• 대한화학회지
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• 제47권2호
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• pp.104-108
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• 2003

$[Cu(L)]Cl_2{\cdot}2H_2O(L=3,14-dimethyl-2,6,13,17-tetraazatricyclo[14,4,0^{1.18},0^{7.12}]docosane)$과 2,5-pyridinedicarboxylate(pdc)의 반응으로부터 $[Cu(L)(H_2O)](pdc){\cdot}6H_2O(1)$가 합성되었다. 화합물 1의 구조가 X-ray 회절법 및 분광학적 방법으로 규명되었다. 중심 copper 원자는 거대고리 리간드로부터 4개의 이차 아민과 축방향 위치의 물분자로 결합된 약간 일그러진 사각뿔 구조를 갖는다. 또한 분자간 수소결합은 삼차원의 분자구조를 형성한다.

• 생명과학회지
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• 제26권3호
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• pp.353-358
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• 2016

Thiolase는 두 분자의 acetyl-CoA를 중합하여 acetoacetyl-CoA를 생산하는 효소이다. 우리는 Clostridium butyricum 유래 thiolase (CbTHL)를 대장균에서 발현하고, 대량으로 정제하여 결정화에 성공하였다. 성장된 결정을 이용하여 엑스선회절 데이터를 획득하였으며, 3차원 입체구조를 2.0 Å으로 규명하였다. 전체적인 구조는 C. acetobutylicum 유래 thiolase (CaTHL)와 같은 type II biosynthetic thiolase와 매우 유사하다는 것을 확인하였다. CbTHL 구조를 CaTHL/CoA 복합체구조와 겹치기를 함으로써 활성화 잔기와 기질결합에 관여하는 잔기를 밝혀낼 수 있었다. CbTHL의 활성화부위는 3개의 잘 보존된 잔기인 Cys88, His349, Cys379로 구성되어 있으며, 이들 잔기는 각각, 공유결합친핵체, 일반염기, 2번째 친핵체의 역할을 하는 것으로 보인다. CbTHL에서 기질결합은, β-mercaptoethyamine과 pantothenic acid 부위는 타 thiolase와 매우 유사한 방법으로 안정화 되지만, ADP 부분은 타 thiolase와는 달리 매우 특이적인 잔기들을 사용한다. CbTHL 구조에서 가장 특징적인 것은 본 단백질이 가역적 이황화결합을 매개로 산화환원스위치를 통하여 그 활성을 조절한다는 것이다.

• 대한화학회지
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• 제18권5호
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• pp.329-340
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• 1974

X-선 회절법을 이용하여 sulfadiazine, $C_{10}H_{10}N_4O_2S$, 의 결정 및 분자 구조를 규명하였다. Acetone 과 ethanol의 혼합용액으로 부터 얻은 결정은 일사축계에 속하며, 단위세포에는 4분자가 있고, 공간군은 P21/c이다. 단위세포 상수는 $a=13.71{\pm}0.04,\;b=5.84{\pm}0.03,\;c=15.11{\pm}0.05{\AA},\;{\beta}=115.0{\pm}0.3^{\circ}$이다. 결정구조는 3차원적인 와이센버그사진으로 부터 얻어진 실험치를 이용하여 패터슨합성과 프리에합성을 하고 이를 해석하여 밝혀냈다. 수소원자를 제외한 원자들의 좌표치는 최소자승법으로 정밀화 하였으며, 최종 R값은 관측된 1517개의 독립반사에 대하여 0.15이다. 벤젠고리와 피리미딘고리의 두 평면이 이루는 각은 $76^{\circ}$이고, S-N(1)결합을 중심으로 한 N(1)-C(1) 결합과 S-C(5)결합이 이루는 conformational angle은 $77^{\circ}$로서 gauche형을 하고 있다. 이미노기의 질소원자, N(1)은 대칭중심에 의하여 옮겨지는 다른 분자의 피리미딘고리의 질소원자, N(3)와 $N-H{\cdots}N$형의 수소결합을 이루고 있으며, 아미노기의 질소원자, N(4)는 b축의 거리만큼 떨어져 있는 다른분자의 산소원자, O(1) 및 O(2)와 두개의 $N-H{\cdots}O$형 수소결합을 이루고 있다. 이들 수소결합의 2차원적 그물은 (100)면에 평행한 무한한 분자층을 형성하며 인접분자층 사이에는 van der Waals의 힘에 의하여 결합되어 있다

