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Structure of Human Toll-like Receptor 3
Choe, Jungwoo 이화여자대학교 세포신호전달연구센터 2007 고사리 세포신호전달 심포지움 Vol. No.9
Toll-like receptors(TLRs) are important pattern recognition receptors of the innate immune system and recognize specific pathogen-associated molecules from various pathogens including bacteria, virus, fungus and parasite. TLR3 is the receptor of the viral double-stranded RNA and play key roles in the defense against viral infection. The crystal structure of the heavily glycosylated human TLR3 extracellular domain at 2.1Å resolution reveals a large horseshoe-shaped structure that is assembled from 23 leucine-rich repeats(LRRs). The overall structure is stabilized by three main interactions 1) hydrophobic interaction inside the LRRs formed by seven conserved hydrophobic residues in the LRR repeats 2) numerous hydrogen bonds in the 25 continous β-sheet and 3) four hydrogen bonding networks made by conserved asparagines at position 10 in 24-residue LRR motif. N-glycosylation is observed in 9 out of the 15 potential glycosylation sites and TLR3 surface is largely masked by carbohydrate, but one face is glycosylation-free. This glycosylation-free surface also contains the most highly conserved surface residues and a TLR3-specific LRR insertion(LRR20) that forms the TLR3 homodimer interface. Two patches of positively-charged residues and a second TLR3-specific LRR insertion(LRR12) also map to this carbohydrate-free face and would provide an appropriate binding site for dsRNA. Thus, the TLR3 structure gives insights into its distinctive architecture, putative ligand binding site and potential mechanism of signaling
사용자-데이터 인터페이스 : 데이터에서 자동 스크롤을 통한 정보 검색 가속화 인터페이스
최민기(Minki Choe),박정우(JungWoo Park),김종현(Jong-Hyun Kim) 한국컴퓨터정보학회 2021 한국컴퓨터정보학회 학술발표논문집 Vol.29 No.1
본 논문에서는 사용자의 관심영역(Region of interests, ROI)를 기반 스크롤을 통해 데이터를 좀 더 빠르고 효율적으로 검색할 수 있는 사용자-데이터 인터페이스를 제안한다. 사용자가 관심있는 정보나 콘텐츠를 찾는 행동에서 착안한 우리의 접근 방식은 주어진 콘텐츠에서 ROI를 효율적으로 계산하고, GMM(Gaussian mixture model, 가우시안 혼합 모델)에서 착안해 개발한 커널을 기반으로 사용자가 관심 있어 하는 정보의 위치로 부드럽고 빠르게 화면을 이동시켜 정보를 탐색한다. 과정을 설명하기 앞서, 다수의 ROI가 있을 때 스크롤의 현 위치는 항상 두 ROI의 사이에 있다. 그 두 사이의 거리가 가장 짧은 두 ROI에 각각 우리의 커널을 적용하면 현 위치에서 스크롤 가속에 적용 가능한 두 개의 관성이 생긴다. 여기에 선형 보간법(Linear interpolation)을 적용하여 한층 부드러운 하나의 관성으로 만들고, 이것을 스크롤에 적용한다. 결과적으로, 오직 사용자의 입력에 따라 정보가 검색되는 기존의 접근법과는 달리, ROI와 DOI(Degree of interests, 중요도)를 기반으로 향상된 스크롤을 통해 사용자가 관심 있어 하는 정보나 콘텐츠를 보다 쉽게 직관적으로 찾아줄 수 있기 때문에 사용자는 탐색 시간을 절약할 수 있다.
