11 results on '"Kim, Su Yeon"'
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2. PMFF: Development of a Physics-Based Molecular Force Field for Protein Simulation and Ligand Docking.
- Author
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Hwang SB, Lee CJ, Lee S, Ma S, Kang YM, Cho KH, Kim SY, Kwon OY, Yoon CN, Kang YK, Yoon JH, Nam KY, Kim SG, In Y, Chai HH, Acree WE Jr, Grant JA, Gibson KD, Jhon MS, Scheraga HA, and No KT
- Subjects
- Crystallography, X-Ray, Ligands, Models, Molecular, Proteins chemistry, Thermodynamics
- Abstract
The physics-based molecular force field (PMFF) was developed by integrating a set of potential energy functions in which each term in an intermolecular potential energy function is derived based on experimental values, such as the dipole moments, lattice energy, proton transfer energy, and X-ray crystal structures. The term "physics-based" is used to emphasize the idea that the experimental observables that are considered to be the most relevant to each term are used for the parameterization rather than parameterizing all observables together against the target value. PMFF uses MM3 intramolecular potential energy terms to describe intramolecular interactions and includes an implicit solvation model specifically developed for the PMFF. We evaluated the PMFF in three ways. We concluded that the PMFF provides reliable information based on the structure in a biological system and interprets the biological phenomena accurately by providing more accurate evidence of the biological phenomena.
- Published
- 2020
- Full Text
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3. Characterization of Site-Specific N-Glycopeptide Isoforms of α-1-Acid Glycoprotein from an Interlaboratory Study Using LC-MS/MS.
- Author
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Lee JY, Lee HK, Park GW, Hwang H, Jeong HK, Yun KN, Ji ES, Kim KH, Kim JS, Kim JW, Yun SH, Choi CW, Kim SI, Lim JS, Jeong SK, Paik YK, Lee SY, Park J, Kim SY, Choi YJ, Kim YI, Seo J, Cho JY, Oh MJ, Seo N, An HJ, Kim JY, and Yoo JS
- Subjects
- Binding Sites, Blood Specimen Collection, Chromatography, Liquid, Glycosylation, Humans, Reproducibility of Results, Tandem Mass Spectrometry, Glycopeptides chemistry, Orosomucoid chemistry, Protein Isoforms analysis
- Abstract
Glycoprotein conformations are complex and heterogeneous. Currently, site-specific characterization of glycopeptides is a challenge. We sought to establish an efficient method of N-glycoprotein characterization using mass spectrometry (MS). Using alpha-1-acid glycoprotein (AGP) as a model N-glycoprotein, we identified its tryptic N-glycopeptides and examined the data reproducibility in seven laboratories running different LC-MS/MS platforms. We used three test samples and one blind sample to evaluate instrument performance with entire sample preparation workflow. 165 site-specific N-glycopeptides representative of all N-glycosylation sites were identified from AGP 1 and AGP 2 isoforms. The glycopeptide fragmentations by collision-induced dissociation or higher-energy collisional dissociation (HCD) varied based on the MS analyzer. Orbitrap Elite identified the greatest number of AGP N-glycopeptides, followed by Triple TOF and Q-Exactive Plus. Reproducible generation of oxonium ions, glycan-cleaved glycopeptide fragment ions, and peptide backbone fragment ions was essential for successful identification. Laboratory proficiency affected the number of identified N-glycopeptides. The relative quantities of the 10 major N-glycopeptide isoforms of AGP detected in four laboratories were compared to assess reproducibility. Quantitative analysis showed that the coefficient of variation was <25% for all test samples. Our analytical protocol yielded identification and quantification of site-specific N-glycopeptide isoforms of AGP from control and disease plasma sample.
- Published
- 2016
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4. Simultaneous enhancement of upconversion and downshifting luminescence via plasmonic structure.
- Author
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Lee KT, Park JH, Kwon SJ, Kwon HK, Kyhm J, Kwak KW, Jang HS, Kim SY, Han JS, Lee SH, Shin DH, Ko H, Han IK, Ju BK, Kwon SH, and Ko DH
- Subjects
- Light, Materials Testing, Scattering, Radiation, Luminescent Measurements methods, Metal Nanoparticles chemistry, Metal Nanoparticles ultrastructure, Molecular Imprinting methods, Silver chemistry, Surface Plasmon Resonance methods
- Abstract
We describe a metal nanodisk-insulator-metal (MIM) structure that enhances lanthanide-based upconversion (UC) and downshifting (DS) simultaneously. The structure was fabricated using a nanotransfer printing method that facilitates large-area applications of nanostructures for optoelectronic devices. The proposed MIM structure is a promising way to harness the entire solar spectrum by converting both ultraviolet and near-infrared to visible light concurrently through resonant-mode excitation. The overall photoluminescence enhancements of the UC and DS were 174- and 29-fold, respectively.
