• Journal of Microbiology and Biotechnology
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• 제27권12호
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• pp.2241-2244
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• 2017

The structure of concanavalin A (ConA) has been studied intensively owing to its specific interactions with carbohydrates and its heterometal ($Ca^{2+}$ and $Mn^{2+}$) coordination. Most structures from X-ray crystallography have shown ConA as a dimer or tetramer, because the complex formation requires specific crystallization conditions. Here, we reported the monomeric structure of ConA with a resolution of $1.6{\AA}$, which revealed that metal coordination could trigger sugar-binding ability. The calcium coordination residue, Asn14, changed the orientation of carbohydrate-binding residues and biophysical details, including structural information, providing valuable clues for the development and application of detection kits using ConA.

• Bulletin of the Korean Chemical Society
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• 제25권7호
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• pp.977-982
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• 2004

The reaction of $cis-[Cr([14]-decane)(OH_2)_2]^+$ ([14]-decane = rac-5,5,7,12,12,14-hexamethyl-1,4,8,11-teraazacyclotetradecane) with auxiliary ligands {$L_a$ = benzoate(bz) or chlorobenzoate(cbz)} leads to a new compound $[Cr([14]-decane)(bz)_2]ClO_4$ or $[Cr([14]-decane)(cbz)_2]ClO_4$. These complexes have been characterized by a combination of elemental analysis, conductivity, IR and Vis spectroscopy, mass spectrometry, and X-ray crystallography. The crystal structure of $[Cr([14]-decane)(cbz)_2]^+$ was determined. The complex shows a distorted octahedral coordination environment with the macrocycle adopting a folded cis-V conformation. The angle $N_{axial}-Cr-N_{axial}$ deviates by $14.5^{\circ}$ from the ideal value of $180^{\circ}$for a perfect octahedron. The bond angle cis-O-Cr-O between the Cr(III) ion and the two carboxylate oxygen atoms of the monodentate p-chlorobenzoate ligands is close to 90$^{\circ}$. The FAB mass spectra of the $cis-[Cr([14]-decane)(La)_2]ClO_4$ display peaks due to the molecular ions $[Cr([14]-decane)(bz)_2-H]^\;,\;[Cr([14]-decane)(cbz)_2-2H]^$ at m/z 578, 646, respectively.

• Bulletin of the Korean Chemical Society
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• 제24권8호
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• pp.1150-1154
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• 2003

The reactions of [Ni(L)(H₂O)₂]Cl₂ (L = 2,5,9,12-tetramethyl-1,4,8,11-tetraazacyclotetradecane) with terephtalate (tp) and 2,5-pyridinedicarboxylate (pdc) generate one-dimensional nickel(II) complexes, [Ni(L)(H₂O)₂](tp) · ₄H₂O (1) and [Ni(L)(H₂O)₂](pdc)·₄H₂O (2). The structures have been characterized by X-ray crystallography, magnetic susceptibility and spectroscopy. The crystal structures of 1 and 2 show a distorted octahedral coordination geometry around the Ni(II) ion, with secondary amines of the macrocycle and two water molecules at the trans position. Complexes 1 and 2 display the one-dimensional hydrogen-bonded infinite chains. The magnetic behavior of all compounds exhibits weak interchain antiferromagnetic interactions with J values of -1.09(3) for 1 and -1.14(2) cm-1 for 2.

• 한국자기공명학회논문지
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• 제19권2호
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• pp.83-87
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• 2015

Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain ($Syn4^{cyto}$) in focal contacts, interacts with various cell adhesion adaptor proteins including $Syn4^{cyto}$ to control cell signaling. Syndesmos consists of 211 amino acids and it exists as a dimer (44kDa) in solution. Recently, we have determined the structure of syndesmos by x-ray crystallography, however, dynamics related to syndecan binding still remain elusive. In this report, we performed NMR experiments to acquire biochemical and structural information of syndesmos. Based on a series of three-dimensional triple resonance experiments on a $^{13}C/^{15}N/^2H$ labeled protein, NMR spectra were obtained with well dispersed and homogeneous NMR data. We present the sequence specific backbone assignment of syndesmos and assigned NMR data with combination structural information can be directly used for the studies on interaction with $Syn4^{cyto}$ and other binding molecules.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2003년도 제2차 연례학술대회 발표논문집
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• pp.268-274
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• 2003

Most currently known molecular structures were determined by X-ray crystallography or Nuclear Magnetic Resonance (NMR). These methods generate a large amount of structure data, even far small molecules, and consist mainly of three-dimensional atomic coordinates. These are useful for analyzing molecular structure, but structure elements at higher level are also needed for a complete understanding of structure, and especially for structure prediction. Computational approaches exist for identifying secondary structural elements in proteins from atomic coordinates. However, similar methods have not been developed for RNA due in part to the very small amount of structure data so far available, and extracting the structural elements of RNA requires substantial manual work. Since the number of three-dimensional RNA structures is increasing, a more systematic and automated method is needed. We have developed a set of algorithms for recognizing secondary and tertiary structural elements in RNA molecules and in the protein-RNA structures in protein data banks (PDB). The present work represents the first attempt at extracting RNA structure elements from atomic coordinates in structure databases. The regularities in the structure elements revealed by the algorithms should provide useful information for predicting the structure of RNA molecules bound to proteins.

