• Genomics & Informatics
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• v.11 no.4
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• pp.282-288
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• 2013

The molecular vibration-activity relationship in the receptor-ligand interaction of adenosine receptors was investigated by structure similarity, molecular vibration, and hierarchical clustering in a dataset of 46 ligands of adenosine receptors. The resulting dendrogram was compared with those of another kind of fingerprint or descriptor. The dendrogram result produced by corralled intensity of molecular vibrational frequency outperformed four other analyses in the current study of adenosine receptor agonism and antagonism. The tree that was produced by clustering analysis of molecular vibration patterns showed its potential for the functional classification of adenosine receptor ligands.

• Environmental Mutagens and Carcinogens
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• v.21 no.2
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• pp.113-117
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• 2001

The screening of various molecular descriptors for predicting carcinogenic, mutagenic and teratogenic activities of chlorinated aliphatic compounds as drinking water disinfection byproducts (DBPs) has been investigated for the application of quantitative structure-activity relationships (QSAR). The present work embodies the study of relationship between molecular descriptors and toxicity parameters of the genotoxicity endpoints for the screening of relevant molecular descriptors. The toxicity Indices for 29 compounds constituting the testing set were computed by the PASS program and active values were chosen. We investigate feasibility of screening descriptors and of their applications among different genotoxic endpoints. The correlation to teratogenicity of all 29 compounds was significantly improved when the same analysis was done with 20 alkanes only without alkene compounds. The HOMO (highest occupied molecular orbital) energy and number of Cl parameters were dominantly contributed.

• Asian Pacific Journal of Cancer Prevention
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• v.15 no.2
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• pp.797-802
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• 2014

We screened a small molecular library that was designed and independently synthesized in vitro and found a new drug (MY-03-01) that is active against ovarian cancer. We established that MY-03-01 effectively inhibited SKOV-3 cell survival in a dose-dependent manner, based on cell viability rates, and that it not only induced SKOV-3 apoptosis by itself, but also did so synergistically with paclitaxel. Secondly, when MY-03-01 was applied at $40{\mu}M$, its hemolytic activity was less than 10%, compared with the control, and there was almost no damage to nor mal cells at this concentration. In addition, we used DAPI staining and flow cytometry to show that MY-03-01 could significantly induce apoptosis of SKOV-3 cells. Finally, we found that MY-03-01 likely induced SKOV-3 apoptosis by activating caspase3 and caspase9 through the mitochondrial pathway.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3553-3560
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• 2010

A new hydrazone derivative compound has been synthesized and characterized by IR, $^1H$-NMR, $^{13}C$-NMR and UV-vis. spectroscopy techniques, elemental analysis and single-crystal X-ray diffraction (XRD). The new compound crystallizes in monoclinic space group C2/c. In addition to the crystal structure from X-ray experiment, the molecular geometry, vibrational frequencies and frontier molecular orbitals analysis of the title compound in the ground state have been calculated by using the HF/6-31G(d, p), B3LYP/6-311G(d, p) and B3LYP/6-31G(d, p) methods. The computed vibrational frequencies are used to determine the types of molecular motions associated with each of the observed experimental bands. To determine conformational flexibility, molecular energy profile of (1) was obtained by semi-empirical (AM1) calculation with respect to a selected degree of torsional freedom, which was varied from $-180^{\circ}$ to $+180^{\circ}$ in steps of $10^{\circ}$. Molecular electrostatic potential of the compound was also performed by the theoretical method.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.17-20
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• 2000

Structural genomics aims to provide a good experimental structure or computational model of every tractable protein in a complete genome. Underlying this goal is the immense value of protein structure, especially in permitting recognition of distant evolutionary relationships for proteins whose sequence analysis has failed to find any significant homolog. A considerable fraction of the genes in all sequenced genomes have no known function, and structure determination provides a direct means of revealing homology that may be used to infer their putative molecular function. The solved structures will be similarly useful for elucidating the biochemical or biophysical role of proteins that have been previously ascribed only phenotypic functions. More generally, knowledge of an increasingly complete repertoire of protein structures will aid structure prediction methods, improve understanding of protein structure, and ultimately lend insight into molecular interactions and pathways. We use computational methods to select families whose structures cannot be predicted and which are likely to be amenable to experimental characterization. Methods to be employed included modern sequence analysis and clustering algorithms. A critical component is consultation of the presage database for structural genomics, which records the community's experimental work underway and computational predictions. The protein families are ranked according to several criteria including taxonomic diversity and known functional information. Individual proteins, often homologs from hyperthermophiles, are selected from these families as targets for structure determination. The solved structures are examined for structural similarity to other proteins of known structure. Homologous proteins in sequence databases are computationally modeled, to provide a resource of protein structure models complementing the experimentally solved protein structures.

