• Proceedings of the Korean Society of Applied Pharmacology
• /
• 1994.04a
• /
• pp.264-264
• /
• 1994

본 연구는 보리 씨앗에 존재하는 리보솜 불활성화 단백질(RIP) 의 삼차원 구조를 X-선 결정학 방법을 이용하여 밝히고, 그 결과로 분자 차원에서 기능을 이해하는 것을 목적으로 하고있다. 리보솜불활성화 단백질은 N-glucosidase 반응을 통하여 단백질 합성을 저해하기 때문에 세포를 죽일 수 있다. 따라서 암세포만을 특정적으로 인식하는 다른 물질과 결합시키면 암세포만을 특정적으로 죽일 수 있는 면역독소로 이용될 수 있다. 또, 최근에는 항바이러스의 작용을 함이 밝혀져 많은 연구가 진행되고 있다. 단백질 삼차원 구조 규명을 위해서는 여러가지 단계가 있는데 지난 번 과제까지 성공적으로 리보솜 불활성화 단백질의 대량 분리와 X-선 결정학의 필수 요건 좋은 결정을 길렀고, 이번에는 구조 해석을 위해 꼭 해결해야하는 위상문제를 극복하기 위하여 여러가지 실험을 진행하였다. 우선, 비슷한 구조인 피마자씨에서 분리한 Ricin의 A-체인과 미국자리공 잎에서 분리한 Pokeweed antiviral protein의 삼차원 분자좌표를 이용하여 분자치환법으로 위상문제 해결을 시도하였다. Ricin 의 A-체인을 이용하였을 때 분자의 위치가 정확히 찾아지지 않았고, 다른 모델인 Pokeweed antiviral protein을 이용하여 X-PLOR 프로그램내의 PC refinement법으로 분자치환을 시도하였다. Euler각도로 (187.37, 22.5, 311.94) 의 회전해 (Rotation solution) 를 가지고 있었고, 이러한 해에 맞추어서 분자를 돌려둔 후, 이동해 (Transaltion solution) 을 구해서 그 위치 (Orientation) 로 분자를 이동하였다. 이 때 R값은 53.9 % (8.0 - 3.5$\AA$) 이였고, 부분좌표 (Fractional coorcdinate) 에서는 0.102, 0.000, 0.261 이고, 직교좌표 (Orthogonal coorclinate) 에서는 4.616, 0.000, 13.167 의 결과를 얻었다.

• Polymer Science and Technology
• /
• v.18 no.4
• /
• pp.338-345
• /
• 2007

• Proceeding of EDISON Challenge
• /
• 2015.03a
• /
• pp.177-183
• /
• 2015

$\text\tiny{D}$-Psicose 3-Epimerase (DPE)는 $\text\tiny{D}$-Fructose의 C3 Epimerase로써 $\text\tiny{D}$-Fructose를 $\text\tiny{D}$-Psicose로 전환해 주는 효소이다. $\text\tiny{D}$-Psicose는 설탕 대신 사용하는 감미료로 몸에 흡수되지 않아 칼로리가 없다고 알려져 있고 자연에서는 오로지 DPE에 의해서만 생산되는 희귀당이다. 이에 따라 DPE를 통한 $\text\tiny{D}$-Psicose 대량생산의 필요성이 대두되고 있는 등 이 분야에 대한 관심이 뜨거운 실정이다. 본 연구팀은 이 당과 관련된 작용기작 연구를 수행하기 위하여 아직 단백질 3차구조가 알려지지 않은 Clostridium hylemonae DPE (chDPE) 단백질의 3차 구조예측 연구를 수행 하였다. 우리는 HHsearch를 이용하여 agrobacterium tumefaciens의 DPE 외 2개의 구조를 호몰로지 모델링 연구를 위한 주형으로 선정하였다. 다음으로 PROMALS3D를 이용하여 주형들과 chDPE의 multiple sequence alignment를 수행하였고 이를 바탕으로 3차구조 예측 연구를 수행 하였다. 예측된 구조를 검증하기 위하여 ProSA와 Ramachandran plot분석을 이용하였고 Ramachandran plot에서 단백질의 94.8%에 해당하는 잔기들이 favoured regions에 위치하였다. ProSA에서는 Z-score값이 -9.3으로 X-선 결정학이나 핵자기 공명법으로 밝혀진 구조들에서 관측되는 범위 내에 위치하였다. 나아가 예측된 구조에 $\text\tiny{D}$-Psicose와 $\text\tiny{D}$-Fructose의 결합모드를 규명하기 위하여 도킹을 시도하였다. 이번 연구를 통하여 chDPE의 구조를 예측 할 수 있었고 이를 바탕으로 이 단백질의 기능을 이해하는데 도움을 줄 것으로 기대된다.

