Structural Bioinformatics Analysis of Disease-related Mutations

Park, Seong-Jin,Oh, Sang-Ho,Park, Dae-Ui,Bhak, Jong Korea Genome Organization 2008 Genomics & informatics Vol.6 No.3

In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and disease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within $20\;{\AA}$ (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.

Polyacetylenic compounds from Atractylodes rhizomes

( Jung-hoon Kim ) 대한본초학회 2016 大韓本草學會誌 Vol.31 No.5

Objectives : Atractylodes rhizomes, which have been widely used to treat gastrointestinal disorders, consist of numerous chemical compounds. Polyacetylenes are the parts of characteristic compounds of importance required to understand the therapeutic properties of Atractylodes rhizomes. It is necessary to understand the physicochemical and pharmacological properties of polyacetylenes in the Atractylodes rhizomes. Methods : The literatures from 1970 to January 2016 were searched using Korean and international electronic databases. The chemical structures of polyacetylenes were drawn by structure-drawing software. Results : The reported polyacetylenes were classified by their chemical skeletons and original resources, and their physicochemical and pharmacological features were discussed. Polyacetylenes with skeletal moieties were reported, such as diene.diyne types (two double and two triple carbon-bonds), triene.diyne types (three double carbon bonds and two triple carbon bonds), and monoene.diyne types (one double carbon bonds and two double carbon bonds), with various functional groups. Atractylodin was most frequently reported from many Atractylodes species. Atractylodin-related polyacetylenes showed chemical instability in both high and freezing temperatures. Processing of the Atractylodes rhizomes by stir-frying with bran could affect the contents of polyacetylenes and their bioavailability in vivo. Several polyacetylenes showed structure-related anti-inflammatory activities and gastrointestinal activities. Conclusion : Polyacetylene compounds in Atractylodes rhizomes were based on three chemical backbones and showed diverse physicochemical and pharmacological features. The present study provides structural, physicochemical, and pharmacological information of polyacetylene from Atractylodes rhizomes. This information provides fundamental data for further research.

Polyacetylenic compounds from Atractylodes rhizomes

Kim, Jung-Hoon The Korea Association of Herbology 2016 大韓本草學會誌 Vol.31 No.5

Objectives : Atractylodes rhizomes, which have been widely used to treat gastrointestinal disorders, consist of numerous chemical compounds. Polyacetylenes are the parts of characteristic compounds of importance required to understand the therapeutic properties of Atractylodes rhizomes. It is necessary to understand the physicochemical and pharmacological properties of polyacetylenes in the Atractylodes rhizomes.Methods : The literatures from 1970 to January 2016 were searched using Korean and international electronic databases. The chemical structures of polyacetylenes were drawn by structure-drawing software.Results : The reported polyacetylenes were classified by their chemical skeletons and original resources, and their physicochemical and pharmacological features were discussed. Polyacetylenes with skeletal moieties were reported, such as diene-diyne types (two double and two triple carbon-bonds), triene-diyne types (three double carbon bonds and two triple carbon bonds), and monoene-diyne types (one double carbon bonds and two double carbon bonds), with various functional groups. Atractylodin was most frequently reported from many Atractylodes species. Atractylodin-related polyacetylenes showed chemical instability in both high and freezing temperatures. Processing of the Atractylodes rhizomes by stir-frying with bran could affect the contents of polyacetylenes and their bioavailability in vivo. Several polyacetylenes showed structure-related anti-inflammatory activities and gastrointestinal activities.Conclusion : Polyacetylene compounds in Atractylodes rhizomes were based on three chemical backbones and showed diverse physicochemical and pharmacological features. The present study provides structural, physicochemical, and pharmacological information of polyacetylene from Atractylodes rhizomes. This information provides fundamental data for further research.

Polyacetylenic compounds from Atractylodes rhizomes

김정훈 대한본초학회 2016 大韓本草學會誌 Vol.31 No.5

Objectives : Atractylodes rhizomes, which have been widely used to treat gastrointestinal disorders, consist of numerous chemical compounds. Polyacetylenes are the parts of characteristic compounds of importance required to understand the therapeutic properties of Atractylodes rhizomes. It is necessary to understand the physicochemical and pharmacological properties of polyacetylenes in the Atractylodes rhizomes. Methods : The literatures from 1970 to January 2016 were searched using Korean and international electronic databases. The chemical structures of polyacetylenes were drawn by structure-drawing software. Results : The reported polyacetylenes were classified by their chemical skeletons and original resources, and their physicochemical and pharmacological features were discussed. Polyacetylenes with skeletal moieties were reported, such as diene–diyne types (two double and two triple carbon-bonds), triene–diyne types (three double carbon bonds and two triple carbon bonds), and monoene–diyne types (one double carbon bonds and two double carbon bonds), with various functional groups. Atractylodin was most frequently reported from many Atractylodes species. Atractylodin-related polyacetylenes showed chemical instability in both high and freezing temperatures. Processing of the Atractylodes rhizomes by stir-frying with bran could affect the contents of polyacetylenes and their bioavailability in vivo. Several polyacetylenes showed structure-related anti-inflammatory activities and gastrointestinal activities. Conclusion : Polyacetylene compounds in Atractylodes rhizomes were based on three chemical backbones and showed diverse physicochemical and pharmacological features. The present study provides structural, physicochemical, and pharmacological information of polyacetylene from Atractylodes rhizomes. This information provides fundamental data for further research.

