• The Microorganisms and Industry
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• v.17 no.1
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• pp.10-18
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• 1991

A phylogenetic comparison of homologous protein can often supplement genetic and biochemical analysis by revealing conserved structures that are critical for function(Waugh et al., 1989). I therefore isolated a secY homologue from B. subtilis, a gram positive bacterium evolutionary distant from E. coli. The comparison and interplay between these two bacterial systems should contribute greatly to our understanding of the functions and interactions within systems evolved for protein translocation in both prokaryotic and eukaryotic organisms.

• Genomics & Informatics
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• v.18 no.4
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• pp.39.1-39.8
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• 2020

Alzheimer's disease (AD) is a chronic, progressive brain disorder that slowly destroys affected individuals' memory and reasoning faculties, and consequently, their ability to perform the simplest tasks. This study investigated the hub genes of AD. Proteins interact with other proteins and non-protein molecules, and these interactions play an important role in understanding protein function. Computational methods are useful for understanding biological problems, in particular, network analyses of protein-protein interactions. Through a protein network analysis, we identified the following top 10 hub genes associated with AD: PTGER3, C3AR1, NPY, ADCY2, CXCL12, CCR5, MTNR1A, CNR2, GRM2, and CXCL8. Through gene enrichment, it was identified that most gene functions could be classified as integral to the plasma membrane, G-protein coupled receptor activity, and cell communication under gene ontology, as well as involvement in signal transduction pathways. Based on the convergent functional genomics ranking, the prioritized genes were NPY, CXCL12, CCR5, and CNR2.

• The Korean Journal of Physiology and Pharmacology
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• v.24 no.6
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• pp.481-492
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• 2020

The present study aimed to examine the effect of allyl isothiocyanate (AITC) on chronic obstructive pulmonary disease and to investigate whether upregulation of multidrug resistance-associated protein 1 (MRP1) associated with the activation of the PARK7 (DJ-1)/nuclear factor erythroid 2-related factor 2 (Nrf2) axis. Lung function indexes and histopathological changes in mice were assessed by lung function detection and H&E staining. The expression levels of Nrf2, MRP1, heme oxygenase-1 (HO-1), and DJ-1 were determined by immunohistochemistry, Western blotting and reverse transcription-quantitative polymerase chain reaction. Next, the expression of DJ-1 in human bronchial epithelial (16HBE) cells was silenced by siRNA, and the effect of DJ-1 expression level on cigarette smoke extract (CSE)-stimulated protein degradation and AITC-induced protein expression was examined. The expression of DJ-1, Nrf2, HO-1, and MRP1 was significantly decreased in the wild type model group, while the expression of each protein was significantly increased after administration of AITC. Silencing the expression of DJ-1 in 16HBE cells accelerated CSE-induced protein degradation, and significantly attenuated the AITC-induced mRNA and protein expression of Nrf2 and MRP1. The present study describes a novel mechanism by which AITC induces MRP1 expression by protecting against CS/CSE-mediated DJ-1 protein degradation via activation of the DJ-1/Nrf2 axis.

• Molecules and Cells
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• v.41 no.2
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• pp.150-159
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• 2018

Animals use their odorant receptors to receive chemical information from the environment. Insect odorant receptors differ from the G protein-coupled odorant receptors in vertebrates and nematodes, and very little is known about their protein-protein interactions. Here, we introduce a mass spectrometric platform designed for the large-scale analysis of insect odorant receptor protein-protein interactions. Using this platform, we obtained the first Orco interactome from Drosophila melanogaster. From a total of 1,186 identified proteins, we narrowed the interaction candidates to 226, of which only two-thirds have been named. These candidates include the known olfactory proteins Or92a and Obp51a. Around 90% of the proteins having published names likely function inside the cell, and nearly half of these intracellular proteins are associated with the endomembrane system. In a basic loss-of-function electrophysiological screen, we found that the disruption of eight (i.e., Rab5, CG32795, Mpcp, Tom70, Vir-1, CG30427, Eaat1, and CG2781) of 28 randomly selected candidates affects olfactory responses in vivo. Thus, because this Orco interactome includes physiologically meaningful candidates, we anticipate that our platform will help guide further research on the molecular mechanisms of the insect odorant receptor family.

• Horticultural Science & Technology
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• v.30 no.6
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• pp.734-742
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• 2012

To compare RNA interference-mediated gene silencing technique and T-DNA integration for gene function analysis in Chinese cabbage, BrSAMS-knockout (KO) line and BrSAMS-knockdown (KD) line were used. The KO line had lost the function of a Brassica rapa S-adenosylmethionine synthetase (BrSAMS) gene by T-DNA insertion and the KD line had shown down-regulated BrSAMS genes' expression by dsRNA cleavage. From microarray results of the KO and KD lines, genes linked to SAMS such as sterol, sucrose, homogalacturonan biosynthesis and glutaredoxin-related protein, serine/threonine protein kinase, and gibberellin-responsive protein showed distinct differences in their expression levels. Even though one BrSAMS gene in the KO line was broken by T-DNA insertion, gene expression pattern of that line did not show remarkable differences compared to wild type control. However, the KD line obtained by RNAi technique showed prominent difference in its gene expression. Besides, change of polyamine and ethylene synthesis genes directly associated with BrSAMS was displayed much more in the KD line. In the microarray analysis of the KO line, BrSAMS function could not be clearly defined because of BrSAMS redundancy due to the genome triplication events in Brassicaceae. In conclusion, we supposed that gene knock-down method by RNAi silencing is more effective than knock-out method by T-DNA insertion for gene function analysis of polyploidy crops such as Chinese cabbage.

