• Genomics & Informatics
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• v.18 no.3
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• pp.30.1-30.7
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• 2020

The novel coronavirus pandemic that has originated from China and spread throughout the world in three months. Genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) predecessor, severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) play an important role in understanding the concept of genetic variation. In this paper, the genomic data accessed from National Center for Biotechnology Information (NCBI) through Molecular Evolutionary Genetic Analysis (MEGA) for statistical analysis. Firstly, the Bayesian information criterion (BIC) and Akaike information criterion (AICc) are used to evaluate the best substitution pattern. Secondly, the maximum likelihood method used to estimate of transition/transversions (R) through Kimura-2, Tamura-3, Hasegawa-Kishino-Yano, and Tamura-Nei nucleotide substitutions model. Thirdly and finally nucleotide frequencies computed based on genomic data of NCBI. The results indicate that general times reversible model has the lowest BIC and AICc score 347,394 and 347,287, respectively. The transition/transversions bias for nucleotide substitutions models varies from 0.56 to 0.59 in MEGA output. The average nitrogenous bases frequency of U, C, A, and G are 31.74, 19.48, 28.04, and 20.74, respectively in percentages. Overall the genomic data analysis of SARS-CoV-2, SARS-CoV, and MERS-CoV highlights the close genetic relationship.

• Journal of Life Science
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• v.14 no.5
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• pp.752-760
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• 2004

The function of the [4Fe-4S] cluster containing iron (Fe-) protein in nitrogenase catalysis is to serve as the nucleotide-dependent electron donor to the MoFe protein which contains the sites for substrate binding and reduction. The ability of the Fe protein to function in this manner is dependent on its ability to adopt the appropriate conformation for productive interaction with the MoFe protein and on its ability to change redox potentials to provide the driving force required for electron transfer. The MgADP-bound (or off) conformational state of the nitrogenase Fe protein structure described reveals mechanisms for long-range communication from the nucleotide-binding sites to control affinity of association with the MoFe protein component. Two pathways, termed switches I and II, appear to be integral to this nucleotide signal transduction mechanism. In addition, the structure of the MgADP bound Fe protein provides the basis for the changes in the biophysical properties of the [4Fe-4S] observed when Fe protein binds nucleotides. The structures of the nitrogenase Fe protein with defined amino acid substitutions in the nucleotide dependent signal transduction pathways of the Switch I and Switch II have been determined by X-ray diffraction methods. These two pathways have been also implicated by site directed mutagenesis studies, structural analysis and analogies to other proteins that utilize similar nucleotide dependent signal transduction pathways. We have examined the validity of the assignment of these pathways in linking the signals generated by MgATP binding and hydrolysis to macromolecular complex formation and intermolecular electron transfer. The results provide a structural basis for the observed biophysical and biochemical properties of the Fe protein variants and interactions within the nitrogenase Fe protein-MoFe protein complex.

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2497-2502
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• 2010

Arg13 is a conserved active-site residue in all known Pi class glutathione S-transferases (GSTs) and in most Alpha class GSTs. To evaluate its contribution to substrate binding and catalysis of this residue, three mutants (R13A, R13K, and R13L) were expressed in Escherichia coli and purified by GSH affinity chromatography. The substitutions of Arg13 significantly affected GSH-conjugation activity, while scarcely affecting glutathione peroxidase or steroid isomerase activities. Mutation of Arg13 into Ala largely reduced the GSH-conjugation activity by approximately 85 - 95%, whereas substitutions by Lys and Leu barely affected activity. These results suggest that, in the GSH-conjugation activity of hGST P1-1, the contribution of Arg13 toward catalytic activity is highly dependent on substrate specificities and the size of the side chain at position 13. From the kinetic parameters, introduction of larger side chains at position 13 results in stronger affinity (Leu > Lys, Arg > Ala) towards GSH. The substitutions of Arg13 with alanine and leucine significantly affected $k_{cat}$, whereas substitution with Lys was similar to that of the wild type, indicating the significance of a positively charged residue at position 13. From the plots of log ($k_{cat}/{K_m}^{CDNB}$) against pH, the $pK_a$ values of the thiol group of GSH bound in R13A, R13K, and R13L were estimated to be 1.8, 1.4, and 1.8 pK units higher than the $pK_a$ value of the wild-type enzyme, demonstrating the contribution of the Arg13 guanidinium group to the electrostatic field in the active site. From these results, we suggest that contribution of Arg13 in substrate binding is highly dependent on the nature of the electrophilic substrates, while in the catalytic mechanism, it stabilizes the GSH thiolate through hydrogen bonding.

