• BMB Reports
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• 제49권9호
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• pp.459-473
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• 2016

Neurodegenerative diseases (NDs) often involve the formation of abnormal and toxic protein aggregates, which are thought to be the primary factor in ND occurrence and progression. Aged neurons exhibit marked increases in aggregated protein levels, which can lead to increased cell death in specific brain regions. As no specific drugs/therapies for treating the symptoms or/and progression of NDs are available, obtaining a complete understanding of the mechanism underlying the formation of protein aggregates is needed for designing a novel and efficient removal strategy. Intracellular proteolysis generally involves either the lysosomal or ubiquitin-proteasome system. In this review, we focus on the structure and assembly of the proteasome, proteasome-mediated protein degradation, and the multiple dynamic regulatory mechanisms governing proteasome activity. We also discuss the plausibility of the correlation between changes in proteasome activity and the occurrence of NDs.

• 대한의생명과학회지
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• 제26권1호
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• pp.47-50
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• 2020

Recently, decades of robust researches on degenerative brain disorder have been highlighted on the interactive connection of gut and brain. In terms of inflammatory cytokine production, others have shown that Nucleotide-Binding Oligomerization Domain Containing 2 (NOD2) is involved with Leucine-Rich Repeat Kinase 2 (LRRK2). HEK293T cells were transiently co-transfected with Myc-tagged LRRK2 and Flag-tagged NOD2 and then followed by co-immunoprecipitation assay. In this study, we provide the novel finding of physical protein-protein interaction between NOD2 and LRRK2. G2019S variant has shown stronger interactions against NOD2 than those of wild type LRRK2. In an axis of NOD2-LRRK2 communication, it is believed to pave a new way in the understanding of the bidirectional molecular mechanism of brain disorder, including Parkinson's disease into gut inflammatory disease, including Crohn's disease.

• Molecules and Cells
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• 제44권8호
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• pp.569-579
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• 2021

Cyclase-associated protein 2 (CAP2) has been addressed as a candidate biomarker in various cancer types. Previously, we have shown that CAP2 is expressed during multi-step hepatocarcinogenesis; however, its underlying mechanisms in liver cancer cells are not fully elucidated yet. Here, we demonstrated that endoplasmic reticulum (ER) stress induced CAP2 expression, and which promoted migration and invasion of liver cancer cells. We also found that the ER stress-induced CAP2 expression is mediated through activation of protein kinase C epsilon (PKCε) and the promotor binding of activating transcription factor 2 (ATF2). In addition, we further demonstrated that CAP2 expression promoted epithelial-mesenchymal transition (EMT) through activation of Rac1 and ERK. In conclusion, we suggest that ER stress induces CAP2 expression promoting EMT in liver cancer cells. Our results shed light on the novel functions of CAP2 in the metastatic process of liver cancer cells.

• 한국식물병리학회:학술대회논문집
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• 한국식물병리학회 2003년도 정기총회 및 추계학술발표회
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• pp.29-29
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• 2003

Incompatible plant-pathogen interactions result in the rapid cell death response known as hypersensitive response (HR) and activation of host defense-related genes. To understand the molecular and cellular mechanism controlling defense response better, several approaches including isolation and characterization of novel genes, promoter analysis of those genes, protein-protein interaction analysis and reverse genetic approach etc. By using the yeast two-hybrid system a clone named Tsipl, Tsil -interacting protein 1, was isolated whose translation product apparently interacted with Tsil, an EREBP/AP2 type DNA binding protein. RNA gel blot analysis showed that the expression of Tsipl was increased by treatment with NaCl, ethylene, salicylic acid, or gibberellic acid. Transient expression analysis using a Tsipl::smGFP fusion gene in Arabidopsis protoplasts indicated that the Tsipl protein was targeted to the outer surface of chloroplasts. The targeted Tsipl::smGFP proteins were diffused to the cytoplasm of protoplasts in the presence of salicylic acid (SA) The PEG-mediated co-transfection analysis showed that Tsipl could interact with Tsil in the nucleus. These results suggest that Tsipl-Tsil interaction might serve to regulate defense-related gene expression. Basically the useful promoters are valuable tools for effective control of gene expression related to various developmental and environmental condition.(중략)