에폭시 도막 철근의 내부식 성능에 관한 실험적 연구

신영수,홍기섭,최완철 한국콘크리트학회 1994 콘크리트학회지 Vol.6 No.6

콘크리트내 철근의 부식을 방지하여 내구성을 증대시키기 위해 국내에서 시험 생산한 에폭시도막 철근의 내부식성능을 실험, 평가하였다. 본 연구에서는 국내 산업규격(KS)과 미국재료시험기준 시험결과로부터 에폭시도막 철근을 내약품성능, 염화물 투과성은 양호하였다. 그러나, 에폭시도막 철근표면의 결함부에서 부식이 발생되었으며 도막두계 $200{\mu}m$ 미만의 시험체에서 부식발생률이 높았다. 4mm 정도의 부분에폭시 도막손상은 전체적인 부식에 영향을 미치지는 않았다. 도막의 결함이 생기지 않도록 에폭시도막 과정에서 철근의 표면처리에 주의가 특별히 필요하다. Epoxy coated bars protecting reinforcing bars from corrosion and enhancing durability of reinforced concrete structures are tested to evaluate corrosion protection properties. Tests are performed based on the relevant sta.ndards of KS and ASTM, such as chenical resistance, salt water spray, salt crock test and chloride ermeability test. with the main varlable of the coating thlckness. Test results show good chemical protection property and chloride permeability. The results of the salt water spray and the salt crock test show that epoxy coating well protects the reinforcing bars from corrosion, cornparing to the biack bars without epoxy coatmg. However, several spots on the coated bars are rusted at the pinholes or un the bars with coating thickness less thar $200{\mu}M$. Special cautions are required i n the process of blast cleanmg when applying the usion-bonded epoxy coating.

Two-stage processed Cu₄SnS₄ thin films for photovoltaics - Effect of (N₂ + S₂) pressure during annealing

Chalapathi, U.,Poornaprakash, B.,Park, Si-Hyun Elsevier 2018 THIN SOLID FILMS - Vol.660 No.-

<P><B>Abstract</B></P> <P>In this paper, we report the fabrication of Cu<SUB>4</SUB>SnS<SUB>4</SUB> thin films by annealing chemically deposited SnS–CuS precursors at 823 K for 90 min, and we studied the effect of the (N<SUB>2</SUB> + S<SUB>2</SUB>) pressure during annealing on the growth and properties of the Cu<SUB>4</SUB>SnS<SUB>4</SUB> films. Films prepared at a (N<SUB>2</SUB> + S<SUB>2</SUB>) pressure of 1.3 kPa exhibited an orthorhombic crystal structure with lattice parameters of a = 1.371 nm, b = 0.766 nm, and c = 0.643 nm, a grain size of 3–6 μm, a direct optical band gap of 1.0 eV, p-type electrical conductivity, and a hole mobility of 69.5 cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP>. Increasing the (N<SUB>2</SUB> + S<SUB>2</SUB>) pressure from 1.3 kPa to 66.7 kPa increased the grain size to more than 6 μm and the hole mobility to 150 cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP> at 26.7 kPa and then decreased to 86 cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP> at 66.7 kPa. Further increasing the (N<SUB>2</SUB> + S<SUB>2</SUB>) pressure to 101.3 kPa resulted in the formation of a monoclinic Cu<SUB>2</SUB>SnS<SUB>3</SUB> secondary phase. This study reveals that an annealing temperature of 823 K and a (N<SUB>2</SUB> + S<SUB>2</SUB>) pressure of 1.3–66.7 kPa are the optimized conditions to obtain large-grained Cu<SUB>4</SUB>SnS<SUB>4</SUB> films free of secondary phases with good optical and electrical properties.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Cu<SUB>4</SUB>SnS<SUB>4</SUB> thin films were grown by annealing SnS–CuS stacks in a graphite box. </LI> <LI> The effect of (N<SUB>2</SUB> + S<SUB>2</SUB>) pressure during annealing on the growth of the films investigated </LI> <LI> (N<SUB>2</SUB> + S<SUB>2</SUB>) pressure significantly enhanced the grain growth and electrical properties of films. </LI> <LI> Large-grained Cu<SUB>4</SUB>SnS<SUB>4</SUB> films obtained at 1.3–66.7 kPa (N<SUB>2</SUB> + S<SUB>2</SUB>) pressure </LI> </UL> </P>

Effects of Mn-doping on the Electrical and the Ferroelectric Properties of Bi6Fe2Ti3O18 Thin Films Prepared by Using Chemical Solution Deposition

J. W. Kim,라그하반,J. Y. Choi,W. J. Kim,S. S. Kim,T. K. Song 한국물리학회 2015 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.66 No.9