• The Pure and Applied Mathematics
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• v.16 no.1
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• pp.13-18
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• 2009

A semilocal convergence analysis is provided for Newton's method in a Banach space. The inverses of the operators involved are only locally $H{\ddot{o}}lderian$. We make use of a point-based approximation and center-$H{\ddot{o}}lderian$ hypotheses for the inverses of the operators involved. Such an approach can be used to approximate solutions of equations involving nonsmooth operators.

• Bulletin of the Korean Chemical Society
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• v.29 no.5
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• pp.1075-1078
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• 2008

• Journal of the Korean Chemical Society
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• v.57 no.6
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• pp.677-683
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• 2013

A theoretical study of the electronic structures of $TiC_{1-x}$ and $Ti_{1-x}W_xC$ (x = 0, 0.25) is presented. The density of states and crystal orbital overlap population calculations were used to interpret variations of elastic properties induced by carbon vacancies and alloying substitutions. Our results show why the introduction of vacancies into TiC reduces bulk moduli, while W substitution at a Ti site increases the elastic modulus. The effect of the point defects on the bonding in TiC is investigated by means of extended Huckel tight-binding band calculations.

• The Pure and Applied Mathematics
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• v.15 no.2
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• pp.111-120
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• 2008

A semi local convergence analysis is provided for Newton's method in a Banach space setting. The operators involved are only locally Holderian. We make use of a point-based approximation and center-Holderian hypotheses. This approach can be used to approximate solutions of equations involving nonsmooth operators.

• Proceedings of the Korea Information Processing Society Conference
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• 2007.11a
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• pp.1131-1134
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• 2007

본 논문에서는 랜덤대치(random substitution) 기법에 대하여 심도 있는 분석을 실시한다. 랜덤대치 기법의 효율적인 구현을 위하여 데이터 재구축(reconstruction) 과정에서 필요로 하는 역행렬을 구하는 공식을 제시한다. 또한, 랜덤대치에 사용되는 다양한 파라미터들의 의미를 실험적으로 밝혀내며, 정확도와 프라이버시를 합리적으로 측정할 수 있는 새로운 측도(measure)들을 제안한다.

• Proceedings of the Korea Information Processing Society Conference
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• 2009.04a
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• pp.1377-1380
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• 2009

랜덤대치 기법은 프라이버시 손상 관점에서 높은 프라이버시를 보존하면서 원본 데이터의 분포를 재구축하여 데이터 유용성을 확보한다. 데이터 유용성을 위한 랜덤대치 기법의 정확성을 높이는 문제는 그동안 면밀히 연구되지 않았다. 본 논문에서는 랜덤대치 기법이 대부분의 데이터에 대해서 상대적으로 낮은 정확성을 보임을 실험을 통해 밝히고, 이론적인 분석과 실험을 바탕으로 정확성을 높일 수 있는 실용적인 알고리즘 개선 방법을 제안한다.

• Proceedings of the Korean Vacuum Society Conference
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• 2016.02a
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• pp.246-246
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• 2016

Tungsten-nitrogen (W-N) co-doping has been known to enhance the photocatalytic activity of anatase titania nanoparticles by utilizing visible light. The doping effects are, however, largely dependent on calcination or annealing conditions, and thus, the massive production of quality-controlled photocatalysts still remains a challenge. Using density functional theory (DFT) thermodynamics and time-dependent DFT (TDDFT) computations, we investigate the atomic structures of N doping and W-N co-doping in anatase titania, as well as the effect of the thermal processing conditions. We find that W and N dopants predominantly constitute two complex structures: an N interstitial site near a Ti vacancy in the triple charge state and the simultaneous substitutions of Ti by W and the nearest O by N. The latter case induces highly localized shallow in-gap levels near the conduction band minimum (CBM) and the valence band maximum (VBM), whereas the defect complex yielded deep levels (1.9 eV above the VBM). Electronic structures suggest that substitutions of Ti by W and the nearest O by N improves the photocatalytic activity of anatase by band gap narrowing, while defective structure degrades the activity by an in-gap state-assisted electron-hole recombination, which explains the experimentally observed deep level-related photon absorption. Through the real-time propagation of TDDFT (rtp-TDDFT), we demonstrate that the presence of defective structure attracts excited electrons from the conduction band to a localized in-gap state within a much shorter time than the flat band lifetime of titania. Based on these results, we suggest that calcination under N-rich and O-poor conditions is desirable to eliminate the deep-level states to improve photocatalysis.