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Sampath Natarajan,강린우,김진광,Tae-Kyun Jung,Thanh Thi Ngoc Doan,Ho-Phuong-Thuy Ngo,홍명기,Seunghwan Kim,Viet Pham Tan,Seok Joon Ahn,이상희,한예선,안예진 한국분자세포생물학회 2012 Molecules and cells Vol.33 No.1
Xanthomonas oryzae pv. oryzae (Xoo) is a plant bacterial pathogen that causes bacterial blight (BB) disease, resulting in serious production losses of rice. The crystal structure of malonyl CoA-acyl carrier protein transacylase (XoMCAT), encoded by the gene fabD (Xoo0880) from Xoo, was determined at 2.3 Å resolution in complex with N-cyclohexyl-2-aminoethansulfonic acid. Malonyl CoA-acyl carrier protein transacylase transfers malonyl group from malonyl CoA to acyl carrier protein (ACP). The transacylation step is essential in fatty acid synthesis. Based on the rationale, XoMCAT has been considered as a target for antibacterial agents against BB. Protein-protein interaction between XoMCAT and ACP was also extensively investigated using computational docking, and the proposed model revealed that ACP bound to the cleft between two XoMCAT subdomains.
설균보,박현재,안예진,강린우 대한화학회 2019 Bulletin of the Korean Chemical Society Vol.40 No.10
Crystal Structure of Enoyl-Acyl Carrier Protein Reductase (FabI) proposes a putative inhibitor binding pocket.
동기식 및 비동기식 원격 협업을 위한 가상현실 기반의 분자 모델링 시스템
이준(Jun Lee),김형석(Hyungseok Kim),강린우(Linwoo Kang),김지인(Jeein Kim) 한국HCI학회 2009 한국HCI학회 논문지 Vol.4 No.1
컴퓨터를 사용한 협업 시스템은 인터넷을 통하여 가상공간에서 여러 명의 사용들이 협력하여 작업을 할 수 있는 시스템을 의미한다. 특히, 협업 가상현실 시스템은 실제로 경험하기 힘든 작업을 사이버 공간에서 가능하게 하여 다양한 과학기술 분야 및 문화기술 분야에 적용이 되고 있다. 하지만 기존의 협업 가상현실 시스템들은 같은 시간대에 동기화되어 이루어지는 작업에만 중점을 두고 있어 시간과 장소의 차이에 따라 이루어지는 다양한 형태의 협업 작업들은 지원 하지 못하고 있다. 본 연구에서는 이러한 문제를 해결하기 위해 동기식 및 비동기식 원격 차이에 따른 협업 작업을 분류하고 이에 따른 동기식 및 비동기식 원격 협업 작업을 지원 해주는 시스템을 제안 한다. 제안된 시스템은 생명공학 분야의 중요한 실험인 도킹 시뮬레이션 및 구조 결정학 분석 실험에 적용 되었다. 실험과정에서는 선정된 분자 시뮬레이션 실험 과정을 본 논문에서 제안한 동기식 및 비동기식 원격 협업 작업을 하는 경우와 일반적인 단일 작업을 하는 경우에 걸리는 시간과 성능을 비교 하였다. A computer supported cooperative work(CSCW) system is a collaboration system, which enables cooperative works among various participants through the Internet. A collaborative virtual reality environment(CRVE) can be used in scientific research and cultural research because it can provide users with virtual experiences of three dimensional molecular models in cyberspace. However, general CVRE systems are only focused on synchronous collaborations. We propose a remote collaboration system, which provides synchronous and asynchronous cooperation in collaborative virtual reality environment. The proposed system can be applied to bioscience experiments such as molecular docking process, and crystallography simulation. The proposed system is evaluated in performance comparison with previous approaches.
벼의 생엽절편을 이용한 병원균 억제물질의 대량 스크리닝 방법 개발
박샛별 ( Sait Byul Park ),이충환 ( Choong Hwan Lee ),김태종 ( Tae Jong Kim ),강린우 ( Lin Woo Kang ),이병무 ( Byoung Moo Lee ),김정구 ( Jeong Gu Kim ) 한국미생물생명공학회 ( 구 한국산업미생물학회 ) 2012 한국미생물·생명공학회지 Vol.40 No.1
A new method for the high throughput screening of antagonistic substances against rice pathogens using rice leaf explants was developed. This method can be used to confirm the activities of any compound or mixture suppressing rice bacterial blight (BB) before field tests. Xanthomonas oryzae pv. oryzae (Xoo) culture medium was distributed in 96 well plates with equally sized explants and the active compounds were added to the wells. The strength suppressing BB was converted into an area percent of the lesion on the rice explants. The explants under BB suppressing activity remained uninfected maintaining their actual green color, while infected explants exhibited pale yellow-colored lesions. Based on the results, this method seems to be faster and easier, dose-dependent, and can be performed all-at-once with a small amount of unspecified compounds. This method also has the potential to be applied to inspection activities for the suppression of other waterborne crop diseases.
Ho-Phuong-Thuy Ngo,Diem-Quynh Nguyen,김승환,김정구,안예진,강린우 한국구조생물학회 2019 Biodesign Vol.7 No.2
Xanthomonas oryzae pv. oryzae (Xoo) is a plant pathogen, which causes a bacterial blight of rice. The bacterial blightis one of the most devastating diseases of rice in most of the rice growing countries and there is no effective pesticideagainst bacterial blight. The β-ketoacyl-acyl carrier protein synthase III (FabH) plays a key role in fatty acid synthesis(FAS) and is a promising drug target for the development of antibacterial agents. Xoo0878 gene, a fabH gene, from Xoowas cloned and its gene product Xoo0878 was expressed, purified and crystallized. Xoo0878 crystal diffracted to 2.1Åresolution and belonged to the triclinic space group P1, with unit-cell parameters a = 57.3Å, b = 64.7Å, c = 104.2Å and α =81.6°, β = 84.7°, γ = 74.4°. There are four monomers in the asymmetric unit, with a corresponding crystal volume per proteinweight of 2.65 Å3 Da−1 and a solvent content of 53.6%. Xoo0878 structure will be useful to develop new antibacterial agentsagainst Xoo.
