• Proceedings of the Korean Society for Bioinformatics Conference
• /
• 2000.11a
• /
• pp.32-34
• /
• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2012.02a
• /
• pp.557-557
• /
• 2012

Silicatein-${\alpha}$, the enzyme extracted from silica spicules in glass sponges, has been studied extensively in the way of chemistry from 1999, in which the pioneering work by Morse, D. E. - the discovery of the enzymatic hydrolysis in Silicatein-${\alpha}$ - was published. Since its reaction conditions are physiologically favored, synthesis of various materials, such as gallium oxide, zirconium oxide, and silicon oxide, was achieved without any hazardous wastes. Although some groups synthesized oxide films and particles, they have not achieved yet controlled morphogenesis in the reaction conditions mentioned above. With the knowledge of catalytic triad involved in hydrolysis of silicone alkoxide and oligomerization of silicic acid, we designed the novel peptide amphiphiles to not only form self-assembled structure, but also display similar activities to silicatein-${\alpha}$. Designed templates were able to self-assemble into left-handed helices for the peptide amphiphiles with L-form amino acid, catalyzing polycondensation of silicic acids onto the surface of them. It led to the formation of silica helices with 30-50 nm diameters. These results were characterized by various techniques, including SEM, TEM, and STEM. Given the situation that nano-bio-technology, the bio-applicable technology in nanometer scale, has been attracting considerable attention; this result could be applied to the latest applications in biotechnology, such as biosensors, lab-on-a-chip, biocompatible nanodevices.

• Publications of The Korean Astronomical Society
• /
• v.30 no.2
• /
• pp.75-78
• /
• 2015

A growing body of evidence has been supporting the existence of so-called "dark molecular gas" (DMG), which is invisible in the most common tracer of molecular gas, i.e., CO rotational emission. DMG is believed to be the main gas component of the intermediate extinction region from Av~0.05-2, roughly corresponding to the self-shielding threshold of $H_2$ and $^{13}CO$. To quantify DMG relative to $H{\small{I}}$ and CO, we are pursuing three observational techniques; $H{\small{I}}$ self-absorption, OH absorption, and THz $C^+$ emission. In this paper, we focus on preliminary results from a CO and OH absorption survey of DMG candidates. Our analysis shows that the OH excitation temperature is close to that of the Galactic continuum background and that OH is a good DMG tracer co-existing with molecular hydrogen in regions without CO. Through systematic "absorption mapping" by the Square Kilometer Array (SKA) and ALMA, we will have unprecedented, comprehensive knowledge of the ISM components including DMG in terms of their temperature and density, which will impact our understanding of galaxy evolution and star formation profoundly.

• Proceedings of the Membrane Society of Korea Conference
• /
• 2003.07a
• /
• pp.91-94
• /
• 2003

In this work, the physicochemical properties for permeant molecules and polyion complex membrane prepared by complexation between SA and chitosan were determined by using molecular modeling methods, and the permeation behaviors of water and alcohol molecules through the PIC membrane have been investigated. In the case of penetrant molecule, the experimental results showed that the prepared membrane was excellent pervaporation performance result in most solution, and the selectivity and permeability of the membrane were dependent on the molecular size, the polarity and the hydrophilic surface of permeant organics. However, the separation behavior of methanol aqueous solution exhibited other permeation tendency with other feed solutions and contradictory result. That is, the membrane were preferentially permeable to methanol over water despite water molecule has stronger polarity and small molecular size than methanol molecule. In this study, the results were discussed from the viewpoint of chemical and physical properties between permeant molecules and membrane in the diffusion state.

• Journal of Microbiology
• /
• v.45 no.3
• /
• pp.275-279
• /
• 2007

The aims of this study were to detect Burkholderia cepacia complex (Bcc) strains in a cohort of Cystic Fibrosis patients (n=276) and to characterize Bcc isolates by molecular techniques. The results showed that 11.23% of patients were infected by Bcc. Burkholderia cenocepacia lineage III-A was the most prevalent species (64.3%) and, of these, 10% was cblA positive and 50% esmR positive. Less than half of the strains were sensitive to ceftazidime, meropenem, piperacillin-tazobactam, and trimethoprim-sulfamethoxazole. About half of the strains (41%) had homogeneous profiles, suggesting cross-transmission. The infection by B. cenocepacia was associated to a high rate of mortality (p=0.01).

• ALGAE
• /
• v.35 no.1
• /
• pp.17-32
• /
• 2020

Asterochloris is one of the most common genera of lichen phycobionts in Trebouxiophyceae. Asterochloris phycobionts associated with the lichenized fungi Cladonia and Stereocaulon in King George Island (Antarctica) and Morro Chico (Chile), were isolated and then used to establish clonal cultures. To understand the phylogenetic relationships and species diversity of Antarctic Asterochloris species, molecular and morphological data were analyzed by using three microscopy techniques (light, confocal laser and transmission electron) and a multi-locus phylogeny with data from the nuclear-encoded internal transcribed spacer (ITS) rDNA and the actin and plastid-encoded ribulose bisphosphate carboxylase large chain (rbcL) coding genes. Morphological data of three Antarctic strains showed significant species-specific features in chloroplast while molecular data segregated the taxa into distinct three clades as well. Each species had unique molecular signatures that could be found in secondary structures of the ITS1 and ITS2. The species diversity of Antarctic Asterochloris was represented by six taxa, namely, A. glomerata, A. italiana, A. sejongensis, and three new species (A. antarctica, A. pseudoirregularis, A. stereocaulonicola).

