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Hyeongseop Jeong,Seong-Gyu Lee,Hee-Seok Kweon,Jaekyung Hyun 한국구조생물학회 2017 Biodesign Vol.5 No.3
Cryo-electron microscopy (cryo-EM) single particle analysis has become a mainstream structural biology tool and therefore access to high-end transmission electron microscope (TEM) dedicated to high resolution cryo-EM is critical. At Korea Basic Science Institute (KBSI), a facility dedicated to biological electron microscopy was established in 2016, and High Resolution Bio-TEM (HR Bio-TEM, Titan Krios, Thermo Fisher Scientific Inc., USA) is now accessible to national and international researchers. This report describes major features of the HR Bio-TEM and the facility, along with overall workflow of cryo-EM image data acquisition.
Jeong, Hyeongseop,Yoo, Seung Jo,Won, Jonghan,Lee, Hyun-Ju,Chung, Jeong Min,Kim, Han-ul,Kim, Gwang Joong,Kim, Jin-Gyu,Jung, Hyun Suk,Hyun, Jaekyung Elsevier 2018 Ultramicroscopy Vol.194 No.-
<P><B>Abstract</B></P> <P>Heavy metal compounds are adsorbed onto biological specimen in order to enhance the contrast as well as to preserve the structural features of the specimen against electron beam-induced radiation damage. In particular, in combination with computational image processing, negative staining is widely used for structural analysis of protein complexes to moderate resolutions. Image analysis of negatively stained biological specimen is known to suffer from limited achievable resolution due to dehydration and large grain size of staining molecules although the extent of such effect remains somewhat dubious.</P> <P>Stain molecules exist as grains under electron beam. However, clear observation of the crystalline nature of the grains and their association with biological specimen has not been thoroughly demonstrated. In this study, we attempted high-resolution TEM (HRTEM) using high voltage electron microscopy and electron crystallography analysis for the detailed characterization of negatively stained biological specimen, focusing on physical state and chemical composition of the stain molecules. The electron crystallography analysis allowed for the identification of the crystal constituents of widely used stains, hence revealing the chemical nature and the morphology of the stain molecules at specimen level. This study re-evaluated generally accepted notions on negative staining, and may help correctly interpreting the structural analysis of stained biological specimen.</P> <P><B>Highlights</B></P> <P> <UL> <LI> High voltage electron microscopy (HVEM) visualized nano-crystals surrounding of heavy metal-embedded biological specimen. </LI> <LI> Electron crystallography determined chemical composition of the stain molecules. </LI> <LI> The grain size of nano-crystals of stained molecules from uranyl acetate and uranyl formate were nearly identical, and consistent with that of uranium dioxide (UO<SUB>2</SUB>). </LI> <LI> It identified that UO<SUB>2</SUB> is the main contributor of image contrast of heavy metal-embedded biological specimen. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>
Lee, Sangmin,Jeong, Hyeongseop,Lee, Ju Huck,Chung, Jeong Min,Kim, Rumi,Yun, Hyung Joong,Won, Jonghan,Jung, Hyun Suk Elsevier 2017 Biochemical and biophysical research communication Vol.489 No.2
<P><B>Abstract</B></P> <P>Alkyl hydroperoxide reductase E (AhpE) is a member of the peroxidase family of enzymes that catalyse the reduction of peroxides, however its structural and functional roles are still unclear in details. In this study, we used the <I>Thermococcus kodakarensis</I> AhpE-like protein as a model to investigate structure–function relationships including the molecular properties of DNA binding activity. Multiple sequence alignment, structural comparison and biochemical analyses revealed that TkAhpE includes conserved peroxidase residues in the active site, and exhibits peroxidase activity with structure-dependent holdase chaperone function. Following electrophoretic mobility shift assays and electron microscopy analysis demonstrated distinctive binding features of TkAhpE to the DNA showing that their dimeric conformer can bind to the double-stranded DNA, but not to the single-stranded DNA, indicating its striking molecular features to double-stranded DNA-specific interactions. Based on our results, we provided that TkAhpE is a multifunctional peroxidase displaying structure-dependent molecular chaperone and DNA binding activities.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Alkyl hydroperoxide reductase E acts as a multi-functional protein displaying peroxidase, holdase and DNA binding activities. </LI> <LI> Thermococcus kodakarensis AhpE(TkAhpE) exhibits peroxidase activities with structure-dependent holdase chaperone function. </LI> <LI> Recombinant TkAhpE is expressed as two different oligomeric forms, the dimeric and octameric conformers. </LI> <LI> Unlikely an octameric conformer, dimeric state of TkAhpE can bind both double stranded circular and linear DNA molecules. </LI> </UL> </P>
Structure of the Tripartite Multidrug Efflux Pump AcrAB-TolC Suggests an Alternative Assembly Mode
Kim, Jin-Sik,Jeong, Hyeongseop,Song, Saemee,Kim, Hye-Yeon,Lee, Kangseok,Hyun, Jaekyung,Ha, Nam-Chul Korean Society for Molecular and Cellular Biology 2015 Molecules and cells Vol.38 No.2
Escherichia coli AcrAB-TolC is a multidrug efflux pump that expels a wide range of toxic substrates. The dynamic nature of the binding or low affinity between the components has impeded elucidation of how the three components assemble in the functional state. Here, we created fusion proteins composed of AcrB, a transmembrane linker, and two copies of AcrA. The fusion protein exhibited acridine pumping activity, suggesting that the protein reflects the functional structure in vivo. To discern the assembling mode with TolC, the AcrBA fusion protein was incubated with TolC or a chimeric protein containing the TolC aperture tip region. Three-dimensional structures of the complex proteins were determined through transmission electron microscopy. The overall structure exemplifies the adaptor bridging model, wherein the funnel-like AcrA hexamer forms an intermeshing cogwheel interaction with the ${\alpha}$-barrel tip region of TolC, and a direct interaction between AcrB and TolC is not allowed. These observations provide a structural blueprint for understanding multidrug resistance in pathogenic Gram-negative bacteria.
