• BMB Reports
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• 제29권4호
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• pp.380-385
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• 1996

Ovomucoid third domain is a serine proteinase inhibitor protein which consists of 56 amino acid residues. A fifty picosecond molecular dynamics (MD) simulation was carried out for ovomucoid third domain protein with 5 $\AA$ layer of water molecules. A comparison of main chain atoms in the MD averaged structure with the crystal structure showed that most of the backbone structures are maintained during the simulation. Investigation of the intramolecular hydrogen bondings indicated that most of the interactions between main chain atoms were conserved, whereas those between side chains were reorganized for the period of the simulation. Especially, the side chain interactions around the scissile bond of reactive site P1 (Met18) were found to be more extensive for the MD structures. During the simulation, hydrogen bonds were maintained between the side chains of Glu19 and Arg21 as well as those of Thr17 and Glu19. Extensive side chain interactions observed in the MD structures may shed light on the question of why protein proteinase inhibitors are strong inhibitors for proteinases rather than good substrates.

• 생약학회지
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• 제27권3호
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• pp.207-211
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• 1996

Cumambrin A has been isolated from the dried flowers of Chrysanthemum boreale Makino. The complete $^1H$ and $^{13}C$ NMR assignment of cumambrin A was achieved from two-dimensional $^1H$-$^1H$ COSY and $^{13}C$-$^1H$ COSY spectra with the aid of homonuclear and heteronuclear double resonance experiments. The its structure has been verified by single crystal X-ray diffraction.

• Bulletin of the Korean Chemical Society
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• 제18권4호
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• pp.415-424
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• 1997

Conformational flexibilities of the GlcNAc(β1,3)Gal(β)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at φ=80° and ψ=60° and N3 at φ=60° and ψ=-40°. We have presented adequate evidences to state that GlcNAc(β1,3)Gal(β)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental NOEs very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(β1,3)Gal(β)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.

• Journal of Microbiology and Biotechnology
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• 제20권10호
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• pp.1393-1396
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• 2010

The attachment of sugar to flavonoids enhances their solubility. Glycosylation is performed primarily by uridine diphosphate-dependent glycosyltransferases (UGTs). The UGT from Bacillus cereus, BcGT-1, transferred three glucose molecules into kaempferol. The structural analysis of BcGT-1 showed that its substrate binding site is wider than that of plant flavonoid monoglucosyltransferases. In order to create monoglucosyltransferase from BcGT-1, the error-prone polymerase chain reaction (PCR) was performed. We analyzed 150 clones. Among them, two mutants generated only kaempferol O-monoglucoside, albeit with reduced reactivity. Unexpectedly, the two mutants harbored mutations in the amino acids located outside of the active sites. Based on the modeled structure of BcGT-1, it was proposed that the local change in the secondary structure of BcGT-1 caused the alteration of triglucosyltransferase into monoglucosyltransferase.

• Macromolecular Research
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• 제12권2호
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• pp.178-188
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• 2004

We performed molecular dynamics (MD) simulations at 300 K on a series of poly(benzyl ether) (PBE) dendrimers having a different core functionalities. We used the rotational isomeric state Metropolis Monte Carlo (RMMC) method to construct the initial configuration in a periodic boundary cell (PBC) before the MD simulations were undertaken. To elucidate the effects that the structural features have on the chain dimension, the overall internal structure, and the morphology, we monitored the radii of gyration, R$\sub$g/ and the conformational changes during the simulations. The PBE dendrimers in a glassy state adopted less-extended structures when compared with the conformations obtained from the RMMC calculations. We found that R$\sub$g/ of the PBE dendrimer depends on the molecular weight, M, according to the relation, R$\sub$g/∼M$\^$0.22/. The radial distributions of the dendrimers were developed identically in the PBC, irrespective of the core functionality. A gradual decrease in radial density resulted from the fact that the terminal branch ends are distributed all over the molecule, except for the core region.

