• Proceedings of the PSK Conference
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• 2003.10b
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• pp.176.2-176.2
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• 2003

Transcription factors (TF) can bind tightly to specific DNA lesions formed by some anticancer agents. The formation these TF:(drug-modified DNA) complex may disrupt expression of genes critical for cell survival, and it was proved to be one of biochemical mechanisms of anticancer activity. Based on this model, we have designed programmable DNA Alkylating agents that can also attract TF, especially nuclear receptors. As a model compound, we designed drug molecules, RA-mustard and Am580-mustard, that enable to bind both retinoic acid receptor (RAR) and DNA by using molecular modeling techniques, and synthesized them by connecting chlorambucil and ligand for RAR with a linker unit. (omitted)

• BMB Reports
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• v.36 no.3
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• pp.299-304
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• 2003

For deciphering the cyclic guanosine monophosphate (cGMP) signaling pathway, we employed chemical proteomics to identify the novel target molecules of cGMP. We used cGMP that was immobilized onto agarose beads with linkers directed at three different positions of cGMP. We performed a pull-down assay using the beads as baits on tissue lysates and identified 9 proteins by MALDI-TOF (Matrix-Assisted Laser Desorption/Ionization Time-of-Flight) mass spectrometry. Some of the identified proteins were previously known cGMP targets, including cGMP-dependent protein kinase and cGMP-stimulated phosphodiesterase. Surprisingly, some of the co-precipitated proteins were never formerly reported to associate with the cGMP signaling pathway. The competition binding assays showed that the interactions are not by nonspecific binding to either the linker or bead itself, but by specific binding to cGMP. Furthermore, we observed that the interactions are highly specific to cGMP against other nucleotides, such as cyclic adenosine monophosphate (cAMP) and 5'-GMP, which are structurally similar to cGMP. As one of the identified targets, MAPK1 was confirmed by immunoblotting with an anti-MAPK1 antibody. For further proof, we observed that the membrane-permeable cGMP (8-bromo cyclic GMP) stimulated mitogen-activated protein kinase 1 signaling in the treated cells. Our present study suggests that chemical proteomics can be a very useful and powerful technique for identifying the target proteins of small bioactive molecules.

• Genomics & Informatics
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• v.4 no.3
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• pp.97-102
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• 2006

In acute leukemia patients, several successful methods of expression profiling have been used for various purposes, i.e., to identify new disease class, to select a therapeutic target, or to predict chemo-sensitivity and clinical outcome. In the present study, we tested the peripheral blood of 47 acute leukemia patients in an attempt to identify differentially expressed genes in AML and ALL using a Korean-made 10K oligo-nucleotide microarray. Methods: Total RNA was prepared from peripheral blood and amplified for microarray experimentation. SAM (significant analysis of microarray) and PAM (prediction analysis of microarray) were used to select significant genes. The selected genes were tested for in a test group, independently of the training group. Results: We identified 345 differentially expressed genes that differentiated AML and ALL patients (FWER<0.05). Genes were selected using the training group (n=35) and tested for in the test group (n=12). Both training group and test group discriminated AML and ALL patients accurately. Genes that showed relatively high expression in AML patients were deoxynucleotidyl transferase, pre-B lymphocyte gene 3, B-cell linker, CD9 antigen, lymphoid enhancer-binding factor 1, CD79B antigen, and early B-cell factor. Genes highly expressed in ALL patients were annexin A 1, amyloid beta (A4) precursor protein, amyloid beta (A4) precursor-like protein 2, cathepsin C, lysozyme (renal amyloidosis), myeloperoxidase, and hematopoietic prostaglandin D2 synthase. Conclusion: This study provided genome wide molecular signatures of Korean acute leukemia patients, which clearly identify AML and ALL. Given with other reported signatures, these molecular signatures provide a means of achieving a molecular diagnosis in Korean acute leukemia patents.