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.133-138
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• 2003

The prediction of protein secondary structure has been an important bioinformatics tool that is an essential component of the template-based protein tertiary structure prediction process. It has been known that the predicted secondary structure information improves both the fold recognition performance and the alignment accuracy. In this paper, we describe several novel ideas that may improve the prediction accuracy. The main idea is motivated by an observation that the protein's structural information, especially when it is combined with the evolutionary information, significantly improves the accuracy of the predicted tertiary structure. From the non-redundant set of protein structures, we derive the 'potential' parameters for the protein secondary structure prediction that contains the structural information of proteins, by following the procedure similar to the way to derive the directional information table of GOR method. Those potential parameters are combined with the frequency matrices obtained by running PSI-BLAST to construct the feature vectors that are used to train the support vector machines (SVM) to build the secondary structure classifiers. Moreover, the problem of huge model file size, which is one of the known shortcomings of SVM, is partially overcome by reducing the size of training data by filtering out the redundancy not only at the protein level but also at the feature vector level. A preliminary result measured by the average three-state prediction accuracy is encouraging.

• Biomolecules & Therapeutics
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• 제25권1호
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• pp.12-25
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• 2017

G protein-coupled receptors (GPCRs) are a family of cell-surface proteins that play critical roles in regulating a variety of pathophysiological processes and thus are targeted by almost a third of currently available therapeutics. It was originally thought that GPCRs convert extracellular stimuli into intracellular signals through activating G proteins, whereas ${\beta}$-arrestins have important roles in internalization and desensitization of the receptor. Over the past decade, several novel functional aspects of ${\beta}$-arrestins in regulating GPCR signaling have been discovered. These previously unanticipated roles of ${\beta}$-arrestins to act as signal transducers and mediators of G protein-independent signaling have led to the concept of biased agonism. Biased GPCR ligands are able to engage with their target receptors in a manner that preferentially activates only G protein- or ${\beta}$-arrestin-mediated downstream signaling. This offers the potential for next generation drugs with high selectivity to therapeutically relevant GPCR signaling pathways. In this review, we provide a summary of the recent studies highlighting G protein- or ${\beta}$-arrestin-biased GPCR signaling and the effects of biased ligands on disease pathogenesis and regulation.

• BMB Reports
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• 제35권4호
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• pp.403-408
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• 2002

A hypothetical 21.0 kDa protein (ORF O197) from Escherichia coli K-12 was cloned, purified, and characterized. The protein sequence of ORF O197(termed EcO197) shares a 33.5% identity with that of a novel NTPase from Methanococcus jannaschii. The EcO197 protein was purified using Ni-NTA affinity chromatography, protease digestion, and gel filtration column. It hydrolyzed nucleoside triphosphates with an O6 atom-containing purine base to nucleoside monophosphate and pyrophosphate. The EcO197 protein had a strong preference for deoxyinosine triphosphate (dITP) and xanthosine triphosphate (XTP), while it had little activity in the standard nucleoside triphosphates (dATP, dCTP, dGTP, and dTTP). These aberrant nucleotides can be produced by oxidative deamination from purine nucleotides in cells; they are potentially mutagenic. The mutation protection mechanisms are caused by the incorporation into DNA of unwelcome nucleotides that are formed spontaneously. The EcO197 protein may function to eliminate specifically damaged purine nucleotide that contains the 6-keto group. This protein appears to be the first eubacterial dITP-and XTP-hydrolyzing enzyme that has been identified.