• Polymer(Korea)
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• v.24 no.4
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• pp.488-498
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• 2000

Molecular bottle-brush was prepared by hydrogen-bonding between poly(4-vinylpyridine)(P4VP) as main chain and 3-pentadecylphenol (PDP) as amphiphilic side chain. Variation of long period ( $L_{p}$), order-disorder transition temperature ( $T_{ODT}$) and mesomorphic structure of bottle-brush were investigated by changing various mole ratio (x) of pyridine group in P4VP and PDP and molecular weight of P4VP. Upper critical solution temperature (UCST) behaviour was observed. For x 0.8-0.9, maximum critical temperature was found. As molecular weight of P4VP was increased, phase transition occurred at higher temperature. It was found that phase behaviour of the bottle-brush was affected by mobility of P4VP as well as size and regularity of lamellar structure. The $L_{p}$ determined from analysis of crystal structure was in the range of 35 $\AA$ and 40 $\AA$ and was more affected by the molecular weight of P4VP than by mole ratio (x). However, if the molecular weight of P4VP was high, LP value was little affected.ted.d.

• Korea-Australia Rheology Journal
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• v.19 no.1
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• pp.1-5
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• 2007

By combining ultrasonic energy which is essential for the chain scission of polymer molecules and a multifunctional agent (MFA) having double bonds at its ends, we were able to modify the molecular structure of polycarbonate (PC) from linear to a branched structure during melt processing. The three double bonds in chain ends of MFA were expected to act as sites for trapping macroradicals of PC during the course of ultrasound-assisted mixing process. The transformation of molecular structure of PC was confirmed by the measurements of rheological properties of the modified PC. After the ultrasonic irradiation of PC together with MFA, increase in complex viscosities and shear-thinning behavior were observed. The Cole-Cole plot and measurement of extensional viscosities revealed the characteristic features of branched structure with well-defined extensional behavior which is comparable to that of a commercial branched PC.

• Asian-Australasian Journal of Animal Sciences
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• v.17 no.7
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• pp.897-902
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• 2004

PSMC5 subunit, which belongs to the 26S proteasomal subunit family, plays an important role in the antigen presentation mediated by MHC class I molecular. Full-length cDNA of porcine PSMC5 was isolated using the in silico cloning and rapid amplification of cDNA ends (RACE). Amino acid was deduced and the primary structure was analyzed. Results revealed that the porcine PSMC5 gene shares the high degree of sequence similarity with its mammalian counterparts at both the nucleotide level and the amino acid level. The RT-PCR was performed to detect the porcine PSMC5 expression pattern in seven tissues and the result showed that high express level was observed in spleen, lung, marrow and liver while the low express level was in muscle. The full-length genomic DNA sequence of porcine PSMC5 gene was amplified by PCR and the genomic structure revealed that this gene was comprised by 12 exons and 11 introns. Best alignment of the cDNA and genomic exon DNA sequence presents 4 mismatches and this information potentially bears further study in gene polymorphisms.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1479-1484
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• 2010

Photosynthesis uses light energy to drive the oxidation of water at an oxygen-evolving catalytic site within photosystem II (PSII). Chlorophyll binding by the photosystem II subunit S protein, PsbS, was found to be necessary for energy-dependent quenching (qE), the major energy-dependent component of non-photochemical quenching (NPQ) in Arabidopsis thaliana. It is proposed that PsbS acts as a trigger of the conformational change that leads to the establishment of nonphotochemical quenching. However, the exact structure and function of PsbS in PSII are still unknown. Here, we clone and express the recombinant PsbS gene from Arabidopsis thaliana in E. coli and purify the resulting homogeneous protein. We used various biochemical and biophysical techniques to elucidate PsbS structure and function, including circular dichroism (CD), fluorescence, and DSC. The protein shows optimal stability at $4^{\circ}C$ and pH 7.5. The CD spectra of PsbS show that the conformational changes of the protein were strongly dependent on pH conditions. The CD curve for PsbS at pH 10.5 curve had the deepest negative peak and the peak of PsbS at pH 4.5 was the least negative. The fluorescence emission spectrum of the purified PsbS protein was also measured, and the ${\lambda}_{max}$ was found to be at 328 nm. PsbS revealed some structural changes under varying temperature and oxygen gas condition.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.14 no.3
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• pp.1512-1518
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• 2013

Polycarbonates (PCs) with six different end capping agents were synthesized from melt polymerization. Chemical structure of the synthesized PC was determined by FT-IR spectroscopy. The average molecular weight and distribution, glass transition and thermal degradation temperatures were determined by GPC, DSC and TGA. Average molecular weight changed with the chemical structure of end capping agent, and 4-tert-butylphenol was estimated as the optimum end capping agent. The average molecular weights of PCs decreased with the concentration of the agent, the number average molecular weight was observed as 20,000 - 30,000 when 0.05-0.15 mol% of 4-tert-butylphenol added in PCs. The melt viscosities and glass transition temperature of the PCs decreased with molecular weight. The change for adding method of the agent affected on both the molecular weight distribution and decrease in power law index.