• 한국음향학회지
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• 제11권2호
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• pp.5-14
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• 1992

천문학, 통신, X선 결정학, 공학등 여러 분야에서 부분정보, 즉 크기 스펙트럼이나 위상 스텍트럼 중 어느 하나만 가지고 원래신호를 근사적으로 복원하는 일은 매우 중요하고도 유용하다. 본 논문에서는 위상정보로부터 크기정보를 추정하여 원래의 저주파신호를 복원하는 반복 알고리즘을 시도하였다. 제안된 방법에서는 기존방법에서 지세도니 일정상수 함수를 초기 크기정보를 택하는 대신에 지수함수를 택하고, 여기에 적응 알고리즘을 부가적용하여 수렴속도는 물론 메모리 사용면에서도 상당한 개선을 이룰 수가 있었다.

• 대한화학회지
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• 제23권4호
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• pp.206-209
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• 1979

Empirical force-field method를 단결정 회절방법으로 구조가 연구된 여덟개의 1,6-anhydropyranose 분자구조$^{13{\sim}21}$에 적용하였다. 이론적 계산에서도 분자들간의 pyranose고리 conformation의 $^1C_4$와 $E_0$ 사이간의 차이는 실험치와 비슷하게 얻어졌다. Five-membered anhydro 고리의 분자들간의 작은 conformation 차이는 잘 예측되지 않았다. C-C결합 길이의 계산치는 실험치와 0.012${\AA}$내에서, C-O결합 길이는 0.027${\AA}$내에서, non-hydrogen atom의 결합각은 1.9$^{\circ}$이내에서 일치되고 있다

• Bulletin of the Korean Chemical Society
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• 제35권11호
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• pp.3319-3325
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• 2014

Eu(III)-doped $CeO_2$ nanorods were prepared by a co-precipitation method at room temperature, and their photoluminescence profiles were examined with different Eu(III)-doping concentrations and thermal annealing temperatures. Scanning electron microscopy, X-ray diffraction crystallography and UV-Vis absorption spectroscopy were employed to examine the morphology, crystal structure and photon absorption profiles of the nanorods, respectively. Additionally, their 2D and 3D-photoluminescence profile maps were obtained to fully understand the photoluminescence mechanism. We found that the magnetic dipole $^5D_0{\rightarrow}^7F_1$ and the electric dipole $^5D_0{\rightarrow}^7F_2$ transitions of Eu(III) were highly dependent on the doping concentration, annealing temperature and excitation wavelength, which was explained by the presence of different Eu(III)-doping sites (with and without an inversion center) in the $CeO_2$ host with a cubic crystal structure.

• 한국결정학회지
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• 제5권1호
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• pp.39-50
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• 1994

Hot Tungsten Filament법에 의해 실리콘(Si), 몰리브데늄(Mo), 타이타늄(Ti), 텅스텐(W) 기판 위에 다이아몬드 박막을 증착시시키고 SEM, X선 회절분석 및 Raman spectroscopy로 분석하였다. 증착시간에 따른 증착실험의 결과로부터 내열금속위에 증착한 다이아몬드박막의 경우에는 먼저 탄화물 층이 형성되고, 그 이후에 다이아몬드가 핵형성되어 성장함을 알 수 있었다. 내열금속에 증착한 다이아몬드 박막은 5기판 위에 증착한 것과 비교할 때, 핵이 많이 형성되었고 facet이 잘 발달된 입자가 적었다. 5기판 뿐만 아니라 내열금속 기판 위에 다이아몬드막을 증착시킬 경우, 다이아몬드의 Raman 피크는 천연 다이아몬드에 비해 높은 주파수쪽으로 이동되었다. 이와같은 Raman 피크의 이동은 다이아몬드와 기판 사이의 열충격보다는 완충층의 역활을 하는 탄화물과 다이아몬드 사이의 열충격을 고려할 때 효과적으로 설명이 가능하였다. 생성된 탄화물의 형태와 다이아몬드 사이에 열충격이 가장 큰 Mo기판의 경우, 다이아몬드 Rarirm 피크의 이동이 가장 크게 나타났으며 Ti, W, Si기판의 순서로 이동이 적게 관찰되었다.

• 한국결정학회지
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• 제10권1호
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• pp.1-8
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• 1999

Two conformational isomers of p-tert-butylcalix[4]arene hexanoate were prepared from the reaction of-p-tert-butylcalix[4]arene and hexanoly chloride in the presence of AlCl3 in CH2Cl2 and their structures were determined by NMR spectra and X-ray diffraction as a cone and a 1,3-alternate conformer, respectively. The crystal of cone conformer (C68H96O8·(CH3)2CO) is triclinic, P, a=15.066(1) , b=16.063(1) , c=16.365(1) , α=79.75(2)o, β=109.95(2)o, γ=80.32(0)o, V=3602.7(4) 3, Z=2. The intensity data were collected on Simens SMART diffractometer/CCD area detector. The structure was solved by direct method and refined by least-squares calculations to a final R value of 0.144 for 4638 observed reflections. The molecular conformation is distorted symmetric cone with the flattening A and D phenyl rings. The crystal of 1,3-alternate conformer (C68H96O8·2CHCl3) is orthorhombic, Pca21, a=34.586(5) , b=10.207(3) , c=20.394(4) , V=7199(3) 3, Z=4. The intensity data were collected on an Enraf-Noninus CAD-4 Diffractometer with a graphite monochromated Mo-K radiation. The structure was solved by direct method and refined by least-squares calculations to a final R value of 0.152 for 2241 observed reflections. The molecule has a pseudo mirror symmetric 1,3-alternate conformation.