• Korean Journal of Crystallography
• /
• v.5 no.1
• /
• pp.20-23
• /
• 1994

Specific binding to the oric region of E, coli chromsome by IciA protein inhibits initiation of chrorrnsomal replication in vitro by blocking the opening of this region effected by the initiator DnaA protein. The IciA protein has been suggested play a critical role in a key stage of the cell cycle. In order to study the structure-function relationship of IciA protein, we are determining the three-dimensional structure of IciA Votein by X-ray crystallography, As a first step toward its structure detumination E. coli IciA protein has been crystallized using sodium formate as a precipitant.

• Journal of Radiation Protection and Research
• /
• v.32 no.4
• /
• pp.140-156
• /
• 2007

This research was performed to investigate the morphological changes of folliculus ovary according to the radiation dose. The whole body radiation of 200 cGy, 400 cGy, and 600 cGy was given to the each groups of 5 months-aged female mouse. Various staining methods used in this research are: Hematosylin-Eosin method, and immunohistochemistrical methods using BrdU, TUNEL, p53, p21, PCNA and inhibin. The minute structural changes of folliculus ovary were observed through an electron microscope with high magnification. The morphological changes of growing folliculus ovary became distinct as the dose of X-rays increased. Especially, the nuclei of granular cells showed manifest condensation and the changes of the transparent zone were distinct. As a result of histochemical reaction according to Masson's trichrome method and reticular fiber method, the changed granular cells, the deformed basilar membrane of folliculus ovary and the abnormal arrangement of the reticular fiber were observed. In the reaction of BrdU, the granular cells of normal folliculus ovary with positive reaction rapidly decreased according to the increase of the dose of X-rays. In TUNEL study, granular cells showing positive reaction in retarded folliculus ovary were expanded to growing folliculus ovary and primordial folliculus ovary according to the increase of the dose of X-rays. In case of 600 cGy of X-rays, oocyte underwent apoptosis. In p53 immunohistochemistry, p53 manifested to be stronger as the dose of X-rays increased. p53 reactivity was manifested distinctively in all cells comprising folliculus ovary following irradiation of 600 cGy. p21 was manifested in granular cells of folliculus ovary and showed very positive reaction around follicular antrum according to the increase of the dose of X-rays. In PCNA, positive reaction was manifested in growing folliculus ovary, mature folliculus ovary and primordial folliculus ovary, but the extent of the reaction decreased as the dose of the X-rays decreased. The finding that the reaction of granular cells around folliculus ovary was stronger than that near follicular membrane indicates that what was damaged first by X-ray was the cells near folliculus ovary and follicular antrum. The reactivity of $inhibin-{\alpha}$ showed difference according to the growing stage of folliculus ovary: $inhibin-{\alpha}$ showed the most strong reaction in mature folliculus ovary with follicular antrum. There was strong reaction in granular cells around follicular membrane but $inhibin-{\alpha}$ did not occur at all in theca cells comprising follicular membrane. $Inhibin-{\alpha}$ in ovary tissue exposed to 400 cGy of X-rays was manifested more strongly than in ovary tissue exposed to 600 cGy of X-rays, which was related to the phenomenon that granular cells of mature folliculus ovary underwent necrosis or apoptosis increasingly due to X-rays. In an electron microscope with high magnification, nuclei and protoplasm of granular cells in growing folliculus ovary abruptly underwent minute structural changes according to the increase of dose of X-rays. Cell residue, by-product of cell decease, neutrophil and macrophage around follicular antrum were observed. The minute structural changes in granular cells showed typical characteristics of apoptosis: the increase of electronic density due to nuclear condensation, fragmentation of nuclei and atrophy of protoplasm. Necrosis of cells was identified but it was not so remarkable. Macrophage with apoptotic bodies was scattered. Proportional to the radiation dose, we found that the generation of heterogeneous substance of normal ovary texture's follicular fluid, the emergence of dyeing characteristic in the basilar membrane of folicle, the generation of apoptosis, and the transformation of macrophages, etc. From this results, we can infer the possible radiation hazard on the ovary of cervix cancer patient with radiation therapy.

