• Molecules and Cells
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• v.45 no.3
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• pp.158-167
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• 2022

Ubiquitin (Ub) is post-translationally modified by Ub itself or Ub-like proteins, phosphorylation, and acetylation, among others, which elicits a variety of Ub topologies and cellular functions. However, N-terminal (Nt) modifications of Ub remain unknown, except the linear head-to-tail ubiquitylation via Nt-Met. Here, using the yeast Saccharomyces cerevisiae and an Nt-arginylated Ub-specific antibody, we found that the detectable level of Ub undergoes Nt-Met excision, Nt-deamination, and Nt-arginylation. The resulting Nt-arginylated Ub and its conjugated proteins are upregulated in the stationary-growth phase or by oxidative stress. We further proved the existence of Nt-arginylated Ub in vivo and identified Nt-arginylated Ub-protein conjugates using stable isotope labeling by amino acids in cell culture (SILAC)-based tandem mass spectrometry. In silico structural modeling of Nt-arginylated Ub predicted that Nt-Arg flexibly protrudes from the surface of the Ub, thereby most likely providing a docking site for the factors that recognize it. Collectively, these results reveal unprecedented Nt-arginylated Ub and the pathway by which it is produced, which greatly expands the known complexity of the Ub code.

• The Korean Journal of Franchise Management
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• v.4 no.1
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• pp.113-129
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• 2013

The realization of agricultural modernization, the solving of the "three rural" issue as well as the increment of farmers' income is one of China's top priority. Thus, under the support and encouragement of government's relevant policies, China has introduced the "Supermarket-Farmer Direct Purchase" which is a new mode for the supply of agricultural products. This is an innovative of agricultural products circulation mode, and the comprehensive promotion will help supermarkets get cheap goods directly from the hands of farmers, thus forming price competitiveness; farmers can also get profits and subsidies from supermarkets which can eliminate middlemen's profit, thus increasing their revenue; consumers can both get a guarantee of food safety and save expenses, and the win-win situation for the supermarkets, farmers, and consumers will be achieved. However, the dilemma between "farmers having difficulty in selling" and "supermarkets having difficulty in buying" is still frequent. So in this thesis, through theoretical research and situation analysis, each relevant part of the "Supermarket-Farmer Direct Purchase" mode will be studied as a whole. Moreover, effectiveness will be evaluated and relevant problems will be identified. Then, based on foreign experience and our national conditions, new modes and advice will be provided for users in different circumstances.

• Proceedings of the Korean Institute of Navigation and Port Research Conference
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• 2022.11a
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• pp.188-188
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• 2022

선박의 운용 효율을 높일 수 있는 방법인 무인 운용체계는 근래에 많은 관심을 받고 연구되어 왔다. 특히 무인수상선과 무인수중체의(USV-AUV)의 복합 운용 분야는 그 동안 어려움이 있었던 심해저 탐사 및 특수 임무 활용에 용이하여 많은 연구가 수행되고 있다. 본 연구에서는 쌍동선 형태인 무인수상선이 모선이 되고 무인수중체가 결합하여 충전하고 다시 진수하여 원거리 및 심해저 조건에서 무인수중체가 운용 가능하도록 하는 시스템의 일부인 USV-AUV의 docking을 위한 DP 시스템을 개발하고 선박해양플랜트연구소 해양공학수조에서 모형시험을 통해 이를 검증하였다. 또한, 실제 제작된 무인쌍동선과 추진 시스템을 활용하여 모형시험을 통해 검증한 DP 알고리즘을 적용하여 화성 제부도 앞바다에서 실선 DP 테스트를 수행하였다. 실 해역에서의 DP 시스템 테스트는 정확한 환경 조건의 계측 및 구현이 어려워 모형시험과 같은 정량적인 평가는 어렵지만, 정성적으로 DP 시스템이 작동하는 것을 확인할 수 있었다.

• BMB Reports
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• v.56 no.11
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• pp.594-599
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• 2023

A number of therapeutic drugs have been developed from functional chemicals found in plants. Knowledge of plants used for medicinal purposes has historically been transmitted by word of mouth or through literature. The aim of the present study is to provide a systemic platform for the development of lead compounds against breast cancer based on a traditional medical text. To verify our systematic approach, integrating processes consisted of text mining of traditional medical texts, 3-D virtual docking screening, and in vitro and in vivo experimental validations were demonstrated. Our text analysis system identified rutin as a specific phytochemical traditionally used for cancer treatment. 3-D virtual screening predicted that rutin could block EGFR signaling. Thus, we validated significant anti-cancer effects of rutin against breast cancer cells through blockade of EGFR signaling pathway in vitro. We also demonstrated in vivo anti-cancer effects of rutin using the breast cancer recurrence in vivo models. In summary, our innovative approach might be proper for discovering new phytochemical lead compounds designing for blockade of malignant neoplasm including breast cancer.

