitude. On the other hand, the some proximate components and cell wall components were significantly affected by season and altitude including the season${\times}$altitude interaction. For the legumes, the in vitro neutral detergent fiber digestibility (IVNDFD) and cellulose content were significantly affected by season. On the other hand, the ether extract (EE) content was significantly affected by season and altitude. The interaction of the season${\times}$altitude for IVDMD, of the year${\times}$season for some proximate components and of the year${\times}$season and the season${\times}$altitude for some cell wall components were significant. These results indicate that the forages grown at highland in dry season have a relatively high quality. The means of the total digestible nutrient (TDN) content estimated from IVDMD in grasses and in legumes were 50.3% and 57.4%, respectively, and the crude protein contents were 7.7% and 17.6%, respectively. The correlation coefficients between IVDMD and the contents of crude fiber, neutral detergent fiber and acid detergent fiber were relatively high in all of forage plants, suggesting that these components would provide an accurate prediction of digestibility or TDN content. A close relationship between IVNDFD and lignin content indicates that the lignin would be the most accurate predictor of cell wall digestibility.

• Journal of Microbiology and Biotechnology
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• 제31권10호
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• pp.1358-1365
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• 2021

To clarify the role of long intergenic nonprotein-coding RNA 1232 (LINC01232) in the progression of gastric cancer and the potential mechanism, we analyzed the expression of LINC01232 in TCGA database using the GEPIA online tool, and the LINC01232 level in gastric cancer cell lines was detected by quantitative real time-polymerase chain reaction (qRT-PCR) as well. Cell proliferation assay, colony formation assay, transwell assay and tumor formation experiment in nude mice were conducted to observe the biological behavior changes of gastric cancer cells through the influence of LINC01232 knockdown. LncATLAS database and subcellular isolation assay were used for subcellular distribution of LINC01232 in gastric cancer cells. The interaction among LINC01232, zeste homolog 2 (EZH2) and kruppel-like factor 2 (KLF2) was clarified by RNA-protein interaction prediction (RPISeq), RNA immunoprecipitation (RIP), qRT-PCR and chromatin immunoprecipitation (ChIP) assay. Rescue experiments were further conducted to elucidate the biological function of LINC01232/KLF2 axis in the progression of gastric cancer. LINC01232 was upregulated in stomach adenocarcinoma (STAD) tissues and gastric cancer lines. LINC01232 knockdown inhibited the proliferative capacities of gastric cancer cells in vitro, and impaired in vivo tumorigenicity. LINC01232 was mainly distributed in the cell nucleus where it epigenetically repressed KLF2 expression via binding to the enhancer of EZH2, which was capable of binding to promoter regions of KLF2 to induce histone H3 lysine 27 trimethylation (H3K27me3). LINC01232 exerts oncogenic activities in gastric cancer via inhibition of KLF2, and therefore, the knockdown of KLF2 could reverse the regulatory effect of LINC01232 in the proliferative ability of gastric cancer cells.

• Bulletin of the Korean Chemical Society
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• 제32권6호
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• pp.2008-2014
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• 2011

Serotonin or 5-hydroxytryptamine subtype 2C ($5-HT_{2C}$) receptor belongs to class A amine subfamily of G-protein-coupled receptor (GPCR) super family and its ligands has therapeutic promise as anti-depressant and -obesity agents. So far, bovine rhodopsin from class A opsin subfamily was the mostly used X-ray crystal template to model this receptor. Here, we explained homology model using beta 2 adrenergic receptor (${\beta}$2AR), the model was energetically minimized and validated by flexible ligand docking with known agonists and antagonists. In the active site Asp134, Ser138 of transmembrane 3 (TM3), Arg195 of extracellular loop 2 (ECL2) and Tyr358 of TM7 were found as important residues to interact with agonists. In addition to these, V208 of ECL2 and N351 of TM7 was found to interact with antagonists. Several conserved residues including Trp324, Phe327 and Phe328 were also found to contribute hydrophobic interaction. The predicted ligand binding mode is in good agreement with published mutagenesis and homology model data. This new template derived homology model can be useful for further virtual screening based lead identification.