• Journal of Life Science
• /
• v.14 no.5
• /
• pp.752-760
• /
• 2004

The function of the [4Fe-4S] cluster containing iron (Fe-) protein in nitrogenase catalysis is to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. The MgADP-bound (or off) conformational state of the nitrogenase Fe protein structure described reveals mechanisms for long-range communication from the nucleotide-binding sites to control affinity of association with the MoFe protein component. Two pathways, termed switches I and II, appear to be integral to this nucleotide signal transduction mechanism. In addition, the structure of the MgADP bound Fe protein provides the basis for the changes in the biophysical properties of the [4Fe-4S] observed when Fe protein binds nucleotides. The structures of the nitrogenase Fe protein with defined amino acid substitutions in the nucleotide dependent signal transduction pathways of the Switch I and Switch II have been determined by X-ray diffraction methods. These two pathways have been also implicated by site directed mutagenesis studies, structural analysis and analogies to other proteins that utilize similar nucleotide dependent signal transduction pathways. We have examined the validity of the assignment of these pathways in linking the signals generated by MgATP binding and hydrolysis to macromolecular complex formation and intermolecular electron transfer. The results provide a structural basis for the observed biophysical and biochemical properties of the Fe protein variants and interactions within the nitrogenase Fe protein-MoFe protein complex.

• Polymer Science and Technology
• /
• v.24 no.6
• /
• pp.590-595
• /
• 2013

• Journal of the Korean Vacuum Society
• /
• v.14 no.3
• /
• pp.138-142
• /
• 2005

We tested performance of the 4C1 beamline for analyzing structures of proteins in solution using small angle X-ray scattering (SAXS) at the Pohang Light Source(PLS). Structurally well-known proteins such as lysozyme and $Bcl-XL(\vartriangle TM/\vartriangle loop)$ were used for the study. Low resolution solution structures of lysozyme and $Bcl-XL(\vartriangle TM/\vartriangle loop)$ were obtained at a resolution of at least i.2 nm, and the structures were basically same as those calculated from the crystal structures of the proteins. We also used $Bcl-XL(\vartriangle TM/\vartriangle loop)$ with a long flexible loop attached [$Bcl-XL(\vartriangleTM))$] and obtained significantly different data from $Bcl-XL(\vartriangle TM/\vartriangle loop)$, although the electron density map of the loop is known to be invisible from the crystal structure of $Bcl-XL(\vartriangleTM))$. We confirm that SAXS experiment is a powerful tool for the structural study of proteins in solution and the 4Cl beamline at the PLS is well-equipped and suitable for the protein solution SAXS experiment.

• Applied Biological Chemistry
• /
• v.48 no.3
• /
• pp.189-200
• /
• 2005

Biological nitrogen fixation is an important process for academic and industrial aspects. This review will briefly compare industrial and biological nitrogen fixation and cover the characteristics of biological nitrogen fixation studied in Azotobacter vinelandii. Various organisms can carry out biological nitrogen fixation and recently the researches on the reaction mechanism were concentrated on the free-living microorganism, A. vinelandii. Nitrogen fixation, which transforms atmospheric $N_2$ into ammonia, is chemically a reduction reaction requiring electron donation. Nitrogenase, the biological nitrgen fixer, accepts electrons from biological electron donors, and transfers them to the active site, FeMo-cofactor, through $Fe_4S_4$ cluster in Fe protein and P-cluster in MoFe protein. The electron transport and the proton transport are very important processes in the nitrogenase catalysis to understand its reaction mechanism, and the interactions between FeMo-cofactor and nitrogen molecule are at the center of biological nitrogen fixation mechanism. Spectroscopic studies including protein X-ray crystallography, EPR and $M{\ddot{o}}ssbauer$, biochemical approaches including substrate and inhibitor interactions as well as site-directed mutation study, and chemical approach to synthesize the FeMo-cofactor model compounds were used for biological nitrogen fixation study. Recent research results from these area were presented, and finally, a new nitrogenase reaction mechanism will be proposed based on the various research results.

• Applied Microscopy
• /
• v.38 no.3
• /
• pp.235-243
• /
• 2008

A compact soft x-ray microscope operated in the 'water window' wavelength region ($2.3{\sim}4.4nm$) was used for observing cells with nano-scale spatial resolution. To obtain cellular imaging captured with colloidal gold nanoparticles using a compact soft x-ray microscope. The colloidal gold nanoparticles showed higher contrast and lower transmission more than 7 times than that of cellular protein on the soft x-ray wavelength region. The structure and thickness of the cell membrane of the Coscinodiscus oculoides (diatome) and red blood cells were seen clearly. The gold nanoparticles within the HT1080 and MDA-MB 231 cells were seen clearly on the soft x-ray microscopy. The gold nanoparticles were aggregated within vesicles by endocytosis.