• Title/Summary/Keyword: Protein screening

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Atom Number and Bounding Sphere Based Search Speedup Technique for Similar Proteins Screening (원자개수와 경계구에 기반한 유사 단백질 스크리닝을 위한 검색 가속 기법)

  • Lee, Jaeho;Park, JoonYoung
    • Korean Journal of Computational Design and Engineering
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    • v.20 no.4
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    • pp.321-327
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    • 2015
  • In the protein database search, 3D structural shape comparison for protein screening plays a important role. Protein databases have big size and have been grown rapidly. Exhaustive search methods cannot provide a satisfactory performance. As protein is composed of a set of spheres, the similarity calculation of two set of spheres is very expensive. Thus, a reasonable filtering method could be an answer for the speedup of protein screening. In this paper, we suggest a speedup method for protein screening with atom number and bounding sphere. We also show some experimental results for the validity of our method.

Screening of New Antibiotics Inhibiting Bacterial Enoyl-Acyl Carrier Protein Reductase (Fabl) (세균의 지방산 생합성 효소 (Enoyl-Acyl Carrier Protein Reductase, FabI)를 저해하는 새로운 항균물질의 스크리닝)

  • 곽진환
    • YAKHAK HOEJI
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    • v.46 no.1
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    • pp.24-29
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    • 2002
  • Enoyl-Acyl Carrier Protein Reductase (Fabl) of bacteria is hem as an important target for new antibacterial drugs and plays a determinant role in completing cycles of elongation in type-H fatty acid synthase system. In this study, a fabI gene from Staphylococcus aureus 6538p cloned in pET-l4b vector and FabI protein was over-produced in Escherichaia coli BL2l (DE3). $NH_2$-terminal His-tagged FabI protein was purified by nickel-nitrilotriacetic acid (Ni-NTA) metalaffinity chromatography Purified 6xHis-tagged FabI showed a catalytic activity on tram - 2 - octenoyl - N -acethlcysteamine by utilizing NADPH as a cofactor. For the discovery of new FabI inhibitors from chemical libraries, a target-oriented screening system using a 96-well plate was developed. About 10,000 chemical libraries from Korea Chemical Bank wore tested in this screening system, and 26 chemicals (0.25%) among them showed an inhibitory activity against FabI enzyme. This result showed that a new screening system can be used for the discovery of new FabI inhibitors.

Parthenolide-Induced Apoptosis, Autophagy and Suppression of Proliferation in HepG2 Cells

  • Sun, Jing;Zhang, Chan;Bao, Yong-Li;Wu, Yin;Chen, Zhong-Liang;Yu, Chun-Lei;Huang, Yan-Xin;Sun, Ying;Zheng, Li-Hua;Wang, Xue;Li, Yu-Xin
    • Asian Pacific Journal of Cancer Prevention
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    • v.15 no.12
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    • pp.4897-4902
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    • 2014
  • Purpose: To investigate the anticancer effects and underlying mechanisms of parthenolide on HepG2 human hepatocellular carcinoma cells. Materials and Methods: Cell viability was assessed by MTT assay and cell apoptosis through DAPI, TUNEL staining and Western blotting. Monodansylcadaverin(MDC) and AO staining were used to detect cell autophagy. Cell proliferation was assessed by Ki67 immunofluorescence staining. Results: Parthenolide induced growth inhibition in HepG2 cells. DAPI and TUNEL staining showed that parthenolide could increase the number of apoptotic nuclei, while reducing the expression of the anti-apoptotic protein Bcl-2 and elevating the expression of related proteins, like p53, Bax, cleaved caspase9 and cleaved caspase3. Parthenolide could induce autophagy in HepG2 cells and inhibited the expression of proliferation-related gene, Ki-67. Conclusions: Parthenolide can exert anti-cancer effects by inducing cell apoptosis, activating autophagy and inhibiting cell proliferation.

