• BMB Reports
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• 제40권5호
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• pp.832-838
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• 2007

A novel inhibitory protein against blood coagulation factor Va (FVa) was purified from muscle protein of granulated ark (Tegillarca granosa, order Arcoida, marine bivalvia) by consecutive FPLC method using anion exchange and gel permeation chromatography. In the results of ESI-QTOF tandem mass analysis and database research, it was revealed that the purified T. granosa anticoagulant protein (TGAP) has 7.7 kDa of molecular mass and its partial sequence, HTHLQRAPHPNALGYHGK, has a high identity (64%) with serine/threonine kinase derived from Rhodopirellula baltica (order Planctomycetales, marine bacteria). TGAP could potently prolong thrombin time (TT), corresponding to inhibition of thrombin (FIIa) formation. Specific factor inhibitory assay showed that TGAP inhibits FVa among the major components of prothrombinase complex. In vitro assay for direct-binding affinity using surface plasmon resonance (SPR) spectrometer indicated that TGAP could be directly bound with FVa. In addition, the binding affinity of FVa to FII was decreased by addition of TGAP in dose-dependant manner ($IC_{50}$ value = 77.9 nM). These results illustrated that TGAP might interact with a heavy chain of FVa ($FVa_H$) bound to FII in prothrombin complex. The present study elucidated that non-cytotoxic T. granosa anticoagulant protein (TGAP) bound to FVa can prolong blood coagulation time by inhibiting conversion of FII to FIIa in blood coagulation cascade. In addition, TGAP did not significantly (P < 0.05) show fibrinolytic activity and cytotoxicity on venous endothelial cell line (ECV 304).

• Genomics & Informatics
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• 제6권4호
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• pp.210-222
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• 2008

Due to the polygenic nature of cancer, it is believed that breast cancer is caused by the perturbation of multiple genes and their complex interactions, which contribute to the wide aspects of disease phenotypes. A systems biology approach for the identification of subnetworks of interconnected genes as functional modules is required to understand the complex nature of diseases such as breast cancer. In this study, we apply a 3-step strategy for the interpretation of microarray data, focusing on identifying significantly perturbed metabolic pathways rather than analyzing a large amount of overexpressed and underexpressed individual genes. The selected pathways are considered to be dysregulated functional modules that putatively contribute to the progression of disease. The subnetwork of protein-protein interactions for these dysregulated pathways are constructed for further detailed analysis. We evaluated the method by analyzing microarray datasets of breast cancer tissues; i.e., normal and invasive breast cancer tissues. Using the strategy of microarray analysis, we selected several significantly perturbed pathways that are implicated in the regulation of progression of breast cancers, including the extracellular matrix-receptor interaction pathway and the focal adhesion pathway. Moreover, these selected pathways include several known breast cancer-related genes. It is concluded from this study that the present strategy is capable of selecting interesting perturbed pathways that putatively play a role in the progression of breast cancer and provides an improved interpretability of networks of protein-protein interactions.

• 한국식품위생안전성학회지
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• 제13권3호
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• pp.206-212
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• 1998

Salmonella spp.의 신속한 검출을 위하여 엷은 박막형태의 수정결정을 사용하는 압전류적(piesoelectric) 항체센서 시스템을 개발하고 증류수, 완충용액, 식염용액 등의 여러 매질 중에서 보여주는 진동 특성을 검토하였다. Salmonella spp. 균 구조항원(Common structural antigen)에 대한 항체를 수정결정에 PEI pre-coating, BSA 가교화, 3-APTES silanizaition, protein A와 DTBP thiolation의 5가지 방법에 의해 고정화한 후 항체 센서의 안정성을 살펴보았다. Salmonella 균을 주입하였을 때 Salmonella 균과 수정 결정에 고정화한 항체와의 결함반응에 의해 수정결정의 질량증가와 이에 따른 진동수 감소가 나타났다. 고정화방법 중 protein A와 DTBP를 이용하여 고정화하는 방법이 센서반응을 가장 안정적이고 재현성 있게 나타내줌을 알 수 있었다. $7.45{\times}10^{7}\;CFU/ml$의 Salmonella 균을 반응 cell 내에 주입하였을 때 protein A를 이용한 고정화의 경우 80Hz, DTBP를 이용한 고정화의 경우 283 Hz의 진동수 감소가 나타났으며, 압전류적 항체센서를 이용할 경우 40분 이내에 Salmonella spp.의 검출이 가능하였다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.56-58
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• 2000