- Published
- 2015
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5. Tangeretin reduces ultraviolet B (UVB)-induced cyclooxygenase-2 expression in mouse epidermal cells by blocking mitogen-activated protein kinase (MAPK) activation and reactive oxygen species (ROS) generation.
- Author
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Yoon JH, Lim TG, Lee KM, Jeon AJ, Kim SY, and Lee KW
- Subjects
- Animals, Cells, Cultured, Citrus sinensis chemistry, Cyclooxygenase 2 metabolism, Enzyme Activation drug effects, Enzyme Activation radiation effects, Epidermis drug effects, Epidermis metabolism, Epidermis radiation effects, Gene Expression Regulation, Enzymologic drug effects, Mice, Mitogen-Activated Protein Kinases genetics, Signal Transduction drug effects, Ultraviolet Rays, Cyclooxygenase 2 genetics, Down-Regulation, Epidermis enzymology, Flavones pharmacology, Gene Expression Regulation, Enzymologic radiation effects, Mitogen-Activated Protein Kinases metabolism, Plant Extracts pharmacology, Reactive Oxygen Species metabolism
- Abstract
The present study examined the effects of tangeretin, a polymethoxylated flavonone present in citrus fruits, on ultraviolet B (UVB)-induced cyclooxygenase-2 (COX-2) expression in JB6 P+ mouse skin epidermal cells. Tangeretin suppressed UVB-induced COX-2 expression and transactivation of nuclear factor-κB and activator protein-1 in JB6 P+ cells. Moreover, tangeretin blocked UVB-induced phosphorylation of Akt and mitogen-activated protein kinases (MAPKs), including extracellular signal-regulated protein kinase, c-Jun N-terminal kinase, and p38, and attenuated the phosphorylation of MAPK kinases 1/2, 3/6, and 4. Tangeretin also limited the endogenous generation of reactive oxygen species (ROS), thereby protecting the cells against oxidative stress. However, tangeretin did not scavenge the stable 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical and influence the nicotinamide adenine dinucleotide phosphate oxidase activity. These results suggest that the anti-inflammatory effects of tangeretin stem from its modulation of cell signaling and suppression of intracellular ROS generation. Tangeretin may have a potent chemopreventive effect in skin cancer.
- Published
- 2011
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6. Simple photoreduction of graphene oxide nanosheet under mild conditions.
- Author
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Matsumoto Y, Koinuma M, Kim SY, Watanabe Y, Taniguchi T, Hatakeyama K, Tateishi H, and Ida S
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- Materials Testing, Nanostructures ultrastructure, Nanotechnology methods, Oxidation-Reduction, Oxides chemistry, Oxides radiation effects, Particle Size, Photochemistry methods, Ultraviolet Rays, Crystallization methods, Graphite chemistry, Graphite radiation effects, Membranes, Artificial, Nanostructures chemistry, Nanostructures radiation effects
- Abstract
Graphene oxide (GO) nanosheets were reduced by UV irradiation in H2 or N2 under mild conditions (at room temperature) without a photocatalyst. Photoreduction proceeded even in an aqueous suspension of nanosheets. The GO nanosheets reduced by this method were analyzed by X-ray photoelectron spectroscopy and Raman spectroscopy. It was found that epoxy groups attached to the interiors of aromatic domains of the GO nanosheet were destroyed during UV irradiation to form relatively large sp2 islands resulting in a high conductivity. I-V curves were measured by conductive atomic force microscopy (AFM; perpendicular to a single nanosheet) and a two-electrode system (parallel to the nanosheet). They revealed that photoreduced GO nanosheets have high conductivities, whereas nonreduced GO nanosheets are nearly insulating. Ag+ adsorbed on GO nanosheets promoted the photoreduction. This photoreduction method was very useful for photopatterning a conducting section of micrometer size on insulating GO. The developed photoreduction process based on a photoreaction will extend the applications of GO to many fields because it can be performed in mild conditions without a photocatalyst.
- Published
- 2010
- Full Text
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7. Influence of electrolyte composition on the photovoltaic performance and stability of dye-sensitized solar cells with multiwalled carbon nanotube catalysts.
