• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.103-113
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• 2014

Hydrophobicity is the key concept to understand the role of water in protein folding, protein self-assembly, and protein-ligand interaction. Conventionally, hydrophobicity of amino acids in a protein has been argued based on hydrophobicity scales determined for individual free amino acids, assuming that those scales are unaltered when amino acids are embedded in a protein. Here, we investigate how the hydrophobicity of constituent amino acids depends on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we compute and analyze the hydration free energy - free energy change upon hydration quantifying the hydrophobicity - of three short proteins based on the integral-equation theory of liquids. We find that the hydration free energy of charged amino acids is significantly affected by the protein total charge and exhibits contrasting behavior depending on the protein net charge being positive or negative. We also observe that amino acids in the central ${\beta}$-strand sandwiched by ${\beta}$-sheets display more enhanced hydrophobicity than free amino acids, whereas those in the ${\alpha}$-helix do not clearly show such a tendency. Our results provide novel insights into the hydrophobicity of amino acids, and will be valuable for rationalizing and predicting the strength of water-mediated interaction involved in the biological activity of proteins.

• Macromolecular Research
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• v.11 no.4
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• pp.283-290
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• 2003

Organic drugs including aspirin, omeprazole, and naproxen with three different levels of octanol/water partition coefficient were examined for their release behavior from the amphiphilic PCL-b-PEO-b-PCL (PCEC) matrix. Scanning electron micrograph (SEM) of PCEC illustrated a well defined two-phase morphology consisted of dispersed poly(ethylene oxide) (PEO) domain and continuous polycaprolactone (PCL) phase. Differential scanning calorimetry (DSC) and X-ray diffractometry (XRD) experiments veri tied that three model drugs are dissolved as a molecular dispersion in PCEC matrix. The release of hydrophilic aspirin closely followed the water absorption profile of the matrix indicating that its major fraction is present in PEO domain. However, substantial amount of aspirin present in less hydrophilic region displayed discontinuous biphasic release pattern. In the case of omeprazole with intermediate hydrophobicity consistent release behavior was observed for a period of 24 hrs after the rapid liberation of ca. 10% of the drug presumably partitioned in PEO phase. It was ascribed to the fact that the progressive hydration of PCEC matrix gradually increased the chance of drug/water exposure to compensate the exhaustion of device. Naproxen with the highest octanol/water distribution coefficient among three model drugs exhibited a limited release of 35% for 24 hrs. Finally, hydroxypropyl methylcellulose phthalate (HPMCP)/PCEC blend matrix demonstrated an accelerated and quantitative release of hydrophobic naproxen by generating high porosity and thereby expanding polymer/water interface.

• Bulletin of the Korean Chemical Society
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• v.26 no.8
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• pp.1225-1228
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• 2005

C-terminal fragments of APP (APP-CTs), that contain A$\beta$ sequence, are found in neurotic plaques, neurofibrillary tangles and the cytosol of lymphoblastoid cells obtained from AD patients. CT26, Thr639-Asp664 (TVIVITLVMLKKKQYTSIHH GVVEVD) includes not only the transmembrane domain but also the cytoplasmic domain of APP. This sequence is produced from cleavage of APP by caspase and $\gamma$-secretase. In this study, the solution structure of CT26 was investigated using NMR spectroscopy and circular dichroism (CD) spectropolarimeter in various membrane-mimicking environments. According to CD spectra and the tertiary structure of CT26 determined in TFE-containing aqueous solution, CT26 has an α-helical structure from $Val^{2}\;to\;Lys^{11}$ in TFE-containing aqueous solution. However, according to CD data, CT26 adopts a $\beta$-sheet structure in the SDS micelles and DPC micelles. This result implies that CT26 may have a conformational transition between $\alpha$-helix and $\beta$-sheet structure. This study may provide an insight into the conformational basis of the pathological activity of the C-terminal fragments of APP in the model membrane.

