• BMB Reports
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• v.42 no.1
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• pp.22-27
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• 2009

Replication Protein A (RPA) is a single stranded DNA-binding protein involved in DNA metabolic activities such as replication, repair, and recombination. RPA-Interacting Protein $\alpha$ ($RIP{\alpha}$) was originally identified as a nuclear transporter of RPA in Xenopus. The human $RIP{\alpha}$ gene encodes several splice isoforms, of which $hRIP{\alpha}$ and $hRIP{\beta}$ are the major translation products in vivo. However, limited information is available about the alternative splicing of $RIP{\alpha}$ in eukaryotes, apart from that in humans. In this study, we examined the alternative splicing of RIP{\alpha} in the Drosophila, Xenopus, and mouse system. We showed that the number of splice isoforms of RIP{\alpha} was species-specific, and displayed a tendency to increase in higher eukaryotes. Moreover, a mouse ortholog of $hRIP{\alpha}$, $mRIP{\beta}2$, was not SUMOylated, in contrast to $hRIP{\alpha}$. Based on these results, we suggest that the $RIP{\alpha}$ gene gains more splice isoforms and additional modifications after molecular evolution.

• IMMUNE NETWORK
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• v.2 no.3
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• pp.125-132
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• 2002

In the past, bioinformatics was often regarded as a difficult and rather remote field, practiced only by computer scientists and not a practical tool available to biologists. However, the various on-going genome projects have had a serious impact on biological sciences in various ways and now there is little doubt that bioinformatics is an essential part of the research environment, with a wealth of biological information to analyze and predict. Fully sequenced genomes made us to have additional insights into the functional properties of the encoded proteins and made it possible to develop new tools and schemes for functional biology on a proteomic scale. Among those are the yeast two-hybrid system, mass spectrometry and microarray: the technology of choice to detect protein-protein interactions. These functional insights emerge as networks of interacting proteins, also known as "pathway informatics" or "interactomics". Without exception it is no longer possible to make advances in the signaling/regulatory pathway studies without integrating information technologies with experimental technologies. In this paper, we will introduce the databases of protein interaction worldwide and discuss several challenging issues regarding the actual implementation of databases.

• Proceedings of the Korea Information Processing Society Conference
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• 2011.11a
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• pp.1115-1118
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• 2011

단백질 사이의 상호작용 네트워크(PPI network: Protein-Protein Interaction network)를 이용하여 단백질 기능을 예측 하는 것은 단백질 기능 예측 기법들 중에서 중요한 작용을 한다. 하지만 PPI를 이용한 단백질 기능 예측은 기능의 복잡도와 다양성으로 인해 제한적인 결과를 나타내 왔다. 따라서 본 논문에서는 기존의 연구들 보다 높은 정확도로 단백질 기능을 예측하기 위해 기능 예측을 하려는 단백질과 상호작용 하는 단백질들에 그래프 마이닝 기법을 적용하여 빈발 2-노드 상호작용 패턴을 찾고, 그 패턴을 이용하여 단백질 기능을 예측하는 접근법을 제안하였다. 실험데이터로 DIP(Database of Interacting Proteins)에서 제공하는 단백질 상호작용 데이터를 사용하였으며, 다른 기존의 단백질 기능 예측 기법들보다 높은 정확도를 보여주었다.

• CELLMED
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• v.2 no.1
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• pp.9.1-9.13
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• 2012

Jeechool-Whan (JW) is a prescription of Ponciri Fructus Immaturus and Atractylodis Rhizoma Alba and improves the functions of the stomach and the spleen. Although it is said in Korean Medicine that the spleen and the stomach are the roots of the body's resistance, the meaning of 'improving the spleen and the stomach' is very comprehensive. Moreover, there are lots of drugs that are said to improve the spleen and the stomach, and the number of prescriptions using these drugs is huge. In this study, we focused on the new effect and mechanism of the JW on the ovalbumin (OVA)-induced allergic rhinitis (AR) model. The increased number of rubs and the increased levels of IgE and histamine in the OVA-sensitized mice were inhibited by JW administration. The balance of Th1/Th2 cytokine level was regulated by JW administration. The levels inflammatory proteins were decreased by JW administration in the nasal mucosa of the OVA-sensitized mice. Eosinophils and mast cells infiltration increased by OVA-sensitization was also decreased in the JW-administered mice. In addition, JW inhibited caspase-1 activity in the same nasal mucosa tissue. In activated human mast cells, JW inhibited the receptor interacting protein-2, I${\kappa}$B kinase-${\beta}$, nuclear factor-${\kappa}$B/Rel A, and caspase-1 activation. In conclusion, this study will be support the clear understanding of the concept of the spleen and the stomach in traditional Korean medicine as well as for a possibility of finding a cure for this AR in traditional medical treatments.

• Molecules and Cells
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• v.21 no.3
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• pp.330-336
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• 2006

Since its identification in 1989, hepatitis C virus has been the subject of extensive research. The biology of the virus and the development of antiviral drugs are closely related. The RNA polymerase activity of nonstructural protein 5B was first demonstrated in 1996. NS5B is believed to localize to the perinuclear region, forming a replicase complex with other viral proteins. It has a typical polymerase structure with thumb, palm, and finger domains encircling the active site. A de novo replication initiation mechanism has been suggested. To date, many small molecule inhibitors are known including nucleoside analogues, non-nucleoside analogues, and pyrophosphate mimics. NS5B interacts with other viral proteins such as core, NS3, 4A, 4B, and 5A. The helicase activity of NS3 seems necessary for RNA strand unwinding during replication, with other nonstructural proteins performing modulatory roles. Cellular proteins interacting with NS5B include VAMP-associated proteins, heIF4AII, hPLIC1, nucleolin, PRK2, ${\alpha}$-actinin, and p68 helicase. The interactions of NS5B with these proteins might play roles in cellular trafficking, signal transduction, and RNA polymerization, as well as the regulation of replication/translation processes.