• Genomics & Informatics
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• v.21 no.3
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• pp.41.1-41.11
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• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

• Biomolecules & Therapeutics
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• v.32 no.4
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• pp.474-480
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• 2024

Streptomyces avermitilis genome includes 33 genes encoding monooxygenation-catalyzing cytochrome P450 enzymes. We investigated the structure of CYP107P2 and its interactions with terpenoid compounds. The recombinant CYP107P2 protein was expressed in Escherichia coli and the purified enzyme exhibited a typical P450 spectrum upon CO-binding in its reduced state. Type-I substrate-binding spectral titrations were observed with various terpenoid compounds, including α-pinene, β-pinene, α-terpinyl acetate, and (+)-3-carene. The calculated binding affinities (Kd) ranged from 15.9 to 50.8 µM. The X-ray crystal structure of CYP107P2 was determined at 1.99 Å resolution, with a well-conserved overall P450 folding conformation. The terpenoid compound docking models illustrated that the structural interaction between monoterpenes and CYP107P2, with the distance between heme and terpenes ranging from 3.4 to 5.4 Å, indicates potential substrate binding for P450 enzyme. This study suggests that CYP107P2 is a Streptomyces P450 enzyme capable of catalyzing terpenes as substrates, signifying noteworthy advancements in comprehending a novel P450 enzyme's involvement in terpene reactions.

• Journal of Integrative Natural Science
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• v.17 no.1
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• pp.13-20
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• 2024

Female breast cancer is the fifth highest cause of mortality. Breast cancer is the most prevalent type of cancer in women globally, while it can also affect men. STAT5A plays a role in its development and progression. Given that activation of STAT5a is frequently linked to the growth and progression of tumors, STAT5a has been identified as a possible target for the therapy of several cancers. STAT5A, in particular, has proven to be overexpressed in various breast cancer cell lines and tumors, and it has been associated to the promotion of tumour cell proliferation and survival. STAT5A inhibition has been shown in vitro and in vivo to reduce the development of breast cancer cells. As a result, we have screened compounds from the FDA database that might serve as potential inhibitors of STAT5a through virtual screening, docking, DFT and MD simulation approaches. The drug Nilotinib has shown promising results inhibiting STAT5a. Further, in-vitro analysis will be carried forward to understand the anti-cancer activity.

• Proceedings of the Korea Committee for Ocean Resources and Engineering Conference
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• 2004.05a
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• pp.249-256
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• 2004

KRISO/KORDI is currently developing a deep-sea unmanned underwater vehicle (UUV) system which is composed of a launcher, an ROV, and an AUV. Two USBL acoustic positioning systems will be used for UUV's navigation. One is for the deep sea positioning of all three vehicles and the other is for AUV's guidance to the docking device on the launcher. In order to increase the position accuracy MFSK(Multiple Frequency Shift Keying) broadband signal will be used. As the first step to the implementation of a USBL system, this paper studies USBL positioning algorithm using MFSK signals. Firstly, the characteristics of MFSK signal is described with various MFSK parameters: number of frequencies, frequency step, center frequency, and pulse length. Time and phase delays between two received signals are estimated by using cross-correlation and cross-spectrum methods. Finally an USBL positioning algorithm is derived by converting the delays to difference of distances and applying trigonometry. The simulation results show that the position accuracy is improved highly when both cross-correlation and cross-spectrum of MFSK signals are used simultaneously.

• Bulletin of the Korean Chemical Society
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• v.31 no.3
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• pp.611-614
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• 2010

Substituted imidazolidin-2-ones deduced as potential inhibitors of IleRS by docking simulations were synthesized from an aziridine-2-carboxaldehyde. Reductive amination of an aziridine-2-carboxaldehyde with dipeptides for the substituents at N1 and followed by aziridine-ring expansion with triphosgene afforded 4-chloromethylimidazolidin-2-ones whose chloride were further manipulated towards phenylurea, pyrimidin-2-yl-urea or benzenesulfonamide at C4.

• The Journal of Korean Association of Computer Education
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• v.12 no.4
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• pp.57-64
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• 2009

Protein structure comparison is a task that requires a lot of computing resources because many atoms in proteins need to be processed. To address the issue, Grid computing environment has been employed for processing time-consuming jobs in a distributed manner. However, controling the Grid computing environment may not be easy for non-experts. In this paper, we present a JXTA-based system for protein structure comparison that can be easily controled by non-experts. To search proteins similar to a query protein, the geometric hashing algorithm that consists of preprocessing and recognition was employed. Experimental results indicate that the system can find the correct protein structure for a given query protein structure and the proposed system can be easily extended to solve the protein docking problem. It is expected that the proposed system can be useful for non-experts, especially users who do not have sophisticated knowledge of distributed systems in general such as college students who major in biology or chemistry.