• Bulletin of the Korean Chemical Society
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• 제16권10호
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• pp.944-952
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• 1995

A generic force field approach has been applied to geometry optimization of penam and cephem crystals. The crystalline state energy and force evaluation with the universal force field (MMFF: Merck Molecular Force Field) results in good agreements with the crystallographic data. Bond lengths are usually correct to within 0.02 Å and bond angles usually to within 2.5°. The conformation of the β-lactam bicyclic rings in the crystal environment is also well reproduced. The results thus demonstrate the applicability of MMFF to modeling of newer molecular constructs in condensed phase.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1997년도 학술발표회
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• pp.13-13
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• 1997

Gaegurin 4 is an antimicrobial peptide found in the skin of a Korean frog, Rana rugosa, known for its "wound-healing" effect for years. This 37-residue basic peptide binds to cell membranes and forms ion channels like other antimicrobial peptides but does not exhibit hemolytic activity.(omitted)

• 한국산학기술학회논문지
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• 제19권7호
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• pp.95-104
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• 2018

이성질체의 형태는 수용액 상태에서 종종 안정성과 반응성 등의 기본상태 뿐만 아니라 사슬성장 및 접힘 과정으로 인하여 형태형성에 영향을 주기 때문에 올리고펩티드의 형태를 이해하는 것이 중요하다. 본 논문에서는 L-알라닌(LA), 글리신(G) 5량체 모델의 무수 및 수화물(수화율; h/1) 상태의 구조와 에너지를 4가지 형태이성질체 (베타-확장형;= t-/t+, $PP_{II}$형; g-/t+, $PP_{II}$-유사형; g-/g+ 및 알파-나선형; g-/g-)에 대하여 B3LYP/6-31G(d,p)를 이용하여 양자화학계산(QCC) 방법으로 분석하였다. 구조최적화는 밀도함수 이론(DFT)으로써 B3LYP를 사용하였으며, 기본설정(Basic set)으로는 6-31G(d,p)를 이용하였다. 이미노 양성자(NH)를 갖는 LA와 G에서 베타-확장형, $PP_{II}$-유사형, 알파-나선형의 3가지 형태가 얻어졌으며, 대부분 물 분자가 $PP_{II}$-유사형과 알파-나선형에서는 CO-HN 분자 내 수소결합 사이에 주로 삽입되었고, 베타-확장형은 CO기에 부착되었다. 또한, LA와 G에서 $PP_{II}$-유사형 형태이성질체가 무수 및 수화물 상태에서 가장 안정적이었으며, $PP_{II}$ 형태이성질체는 얻어지지 않았다. LA에 대한 결과는 알라닌 올리고펩티드의 안정적인 형태가 주로 $PP_{II}$라고 보고한 다른 연구의 실험적 및 이론적인 결과와는 상이했다. 올리고펩티드 형태이성질체의 생성패턴과 안정성이 CO-HN의 분자 내 수소결합의 존재 여부 또는 출발 아미노산 내 $NH_2$기의 존재 여부에 강한 영향을 받는 것을 알 수 있었다.

• BMB Reports
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• 제30권5호
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• pp.352-355
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• 1997

The surface adsorbed protein conformations onto the vaccine adjuvants were observed with a Raman spectroscopy by using the maximum adsorption conditions described previously. The adsorbed state Raman vibrational spectra and subsequent spectral analysis display no conformational changes for BSA or IgG relative to their native species in solution.

• Bulletin of the Korean Chemical Society
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• 제35권8호
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• pp.2494-2504
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• 2014

P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.

• Bulletin of the Korean Chemical Society
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• 제25권6호
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• pp.838-842
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• 2004

Amyloid peptide (A${\beta}$) is the major component of senile plaques found in the brain of patient of Alzheimer's disease. ${\beta}$-amyloid peptide (25-35) (A${\beta}$25-35) is biologically active fragment of A${\beta}$. The three-dimensional structure of A${\beta}$25-35 in aqueous solution with 50% (vol/vol) TFE determined by NMR spectroscopy previously adopts an ${\alpha}$-helical conformation from $Ala^{30}$ to $Met^{35}$. It has been proposed that A${\beta}$(25-35) exhibits pH- and concentration-dependent ${\alpha}-helix{\leftrightarrow}{\beta}$sheet transition. This conformational transition with concomitant peptide aggregation is a possible mechanism of plaque formation. Here, in order to gain more insight into the mechanism of ${\alpha}$-helix formation of A${\beta}$25-35 peptide by TFE, which particularly stabilizes ${\alpha}$-helical conformation, we studied the secondary-structural elements of A${\beta}$25-35 peptide by molecular dynamics simulations. Secondary structural elements determined from NMR spectroscopy in aqueous TFE solution are preserved during the MD simulation. TFE/water mixed solvent has reduced capacity for forming hydrogen bond to the peptide compared to pure water solvent. TFE allows A${\beta}$25-35 to form bifurcated hydrogen bonds to TFE as well as to residues in peptide itself. MD simulation in this study supports the notion that TFE can act as an ${\alpha}$-helical structure forming solvent.

• BMB Reports
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• 제32권6호
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• pp.529-534
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• 1999

Asymmetric PCR and single-strand conformation polymorphism (SSCP) methods were combined to analyze human leukocyte antigen (HLA)-DRB allele polymorphism. Asymmetric PCR amplification was applied to generate single-stranded DNA (ssDNA) using the nonradioactive oligonucleotide primers desinged for the polymorphic exon 2 region. The conformational differences of ssDNAs, depending on the allele type, were analyzed by nondenaturing polyacrylamide gel electrophoresis and visualized by ethidium bromide staining. The ssDNAs were clearly separated from double-stranded DNA without interference and obviously migrated depending on their allele type. This method was applied to the genomic DNA either from homozygous or from heterozygous cell lines containing the DR4 allele as template DNA using DR4-specific primers, and satisfying results were obtained. Compared to the standard PCR-SSCP method, this asymmetric PCR-SSCP method has advantages of increased speed, reproducibility, and convenience. Along with PCR-SSP or sequence-based typing, this method will be useful in routine typing of HLA-DRB allele.

• 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

• 한국식품과학회지
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• 제25권3호
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• pp.277-281
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• 1993

콜로이드 식품에서의 단백질의 구조적 안정성을 연구하기 위하여 7개의 BSA structural intermediates, succinylated ${\beta}-lactoglobulin$을 만든 후 CD, 이황화물 결합함량, hydrodynamic radius 등을 측정하여 그 구조적 특성을 규명했다. Refolding time이 길수록 BSA intermediates들은 native BSA 구조에 근접하는 것을 나타냈고 succinylation은 ${\beta}-lactoglobulin$의 순 음전하를 변화시켜 보다 aperiodic structure를 갖게하였다. Perchlorate 존재하 ${\beta}-casein$의 구조는 소수성 상호작용에 크게 영향 받는 것으로 나타났다.

• 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.