Post-genomics may be defined in different ways depending on how one views the challenges after the genome. A popular view is to follow the concept of the central dogma in molecular biology, namely from genome to transcriptome to proteome. Projects are going on to analyze gene expression profiles both at the mRNA and protein levels and to catalog protein 3D structure families, which will no doubt help the understanding of information in the genome. However complete, such catalogs of genes, RNAs, and proteins only tell us about the building blocks of life. They do not tell us much about the wiring (interaction) of building blocks, which is essential for uncovering systemic functional behaviors of the cell or the organism. Thus, an alternative view of post-genomics is to go up from the molecular level to the cellular level, and to understand, what I call, the "interactome"or a complete picture of molecular interactions in the cell. KEGG (http://www.genome.ad.jp/kegg/) is our attempt to computerize current knowledge on various cellular processes as a collection of "generalized"protein-protein interaction networks, to develop new graph-based algorithms for predicting such networks from the genome information, and to actually reconstruct the interactomes for all the completely sequenced genomes and some partial genomes. During the reconstruction process, it becomes readily apparent that certain pathways and molecular complexes are present or absent in each organism, indicating modular structures of the interactome. In addition, the reconstruction uncovers missing components in an otherwise complete pathway or complex, which may result from misannotation of the genome or misrepresentation of the KEGG pathway. When combined with additional experimental data on protein-protein interactions, such as by yeast two-hybrid systems, the reconstruction possibly uncovers unknown partners for a particular pathway or complex. Thus, the reconstruction is tightly coupled with the annotation of individual genes, which is maintained in the GENES database in KEGG. We are also trying to expand our literature surrey to include in the GENES database most up-to-date information about gene functions.

• Animal cells and systems
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• 제16권4호
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• pp.280-288
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• 2012

Targeted degradation of proteins through ubiquitin-mediated proteolysis is an important control mechanism in various cellular processes. The process of ubiquitin conjugation is achieved by three enzyme complexes, among which the ubiquitin ligase complex (E3) is in charge of substrate specificity. The SCF (SKP1-CUL1-F-box) family portrays the largest and the most characterized member of the E3 ligases. For each SCF complex, the ubiquitination target is recognized by the F-box protein subunit, which interacts with the substrate through a unique C-terminal domain. We have characterized a novel F-box protein CFL-1 that represents a single LRR-type F-box (FBXL) in the Caenorhabditis elegans genome. CFL-1 is highly homologous to FBXL20 and FBXL2 of mammals, which are known to regulate synaptic vesicle release and cell cycle, respectively. A green fluorescence protein (GFP)-reporter gene fused to the cfl-1 promoter showed restricted expression around the amphid and the anus. Modulation of CFL-1 activity by RNAi affected the time interval between defecations. RNAi-treated worms also exhibited reduced tendency to form dauer when exposed to daumone. The potential involvement of CFL-1 in the control of defecation and pheromone response adds to the ever expanding list of cellular processes controlled by ubiquitin-mediated proteolysis in C. elegans. We suggest that CFL-1, as a single LRR-type F-box protein in C. elegans, may portray a prototype gene exerting diverse functions that are allocated among multiple FBXLs in higher organisms.

• Journal of Ginseng Research
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• 제46권6호
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• pp.750-758
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• 2022

Background: Mild cognitive impairment (MCI) is a transitional condition between normality and dementia. Ginseng is known to have effects on attenuating cognitive deficits in neurogenerative diseases. Ginsenosides are the main bioactive component of ginseng, and their protein targets have not been fully understood. Furthermore, no thorough analysis is reported in ginsenoside-related protein targets in MCI. Methods: The candidate protein targets of ginsenosides in brain tissues were identified by drug affinity responsive target stability (DARTS) coupled with label-free liquid chromatography-mass spectrometry (LC-MS) analysis. Network pharmacology approach was used to collect the therapeutic targets for MCI. Based on the above-mentioned overlapping targets, we built up a proteineprotein interaction (PPI) network in STRING database and conducted gene ontology (GO) enrichment analysis. Finally, we assessed the effects of ginseng total saponins (GTS) and different ginsenosides on mitochondrial function by measuring the activity of the mitochondrial respiratory chain complex and performing molecular docking. Results: We screened 2526 MCI-related protein targets by databases and 349 ginsenoside-related protein targets by DARTS. On the basis of these 81 overlapping genes, enrichment analysis showed the mitochondria played an important role in GTS-mediated MCI pharmacological process. Mitochondrial function analysis showed GTS, protopanaxatriol (PPT), and Rd increased the activities of complex I in a dose-dependent manner. Molecular docking also predicted the docking pockets between PPT or Rd and mitochondrial respiratory chain complex I. Conclusion: This study indicated that ginsenosides might alleviate MCI by targeting respiratory chain complex I and regulating mitochondrial function, supporting ginseng's therapeutic application in cognitive deficits.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.26-51
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• 2003