- Author
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Seo SH, Kim SY, Koo BK, Cha SI, and Lee DY
- Abstract
Efficient dye-sensitized solar cells (DSCs) were realized by using multiwalled carbon nanotubes (CNTs) as the counter-electrode catalyst. The catalytic layers were produced from an aqueous paste of mass-produced raw CNTs with carboxymethylcellulose polymer by low-temperature (70 degrees C) drying. We found that the highly disordered CNTs played the important role of increasing the fill factor of DSCs with electrolytes including large molecules and that the presence of Li(+) as the counter charges for I(3)(-)/I(-) redox couples reduced the chemical stability when using the CNT catalyst. Our experiments showed that by replacing the conventional Pt catalyst and Li(+)-based electrolyte with the proposed CNT catalyst and an electrolyte containing 1-butyl-3-methylimidazolium cations instead of Li(+), the energy conversion efficiency increased from 6.51% to 7.13%. This result suggests that highly defective CNT catalysts prepared by low-temperature drying are viable cost-effective alternatives for DSCs, as long as the electrolytes composition is optimized.
- Published
- 2010
- Full Text
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8. Regioselectivity prediction of CYP1A2-mediated phase I metabolism.
- Author
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Jung J, Kim ND, Kim SY, Choi I, Cho KH, Oh WS, Kim DN, and No KT
- Subjects
- Binding Sites, Drug Design, Kinetics, Models, Molecular, Oxidation-Reduction, Pharmaceutical Preparations chemistry, Pharmaceutical Preparations metabolism, Protein Binding, Protein Conformation, Stereoisomerism, Substrate Specificity, Thermodynamics, Cytochrome P-450 CYP1A2 chemistry, Cytochrome P-450 CYP1A2 metabolism, Models, Biological
- Abstract
A kinetic, reactivity-binding model has been proposed to predict the regioselectivity of substrates meditated by the CYP1A2 enzyme, which is responsible for the metabolism of planar-conjugated compounds such as caffeine. This model consists of a docking simulation for binding energy and a semiempirical molecular orbital calculation for activation energy. Possible binding modes of CYP1A2 substrates were first examined using automated docking based on the crystal structure of CYP1A2, and binding energy was calculated. Then, activation energies for CYP1A2-mediated metabolism reactions were calculated using the semiempirical molecular orbital calculation, AM1. Finally, the metabolic probability obtained from two energy terms, binding and activation energies, was used for predicting the most probable metabolic site. This model predicted 8 out of 12 substrates accurately as the primary preferred site among all possible metabolic sites, and the other four substrates were predicted into the secondary preferred site. This method can be applied for qualitative prediction of drug metabolism mediated by CYP1A2 and other CYP450 family enzymes, helping to develop drugs efficiently.
- Published
- 2008
- Full Text
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9. Stereospecific high-affinity TRPV1 antagonists: chiral N-(2-benzyl-3-pivaloyloxypropyl) 2-[4-(methylsulfonylamino)phenyl]propionamide analogues.
- Author
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Ryu H, Jin MK, Kim SY, Choi HK, Kang SU, Kang DW, Lee J, Pearce LV, Pavlyukovets VA, Morgan MA, Tran R, Toth A, Lundberg DJ, and Blumberg PM
- Subjects
- Animals, Benzeneacetamides chemistry, Benzeneacetamides pharmacology, Binding Sites, Binding, Competitive, CHO Cells, Calcium metabolism, Cricetinae, Cricetulus, Hydrophobic and Hydrophilic Interactions, Mesylates chemistry, Mesylates pharmacology, Models, Molecular, Radioligand Assay, Rats, Stereoisomerism, Structure-Activity Relationship, TRPV Cation Channels agonists, Benzeneacetamides chemical synthesis, Mesylates chemical synthesis, TRPV Cation Channels antagonists & inhibitors
- Abstract
Previously, we reported the thiourea antagonists 2a and 2b as potent and high affinity TRPV1 antagonists. For further optimization of the lead compounds, a series of their amide and alpha-substituted amide surrogates were investigated and novel chiral N-(2-benzyl-3-pivaloyloxypropyl) 2-[4-(methylsulfonylamino)phenyl]propionamide analogues were characterized as potent and stereospecific rTRPV1 antagonists. In particular, compounds 72 and 73 displayed high binding affinities, with K i values of 4.12 and 1.83 nM and potent antagonism with K i values of 0.58 and 5.2 nM, respectively, in rTRPV1/CHO cells. These values are comparable or more potent than those of 5-iodoRTX under the same assay conditions. A distinctive binding model that includes two hydrophobic pockets is proposed for this series of compounds based on docking studies of 57 and 72 with a homology model of the TM3/4 region of TRPV1.