Mn-doped Bi6Fe2Ti3O18 (Bi6Fe2−xMnxTi3O18, x = 0.0, 0.5, 1.0 and 1.5, represented as BFMTO00, BFMTO05, BFMTO10 and BFMTO15, respectively) thin films were prepared on Pt(111)/Ti/SiO2/Si(100) substrates by using a chemical solution deposition method. Among the thin films, the BFMTO05 thin film exhibited superior electrical and ferroelectric properties. The values of the remnant polarization (2Pr) and the coercive field (2Ec) of the BFMTO05 thin film were 22 μC/cm2 and 207 kV/cm at an electric field of 530 kV/cm, respectively. The leakage current density of the BFMTO05 thin film was 5.45 × 10 −6 A/cm2 at an electric field of 100 kV/cm. The dielectric constant for the BFMTO05 thin film was 467 at a frequency of 1 kHz. Our work confirms that the enhanced electrical and ferroelectric properties may be related to a decrease in the oxygen vacancy density, a stabilization of the perovskite structure and small changes in the lattice parameter caused by doping of Mn3+ ions into the Fe3+ ion sites.

Predictability of physicochemical properties of polychlorinated dibenzo-p-dioxins (PCDDs) based on single-molecular descriptor models

Kim, M.,Li, L.Y.,Grace, J.R. Elsevier Applied Science Publishers 2016 Environmental pollution Vol.213 No.-

Polychlorinated dibenzo-p-dioxins (PCDDs) are of global concern due to their persistence, bioaccumulation and toxicity. Although the fate of PCDDs in the environment is determined by their physical-chemical properties, such as aqueous solubility, vapor pressure, octanol/water-, air/water-, and octanol/water-partition coefficients, experimental property data on the entire set of 75 PCDD congeners are limited. The quantitative structure-property relationship (QSPR) approach is applied to predict the properties of all PCDD congeners. Experimental property data available from the literature are correlated against 16 molecular descriptors of five types. Reported and newly developed QSPR models for PCDDs are presented and reviewed. The values calculated by the best QSPRs are further adjusted to satisfy fundamental thermodynamic relationships. Although the single-descriptor models with chlorine number, molar volume, solvent accessible surface area and polarizability are based on good statistical results, these models cannot distinguish among PCDDs having the same chlorine number. The QSPR model based on the hyper-Wiener index of quantum-chemical descriptor gives useful statistical results and is able to distinguish among congeners with the same chlorine number, as well as satisfying thermodynamic relationships. The resulting consistent properties of the 75 PCDD congeners can be used for environmental modeling.

Iron oxide nanopowder synthesized by electroerosion dispersion (EED) – Properties and potential for microwave applications

Bernd Halbedel,Tatiana Prikhna,Pamela Quiroz,Jens Schawohl,Thomas Kups,Mykola Monastyrov 한국물리학회 2018 Current Applied Physics Vol.18 No.11

Magnetic nanoparticles (MNP) have attracted considerable interest in many fields of research and applied science due to their impressive properties. In the past, especially biomedical problems have promoted the development of MNPs. For technical applications e.g. wastewater treatment and absorption of electromagnetic waves, the existing synthesis approaches are too expensive and/or the producible quantities are too low. In this work we present a method for simple preparation of size-controlled magnetic iron oxide nanoparticles by electroerosion dispersion (EED) of carbon steel in water. We describe the synthesis method, the laboratory installation and discuss the structural, chemical and electromagnetic properties of the synthetized EED powders as well as their applicability for microwave absorption compared to other available ferrite powders.

Comparison of the Effects of Solid Solution Elements and Epsilon Particles on the Structure and Properties of Nuclear Fuel

Jeongmook Lee,Dong Woo Lee,Junghwan Park,Tae-Hyeong Kim,Hye Ran Noh,Jong-Yun Kim,Sang Ho Lim 한국방사성폐기물학회 2022 한국방사성폐기물학회 학술논문요약집 Vol.20 No.1

Spent nuclear fuel is a very complex material because various elements such as fission products, transuranium elements and activation products are produced from initial fresh UO2 fuel after irradiation. These elements exist in UO2 with various forms and can change the structure and of physicochemical properties of UO2. These changes could provide the surface activation site that could enhance chemical reactions and corrosion processes, and would significantly affect the storage environment for long-term disposal of spent nuclear fuel. Therefore, it can be important to understand the characteristics of spent nuclear fuel to design reliable and safe geological repositories. However, it is too hard to study the characteristics of spent nuclear fuel, because it is a very complex material by itself and not easy to handle due to its radioactivity, and it is also difficult to independently understand the effects of each element. Therefore, a simulated spent nuclear fuel containing an element that forms a solid solution and epsilon particle was manufactured to understand the change in characteristics of each element. Most of the elements that form solid solutions are lanthanides or actinides and can change the structure of the UO2 lattice itself. The epsilon particles exist as metals at the grain boundaries of UO2. In this study, structural changes were measured using XRD, SEM, and Raman spectroscopy, and physical and chemical properties were also identified by measuring electrical conductivity and electrochemical properties. The results were summarized, and the effects of solid solution elements and epsilon particles on the structure and properties of UO2 matrix were compared and discussed.