Identification of HUGT1 as a Potential BiP Activator and a Cellular Target for Improvement of Recombinant Protein Production Using a cDNA Screening System

  • Ku, Sebastian Chih Yuan;Lwa, Teng Rhui;Giam, Maybelline;Yap, Miranda Gek Sim;Chao, Sheng-Hao
    • Molecules and Cells
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    • v.27 no.5
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    • pp.577-582
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    • 2009
  • The development of a high-throughput functional genomic screening provides a novel and expeditious approach in identifying critical genes involved in specific biological processes. Here we describe a cell-based cDNA screening system to identify the transcription activators of BiP, an endoplasmic reticulum (ER) chaperone protein. BiP promoter contains the ER stress element which is commonly present in the genes involved in unfolded protein response (UPR) that regulates protein secretion in cells. Therefore, the positive regulators of BiP may also be utilized to improve the recombinant protein production through modulation of UPR. Four BiP activators, including human UDP-glucose:glycoprotein glucosyltransferase 1 (HUGT1), are identified by the cDNA screening. Overexpression of HUGT1 leads to a significant increase in the production of recombinant erythropoietin, interferon ${\gamma}$, and monoclonal antibody in HEK293 cells. Our results demonstrate that the cDNA screening for BiP activators may be effective to identify the novel BiP regulators and HUGT1 may serve as an ideal target gene for improving the recombinant protein production in mammalian cells.

Detergent Screening for NMR-Based Structural Study of the Integral Membrane Protein, Emopamil Binding Protein (Human Sterol Δ8-Δ7 Isomerase)

  • Won, Hyung-Sik
    • Journal of the Korean Magnetic Resonance Society
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    • v.21 no.1
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    • pp.13-19
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    • 2017
  • Human sterol ${\Delta}8-{\Delta}7$ isomerase, commonly known as emopamil binding protein (EBP), is an essential protein in the cholesterol-synthetic pathway, and mutations of this protein are critically associated with human diseases such as Conradi-Hunermann-Happle or male EBP disorder with neurological defects syndrome. Due to such a clinical importance, EBP has been intensively investigated and some important features have been reported. EBP is a tetra-spanning membrane protein, of which $2^{nd}$, $3^{rd}$, and $4^{th}$ membrane-spanning ${\alpha}$ helices play an important role in its enzymatic function. However, detailed structural feature at atomic resolution has not yet been elucidated, due to characteristic difficulties in dealing with membrane protein. Here, we over-expressed EBP using Escherichia coli and performed detergent screening to find suitable membrane mimetics for structural studies of the protein by NMR. As results, DPC and LMPG could be evaluated as the most favorable detergents to acquire promising NMR spectra for structural study of EBP.

EMPAS: Electron Microscopy Screening for Endogenous Protein Architectures

  • Kim, Gijeong;Jang, Seongmin;Lee, Eunhye;Song, Ji-Joon
    • Molecules and Cells
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    • v.43 no.9
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    • pp.804-812
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    • 2020
  • In cells, proteins form macromolecular complexes to execute their own unique roles in biological processes. Conventional structural biology methods adopt a bottom-up approach starting from defined sets of proteins to investigate the structures and interactions of protein complexes. However, this approach does not reflect the diverse and complex landscape of endogenous molecular architectures. Here, we introduce a top-down approach called Electron Microscopy screening for endogenous Protein ArchitectureS (EMPAS) to investigate the diverse and complex landscape of endogenous macromolecular architectures in an unbiased manner. By applying EMPAS, we discovered a spiral architecture and identified it as AdhE. Furthermore, we performed screening to examine endogenous molecular architectures of human embryonic stem cells (hESCs), mouse brains, cyanobacteria and plant leaves, revealing their diverse repertoires of molecular architectures. This study suggests that EMPAS may serve as a tool to investigate the molecular architectures of endogenous macromolecular proteins.

Pristimerin Inhibits Breast Cancer Cell Migration by Up-regulating Regulator of G Protein Signaling 4 Expression

  • Mu, Xian-Min;Shi, Wei;Sun, Li-Xin;Li, Han;Wang, Yu-Rong;Jiang, Zhen-Zhou;Zhang, Lu-Yong
    • Asian Pacific Journal of Cancer Prevention
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    • v.13 no.4
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    • pp.1097-1104
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    • 2012
  • Background/Aim: Pristimerin isolated from Celastrus and Maytenus spp can inhibit proteasome activity. However, whether pristimerin can modulate cancer metastasis is unknown. Methods: The impacts of pristimerin on the purified and intracellular chymotrypsin proteasomal activity, the levels of regulator of G protein signaling 4 (RGS 4) expression and breast cancer cell lamellipodia formation, and the migration and invasion were determined by enzymatic, Western blot, immunofluorescent, and transwell assays, respectively. Results: We found that pristimerin inhibited human chymotrypsin proteasomal activity in MDA-MB-231 cells in a dose-dependent manner. Pristimerin also inhibited breast cancer cell lamellipodia formation, migration, and invasion in vitro by up-regulating RGS4 expression. Thus, knockdown of RGS4 attenuated pristimerin-mediated inhibition of breast cancer cell migration and invasion. Furthermore, pristimerin inhibited growth and invasion of implanted breast tumors in mice. Conclusion: Pristmerin inhibits proteasomal activity and increases the levels of RGS4, inhibiting the migration and invasion of breast cancer cells.