• 대한화학회지
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• 제37권5호
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• pp.473-476
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• 1993

디프로파질디페니메탄$(C_{19}H_{16})$는 단사정계의 공간군 $C2/_c$에$ 속하며 a = 11304(3), b = 20.799(5), c = $6.622(2)\AA$, $\beta$ = $112.8(3)^{\circ}$, Z = 4, V = $1435.3\AA^3,\;F(000)\;=\;520,\;D_c\;=\;1.14g{\cdot}cm^{-3}$ and $\mu$ = 0.32 cm$^{-1}$이며 I $\geq$ -1.0 $\sigma(I)$인 1328개의 회절반점에 대한 최종 R값은 0.055였다. 직접법에 의하여 구조를 풀었으며 수소를 제외한 모든 원자는 E-map에서 찾았다. 한 분자는 단위세포내에 있는 결정학적 2-회전축과 일치하는 대칭축을 분자내의 메탄의 탄소원자에 가짐으로서 $C_2$ 점군에 속한다. 직선인 프로파질 부분은 벤젠기의 분자평면과 거의 수직$(94.2^{\circ})$을 이루고 있으며, 메탄의 탄소원자의 내부각은 $108.1(1)^{\circ}으로$ 벤젠기와는 $1.530(2)\AA$, 프로파질기와는 $1.560(2)\AA$의 길이로 결합하고 있다. 분자사이의 가장 짧은 접촉은 C(9)과 C(9)(-x,y, -1/2-z)사이의 $3.538(2)\AA$ 이다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2005년도 BIOINFO 2005
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• pp.325-330
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• 2005

We are generally interested in the analysis, detection and prediction of structural motifs in proteins, in order to infer compatibility of amino acid sequence to structure in proteins of known three-dimensional structure available in the Protein Data Bank. In this context, we are analyzing some of the well-characterized structural motifs in proteins. We have analyzed simple structural motifs, such as, ${\beta}$-turns and ${\gamma}$-turns by evaluating the statistically significant type-dependent amino acid positional preferences in enlarged representative protein datasets and revised the amino acid preferences. In doing so, we identified a number of ‘unexpected’ isolated ${\beta}$-turns with a proline amino acid residue at the (i+2) position. We extended our study to the identification of multiple turns, continuous turns and to peptides that correspond to the combinations of individual ${\beta}$ and ${\gamma}$-turns in proteins and examined the hydrogen-bond interactions likely to stabilize these peptides. This led us to develop a database of structural motifs in proteins (DSMP) that would primarily allow us to make queries based on the various fields in the database for some well-characterized structural motifs, such as, helices, ${\beta}$-strands, turns, ${\beta}$-hairpins, ${\beta}$-${\alpha}$-${\beta}$, ${\psi}$-loops, ${\beta}$-sheets, disulphide bridges. We have recently implemented this information for all entries in the current PDB in a relational database called ODSMP using Oracle9i that is easy to update and maintain and added few additional structural motifs. We have also developed another relational database corresponding to amino acid sequences and their associated secondary structure for representative proteins in the PDB called PSSARD. This database allows flexible queries to be made on the compatibility of amino acid sequences in the PDB to ‘user-defined’ super-secondary structure conformation and vice-versa. Currently, we have extended this database to include nearly 23,000 protein crystal structures available in the PDB. Further, we have analyzed the ‘structural plasticity’ associated with the ${\beta}$-propeller structural motif We have developed a method to automatically detect ${\beta}$-propellers from the PDB codes. We evaluated the accuracy and consistency of predicting ${\beta}$ and ${\gamma}$-turns in proteins using the residue-coupled model. I will discuss results of our work and describe databases and software applications that have been developed.