• BMB Reports
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• v.40 no.5
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• pp.644-648
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• 2007

Exposure of algae or plants to irradiance from above the light saturation point of photosynthesis is known as high light stress. This high light stress induces various responses including photoinhibition of the photosynthetic apparatus. The degree of photoinhibition could be clearly determined by measuring the parameters such as absorption and fluorescence of chromoproteins. In cyanobacteria and red algae, most of the photosystem (PS) II associated light harvesting is performed by a membrane attached complex called the phycobilisome (PBS). The effects of high intensity light (1000-4000 ${\mu}mol$ photons $m^{-2}s^{-1}$) on excitation energy transfer from PBSs to PS II in a cyanobacterium Spirulina platensis were studied by measuring room temperature PC fluorescence emission spectra. High light (3000 ${\mu}mol$ photons $m^{-2}s^{-1}$) stress had a significant effect on PC fluorescence emission spectra. On the other hand, light stress induced an increase in the ratio of PC fluorescence intensity of PBS indicating that light stress inhibits excitation energy transfer from PBS to PS II. The high light treatment to 3000 ${\mu}mol$ photons $m^{-2}s^{-1}$ caused disappearance of 31.5 kDa linker polypeptide which is known to link PC discs together. In addition we observed the similar decrease in the other polypeptide contents. Our data concludes that the Spirulina cells upon light treatment causes alterations in the phycobiliproteins (PBPs) and affects the energy transfer process within the PBSs.

• Journal of the Korean Applied Science and Technology
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• v.32 no.2
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• pp.202-214
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• 2015

Stimuli-responsive biomaterials that alter their function through sensing local molecular cues may enable technological advances in the fields of drug delivery, gene delivery, actuators, biosensors, and tissue engineering. In this research, pH-responsive hydrogel which is comprised of dimethylaminoethyl methacylate (DMAEMA) and 2-hydroxyethyl methacrylate (HEMA) was synthesized for the effective delivery of doxorubicin (Dox) to breast cancer cells. Cancer and tumor tissues show a lower extracellular pH than normal tissues. DMAEMA/HEMA hydrogels showed significant sensitivity by small pH changes and each formulation of hydrogels was examined by scanning electron microscopy, mechanical test, equilibrium mass swelling, controlled Dox release, and cytotoxicity. High swelling ratios and Dox release were obtained at low pH buffer condition, low cross-linker concentration, and high content of DMAEMA. Dox release was accelerated to 67.3% at pH 5.5 for 6-h incubation at $37^{\circ}C$, while it was limited to 13.8% at pH7.4 at the same time and temperature. Cell toxicity results to breast cancer cells indicate that pH-responsive DMAEMA/HEMA hydrogels may be used as an efficient matrix for anti-cancer drug delivery with various transporting manners. Also, pH-responsive DMAEMA/HEMA hydrogels may be useful in therapeutic treatment which is required a triggered release at low pH range such as gene delivery, ischemia, and diabetic ketoacidosis.

• BMB Reports
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• v.34 no.1
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• pp.59-65
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• 2001

In subtractive hybridization, target sequences in the tester are enriched by hybridizing with an excess amount of driver, followed by removing the tester hybridized with the driver. All of existing subtractive cloning methods are designed to remove the tester/driver hybrid. The removal of hybrid, however, is often unsatisfactory For various reasons. In this study we developed a subtractive enrichment protocol in which the tester/driver can be completely removed by selecting only the tester/tester after hybridization. In this protocol both the tester and driver DNAs are ligated with same linker DNAs and amplified by polymerase chain reaction (PCR). The tester DNA is then digested with two different enzymes and used in subsequent hybridization with an excess driver. After hybridization, the DNA is ligated with the adaptor that is only compatible with the tester/tester. Since only the tester/tester can have the new adaptor, no tester/driver can be amplified by PCR in this protocol. Unlike other methods, a 100% subtraction efficiency can be achieved even though the enzymatic treatments used in the enrichment procedure are incomplete. Furthermore, only the hybridized tester DNA can have the new adaptor and be amplified by PCR, resulting in 100% denaturation in effect. The efficacy of this novel method was verified with the model system in which a known amount of the target sequence is included.