Lee Ji Joo,Choe Young June,Jeong Hyeongseop,Kim Moonsu,Kim Seonggon,Yoo Hanna,Park Kunhee,Kim Chanhee,Choi Sojin,Sim JiWoo,Park Yoojin,Huh In Sil,Hong Gasil,Kim Mi Young,Song Jin Su,Lee Jihee,Kim Eun- 대한의학회 2021 Journal of Korean medical science Vol.36 No.50
In November 2021, 14 international travel-related severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.529 (omicron) variant of concern (VOC) patients were detected in South Korea. Epidemiologic investigation revealed community transmission of the omicron VOC. A total of 80 SARS-CoV-2 omicron VOC-positive patients were identified until December 10, 2021 and 66 of them reported no relation to the international travel. There may be more transmissions with this VOC in Korea than reported.
대용량 교통이력자료의 전처리를 위한 설계 및 응용프로그램 최적화
전세길(Segil Jeon),남궁성(Seong Namkoong),정형섭(Hyeongseop Jeong) 한국정보과학회 2009 한국정보과학회 학술발표논문집 Vol.36 No.1
한국도로공사에서는 고속도로에서 발생하는 고속도로 검지기 데이터, 돌발상황 데이터, 기상데이터, 문자메시지 데이터, 고속도로 TCS 데이터, Hi-pass 데이터 등 대용량 원시 데이터를 매일 데이터베이스에 축적하고 있다. 기존시스템에서 수집된 자료를 위한 자료처리 과정은 단순 SQL구문과 단일 CPU만을 활용해서 알고리즘 구현에 중심을 두고 구현하여 많은 시간이 소요되고 있으며, 특히, 선처리 작업과 결측보정 작업에 많은 시간이 소요되고 있다. 본 논문에서는 기본 자료처리와 품질관리 과정의 성능 향상을 위한 개선 방안을 제시하고, 이러한 개선방안을 적용한 적용 내용과 적용 후 효과에 대해서 기술한다.
Ahn, Jinsook,Lee, Dukwon,Jo, Inseong,Jeong, Hyeongseop,Hyun, Jae-Kyung,Woo, Jae-Sung,Choi, Sang-Ho,Ha, Nam-Chul Korean Society for Molecular and Cellular Biology 2020 Molecules and cells Vol.43 No.3
Cryo-electron microscopy (cryo-EM) is now the first choice to determine the high-resolution structures of huge protein complexes. Grids with two-dimensional arrays of holes covered with a carbon film are typically used in cryo-EM. Although semi-automatic plungers are available, notable trial-and-error is still required to obtain a suitable grid specimen. Herein, we introduce a new method to obtain thin ice specimens using real-time measurement of the liquid amounts in cryo-EM grids. The grids for cryo-EM strongly diffracted laser light, and the diffraction intensity of each spot was measurable in real-time. The measured diffraction patterns represented the states of the liquid in the holes due to the curvature of the liquid around them. Using the diffraction patterns, the optimal time point for freezing the grids for cryo-EM was obtained in real-time. This development will help researchers rapidly determine high-resolution protein structures using the limited resource of cryo-EM instrument access.
Development of New Preventive and Therapeutic Vaccines for Tuberculosis
Kwon, Bo-Eun,Ahn, Jae-Hee,Min, Seunghwan,Kim, Hyeongseop,Seo, Jungheun,Yeo, Sang-Gu,Ko, Hyun-Jeong 한국조명·전기설비학회 2018 한국조명·전기설비학회 학술대회논문집 Vol. No.
<P>Tuberculosis (TB) is a contagious disease that has been responsible for the death of one billion people in the last 200 years. Until now, the only vaccine approved for the prevention of TB is Bacillus Calmette-Guérin (BCG), which is prepared by attenuating <I>Mycobacterium bovis</I>. However, one of the limitations of BCG is that its preventive effect against pulmonary TB varies from person to person. Therefore, there arises a need for a new TB vaccine to replace or supplement BCG. In this review, we have summarized the findings of current clinical trials on preventive and therapeutic TB vaccine candidates. In addition, we have discussed a novel vaccination approach using the cell-based vaccine presenting early secretory antigenic target-6 (ESAT-6), which is a potent immunogenic antigen. The role of ESAT-6 in hosts has also been described.</P>