• Korean Chemical Engineering Research
• /
• v.44 no.4
• /
• pp.329-339
• /
• 2006

The production of lower olefins from methanol becomes an attractive process because of the rapid increase in crude oil price. This paper reivews the conversion mechanisms of methanol to hydrocarbons over zeolite and SAPO molecular sieve catalysts to understand the formation steps of lower olefins from methanol. The feasibility of the conversion mechanisms such as the direct mechanism based on well-defined intermediates and the hydrocarbon pool mechanism involving hydrocarbon moieties as an active centers is discussed with reepect to the induction period, the selectivity for products and the deactivation phenomena of the methanol conversion. The literature appeered since 1999 for the structure of the hydrocarbon pool and its catalytic role in the methanol conversion are summariged, and the prospect for the methanol-to-olefins process is described.

• Parasites, Hosts and Diseases
• /
• v.56 no.2
• /
• pp.175-181
• /
• 2018

The giant roundworm Ascaris infects pigs and people worldwide and causes serious diseases. The taxonomic relationship between Ascaris suum and Ascaris lumbricoides is still unclear. The purpose of the present study was to investigate the genetic diversity and population genetic structure of 258 Ascaris specimens from humans and pigs from 6 sympatric regions in Ascaris-endemic regions of China using existing simple sequence repeat data. The microsatellite markers showed a high level of allelic richness and genetic diversity in the samples. Each of the populations demonstrated excess homozygosity (Ho0). According to a genetic differentiation index (Fst=0.0593), there was a high-level of gene flow in the Ascaris populations. A hierarchical analysis on molecular variance revealed remarkably high levels of variation within the populations. Moreover, a population structure analysis indicated that Ascaris populations fell into 3 main genetic clusters, interpreted as A. suum, A. lumbricoides, and a hybrid of the species. We speculated that humans can be infected with A. lumbricoides, A. suum, and the hybrid, but pigs were mainly infected with A. suum. This study provided new information on the genetic diversity and population structure of Ascaris from human and pigs in China, which can be used for designing Ascaris control strategies. It can also be beneficial to understand the introgression of host affiliation.

• Molecules and Cells
• /
• v.42 no.1
• /
• pp.79-86
• /
• 2019

Endolysins are bacteriophage-derived enzymes that hydrolyze the peptidoglycan of host bacteria. Endolysins are considered to be promising tools for the control of pathogenic bacteria. LysB4 is an endolysin produced by Bacillus cereus-infecting bacteriophage B4, and consists of an N-terminal enzymatic active domain (EAD) and a C-terminal cell wall binding domain (CBD). LysB4 was discovered for the first time as an L-alanoyl-D-glutamate endopeptidase with the ability to breakdown the peptidoglycan among B. cereus-infecting phages. To understand the activity of LysB4 at the molecular level, this study determined the X-ray crystal structure of the LysB4 EAD, using the full-length LysB4 endolysin. The LysB4 EAD has an active site that is typical of LAS-type enzymes, where $Zn^{2+}$ is tetrahedrally coordinated by three amino acid residues and one water molecule. Mutational studies identified essential residues that are involved in lytic activity. Based on the structural and biochemical information about LysB4, we suggest a ligand-docking model and a putative endopeptidase mechanism for the LysB4 EAD. These suggestions add insight into the molecular mechanism of the endolysin LysB4 in B. cereus-infecting phages.

• Reproductive and Developmental Biology
• /
• v.39 no.4
• /
• pp.105-115
• /
• 2015

Toll-like receptor 7 (TLR7) is critical for the triggering of innate immune response by recognizing the conserved molecular patterns of single-stranded RNA (ssRNA) viruses and mediated antigenic adaptive immunity. To understand how TLR7 distinguish pathogen-derived molecular patterns from the host self, it is essential to be able to identify TLR7 receptor interaction interfaces, such as active sites or R848-agonist binding sites. The functional interfaces of TLR7 can serve as targets for structure-based drug design in studying the TLR7 receptor's structure-function relationship. In contrast to mammalian TLR7, chicken TLR7 (chTLR7) is unknown for its important biological function. Therefore, it has been targeted to mediate contrasting evolutionary patterns of positive selection into non-synonymous SNPs across eleven species using TLR7 conservation patterns (evolutionary conserved and class-specific trace residues), where protein sequence differences to the TLR7 receptors of interest record mutation that have passed positive section across the species. In this study, we characterized the Lys609 residue on chTLR7-ECD homodimer interfaces to reflect the current tendency of evolving positive selection to be transfer into a stabilization direction of the R848-agonist/chTLR7-ECDs complex under the phylogenetically variable position across species and we suggest a potential indicator for contrasting evolutionary patterns of both the species TLR-ECDs.