• Nuclear Medicine and Molecular Imaging
• /
• v.40 no.2
• /
• pp.74-81
• /
• 2006

Molecular targeting may be defined as the specific concentration of a diagnostic or therapeutic tracer by its Interaction with a molecular species that is distinctly present or absent in a disease state. Monoclonal antibody (mAb) is one of the successful agents for targeted therapy in cancer. To enhance the therapeutic effect, the concept of targeting radionuclides to tumors using radiolabeled mAbs against tumor-associated antigens, radioimmunotherapy, was proposed. The efficacy of radioimmunotherapy, however, has to be further optimized. Several strategies to improve targeting of tumors with radiolabeled mAbs have been developed, such as the use of mAb fragments, the use of high-affinity mAbs, the use of labeling techniques that are stable in vivo, active removal of the radiolabeled mAb from the circulation, and pretargeting strategies. Until now, however, there are many kinds of obstacles to be solved in the use of mAb for the targeted therapy. Major technical challenges to molecular targeting are related to the rapid and specific delivery of tracers to the target, the elimination of unwanted background activity, and the development of more specific targets to create a cytocidal effect. further development of this field will be determined by success in solving these challenges.

• Mycobiology
• /
• v.51 no.5
• /
• pp.300-312
• /
• 2023

Hydnum is a genus of ectomycorrhizal fungi belonging to the Hydnaceae family. It is widely distributed across different regions of the world, including North America, Europe, and Asia; however, some of them showed disjunct distributions. In recent years, with the integration of molecular techniques, the taxonomy and classification of Hydnum have undergone several revisions and advancements. However, these changes have not yet been applied in the Republic of Korea. In this study, we conducted an integrated analysis combining the morphological and molecular analyses of 30 specimens collected over a period of approximately 10 years in the Republic of Korea. For molecular analysis, the sequence data of the internal transcribed spacer (ITS) region, the large subunit of nuclear ribosomal RNA gene (nrLSU), and a portion of translation elongation factor 1-a (TEF1) were employed as molecular markers. Through this study, we identified eight species that had previously not been reported to occur in the Republic of Korea, including one new species, Hydnum paucispinum. A taxonomic key and detailed descriptions of the eight Hydnum species are provided in this study.

• Journal of Environmental Science International
• /
• v.13 no.4
• /
• pp.403-412
• /
• 2004

Waste water-soluble cutting oil was treated with WI type #1 and WI type #2. The properties of the original water-soluble cutting oil were pH=l0.4, viscosity=1.4cP, CODcr=44,750 ppm, and TOC=10,569 ppm. However, the properties of the oil used for more than 3 months were changed to pH=7.82, viscosity=2.1cP, CODcr=151,000 ppm, and TOC=74,556 ppm. It might be attributed to the fact that molecular chains were cut due to thermal oxidation and impurities such as metal chips were incorporated in to the oil during the operation processes. To prevent the putrefaction of oil, the sterilization effect of ozone and UV on the microorganism in the oil was investigated. Ozone treatment showed that 99.99% of the microorganism was annihilated with 30 minutes contact time and 60 minutes were necessary for the same effect when UV was used. Ozone treatment could cut molecular chains of the oil due to strong sterilization power, which was evidenced by the increase of TOC from 25,132 ppm at instantaneous contact to 28,888 ppm at 30 minutes contact time. However, UV treatment didn't show severe changes in TOC values and thus, seemed to cause of severe cut of molecular chains. When the activated carbon was used to treat the waste water-soluble cutting oil, TOC decreased to 25,417 ppm with 0.lg carbon and to 15,946 ppm with 5.0g carbon. This results indicated that the waste oil of small molecular chains could be eliminated by adsorption. From the results, it could be concluded that these treatment techniques could be proposed to remove the waste oil of small molecular chains resulting in the degradation of the oil properties. In addition, these experimental results could be used for the correlation with future works such as investigation of the molecular distribution according to the sizes, lengths, and molecular weight of the chains.

• Journal of Integrative Natural Science
• /
• v.3 no.3
• /
• pp.143-147
• /
• 2010

Since it is of great importance to know how a ligand binds to a receptor, there have been a lot of efforts to improve the quality of prediction of docking poses. Earlier efforts were focused on improving search algorithm and scoring function in a docking program resulting in a partial improvement with a lot of variations. Although these are basically very important and essential, more tangible improvements came from the reduction of search space. In a normal docking study, the approximate active site is assumed to be known. After defining active site, scoring functions and search algorithms are used to locate the expected binding pose within this search space. A good search algorithm will sample wisely toward the correct binding pose. By careful study of receptor structure, it was possible to prioritize sub-space in the active site using "receptor-based pharmacophores" or "hot spots". In a sense, these techniques reduce the search space from the beginning. Further improvements were made when the bound ligand structure is available, i.e., the searching could be directed by molecular similarity using ligand information. This could be very helpful to increase the accuracy of binding pose. In addition, if the biological activity data is available, docking program could be improved to the level of being useful in affinity prediction for a series of congeneric ligands. Since the number of co-crystal structures is increasing in protein databank, "Ligand-Guided Docking" to reduce the search space would be more important to improve the accuracy of docking pose prediction and the efficiency of virtual screening. Further improvements in this area would be useful to produce more reliable docking programs.