• 생약학회지
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• 제17권2호
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• pp.153-160
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• 1986

We have isolated two new metabolites of territrem, designated as territrem $A'\;(TRA';\;C_{28}H_{30}O_{10})$ and $B'\;(TRB';\; C_{29}H_{34}O_{10})$ from chloroform extract of rice culture of Aspergillus terreus 23-1, using the same isolation procedure as that for territrem A, B and C(TRA, TRB, TRC). The present isolation procedure gave about 5 mg of TRA' and 10 mg of TRB' from 4 kg of rice culture per batch. Analysis of the high resolution mass spectrum showed that the molecular composition of TRA' and TRB' are $C_{28}H_{30}O_{10}$ and $C_{29}H_{34}O_{10}$ respectively, Some results of physicochemical properties were presented in this paper. Single crystal X-ray diffractometry of TRB' showed that the three dimensional structure of TRB' has not changed significantly from that of $TRB\;(C_{29}H_{34}O_9)$, except for the insertion of one oxygen atom into TRB to make additional pyran in the E-ring. It is also suggested that the aromatic moiety of TRA' is similar to that of $TRA\;(C_{28}H_{30}O_9)$ and the rest non-aromatic portions resemble to those of TRB'. The tremorgenic activity, lethality and inhibitory effect on acetylcholine esterase of TRA' and TRB' are greatly reduced comparing to that of TRA and TRB.

• Tribology and Lubricants
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• 제11권5호
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• pp.128-135
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• 1995

Atomic force microscopy/friction force microscopy (AFM/FFM) techniques are increasingly used for tribological studies of engineering surfaces at scales, ranging from atomic and molecular to microscales. These techniques have been used to study surface roughness, adhesion, friction, scratching/wear, indentation, detection of material transfer, and boundary lubrication and for nanofabrication/nanomachining purposes. Micro/nanotribological studies of single-crystal silicon, natural diamond, magnetic media (magnetic tapes and disks) and magnetic heads have been conducted. Commonly measured roughness parameters are found to be scale dependent, requiring the need of scale-independent fractal parameters to characterize surface roughness. Measurements of atomic-scale friction of a freshly-cleaved highly-oriented pyrolytic graphite exhibited the same periodicity as that of corresponding topography. However, the peaks in friction and those in corresponding topography were displaced relative to each other. Variations in atomic-scale friction and the observed displacement has been explained by the variations in interatomic forces in the normal and lateral directions. Local variation in microscale friction is found to correspond to the local slope suggesting that a ratchet mechanism is responsible for this variation. Directionality in the friction is observed on both micro- and macro scales which results from the surface preparation and anisotropy in surface roughness. Microscale friction is generally found to be smaller than the macrofriction as there is less ploughing contribution in microscale measurements. Microscale friction is load dependent and friction values increase with an increase in the normal load approaching to the macrofriction at contact stresses higher than the hardness of the softer material. Wear rate for single-crystal silicon is approximately constant for various loads and test durations. However, for magnetic disks with a multilayered thin-film structure, the wear of the diamond like carbon overcoat is catastrophic. Breakdown of thin films can be detected with AFM. Evolution of the wear has also been studied using AFM. Wear is found to be initiated at nono scratches. AFM has been modified to obtain load-displacement curves and for nanoindentation hardness measurements with depth of indentation as low as 1 mm. Scratching and indentation on nanoscales are the powerful ways to screen for adhesion and resistance to deformation of ultrathin fdms. Detection of material transfer on a nanoscale is possible with AFM. Boundary lubrication studies and measurement of lubricant-film thichness with a lateral resolution on a nanoscale have been conducted using AFM. Self-assembled monolyers and chemically-bonded lubricant films with a mobile fraction are superior in wear resistance. Finally, AFM has also shown to be useful for nanofabrication/nanomachining. Friction and wear on micro-and nanoscales have been found to be generally smaller compared to that at macroscales. Therefore, micro/nanotribological studies may help def'me the regimes for ultra-low friction and near zero wear.