• 아시안잔디학회지
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• 제4권1호
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• pp.12-23
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• 1990

The chlorophyll-protein complexes were separated from thylakoid membranes of Spinach oleracea and Zoysia japonica by two gel Systems of LiDodSO4-PAGE and LiDodSo4/Urea- PAGE under nondenaturing conditions. Seven chlorophyll~protein complexes of CPI*, CPI, CPII*. CP47, CP43, CP29 and CPII were fractionated from both S,oleracea and Zjaponica by LiDodSO4-PAGE. CPI, CP47 and CP43 contained more chlorophyll a than chlorophyll b. The patterns of their absorption spectra at room temperature were similliar to that of chlorophyll a, judging by their UV-spedtroscopy. On the other hand, CPII* and CPII contained approximately equim-olar quantities of chlorophyll a and b. Additional five chlorophyll-protein complexes not separated in the LiDodSO4-PAGE system were electrophoretically isolated from both S, oleracea and Zjaponica by LiDodSO4/Urca-PAGE. The chlorophyll-protein complex just above LRCII $\alpha$in the gel appears CCII-RC separeted recently. 23 kDa and 20 kDa cho-protein complexes is probably LHCIa and LHCIb as judged from their molecular weight. Two novel chlorophyll~protein complexes designated "CPI7" and "CPI6" were fractionate by this gel system. Their molecular weights respectively. Although the stoichiometry of their components and their roles in thylakoid membranes are not apparant, It is thought that they are another kinds of LHCI.other kinds of LHCI.

• 한국콘텐츠학회논문지
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• 제9권5호
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• pp.332-336
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• 2009

유전체 분석에서 중요한 부분 중 하나는 기능이 알려지지 않은 미지 단백질에 대한 기능 예측이다. 단백질-단백질 상호작용 네트워크를 분석하는 것은 미지 단백질에 대한 기능을 보다 쉽게 예측할 수 있게 한다. 단백질-단백질 상호작용 네트워크로부터 미지 단백질의 기능을 예측하기 위한 다양한 연구들이 시도되어 왔다. 카이-제곱(Chi-square) 방식은 단백질-단백질 상호작용 네트워크를 통해 기능을 예측하고자 하는 연구 중 대표적인 방식이다. 하지만 카이-제곱 방식은 네트워크의 토폴로지를 반영하지 않아 네트워크 크기에 따라 예측의 정확성이 떨어지는 문제점이 있다. 따라서 본 논문에서는 카이-제곱 방식을 보완하여 정확성을 높인 새로운 기능 예측 방법을 제안한다 이를 위해 MIPS, DIP 그리고 SGD와 같은 공개된 단백질 상호작용 데이터베이스들로부터 데이터를 수집하여 분석하였다. 그리고 제안된 방식의 우수성을 입증하기 위해 각 데이터베이스들에 대해 카이-제곱방식과 제안하는 보완된 카이-제곱(Modified Chi-square)방식으로 예측해보고 이들의 정확성을 평가하였다.

• Parasites, Hosts and Diseases
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• 제44권4호
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• pp.331-341
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• 2006

Actin binding proteins play key roles in cell structure and movement particularly as regulators of the assembly, stability and localization of actin filaments in the cytoplasm. In the present study, a cDNA clone encoding an actin bundling protein named as AhABP was isolated from Acanthamoeba healyi, a causative agent of granulomatous amebic encephalitis. This clone exhibited high similarity with genes of Physarum polycephalum and Dictyostelium discoideum, which encode actin bundling proteins. Domain search analysis revealed the presence of essential conserved regions, i.e., an active actin binding site and 2 putative calcium binding EF-hands. Transfected amoeba cells demonstrated that AhABP is primarily localized in phagocytic cups, peripheral edges, pseudopods, and in cortical cytoplasm where actins are most abundant. Moreover, AhABP after the deletion of essential regions formed ellipsoidal inclusions within transfected cells. High-speed co-sedimentation assays revealed that AhABP directly interacted with actin in the presence of up to $10{\mu}M$ of calcium. Under the electron microscope, thick parallel bundles were formed by full length AhABP, in contrast to the thin actin bundles formed by constructs with deletion sites. In the light of these results, we conclude that AhABP is a novel actin bundling protein that is importantly associated with actin filaments in the cytoplasm.