• Molecules and Cells
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• v.27 no.5
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• pp.533-538
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• 2009

Heat shock protein 27 (Hsp27) is a molecular chaperone protein which regulates cell apoptosis by interacting directly with the caspase activation components in the apoptotic pathways. With the assistance of the Tat protein transduction domain we directly delivered the Hsp27 into the myocardial cell line, H9c2 and demonstrate that this protein can reverse hypoxia-induced apoptosis of cells. In order to characterize the contribution of Hsp27 in blocking the two major apoptotic pathways operational within cells, we exposed H9c2 cells to staurosporine and cobalt chloride, agents that induce mitochondria-dependent (intrinsic) and -independent (extrinsic) pathways of apoptosis in cells respectively. The Tat-Hsp27 fusion protein showed a greater propensity to inhibit the effect induced by the cobalt chloride treatment. These data suggest that the Hsp27 predominantly exerts its protective effect by interfering with the components of the extrinsic pathway of apoptosis.

• Proceedings of the SCSK Conference
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• 2003.09a
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• pp.590-600
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• 2003

The matrix metalloproteinases (MMPs) are a family of enzymes responsible for degrading connective tissue. MMPs catalyze the breakdown of collagen from the extracellular matrix, leading to wrinkle formation and accelerated skin aging. Furthermore, ultraviolet irradiation causes increased expression of certain MMPs. In the extracellular matrix turnover, MMPs are interacting with endogenous regulators named tissue inhibitors of metalloproteinases (TIMPs). Using peptide substrate assays, it has been demonstrated that TIMP-MMP complexes interact highly specifically with $K_{i}$ values of 10$^{-9}$ -10$^{-16}$ M. Therefore applications for TIMP as inhibitor of collagen degradation are suggested for cosmetic anti-aging products to prevent wrinkle formation and loss of elasticity. To date four TIMP proteins (TIMP-1, TIMP-2, TIMP-3 and TIMP-4) have been identified which show a high degree in sequence similarity. The production of human TIMP-2, a 194-residue nonglycosylated protein, was performed by fed-batch culture of Escherichia coli. TIMP-2 accumulated in the bacterial cells in an insoluble form as inclusion bodies. The inclusion bodies were solubilized and the protein refolded to yield the native TIMP-2 in the active form. The integrity of the protein was confirmed by mass analysis, Edman sequencing and gel shift experiments with authentic samples. The inhibitory activity of the refolded and purified TIMP-2 was demonstrated with MMP-1 and MMP-2 assays using synthetic fluorogenic peptide substrates.s.

• Journal of Life Science
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• v.22 no.9
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• pp.1159-1165
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• 2012

The action of neuronally released ${\gamma}$-aminobutyric acid (GABA) is terminated by uptake into the neurons by GABA transporters (GATs). The mechanism underlying the stabilization and regulation of GAT2 has not yet been elucidated. We used the yeast two-hybrid system to identify proteins that interact with and, thereby, regulate betaine-${\gamma}$-aminobutyric acid transporter 1 (BGT-1/mGAT2). We found an interaction between BGT-1/mGAT2 and Munc-18-interacting proteins (Mints). The "T-H-L" motif at the C-terminal end of BGT-1/mGAT2 was essential for the interaction with Mint2 in the yeast two-hybrid assay. Mint2 bound to the tail region of BGT-1/mGAT2, but not to other GAT members. When co-expressed in HEK-293T cells, Mint2 was co-immunoprecipitated with BGT-1/mGAT2. In addition, we demonstrated the cellular co-localization of BGT-1/mGAT2 and Mint2 in the cells. These results suggest that Mint2 contributes to the regulation of BGT-1/mGAT2.

• Animal cells and systems
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• v.13 no.3
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• pp.283-288
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• 2009

The ubiquitous plasma membrane $Na^+/H^+$ exchanger 1 (NHE1) is rapidly activated in response to various extracellular stimuli and maintains normal cytoplasmic pH. Yeast two-hybrid screening was used in order to identify proteins interacting with NHE1 using its cytoplasmic domain as a bait from HeLa cDNA library. One of the interacting cDNA clones was human Lactate dehydrogenase B (LDHB). In vitro translated LDHB was pulled down together with GST-NHE1.cd protein in the GST pull down assay, confirming the interaction in vitro. LDHB antibody immunoprecipitated endogenous LDHB together with NHE1 from H9c2 cells, validating cellular interaction between NHE1 and LDHB. Subsequent analysis revealed that the overexpression of LDHB increased intracellular PH, implying opening of the NHE1 transporter. Moreover, overexpression of LDHB activated caspase 3 and induced cell death, consistent with the expected phenotype of hyper-activation of NHE1. Collectively, our data indicate that LDHB modulates NHE1 activity via physical interaction.

• Biomedical Science Letters
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• v.13 no.2
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• pp.127-133
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• 2007

Heterotrimeric GTP binding proteins (G proteins) mediate signal generated by neurotransmitter and hormones. Among all G proteins, Go is the most abundant in brain but its role in brain is not clearly understood. To determine the function of the alpha subunit of Go (Go$\alpha$), we search for the interacting partner of Go$\alpha$ in brain using yeast two-hybrid system. A resistant to inhibitor of cholinesterase (Ric-8B) was identified as a Go$\alpha$ interacting protein. We confirmed interaction between Go$\alpha$ and Ric-8b employing in vitro affinity binding assay and showed that the Ric-8b increased the function of Go$\alpha$. Our findings indicate that Ric-8b is possible guanine nucleotide exchange factor for Go$\alpha$.