Identification of pathways and genes associated with cerebral palsy

  • Zhu, Qingwen;Ni, Yufei;Wang, Jing;Yin, Honggang;Zhang, Qin;Zhang, Lingli;Bian, Wenjun;Liang, Bo;Kong, Lingyin;Xuan, Liming;Lu, Naru
    • Genes and Genomics
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    • v.40 no.12
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    • pp.1339-1349
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    • 2018
  • Cerebral palsy (CP) is a non-progressive neurological disease, of which susceptibility is linked to genetic and environmental risk factors. More and more studies have shown that CP might be caused by multiple genetic factors, similar to other neurodevelopmental disorders. Due to the high genetic heterogeneity of CP, we focused on investigating related molecular pathways. Ten children with CP were collected for whole-exome sequencing by next-generation sequencing (NGS) technology. Customized processes were used to identify potential pathogenic pathways and variants. Three pathways (axon guidance, transmission across chemical synapses, protein-protein interactions at synapses) with twenty-three genes were identified to be highly correlated with CP. This study showed that the three pathways associated with CP might be the molecular mechanism of pathogenesis. These findings could provide useful clues for developing pathway-based pharmacotherapies. Further studies are required to confirm potential roles for these pathways in the pathogenesis of CP.

Development of ELISA System for Screening of Specific Binding Inhibitors for Src Homology (SH)2 Domain and Phosphotyrosine Interactions

  • Lee, Sang-Seop;Lee, Kyung-Im;Yoo, Ji-Yun;Jeong, Moon-Jin;Park, Young-Mee;Kwon, Byoung-Mog;Bae, Yun-Soo;Han, Mi-Young
    • BMB Reports
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    • v.34 no.6
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    • pp.537-543
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    • 2001
  • In the present study, an in vitro ELISA system to assess the interaction between Src homology (SH)2 domains and phosphotyrosine that contain peptides was established using purified GST-conjugated SH2 proteins and synthetic biotinylated phosphotyrosine that contain oligopeptides. The SH2 domains bound the relevant phosphopeptides that were immobilized in the streptavidin-coated microtiter plate in a highly specific and dose-dependent manner. The epidermal growth factor receptor (EGFR)-, T antigen (T Ag)-, and platelet-derived growth factor receptor (PDGFR)-derived phosphopeptides interacted with the growth factor receptor binding protein (Grb)2/SH2, Lck/SH2, and phosphatidyl inositol 3-kinase (PI3K) p85/SH2, respectively. No cross-reactions were observed. Competitive inhibition experiments showed that a short phosphopeptide of only four amino acids was long enough to determine the binding specificity. Optimal concentrations of the GST-SH2 fusion protein and phosphopeptide in this new ELISA system for screening the binding blockers were chosen at 2nM and 500nM, respectively. When two candidate compounds were tested in our ELISA system, they specifically inhibited the Lck/SH2 and/or p85/SH2 binding to the relevant phosphopeptides. Our results indicate that this ELISA system could be used as an easy screening method for the discovery of specific binding blockers of protein-protein interactions via SH2 domains.

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Quantitative Screening of Insect Cell Transformants Stably Expressing $GFP_{uv}-{\beta}1$, 3-N-acetylglucosaminyltransferase 2 Fusion Protein

  • Deo Vipin Kumar;Kato Tatsuya;Asari Naoko;Park Enoch Y.
    • Biotechnology and Bioprocess Engineering:BBE
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    • v.10 no.3
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    • pp.275-279
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    • 2005
  • Insect cell transformants, stably expressing human $GFP_{uv}-{\beta}1$, 3-N-acetylglucosaminyltransferase 2 $({\beta}3GnT2)$ as the green fluorescent protein $(GFP_{uv})-fused$ protein, were efficiently isolated on Western blot by the quantification of the densitometric intensity of the fusion protein. From almost 150 transformants containing the fusion gene linked to three different types of signal sequence, two transformants, Tn-pXme4a and -pX28a, were successfully selected, showing 8.3 and 8.6 mU/mL ${\beta}3GnT$ activity, respectively. This method requires a screening time almost one-half that required in the isolation of stably transformed cells with high expression levels, and at the same time allows the handling a large number of transformants.