Bacillus subtilis HmoB is a heme oxygenase with a novel structure
( Seonghun Park ),( Sarah Choi ),( Jungwoo Choe ) 생화학분자생물학회 2012 BMB Reports Vol.45 No.4
Iron availability is limited in the environment and most bacteria have developed a system to acquire iron from host hemoproteins. Heme oxygenase plays an important role by degrading heme group and releasing the essential nutrient iron. The structure of Bacillus subtilis HmoB was determined to 2.0 A resolution. B. subtilis HmoB contains a typical antibiotic biosynthesis monooxygenase (ABM) domain that spans from 71 to 146 residues and belongs to the IsdG family heme oxygenases. Comparison of HmoB and IsdG family proteins showed that the C-terminal region of HmoB has similar sequence and structure to IsdG family proteins and contains conserved critical residues for heme degradation. However, HmoB is distinct from other IsdG family proteins in that HmoB is about 60 amino acids longer in the N-terminus and does not form a dimer whereas previously studied IsdG family heme oxygenases form functional homodimers. Interestingly, the structure of monomeric HmoB resembles the dimeric structure of IsdG family proteins. Hence, B. subtilis HmoB is a heme oxygenase with a novel structural feature. [BMB reports 2012; 45(4): 239-241]
Gold Nanoparticles as Nucleation-Inducing Reagents for Protein Crystallization
Ko, Sanga,Kim, Hye Young,Choi, Inhee,Choe, Jungwoo The American Chemical Society 2017 CRYSTAL GROWTH AND DESIGN Vol.17 No.2
<P>Protein crystallization is a necessary but time-consuming and difficult step in structure determination by crystallography. The rate-limiting step of crystallization is nucleation, where protein monomers in solution cluster in an ordered fashion to form a stable nucleus. Here, we propose the use of gold nanopartides to accelerate nucleation and enhance crystal formation. We tested whether gold nanoparticles can facilitate nucleation by interacting with target proteins and inducing favorable clustering. We used differently sized gold nanospheres and gold nanostars to crystallize hen egg-white lysozyme. Our results indicated that gold nanopartides significantly increased the number of crystallization conditions (by about 20%). Spherical and larger gold particles were found to be more efficient. Furthermore, the use of gold nanopartides did not have any adverse effect on data collection or structure determination. Our findings indicate that the use of nanopartides as protein nucleation-inducing reagents can greatly accelerate structure determination by X-ray crystallography.</P>
Kim, Yongwoon,Lee, Hasup,Heo, Lim,Seok, Chaok,Choe, Jungwoo Wiley-Blackwell Publishing, Inc. 2014 Protein science Vol. No.
<P>Vaccinia virus (VACV) encodes many proteins that interfere with the host immune system. Vaccinia virus A46 protein specifically targets the BB-loop motif of TIR-domain-containing proteins to disrupt receptor:adaptor (e.g., TLR4:MAL and TLR4:TRAM) interactions of the toll-like receptor signaling. The crystal structure of A46 (75-227) determined at 2.58 ? resolution showed that A46 formed a homodimer and adopted a Bcl-2-like fold similar to other VACV proteins such as A52, B14, and K7. Our structure also revealed that VIPER (viral inhibitory peptide of TLR4) motif resides in the α1-helix and six residues of the VIPER region were exposed to surface for binding to target proteins. In vitro binding assays between wild type and six mutants A46 (75-227) and full-length MAL identified critical residues in the VIPER motif. Computational modeling of the A46:MAL complex structure showed that the VIPER region of A46 and AB loop of MAL protein formed a major binding interface. In summary, A46 is a homodimer with a Bcl-2-like fold and VIPER motif is believed to be involved in the interaction with MAL protein based on our binding assays.</P>
Facile Fabrication of Stimuli-responsive Nanoparticles for Peptide Delivery
Donghun SHIN,Seungki LEE,Ji Hyeon OH,Sunho HONG,Jungwoo CHOE,Inhee CHOI 한국생물공학회 2021 한국생물공학회 학술대회 Vol.2021 No.10
Stimuli-responsive nanocarriers have been extensively studied to enhance controlled molecular delivery. To this end, hydrogels have considered to be promising since they can store various cargos with minimizing the loss of activity. Here, we present the stimuli-responsive collagen-based nanoparticles (CNPs) via facile radical polymerization. CNPs are composed of biocompatible fish-derived collagen and thermo-sensitive polymers (i.e., N-isopropylacrylamide) to fabricate thermo-responsive nanoparticles. By adding gold precursor ions in a synthetic solution, hybrid nanoparticles integrated with light-responsive gold nanoparticles are easily obtained. Physicochemical properties including morphology and degree of integration between the building components are tuned to optimize the stimuli-responsive hybrid nanoparticles. The peptide loading efficiency of synthesized nanoparticles are calculated and stimuli-responsive release are investigated. Finally, we show that effective cellular delivery is achieved in presence of light- or thermo-stimuli without any cytotoxic issue. Collectively, we expect that the proposed hybrid nanoparticles would be beneficial in performing controlled peptide delivery.