Crystal Structure of XoLAP, a Leucine Aminopeptidase, from Xanthomonas oryzae pv. oryzae
김진광,Sampath Natarajan,박한슬,Kim-Hung Huynh,이상희,김정구,안예진,강린우 한국미생물학회 2013 The journal of microbiology Vol.51 No.5
Aminopeptidases are metalloproteinases that degrade N-terminal residues from protein and play important roles in cell growth and development by controlling cell homeostasis and protein maturation. We determined the crystal structure of XoLAP, a leucyl aminopeptidase, at 2.6 Å resolution from Xanthomonas oryzae pv. oryzae, causing the destructive rice disease of bacterial blight. It is the first crystal structure of aminopeptidase from phytopathogens as a drug target. XoLAP existed as a hexamer and the monomer structure consisted of an N-terminal cap domain and a C-terminal peptidase domain with two divalent zinc ions. XoLAP structure was compared with BlLAP and EcLAP (EcPepA) structures. Based on the structural comparison, the molecular model of XoLAP in complex with the natural aminopeptidase inhibitor of microginin FR1 was proposed. The model structure will be useful to develop a novel antibacterial drug against Xoo.
The role of serine 190 in FOXO nuclear export and cell death induction in Drosophila melanogaster
홍윤기,조경상,차광호,이다혜,황수진,방세민,정해민,최서윤,Tan-Viet Phamd,강린우,이영하 한국유전학회 2014 Genes & Genomics Vol.36 No.4
Proteins in the forkhead box O (FOXO) familycontain three Akt phosphorylation sites that are important forexport of the protein from the nucleus to the cytosol. Inmammalian FOXO1, phosphorylation of serine 256 (S256)is a prerequisite for the phosphorylation of the other twosites. Although Drosophila FOXO (dFOXO) contains threewell-conserved Akt phosphorylation sites, their role in theregulation of Drosophila physiology is not well understood. In the present study, we examine the regulation and functionof phosphorylation at serine 190 (S190), which correspondsto S256 of mammalian FOXO1. Insulin and Akt were shownto increase S190 phosphorylation of dFOXO. Moreover,dFOXO nuclear export was induced by insulin treatment inboth fly tissues and transfected Drosophila and human cells,and a protein containing an alanine substitution at S190(dFOXOS190A) was defective in these insulin-dependentresponses, suggesting that S190 phosphorylation is requiredfor dFOXO nuclear export. Interestingly, dFOXOS190A anddFOXOS190D mutants showed lower target gene expressionand a reduced ability to induce cell death compared to wildtypedFOXO. These results suggest that the S190 residue isrequired for dFOXO translocation and is important for thepro-apoptotic function of dFOXO.
Kim-Hung Huynh,홍명기,Clarice Lee,Huyen-Thi Tran,이상희,안예진,차선신,강린우 한국미생물학회 2015 The journal of microbiology Vol.53 No.11
Acinetobacter baumannii, which is emerging as a multidrugresistant nosocomial pathogen, causes a number of diseases, including pneumonia, bacteremia, meningitis, and skin infections. With ATP hydrolysis, the D-alanine-D-alanine ligase (DDL) catalyzes the synthesis of D-alanyl-D-alanine, which is an essential component of bacterial peptidoglycan. In this study, we determined the crystal structure of DDL from A. baumannii (AbDDL) at a resolution of 2.2 Å. The asymmetric unit contained six protomers of AbDDL. Five protomers had a closed conformation in the central domain, while one protomer had an open conformation in the central domain. The central domain with an open conformation did not interact with crystallographic symmetry-related protomers and the conformational change of the central domain was not due to crystal packing. The central domain of AbDDL can have an ensemble of the open and closed conformations before the binding of substrate ATP. The conformational change of the central domain is important for the catalytic activity and the detail information will be useful for the development of inhibitors against AbDDL and putative antibacterial agents against A. baumannii. The AbDDL structure was compared with that of other DDLs that were in complex with potent inhibitors and the catalytic activity of AbDDL was confirmed using enzyme kinetics assays.
Conformational change of organic cofactor PLP is essential for catalysis in PLP-dependent enzymes
Ho-Phuong-Thuy Ngo,Diem-Quynh Nguyen,Hyunjae Park,Yoon Sik Park,Kiwoong Kwak,Taejoon Kim,Jang Ho Lee,Kyoung Sang Cho,강린우 생화학분자생물학회 2022 BMB Reports Vol.55 No.9
Pyridoxal 5’-phosphate (PLP)-dependent enzymes are ubiquitous,catalyzing various biochemical reactions of approximately 4%of all classified enzymatic activities. They transform amines andamino acids into important metabolites or signaling moleculesand are important drug targets in many diseases. In the crystalstructures of PLP-dependent enzymes, organic cofactor PLPshowed diverse conformations depending on the catalytic step. The conformational change of PLP is essential in the catalyticmechanism. In the study, we review the sophisticated catalyticmechanism of PLP, especially in transaldimination reactions. Most drugs targeting PLP-dependent enzymes make a covalentbond to PLP with the transaldimination reaction. A detailedunderstanding of organic cofactor PLP will help develop a newdrug against PLP-dependent enzymes.