• Polymer(Korea)
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• v.37 no.3
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• pp.288-293
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• 2013

A group of molecularly imprinted polymers (MIPs) with specific recognition for chiral (S)-ibuprofen were successfully prepared based on hydrogen bonds, utilizing ${\alpha}$-methacrylic acid as a functional monomer. The IR analysis of MIPs showed that the blue- and red-shifted hydrogen bonds were formed between templates and functional monomers in the process of self-assembly imprinting and re-recognition, respectively. According to UV-Vis analysis, we found that the ratio of host-guest complexes between template molecule and functional monomer was 1:1. The effect of cross-linker's quantity on the polymerization was studied by transmission electron microscope (TEM). The adsorption selectivity experiments indicated that MIPs exhibited higher selectivity to (S)-ibuprofen than those to ketoprofen and (R)-ibuprofen, (S)-ibuprofen's structural analogs.

• BMB Reports
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• v.46 no.12
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• pp.606-610
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• 2013

Glucagon like peptide-1 (GLP-1) regulates glucose mediated-insulin secretion, nutrient accumulation, and ${\beta}$-cell growth. Despite the potential therapeutic usage for type 2 diabetes (T2D), GLP-1 has a short half-life in vivo ($t_{1/2}$ <2 min). In an attempt to prolong half-life, GLP-1 fusion proteins were genetically engineered: GLP-1 human serum albumin fusion (GLP-1/HSA), AGLP-1/HSA which has an additional alanine at the N-terminus of GLP-1, and AGLP-1-L/HSA, in which a peptide linker is inserted between AGLP-1 and HSA. Recombinant fusion proteins secreted from the Chinese Hamster Ovary-K1 (CHO-K1) cell line were purified with high purity (>96%). AGLP-1 fusion protein was resistant against the dipeptidyl peptidase-IV (DPP-IV). The fusion proteins activated cAMP-mediated signaling in rat insulinoma INS-1 cells. Furthermore, a C57BL/6N mice pharmacodynamics study exhibited that AGLP-1-L/HSA effectively reduced blood glucose level compared to AGLP-1/HSA.

• Biodesign
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• v.5 no.4
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• pp.136-140
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• 2017

Lam6 is a member of sterol-specific ${\underline{l}ipid$ transfer proteins ${\underline{a}}nchored$ at ${\underline{m}ebrane$ contact sites (LAMs). Lam6 localizes to the ER-mitochondria contact sites by its PH-like domain and the C-terminal transmembrane helix. Here, we purified and crystallized the Lam6 PH-like domain from Saccharomyces cerevisiae. To aid crystallization of the Lam6 PH-like domain, T4 lysozyme was fused to the N-terminus of the Lam6 PH-like domain with a short dipeptide linker, GlySer. The fusion protein was crystallized under the condition of 0.1 M HEPES-HCl pH 7.0, 10% (w/v) PEG 8000, and 0.1 M $Na_3$ Citrate at 293K. X-ray diffraction data of the crystals were collected to $2.4{\AA}$ resolution using synchrotron radiation. The crystals belong to the orthorhombic space group $P2_12_12_1$ with unit cell parameters $a=59.5{\AA}$, $b=60.1{\AA}$, and $c=105.6{\AA}$. The asymmetric unit contains one T4L-Lam6 molecule with a solvent content of 58.7%. The initial attempt to solve the structure by molecular replacement using the T4 lysozyme structure was successful.

• Transactions of the Korean hydrogen and new energy society
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• v.15 no.2
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• pp.108-118
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• 2004

To find out rational design and synthetic strategies toward efficient hydrogen storage materials, molecular modeling and quantum mechanical studies have been carried out on the MOFs(Metal-Organic Frameworks) having various organic linkers and nanocube frameworks. The calculation results about the free volume ratio, surface area, and electron density variation of the frameworks indicated that the capacity of the hydrogen storage of MOFs was largely dependent on the specific surface area and electron localization around benzene ring rather than the free volume of MOFs. The prediction of the modeling study could be supported by the hydrogen adsorption experiments using IRMOF-1 and -3, which showed more enhanced hydrogen storage capacities of IRMOF-3 compared with the IRMOF-1's at both experimental conditions, 77K, ∠ $H_2$ 1 atm and ambient temperature, ∠ $H_2$ 35 atm.