• 전기학회논문지
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• 제59권12호
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• pp.2245-2249
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• 2010

The physical properties of the LB films with merocyanine dyes have been published and attract attention due to the possibility of molecular structure control. The evaluation of the thin films was focused for the purpose of molecular structure control. The molecular structure in the case of the thin films with dyes can be examine by optical absorption spectra measurements. In the result measured by optical absorption spectra, the $[DX]_{1-x}[DO]_x$ LB films shows a large in-plane anisotropy and the transition dipole moment of red-shifted band is preferentially oriented perpendicular to the dipping direction of the film, while that of the blue-shifted band prefers the dipping direction. The spectrum for $0_{\circ}$, $90_{\circ}$-polarized light coincides with the spectrum for non-polarized light and also with the spectrum was observed in the LB film deposited using a fresh solution. These results show that the aging process does not cause a structural change in chromophore but a change in the degree of molecular orientation. In the results, study of the merocyanine dyes LB films using optical absorption spectra would an interesting problem of absorbance peak shifts and mixed components.

• 한국잠사곤충학회지
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• 제39권1호
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• pp.73-78
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• 1997

분자량 약 7000의 Fcp는 효소분해역반응을 이용하는 것에 의해 분자량 약 17000과 약 24000까지 고분자량화된 PIFcp가 얻어졌다. 또, 효소분해의 역반응에 의해 고분자량화되는 것은 일부의 Fcp이며 Silk II형결정으로부터 Silk I형결정으로 전이하는 것은 대부분의 Fcp에서 나타났다. 이 PIFcp는 X선회절과 시차열분석(DTA)의 결과로부터 어느정도 안정한 Silk I형의 결정구조를 가지는 것이 확인되었다.

• BMB Reports
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• 제33권3호
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• pp.268-275
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• 2000

In contrast to the pyrimidine (6-4)pyrimidone photoproduct [(6-4) adduct], its Dewar valence isomer (Dewar product) is low mutagenic and produces a broad range of mutations with a 42 % replicating error frequency. In order to determine the origin of the mutagenic property of the Dewar product, we used experimental NMR restraints and molecular dynamics to determine the solution structure of a Dewar·lesion DNA decamer duplex, which contains a mismatched base pair between the 3'-T residue and an opposed G residue. The 3'-T of the Dewar lesion forms stable hydrogen bonds with the opposite G residue. The helical bending and unwinding angles of the DW/GA duplex, however, are much higher than those of the DW/AA duplex. The stable hydrogen bonding of the G 15 residue does not increase the thermal stability of the overall helix. It also does not restore the distorted backbone conformation of the DNA helix that is caused by the forming of a Dewar lesion. These structural features implicate that no thermal stability, or conformational benefits of G over A opposite the 3'-T of the Dewar lesion, facilitate the preferential incorporation of an A. This is in accordance with the A rule during translesion replication and leads to the low frequent $3'-T{\rightarrow}C$ mutation at this site.

• Bulletin of the Korean Chemical Society
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• 제32권2호
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• pp.673-680
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• 2011

The compound 3-(2-Mercaptopyridine)phthalonitrile has been synthesized and characterized by IR, UV-vis, and X-ray single-crystal determination. The molecular geometry from X-ray determination of the title compound in the ground state has been compared using the Hartree-Fock (HF) and density functional theory (DFT) with the 6-31G(d) basis set. The calculated results show that the DFT and HF can well reproduce the structure of the title compound. The energetic behavior of the title compound in solvent media was examined using the B3LYP method with the 6-31G(d) basis set by applying the Onsager and polarizable continuum model. Using the TD-DFT and TD-HF methods, electronic absorption spectra of the title compound have been predicted and good agreement with the TD-DFT method and the experimental determination was found. The predicted nonlinear optical properties of the title compound are much greater than those of urea. Besides, molecular electrostatic potential of the title compound were investigated by theoretical calculations. The thermodynamic properties of the compound at different temperatures have been calculated and corresponding relations between the properties and temperature have also been obtained.

• 대한의용생체공학회:의공학회지
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• 제43권4호
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• pp.230-240
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• 2022

Drug regeneration technology is an efficient strategy than the existing new drug development process, which requires large costs and time by using drugs that have already been proven safe. In this study, we recognize the importance of the new drug regeneration aspect of new drug development and research in predicting functional similarities through the basic molecular structure that forms drugs. We test four string-based algorithms by using SMILES data and searching for their similarities. And by using the ATC codes, pair them with functional similarities, which we compare and validate to select the optimal model. We confirmed that the higher the molecular structure similarity, the higher the ATC code matching rate. We suggest the possibility of additional potency of random drugs, which can be predicted through data that give information on drugs with high molecular similarities. This model has the advantage of being a great combination with additional data, so we look forward to using this model in future research.