• Genomics & Informatics
• /
• v.13 no.1
• /
• pp.15-24
• /
• 2015

Fatty acid synthase (FASN, EC 2.3.1.85), is a multi-enzyme dimer complex that plays a critical role in lipogenesis. This lipogenic enzyme has gained importance beyond its physiological role due to its implications in several clinical conditions-cancers, obesity, and diabetes. This has made FASN an attractive pharmacological target. Here, we have attempted to predict the theoretical models for the human enoyl reductase (ER) and ${\beta}$-ketoacyl reductase (KR) domains based on the porcine FASN crystal structure, which was the structurally closest template available at the time of this study. Comparative modeling methods were used for studying the structure-function relationships. Different validation studies revealed the predicted structures to be highly plausible. The respective substrates of ER and KR domains-namely, trans-butenoyl and ${\beta}$-ketobutyryl-were computationally docked into active sites using Glide in order to understand the probable binding mode. The molecular dynamics simulations of the apo and holo states of ER and KR showed stable backbone root mean square deviation trajectories with minimal deviation. Ramachandran plot analysis showed 96.0% of residues in the most favorable region for ER and 90.3% for the KR domain, respectively. Thus, the predicted models yielded significant insights into the substrate binding modes of the ER and KR catalytic domains and will aid in identifying novel chemical inhibitors of human FASN that target these domains.

• BMB Reports
• /
• v.45 no.1
• /
• pp.26-31
• /
• 2012

TRIM72 is known to play a critical role in skeletal muscle membrane repair. To better understand the molecular mechanisms of this protein, we carried out an in vitro binding study with TRIM72. Our study proved that TRIM72 binds various lipids with dissociation constants ($K_d$) ranging from 88.2 ${\pm}$ 9.9 nM to 550.5 ${\pm}$ 134.5 nM. In addition, the intrinsic fluorescence of TRIM72 exponentially decreased when the protein was diluted with stirring. The time-resolved fluorescence decay occurred in a concentration-independent manner. The fluorescence-decayed TRIM72 remained in its secondary structure, but its binding properties were significantly reduced. The dissociation constants ($K_d$) of fluorescence-decayed TRIM72 for palmitate and stearate were 159.1 ${\pm}$ 39.9 nM and 355.4 ${\pm}$ 106.0 nM, respectively. This study suggests that TRIM72 can be dynamically converted by various stimuli. The results of this study also provide insight into the role of TRIM72 in the repair of sarcolemma damage.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2014.02a
• /
• pp.125-125
• /
• 2014

In 1991, Prof. Toshio Masuda of Kyoto University for the first time synthesized a representative of diphenylacetylene polymer derivatives, poly[1-phenyl-2-(p-trimethylsilyl)phenylacetylene] [PTMSDPA]. This polymer is highly soluble nevertheless a ultra-high molecular weight (Mw) of > $1.0{\times}10^6$ which showed excellent chemical, physical, mechanical properties [1]. As one of the most interesting features of PTMSDPA, Prof. Katsumi Yoshino of Osaka Univ. reported that this polymer emits an intense fluorescence (FL) in a visible region because of the effective exciton confinement within the resonant structure between the polyene pi-conjugated chain and side phenyl full-aromatic bulky groups [2]. Very recently, Prof. Ben-Zhong Tang of Hong-Kong Institute of Science and Technology clarified the idea that the FL emission of disubstituted acetylene polymer derivatives originates from intramolecular excimer due to the face-to-face stacking of the side phenyl groups [3]. Thus, to know what influence to intramolecular excimer emission in the film as well as to further understand how the intramolecular excimer forms in the film became more crucial in order to further precisely design the optimized molecular structure for highly emissive, substituted acetylene polymers in the solid state. In recent studies, we have focused our interests on the origin of the FL emission in order to expand our knowledge to developments of novel sensor applications. It was found that the intramolecular phenyl-pheyl stack structure of PTMSDPA in film was variable in response to various external chemical stimuli. Using PTMSDPA and its derivatives, we have developed various potential applications such as latent fingerprint identification, viscosity sensor, chemical-responsive actuator, gum-like soft conjugated polymer, and bioimaging. The details will be presented in the 49th KVS Symposium held in Pyong Chang city.

