• Bulletin of the Korean Chemical Society
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• v.35 no.6
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• pp.1713-1719
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• 2014

1FSD is a 28-residue designed protein with a ${\beta}{\beta}{\alpha}$ motif. Since this protein displays most essential features of protein structures in such a small size, this model protein can be an outstanding system for evaluating the balance in the propensity of the secondary structures and the quality of all-atom protein force fields. Particularly, this protein would be difficult to fold to its correct native structure without establishing proper balances between the secondary structure elements in all-atom energy functions. In this work, a series of the recently optimized five amber protein force fields [$ff03^*$, $f99sb^*$-ildn, ff99sb-${\phi}^{\prime}$-ildn, ff99sb-nmr1-ildn, ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn] were investigated for the simulations of 1FSD using a conventional molecular dynamics (MD) and a biased-exchange meta-dynamics (BEMD) methods. Among those tested force fields, we found that ff99sb-nmr1-ildn and ff99sb-${\Phi}{\Psi}$(G24, CS)-ildn are promising in that both force fields can locate the native state of 1FSD with a high accuracy (backbone rmsd ${\leq}1.7{\AA}$) in the global free energy minimum basin with a reasonable energetics conforming to a previous circular dichroism (CD) experiment. Furthermore, both force fields led to a common set of two distinct folding pathways with a heterogeneous nature of the transition state to the folding. We anticipate that these force fields are reasonably well balanced, thereby transferable to many other protein folds.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.45 no.3
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• pp.238-245
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• 2012

In this study, the molecular structures of tet(M) and tet(G) carried by tetracycline (Tc) resistant bacteria in intestinal microflora from the imported ornamental fish were characterized and compared with each other depend on the imported countries. Of the total isolates, approximately 8.9% of the Ent-lac+(lactose fermentative bacteria on coliform media) Tc resistant isolates in fish from three different countries, Singapore, Taiwan and Brazil, were appeared to contain tet(M). Three representative isolates of different countries, Aeromonas spp. JSM-1 (Singapore), JTM-1 (Taiwan) and JBM-1 (Brazil), were isolated and analyzed the molecular structures of tet(M) gene. Interestingly, partial sequence of tet(M) genes (1099 bp) in JBM-1 (Brazil) showed 99.5% homology with the tet(M) found in the Vibrio spp. RV16 isolate, obtained from marine fish in Korea and known to carry Tn1545 parent type of tet(M). In contrast, tet(M) gene in JSM-1 and JTM-1 showed mosaic structure of Tn1545 and Tn916, and 100% homology with each other. It may suggest the presence of various characteristics in terms of tet(M) gene structure. The determined sequence of the tet(G) from Aeromonas spp. JSG-1 and JBG-1 isolated from Singapore and Indonesia ornamental fish respectively showed similar nucleotide sequence homology but revealed a few nucleotide changes in comparison with the sequence of the prototype tet(G) gene (S52437 in GenBank).

• Bulletin of the Korean Chemical Society
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• v.29 no.3
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• pp.627-640
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• 2008

The geometrical structures, atomic charges, and relative energies of tetracoordinated Pd complexes [PdCl3Z (Z = Cl-, Br-, OH?-, H2O, NH3, PH3), PdCl2Z2 (Z = Br-, OH?-, H2O, NH3, PH3), PdZ?2X (Z = Cl-, OH?-, H2O, NH3, PH3; X = oxalate, O2-?CCO2-), and PdZ2Y (Z = Cl?-, OH?-, H2O, NH3, PH3; Y = succinate, CO2-?CHCHCO2-?)] and the ligand exchange reactions of the Pd complexes were investigated using the ab initio second order Mller-Plesset perturbation (MP2) and Density Functional Theory (DFT) methods. The geometrical characteristics of the tetracoordinated Pd(II) complexes with mono- and bidentate ligands, the effects of the atomic charges for the charged and uncharged ligands, the (dz2-p ) interactions between the dz2-orbital of Pd(II) and the p -orbital of bidentates, and the relative stabilities between the isomers of PdCl2Z2 and PdZ2Y were investigated in detail. The potential energy surfaces for the ligand exchange reactions used for the conversions of {[PdCl2(NH3)2] + H2O} to {[PdCl(NH3)2(H2O)]+ + Cl?-?} and {[PdCl2(PH3)2] + H2O} to {[PdCl(PH3)2(H2O)]+ + Cl?-?]} were investigated. The geometrical structure variations, molecular orbital variations (HOMO and LUMO), and relative stabilities for the ligand exchange processes were also examined quantitatively.

• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2549-2554
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• 2009

The structures of 1,n-alkanedithiol (n = 2, 4, 6, 8, 10) self-assembled monolayers (SAMs) on a Au(111) substrate were investigated by electrochemical measurements and theoretical calculations. The results of the experimental techniques indicated that the dithiols, except n = 2, showed an upright molecular structure in the SAMs, in which alkanedithiols were bound to the Au surface via only one thiol functionality and the other one faced up to the air. The results also suggested that the formed dithiol SAMs were densely packed and highly oriented. Except ethanedithiol, which was thought to form a bilayer, the reductive desorption peak potentials of 1,n-alkanedithiol (n = 4, 6, 8, 10) SAMs were more negative than those of the corresponding monothiol ones in 0.1 M KOH solutions. This illustrates that the dithiol SAMs had higher stability than the corresponding monothiol ones. The major part of the high stability may be attributed to the van der Waals interaction among the sulfur atoms on top of the dithiol SAMs. The molecular modeling calculation showed that the structures of dithiol SAMs were similar to those of the corresponding monothiol SAMs and that all the dithiol SAMs, except ethanedithiol, were more stable than the corresponding monothiol SAMs. The calculated energy differences between dithiol and monothiol SAMs decreased with the increment of alkyl-chain length.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.558-564
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• 2013

A simple and effective method is introduced to synthesize a series of polystyrene-b-poly(oligo(ethylene oxide) monomethyl ether methacrylate)-b-polystyrene (PSt-b-POEOMA-b-PSt) triblock copolymers. The structures of PSt-b-POEOMA-b-PSt copolymers were characterized by Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance ($^1H$ NMR) spectroscopy. The molecular weight and molecular weight distribution of the copolymer were measured by gel permeation chromatography (GPC). Furthermore, the self-assembling and drug-loaded behaviours of three different ratios of PSt-b-POEOMA-b-PSt were studied. These copolymers could readily self-assemble into micelles in aqueous solution. The vitamin E-loaded copolymer micelles were produced by the dialysis method. The micelle size and core-shell structure of the block copolymer micelles and the drug-loaded micelles were confirmed by dynamic light scattering (DLS) and transmission electron microscopy (TEM). The thermal properties of the copolymer micelles before and after drug-loaded were investigated by different scanning calorimetry (DSC). The results show that the micelle size is slightly increased with increasing the content of hydrophobic segments and the micelles are still core-shell spherical structures after drug-loaded. Moreover, the glass transition temperature (Tg) of polystyrene is reduced after the drug loaded. The drug loading content (DLC) of the copolymer micelles is 70%-80% by ultraviolet (UV) photolithography analysis. These properties indicate the micelles self-assembled from PSt-b-POEOMA-b-PSt copolymers would have potential as carriers for the encapsulation of hydrophobic drugs.

• Microbiology and Biotechnology Letters
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• v.31 no.4
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• pp.311-321
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• 2003

Bacteria produce lipases, which can catalyze both the hydrolysis and the synthesis of long chain triglycerides. These reactions usually proceed with high regioselectivity and enantioselectivity, and, therefore, lipases have become very important biocatalysts used in organic chemistry. 3D lipase structures were solved from several bacterial lipases. They have an $\alpha/\beta$ hydrolase fold and a catalytic triad consisting of a nucleophilic serine, and an aspartate or glutamate residue that is hydrogen bonded to a histindine. Active sites are covered with $\alpha$-helical lid structure, of which movement is involved in the enzyme's activation at oil/water interface. Four substrate binding pockets were identified for triglycerides: an oxyanion hole and three pockets accommodating the fatty acids bound at positions sn-1, sn-2, and sn-3. These pockets determine the enantiopreference of a lipase. The understanding of structure-function relationships as well as the development of molecular evolution techniques will enable researchers to tailor new lipases for biotechnological applications.

• Journal of Ginseng Research
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• v.43 no.3
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• pp.482-487
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• 2019

Background: The mixed-cultivation of different Panax ginseng cultivars can cause adverse effects on stability of yield and quality. K-1 is a superior cultivar with good root shape and stronger disease resistance. DNA markers mined from functional genes are clearly desirable for K-1, as they may associate with major traits and can be used for marker-assisted selection to maintain the high quality of Korean ginseng. Methods: Five genes encoding pathogenesis-related (PR) proteins of P. ginseng were amplified and compared for polymorphism mining. Primary, secondary, and tertiary structures of PR5 protein were analyzed by ExPASy-ProtParam, PSSpred, and I-TASSER methods, respectively. A coding single nucleotide polymorphism (SNP)-based specific primer was designed for K-1 by introducing a destabilizing mismatch within the 3' end. Allele-specific polymerase chain reaction (PCR) and real-time allele-specific PCR assays were conducted for molecular discrimination of K-1 from other cultivars and landraces. Results: A coding SNP leading to the modification of amino acid residue from aspartic acid to asparagine was exploited in PR5 gene of K-1 cultivar. Bioinformatics analysis showed that the modification of amino acid residue changed the secondary and tertiary structures of the PR5 protein. Primer KSR was designed for specific discrimination of K-1 from other ginseng cultivars and landraces. The developed real-time allele-specific PCR assay enabled easier automation and accurate genotyping of K-1 from a large number of ginseng samples. Conclusion: The SNP marker and the developed real-time allele-specific PCR assay will be useful not only for marker-assisted selection of K-1 cultivar but also for quality control in breeding and seed programs of P. ginseng.