- Published
- 2008
- Full Text
- View/download PDF
10. Branched diacylglycerol-lactones as potent protein kinase C ligands and alpha-secretase activators.
- Author
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Lee J, Kang JH, Han KC, Kim Y, Kim SY, Youn HS, Mook-Jung I, Kim H, Lo Han JH, Ha HJ, Kim YH, Marquez VE, Lewin NE, Pearce LV, Lundberg DJ, and Blumberg PM
- Subjects
- Amyloid Precursor Protein Secretases, Animals, Aspartic Acid Endopeptidases, Cell Line, Tumor, Diglycerides chemistry, Diglycerides pharmacology, Enzyme Activators chemistry, Enzyme Activators pharmacology, Humans, Lactones chemistry, Lactones pharmacology, Ligands, Phorbol 12,13-Dibutyrate metabolism, Phorbol 12,13-Dibutyrate pharmacology, Protein Binding, Rats, Stereoisomerism, Structure-Activity Relationship, Diglycerides chemical synthesis, Endopeptidases metabolism, Enzyme Activators chemical synthesis, Lactones chemical synthesis, Protein Kinase C-alpha metabolism
- Abstract
Using as our lead structure a potent PKC ligand (1) that we had previously described, we investigated a series of branched DAG-lactones to optimize the scaffold for PKC binding affinity and reduced lipophilicity, and we examined the potential utility of select compounds as alpha-secretase activators. Activation of alpha-secretase upon PKC stimulation by ligands causes increased degradation of the amyloid precursor protein (APP), resulting in enhanced secretion of sAPPalpha and reduced deposition of beta-amyloid peptide (Abeta), which is implicated in the pathogenesis of Alzheimer's disease. We modified in a systematic manner the C5-acyl group, the 3-alkylidene, and the lactone ring in 1 and established structure-activity relationships for this series of potent PKC ligands. Select DAG-lactones with high binding affinities for PKC were evaluated for their abilities to lead to increased sAPPalpha secretion as a result of alpha-secretase activation. The DAG-lactones potently induced alpha-secretase activation, and their potencies correlated with the corresponding PKC binding affinities and lipophilicities. Further investigation indicated that 2 exhibited a modestly higher level of sAPPalpha secretion than did phorbol 12,13-dibutyrate (PDBu).
- Published
- 2006
- Full Text
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11. Macrocyclic diacylglycerol-bis-lactones as conformationally constrained analogues of diacylglycerol-lactones. Interactions with protein kinase C.
- Author
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Kang JH, Kim SY, Lee J, Marquez VE, Lewin NE, Pearce LV, and Blumberg PM
- Subjects
- Diglycerides chemistry, Lactones chemistry, Ligands, Models, Molecular, Molecular Conformation, Protein Binding, Diglycerides chemical synthesis, Lactones chemical synthesis, Protein Kinase C chemistry
- Abstract
A series of macrocyclic diacylglycerol (DAG)-bis-lactones were investigated as extreme conformationally constrained analogues of DAG-lactones in order to seek more potent protein kinase C (PKC) ligands with higher binding affinities and less lipophilicity than previous compounds. The additional constraint achieved the desired objective as exemplified by the macrocyclic DAG-bis-lactone 57, which exhibited a 6-fold higher binding affinity for PKCalpha (K(i) = 6.07 nM) than the corresponding nonmacrocyclic 3-alkylidene DAG-lactone 6. A structure-activity relationship (SAR) analysis of the macrocyclic DAG-bis-lactones demonstrated a parabolic relationship between activity and lipophilicity, as well as a predilection for the Z-alkylidene isomers as the preferred ligands. Molecular docking studies revealed that macrocyclic DAG-bis-lactone 57 bound to the C1b domain of PKCalpha exclusively in the sn-1 binding mode in contrast to DAG-lactone 6, which showed both sn-1 and sn-2 binding modes. It is proposed that the high potency displayed by these macrocyclic DAG-bis-lactones results from a set of more favorable hydrogen bonding and hydrophobic interactions with PKCalpha as well as from a reduced entropy penalty due to conformational restriction.
- Published
- 2004
- Full Text
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