• Bulletin of the Korean Chemical Society
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• v.29 no.12
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• pp.2449-2452
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• 2008

• BMB Reports
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• v.43 no.3
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• pp.193-198
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• 2010

In this study, we report the identification and characterization of a novel C2H2 zinc finger protein, ZNF552, from a human embryonic heart cDNA library. ZNF552 is composed of three exons and two introns and maps to chromosome 19q13.43. The cDNA of ZNF552 is 2.3 kb, encoding 407 amino acids with an amino-terminal KRAB domain and seven carboxyl-terminal C2H2 zinc finger motifs in the nucleus and cytoplasm. Northern blotting analysis indicated that a 2.3 kb transcript specific for ZNF552 was expressed in liver, lung, spleen, testis and kidney, especially with a higher level in the lung and testis in human adult tissues. Reporter gene assays showed that ZNF552 was a transcriptional repressor, and overexpression of ZNF552 in the COS-7 cells inhibited the transcriptional activities of AP-1 and SRE, which could be relieved through RNAi analysis. Deletion studies showed that the KRAB domain of ZNF552 may be involved in this inhibition.

• BMB Reports
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• v.43 no.1
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• pp.17-22
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• 2010

In this study, a novel member of BTB-kelch proteins, named KBTBD7, was cloned from a human embryonic heart cDNA library. The cDNA of KBTBD7 is 3,008 bp long and encodes a protein product of 684 amino acids (77.2 kD). This protein is highly conserved in evolution across different species. Western blot analysis indicates that a 77 kD protein specific for KBTBD7 is wildly expressed in all embryonic tissues examined. In COS-7 cells, KBTBD7 proteins are localized to the cytoplasm. KBTBD7 is a transcription activator when fused to GAL4 DNA-binding domain. Deletion analysis indicates that the BTB domain and kelch repeat motif are main regions for transcriptional activation. Overexpression of KBTBD7 in MCF-7 cells activates the transcriptional activities of activator protein-1 (AP-1) and serum response element (SRE), which can be relieved by siRNA. These results suggest that KBTBD7 proteins may act as a new transcriptional activator in mitogen-activated protein kinase (MAPK) signaling.

• Bulletin of the Korean Chemical Society
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• v.7 no.3
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• pp.204-210
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• 1986

It is shown that the linear stability coincides with the thermodynamic stability in the case of stress tensor evolution for simple dense fluids even if the constitutive (evolution) equation for the stress tensor is nolinear. The domain of coincidence can be defined in the space of parameters appearing in the constitutive equation and we find the domain is confined in an elliptical cone in a three-dimensional parameter space. The corresponding state theory in rheology of simple dense fluids is also further examined. The validity of the idea is strengthened by the examination.

• Journal of Magnetics
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• v.13 no.3
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• pp.102-105
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• 2008

This study examined the feasibility of the combining HDDR-process (hydrogenation, disproportionation, desorption and recombination) with mechanical milling to prepare single domain $Nd_2Fe_{14}B$ particles from a Nd-Fe-B alloy ingot. The $Nd_{15}Fe_{77}B_8$ alloy was HDDR-treated and then subjected to a roller-milling. In the HDDR-treated $Nd_{15}Fe_{77}B_8$ alloy, very small $Nd_2Fe_{14}B$ grains comparable to their critical single domain size(0.3 ${\mu}m$) were observed. These fine individual grains were separated successfully along the grain boundaries by a roller-milling. The separated $Nd_2Fe_{14}B$ grains were found to be single domain particles. These results suggest that single domain particles of the $Nd_2Fe_{14}B$ phase can be prepared from a Nd-Fe-B ingot alloy by combining a HDDR-process with mechanical milling.

• Bulletin of the Korean Chemical Society
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• v.32 no.2
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• pp.719-721
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• 2011

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.342-346
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• 2008

Aurintricarboxylic acid (ATA) prevents apoptosis in a wide range of cell types, including PC12 cells. ATA is known to increase the phosphorylation level of IGF-1 receptor (IGF-1R) and downstream signaling proteins. ATA can translocate across the plasma membrane of PC12 cells and inhibit protein tyrosine phosphatases (PTPs) and, therefore, it is not clear whether ATA exerted its antiapoptotic effect through activation of IGF-1R or by inhibition of cytosolic PTPs. When PC12 cells, deprived of serum, were treated with Fab fragment of anti-IGF-1R antibody to prevent the binding of ATA to the extracellular domain of IGF-1R, ATA was found to penetrate into the cytosolic space of the cells. Under these conditions, the survival-promoting effects of ATA were abolished, and the increase of phosphorylation and characteristic cleavage of IGF-1R were not observed. These results indicate that the antiapoptotic effect of ATA in PC12 cells is due to the binding of ATA to the extracellular domain of IGF-1R and subsequent activation of the IGF-1R, not inhibition of cytosolic PTP(s).