• Fisheries and Aquatic Sciences
• /
• v.14 no.1
• /
• pp.43-54
• /
• 2011

Gene structure of copper/zinc-superoxide dismutase (Cu/Zn-SOD; sod1) was characterized in Hemibarbus mylodon (Teleostei; Cypriniformes), an endangered freshwater fish species in Korean peninsula. Full-length cDNA of H. mylodon SOD1 consisted of a 796-bp open reading frame sequence encoding 154 amino acids, and the deduced polypeptide sequence shared high sequence homology with other orthologs, particularly with regard to metal-coordinating ligands. Genomic structure of the H. mylodon sod1 gene (hmsod1; 1,911 bp from the ATG start codon to the stop codon) was typical quinquepartite (i.e., five exons interrupted by four introns); the lengths of the exons were similar among species belonging to various taxonomic positions. The molecular phylogeny inferred from sod1 genes in the teleost lineage was in accordance with the conventional taxonomic assumptions. 5'-flanking upstream region of hmsod1, obtained using the genome walking method, contained typical TATA and CAAT boxes. It also showed various transcription factor binding motifs that may be potentially involved in stress/immune response (e.g., sites for activating proteins or nuclear factor kappa B) or metabolism of xenobiotic compounds (e.g., xenobiotic response element; XRE). The hmsod1 transcripts were ubiquitously detected among tissues, with the liver and spleen showing the highest and lowest expression, respectively. An experimental challenge with Edwardsiella tarda revealed significant upregulation of the hmsod1 in kidney (4.3-fold) and spleen (3.1-fold), based on a real-time RT-PCR assay. Information on the molecular characteristics of this key antioxidant enzyme gene could be a useful basis for a biomarker-based assay to understand cellular stresses in this endangered fish species.

• BMB Reports
• /
• v.41 no.4
• /
• pp.305-309
• /
• 2008

Cobalt is an essential microelements in many biological processes involving enzymatic activity. We found that $Zn^{2+}$ and $Mg^{2+}$, which are in the active site of native calf intestine alkaline phosphatase (CIP), can be replaced by $Co^{2+}$ directly in solution. The effect of $Co^{2+}$ concentration on the substitution reaction was examined at ratios of [$Co^{2+}$]/[CIP] from 0:1 to 8:1. The quantity of $Zn^{2+}$ in CIP decreased progressively as the ratio was increased, but the amount of $Mg^{2+}$ changed in irrregular fashion. A series of active site models of the reaction mechanism of CIP are proposed. Low pH was found to promote the replacement of $Mg^{2+}$ by $Co^{2+}$. To understand how the substitution affects the enzyme, we also solved the secondary structure of CIP after reaction with $Co^{2+}$ in different conditions.

• Journal of the Korean Magnetic Resonance Society
• /
• v.20 no.2
• /
• pp.46-49
• /
• 2016

MiRNA-155, upregulated in various cancers, is one of the miRNAs that suppress apoptosis of human cancer. Thus, inhibition of the maturation of miRNA-155 could be an effective way to induce apoptotic cancer cell death. The apical stem-loop of the pre-miRNA-155 has been known as a Dicer biding site for RNA cleavage. Here, to understand the molecular basis of the tertiary interaction between pre-miRNA-155 with Dicer, we characterize the structure of the apical stem-loop of pre-miRNA-155 using NMR spectroscopy. The RNA has a stem-bulge-stem-loop-stem structure, which is consist of G-C Watson-Crick and G-U Wobble base pairs. The assignments of imino- protons were further confirmed by 2D $^{15}N-^1H$ HSQC NMR spectrum. The NMR parameters obtained in this study can be further used to investigate the tertiary interaction between pre-miRNA-155 and other biomolecules such as protein, nucleic acids, or small chemicals which might be used to control the apoptosis of cancer.