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Crystal Structure of a Putative Histidine-containing Phosphotransfer Protein from Oryza sativa
Euiyoung Bae,Eduard Bitto,Craig A. Bingman,Simon T. Allard,Gary E. Wesenberg,Russell L. Wrobel,Brian G. Fox,George N. Phillips, Jr 한국응용생명화학회 2010 Applied Biological Chemistry (Appl Biol Chem) Vol.53 No.6
Os09g0567400 codes for a hypothetical protein from Oryza sativa that is annotated as the “Histidine-containing phosphotransfer (Hpt) protein”. Hpt domain is a protein module with a histidine residue mediating phosphotransfer reaction in the histidine-aspartate phosphorelay system. We report here the crystal structure and analysis of Os09g0567400.
Molecular dynamics simulation of a psychrophilic adenylate kinase
Bae, Euiyoung,Moon, Sojin,Phillips, George N. Jr. The Korean Society for Applied Biological Chemistr 2015 Applied Biological Chemistry (Appl Biol Chem) Vol.58 No.2
Proteins from psychrophilic organisms can function at low temperatures and have shown potential for industrial applications. In the present study, thermal denaturation of a psychrophilic adenylate kinase (AKpsychro) from Bacillus globisporus was measured using circular dichroism spectroscopy and its molecular dynamics (MD) simulations were performed. The results fromthe unfolding experiment andMD simulations of AKpsychro were compared with those of its mesophilic and thermophilic homologues to study the relationship between dynamic motion and the cold adaptation of proteins.
A first record of Gaphara conspersa (Matsumura, 1931)(Lepidoptera, Tineidae) in Korea
Neung-Ho Ahn,Yang-Seop Bae,Euiyoung Kang 한국응용곤충학회 2014 한국응용곤충학회 학술대회논문집 Vol.2014 No.04
A tineid moth, Gaphara conspersa (Matsumura, 1931) is newly reported in Korea. Gaphara conspersa is myrmecophilous, associated with some species of ants such as Lasius (Lasius) japonicus, L. (Dendrolasius) spp., Polyrhachis spp., Camponotus spp., Pristomyrmex punctatus was known in Japan. The larva lives in a 8-shaped or gourd-shaped flat case are made of soil and sand. Larva scavenges food, dead ants and shed skins of ant larvae that are carried out by ants. Females lays eggs around the nests (Maruyama et al., 2013). In this study, Gaphara conspersa (Matsumura, 1931) was found for the first time from Korea. The larvae were collected in the ant nests at Mt. Cheonggye, Geumto-dong, Seongnam City, in 22. May 2013 and 16. June 2013. The larval cases have three level sizes (small, middle and large) were found at the same time. Figures of the adults, larvae and pupae, are given in this study.
Moon, Sojin,Bae, Euiyoung The Korean Society for Applied Biological Chemistr 2014 Applied Biological Chemistry (Appl Biol Chem) Vol.57 No.5
Thermally stable proteins are desirable in many industrial and laboratory settings, and numerous approaches have been developed to redesign proteins for higher thermal stability. Here, we report the crystal structures of two thermally stable adenylate kinase (AK) mutants that were designed by applying a combination of local structural entropy (LSE) optimization and structure-guided mutagenesis. Structure-guided mutagenesis resulted in stabilizing interactions connecting distant regions of the LSE-optimized AK sequence. This demonstrates the feasibility and importance of simultaneous optimization of local and global features in protein thermal stabilization. An additional AK mutant showed that small changes in side-chain configuration can greatly impact thermal stability.