Large scale protein interaction maps provide a new, global perspective with which to analyse protein function. PSIMAP, the Protein Structural Interactome Map, is a database of all the structurally observed interactions between superfamilies of protein domains with known three-dimensional structure in thePDB. PSIMAP incorporates both functional and evolutionary information into a single network. It makes it possible to age protein domains in terms of taxonomic diversity, interaction and function. One consequence of it is to predict the most important protein domain structure in evolution. We present a global analysis of PSIMAP using several distinct network measures relating to centrality, interactivity, fault-tolerance, and taxonomic diversity. We found the following results: ${\bullet}$ Centrality: we show that the center and barycenter of PSIMAP do not coincide, and that the superfamilies forming the barycenter relate to very general functions, while those constituting the center relate to enzymatic activity. ${\bullet}$ Interactivity: we identify the P-loop and immunoglobulin superfamilies as the most highly interactive. We successfully use connectivity and cluster index, which characterise the connectivity of a superfamily's neighbourhood, to discover superfamilies of complex I and II. This is particularly significant as the structure of complex I is not yet solved. ${\bullet}$ Taxonomic diversity: we found that highly interactive superfamilies are in general taxonomically very diverse and are thus amongst the oldest. This led to the prediction of the oldest and most important protein domain in evolution of lift. ${\bullet}$ Fault-tolerance: we found that the network is very robust as for the majority of superfamilies removal from the network will not break up the network. Overall, we can single out the P-loop containing nucleotide triphosphate hydrolases superfamily as it is the most highly connected and has the highest taxonomic diversity. In addition, this superfamily has the highest interaction rank, is the barycenter of the network (it has the shortest average path to every other superfamily in the network), and is an articulation vertex, whose removal will disconnect the network. More generally, we conclude that the graph-theoretic and taxonomic analysis of PSIMAP is an important step towards the understanding of protein function and could be an important tool for tracing the evolution of life at the molecular level.

• BMB Reports
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• 제41권3호
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• pp.194-203
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• 2008

Nitrosative modifications regulate cellular signal transduction and pathogenesis of inflammatory responses and neuro-degenerative diseases. Protein tyrosine nitration is a biomarker of oxidative stress and also influences protein structure and function. Recent advances in mass spectrometry have made it possible to identify modified proteins and specific modified amino acid residues. For analysis of nitrated peptides with low yields or only a subset of peptides, affinity 'tags' can be bait for 'fishing out' target analytes from complex mixtures. These tagged peptides are then extracted to a solid phase, followed by mass analysis. In this review, we focus on protein tyrosine modifications caused by nitrosative stresses and proteomic methods for selective enrichment and identification of nitrosative protein modifications.

• Biomolecules & Therapeutics
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• 제25권1호
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• pp.4-11
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• 2017

Heterotrimeric G proteins are key intracellular coordinators that receive signals from cells through activation of cognate G protein-coupled receptors (GPCRs). The details of their atomic interactions and structural mechanisms have been described by many biochemical and biophysical studies. Specifically, a framework for understanding conformational changes in the receptor upon ligand binding and associated G protein activation was provided by description of the crystal structure of the ${\beta}2$-adrenoceptor-Gs complex in 2011. This review focused on recent findings in the conformational dynamics of G proteins and GPCRs during activation processes.

• International Journal of Industrial Entomology and Biomaterials
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• 제10권2호
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• pp.125-129
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• 2005

Ribosome-associated membrane protein 4 (RAMP4) is a membrane protein that exposes its N-terminal hydrophilic portion on the cytoplasmic side and spans the membrane close to the C-terminal end. RAMP4 has previously been reported to belong to the set of proteins that remains associated with membrane-bound ribosomes, and controls the glycosylation of major histocompatbility complex class II-associated invariant chain. RAMP4 also may be relative to the stabilization of membrane proteins in response to stress, with other components of translocon, and molecular chaperons in ER. Application of 5'-RACE technique with specially designed primer, we cloned a 715 bp cDNA fragment which contains a 195 bp ORF, termed RAMP4. The deduced protein has 64 amino acid residues and contains a putative transmembrane-spanning domain at the COOH terminus.