• Molecules and Cells
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• 제37권2호
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• pp.100-108
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• 2014

Salmonella enterica serovar Typhimurium (S. Typhimurium) is an intracellular pathogen that has evolved to survive in the phagosome of macrophages. The periplasmic copper-binding protein CueP was initially known to confer copper resistance to S. Typhimurium. Crystal structure and biochemical studies on CueP revealed a putative copper binding site surrounded by the conserved cysteine and histidine residues. A recent study reported that CueP supplies copper ions to periplasmic Cu,Zn-superoxide dismutase (SodCII) at a low copper concentration and thus enables the sustained SodCII activity in the periplasm. In this study, we investigated the role of CueP in copper resistance at a high copper concentration. We observed that the survival of a cueP-deleted strain of Salmonella in macrophage phagosome was significantly reduced. Subsequent biochemical experiments revealed that CueP specifically mediates the reduction of copper ion using electrons released during the formation of the disulfide bond. We observed that the copper ion-mediated Fenton reaction in the presence of hydrogen peroxide was blocked by CueP. This study provides insight into how CueP confers copper resistance to S. Typhimurium in copper-rich environments such as the phagosome of macrophages.

• Bulletin of the Korean Chemical Society
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• 제29권3호
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• pp.546-550
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• 2008

The title compound of nicotinato lead(II) complex [Pb$(C_5H_4NCOO)_2$] has been optimized at B3LYP/LANL2DZ and HF/LANL2DZ levels of theory. The calculated results show that the lead(II) ion adopts 2- coordinate geometry, which is the same as its crystal structure and different from the 4-coordinate geometry of isonicotinato lead(II) complex. Atomic charge distributions indicate that during forming the title compound, each nicotinic acid ion transfers their negative charges to central lead(II) ion. The electronic spectra calculated by B3LYP/LANL2DZ level show that there exist two absorption bands, which have some red shifts compared with those of isonicotinato lead(II) complex and the electronic transitions are mainly derived from intraligand $\pi$ -$\pi$ transition and ligand-to-metal charge transfer (LMCT) transition. CIS-HF method is not suitable for the system studied here. The thermodynamic properties of the title compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained. The second order optical nonlinearity was calculated, and the molecular hyperpolarizability was $1.147754{\times}10^{-30}$ esu.

• Applied Microscopy
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• 제47권4호
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• pp.223-225
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• 2017

Cryo-electron microscopy (cryo-EM) is arguably the most powerful tool used in structural biology. It is an important analytical technique that is used for gaining insight into the functional and molecular mechanisms of biomolecules involved in several physiological processes. Cryo-EM can be separated into the following three groups according to the analytical purposes and the features of the biological samples: cryo-electron tomography (cryo-ET), cryo-single-particle reconstruction, and cryo-electron crystallography. Cryo-tomography is a unique EM technique that is used to study intact biomolecular complexes within their original environments; it can provide mechanistic insights that are challenging for other EM-methods. However, the resolution of reconstructed three-dimensional (3D) models generated by cryo-ET is relatively low, while single-particle reconstruction can reproduce biomolecular structures having near-atomic resolution without the need for crystallization unless the samples are large (>200 kDa) and highly symmetrical. Cryo-electron crystallography is subdivided into the following two categories according to the types of samples: one category that deals with two-dimensional (2D) crystalline arrays and the other category that uses 3D crystals. These two categories of electron-crystallographic techniques use different diffraction data obtained from still diffraction and continuous-rotation diffraction. In this paper, we review crystal-based cryo-EM techniques and focus on the recently developed 3D electron-crystallographic technique called microcrystal-electron diffraction.