• Journal of the Korea Society of Computer and Information
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• v.27 no.8
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• pp.49-59
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• 2022

In this paper, we designed a new enzyme function prediction model PSCREM based on a study that compared and evaluated CNN and LSTM/GRU models, which are the most widely used deep learning models in the field of predicting functions and structures using protein sequences in 2020, under the same conditions. Sequence evolution information was used to preserve detailed patterns which would miss in CNN convolution, and the relationship information between amino acids with functional significance was extracted through overlapping RNNs. It was referenced to feature map production. The RNN family of algorithms used in small CNN-RNN models are LSTM algorithms and GRU algorithms, which are usually stacked two to three times over 100 units, but in this paper, small RNNs consisting of 10 and 20 units are overlapped. The model used the PSSM profile, which is transformed from protein sequence data. The experiment proved 86.4% the performance for the problem of predicting the main classes of enzyme number, and it was confirmed that the performance was 84.4% accurate up to the sub-sub classes of enzyme number. Thus, PSCREM better identifies unique patterns related to protein function through overlapped RNN, and Overlapped RNN is proposed as a novel methodology for protein function and structure prediction extraction.

• Journal of the Korean Society of Food Science and Nutrition
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• v.28 no.1
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• pp.178-190
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• 1999

This study was conducted to develop a simulation model for the growth dynamics of pigs and to describe quantitatively protein deposition depending on the amino acid composition of feed protein. In the model it is assumed that the essential processes that determine the utilization of feed protein in the whole body are protein synthesis, breakdown of protein, and oxidation of amino acid. Besides, it is also assumed that occurrence of protein deposition depends on genetic potential and amino acid composition of feed protein. The genetic potential for the protein deposition is the maximum capacity of protein synthesis, being dependent on the protein mass of the whole body. To describe the effect of amino acid composition of feed on the protein deposition, a factor, which consist of ten amino acid functions and lie between 0 and 1, is introduced. Accordingly a model was developed, which is described with 15 flux equations and 11 differential equations and is composed of two compartments. The model describes non linear structure of the protein utilization system of an organism, which is in non steady state. The objective function for the simulation was protein deposition(g/day) cal culated according to the empirical model, PAF(product of amino acid functions) of Menke. The mean of relative difference between the simulated protein deposition and PAF calculated values, lied in a range of 11.8%. The simulated protein synthesis and breakdown rates(g/day) in the whole body showed a parallel behavior in the course of growth.

• Korean Journal of Microbiology
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• v.34 no.3
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• pp.87-90
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• 1998

Various bacterial strains that secret extracellular fibrinolytic enzyme were screened from Doen-Jang, a traditional soybean fermented food in Korea. Five microbes of them were identified to be Bacillus sp. strains according to Bergey's manual of systematic bacteriology. The culture filtrates of B. amyloliquefaciens (2.46 plasmin unit/ml) and B. pantothenticus (3.82 plasmin unit/ml) showed a level of fibrinolytic activity that was about three times higher than that of plasmin 1.0 unit and Bacillus subtilis showed the highest fibrinolytic activity (4.94 plasmin unit/ml). All of the extracellular proteases showing the fibrinolytic activity are confirmed by SDS-PAGE followed by reverse fibrin zymogram activity assay and we proposed that some of the fibrinolytic enzymes from this work are novel enzymes.

• Interdisciplinary Bio Central
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• v.2 no.3
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• pp.8.1-8.5
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• 2010

Introduction: Recently identified human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Bioinformatics study of hABH2 and hABH3 had led to the discovery of a novel DNA repair mechanism. Very little is known about structure and function of hABH4, one of the members of this superfamily. Therefore, in present study we are intended to predict its structure and function through various bioinformatics tools. Materials and Methods: Modeling was done with modeler 9v7 to predict the 3D structure of the hABH4 protein. This model was validated with the program Procheck using Ramachandran plot statistics and was submitted to PMDB with ID PM0076284. The 3d2GO server was used to predict the functions. Residues at protein ligand and protein RNA binding sites were predicted with 3dLigandSite and KYG programs respectively. Results and Discussion: 3-D model of hABH4, ALKBH4.B99990003.pdb was predicted and evaluated. Validation result showed that 96.4 % residues lies in favored and additional allowed region of Ramachandran plot. Ligand binding residues prediction showed four Ligand clusters, having 24 ligands in cluster 1. Importantly, conserved pattern of Glu196-X-Pro198- Xn-His254 in the functional domain was detected. DNA and RNA binding sites were also predicted in the model. Conclusion and Prospects: The predicted and validated model of human homologue hABH4 resulted from this study may unveil the mechanism of DNA damage repair in human and accelerate the research on designing of appropriate inhibitors aiding in chemotherapy and cancer related diseases.

• Korean Journal of Food Science and Technology
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• v.31 no.1
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• pp.219-223
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• 1999

Various bacterial strains that secret extracellular fibrinolytic enzyme were screened from kimchi, a traditional vegetable fermented food in Korea. Three microbes of them were identified to be Bacillus amyloliquefaciens, Bacillus brevis and Micrococcus luteus strains according to Bergey's Manual of Systematic Bacteriology. It was found that B. amyloliquefaciens, B. brevis and M. luteus produced 2.58, 1.48 and 2.03 plasmin unit/mL of fibrinolytic enzyme, respectively. All extracellular proteases showing the fibrinolytic activity were confirmed by SDS-PAGE and fibrin zymography assay and we propose that some of the fibrinolytic enzymes from this work are novel enzymes.