• Advances in nano research
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• v.12 no.5
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• pp.529-547
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• 2022

Graphene is one of the strongest, stiffest, and lightest nanoscale materials known to date, making it a potentially viable and attractive candidate for developing lightweight structural composites to prevent high-velocity ballistic impact, as commonly encountered in defense and space sectors. In-plane twist in bilayer graphene has recently revealed unprecedented electronic properties like superconductivity, which has now started attracting the attention for other multi-physical properties of such twisted structures. For example, the latest studies show that twisting can enhance the strength and stiffness of graphene by many folds, which in turn creates a strong rationale for their prospective exploitation in high-velocity impact. The present article investigates the ballistic performance of twisted bilayer graphene (tBLG) nanostructures. We have employed molecular dynamics (MD) simulations, augmented further by coupling gaussian process-based machine learning, for the nanoscale characterization of various tBLG structures with varying relative rotation angle (RRA). Spherical diamond impactors (with a diameter of 25Å) are enforced with high initial velocity (V_i) in the range of 1 km/s to 6.5 km/s to observe the ballistic performance of tBLG nanostructures. The specific penetration energy (E_p^*) of the impacted nanostructures and residual velocity (V_r) of the impactor are considered as the quantities of interest, wherein the effect of stochastic system parameters is computationally captured based on an efficient Gaussian process regression (GPR) based Monte Carlo simulation approach. A data-driven sensitivity analysis is carried out to quantify the relative importance of different critical system parameters. As an integral part of this study, we have deterministically investigated the resonant behaviour of graphene nanostructures, wherein the high-velocity impact is used as the initial actuation mechanism. The comprehensive dynamic investigation of bilayer graphene under the ballistic impact, as presented in this paper including the effect of twisting and random disorder for their prospective exploitation, would lead to the development of improved impact-resistant lightweight materials.

• Journal of Powder Materials
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• v.30 no.4
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• pp.346-355
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• 2023

Epoxy-based composites find extensive application in electronic packaging due to their excellent processability and insulation properties. However, conventional epoxy-based polymers exhibit limitations in terms of thermal properties and insulation performance. In this study, we develop epoxy-based siloxane/silica composites that enhance the thermal, mechanical, and insulating properties of epoxy resins. This is achieved by employing a sol-gel-synthesized siloxane hybrid and spherical fused silica particles. Herein, we fabricate two types of epoxy-based siloxane/silica composites with different siloxane molecular structures (branched and linear siloxane networks) and investigate the changes in their properties for different compositions (with or without silica particles) and siloxane structures. The presence of a branched siloxane structure results in hardness and low insulating properties, while a linear siloxane structure yields softness and highly insulating properties. Both types of epoxy-based siloxane/silica composites exhibit high thermal stability and low thermal expansion. These properties are considerably improved by incorporating silica particles. We expect that our developed epoxy-based composites to hold significant potential as advanced electronic packaging materials, offering high-performance and robustness.

• ALGAE
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• v.38 no.4
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• pp.241-252
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• 2023

The genera Carolibrandtia and Chlorella have been described as small green algae with spherical cell shapes that inhabit various environments. Species of these genera are often difficult to identify because of their simple morphology and high phenotypic plasticity. We investigated two small coccoid strains from Antarctica based on morphology, molecular phylogeny by two alignment methods which have been applied to previous phylogenetic studies of the genus Chlorella, and comparison of the secondary structures of nuclear small subunit (SSU) and internal transcribed spacer (ITS) rDNA sequences. Light microscopy of two strains revealed spherical cells containing chloroplasts with pyrenoids, and the morphological characteristics of the strains were nearly identical to those of other Chlorella species. However, based on the phylogenetic analyses of nuclear SSU and ITS rDNA sequences, it was determined that the Antarctic microalgal strains belonged to two genera, as the Chlorella and Carolibrandtia. In addition, the secondary structures of the SSU and ITS2 sequences were analyzed to detect compensatory base changes (CBCs) that were used to identify and describe the two strains. A unique CBC in the SSU rDNA gene was decisive for distinguishing strain CCAP 211/45. The ITS2 rDNA sequences for each strain were compared to those obtained previously from other closely related species. Following the comparison of morphological and molecular characteristics, we propose KSF0092 as a new species, Chlorella terrestris sp. nov., and the reassignment of the strain Chlorella antarctica CCAP 211/45 into Carolibrandtia antarctica comb. nov.