Backbone NMR assignments of the anti-CRISPR AcrIIA5 from phages infecting Streptococcus thermophilus
An, So Young,Kim, Eun-Hee,Bae, Euiyoung,Suh, Jeong-Yong Korean Magnetic Resonance Society 2020 Journal of the Korean Magnetic Resonance Society Vol.24 No.3
The CRISPR-Cas system provides an adaptive immunity for bacteria and archaea against invading phages or foreign plasmids. In the type II CRISPR-Cas system, a single effector protein Cas9 and a guide RNA form an RNA-guided endonuclease complex that can degrade DNA targets of foreign origin. To avoid the Cas9-mediated destruction, phages evolved anti-CRISPR (Acr) proteins that neutralize the host bacterial immunity by inactivating the CRISPR-Cas system. Here we report the backbone <sup>1</sup>H, <sup>15</sup>N, and <sup>13</sup>C resonance assignments of AcrIIA5 that inhibits the endonuclease activity of type II-A Streptococcus thermophilus Cas9 and also Streptococcus pyogenesis Cas9 using triple resonance nuclear magnetic resonance spectroscopy. The backbone chemical shifts of AcrIIA5 predict a disordered region at the N-terminus, followed by an αββββαβββ fold.
Crystal structure of an anti-CRISPR protein, AcrIIA1
Ka, Donghyun,An, So Young,Suh, Jeong-Yong,Bae, Euiyoung Oxford University Press 2018 Nucleic acids research Vol.46 No.d1
<P><B>Abstract</B></P><P>Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide bacteria with RNA-based adaptive immunity against phage infection. To counteract this defense mechanism, phages evolved anti-CRISPR (Acr) proteins that inactivate the CRISPR-Cas systems. AcrIIA1, encoded by <I>Listeria monocytogenes</I> prophages, is the most prevalent among the Acr proteins targeting type II-A CRISPR-Cas systems and has been used as a marker to identify other Acr proteins. Here, we report the crystal structure of AcrIIA1 and its RNA-binding affinity. AcrIIA1 forms a dimer with a novel two helical-domain architecture. The N-terminal domain of AcrIIA1 exhibits a helix-turn-helix motif similar to transcriptional factors. When overexpressed in <I>Escherichia coli</I>, AcrIIA1 associates with RNAs, suggesting that AcrIIA1 functions via nucleic acid recognition. Taken together, the unique structural and functional features of AcrIIA1 suggest its distinct mode of Acr activity, expanding the diversity of the inhibitory mechanisms employed by Acr proteins.</P>
김명원(Myeongwon Kim),박창민(Changmin Park),배현주(Hyunjoo Bae),차의영(Euiyoung Cha) 한국정보과학회 1989 한국정보과학회 학술발표논문집 Vol.16 No.2
역전파 학습 모델은 최근 가장 인기있는 학습 규칙으로 알려지고 있다[1]. 본 논문에서는 역전파 신경망을 이용하여 한글 문자 인식에 관하여 연구하였다. 먼저 한글의 형태를 분류하고 그 형태에 따라 각 각의 음소를 인식하여 완전한 한글 문자를 인식하고자 하였다. 또한 학습 규칙에서의 변수의 변화에 따른 인식률을 비교 분석하였다. 이를 위하여 본 논문에서는 인식 시스템은 C 프로그래밍 언어를 이용하여 구현하였다.
Ka, Donghyun,Jang, Dong ,Man,Han, Byung ,Woo,Bae, Euiyoung Oxford University Press 2018 Nucleic acids research Vol.46 No.18
<P><B>Abstract</B></P><P>Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) proteins provide microbial adaptive immunity against invading foreign nucleic acids. In type II-A CRISPR–Cas systems, the Cas1–Cas2 integrase complex and the subtype-specific Csn2 comprise the CRISPR adaptation module, which cooperates with the Cas9 nuclease effector for spacer selection. Here, we report the molecular organization of the <I>Streptococcus pyogenes</I> type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. We determined the crystal structure of <I>S. pyogenes</I> type II-A Cas2. Chromatographic and calorimetric analyses revealed the stoichiometry and topology of the type II-A adaptation module composed of Cas1, Cas2 and Csn2. We also demonstrated that Cas9 interacts with Csn2 in a direct and stoichiometric manner. Our results reveal a network of molecular interactions among type II-A Cas proteins and highlight the role of Csn2 in coordinating Cas components involved in the adaptation and interference stages of CRISPR-mediated immunity.</P>