• Proceeding of EDISON Challenge
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• 2016.03a
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• pp.163-166
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• 2016

Hydrophobicity is the key concept to understand the water plays in protein folding, protein aggregation, and protein-protein interaction. Traditionally, the hydrophobicity of protein is defined based on the scales of the hydrophobicity of residue, assuming that the hydrophobicity of free amino acids is maintained. Here, we explore how the hydrophobicity of constituting amino acids in protein rely on the protein context, in particular, on the total charge and secondary structures of a protein. To this end, we calculate and investigate the hydration free energy 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 total charge being positive or negative. We also observe that amino acids in the ${\beta}-sheets$ display more enhanced the hydrophobicity than amino acids in the loop, whereas those in the ${\alpha}-helix$ do not clearly show such a tendency. And the salt-bridge forming amino acids also exhibit increase of the hydrophobicity than that with no salt bridge. 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.

• Journal of Microbiology and Biotechnology
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• v.7 no.2
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• pp.132-137
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• 1997

A novel protein (HEAAE, High Essential Amino Acid Encoding Protein), rich in essential amino acids ($75{\%}$ of total), was designed and constructed in our laboratory. The designed peptides were analyzed by SYBLE and stable secondary and tertiary structures were predicted. The monomeric form (HEAAE-1) of the protein consists of 20 amino acid residues with four additional amino acids comprising a potential ${\beta}$-turn (HEAAE-4). Size exclusion analysis demonstrated that the monomer is self-aggregates in aqueous solution to form higher ordered multimeric structures, which are very reminiscent of natural plant storage proteins. The DNA encoding this amino acid sequence was synthesized, and from this monomeric gene fragment (heaae-1), the stable tetrameric form of the gene (heaae-4) was generated by subcloning into the E. coli expression vector pKK223-3. A clear 6 kDa polypeptide band corresponding to the molecular weight of the dimeric form (HEAAE-2) was detected. The smeared band which appeared around the molecular weight corresponding to HEAAE-4 of 11 kDa suggested that the tetramer form of this protein might be processed into smaller size products.

• Journal of the Korean Magnetic Resonance Society
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• v.10 no.2
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• pp.175-187
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• 2006

Binding interactions between a positively charged porphyrin derivative TMAP(meso-tetra(p-trimethylanilinium-4-yl)porphyrin) and triple helical $(dT)_{12}{\cdot}(dA)_{12}{\cdot}(dT)_{12}$, as well as double helical $(dA)_{12}{\cdot}(dT)_{12}$ have been studied with NMR, UV and CD spectroscopy to obtain the detailed information about the binding mode and binding site. UV melting studies showed both DNA duplex and triple helix represented very similar UV absorption patterns upon binding TMAP, but the presence of third strand of triple helical $(dT)_{12}{\cdot}(dA)_{12}{\cdot}(dT)_{12}$, inhibited improvement in thermal stability in terms of melting temperature, $T_m$. In addition, the TMAP molecule is thought to bind to the major groove, according to CD and NMR data. But absence of the clear isosbestic point in UV absorption spectra represented that binding of TMAP to DNA duplex as well as DNA triplex did not show a single binding mode, rather complex binding modes.

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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• pp.49-53
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• 2015

MRA1997 is a 76-residue conserved hypothetical protein of Mycobacterium tuberculosis H37Ra, one of the most pathogenic bacterial species and the causative agent of tuberculosis. In this study, the sequence-specific backbone resonance assignment of MRA1997 was performed using NMR spectroscopy. Approximately 88.3% of the total resonances could be unambiguously assigned. By analyzing deviations of the $C{\alpha}$ and $C{\beta}$ chemical shift values, the secondary structure of MRA1997 was calculated. The result revealed that secondary structure of MRA 1997 consists of one ${\alpha}$-helix and five ${\beta}$-sheets. Our structural study will be a footstone towards the characterization of the three-dimensional structure of MRA1997.

• Journal of the Korean Magnetic Resonance Society
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• v.21 no.2
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• pp.50-54
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• 2017

Cupin-superfamily proteins represent the most functionally diverse groups of proteins and include a huge number of functionally uncharacterized proteins. Recently, YaiE, a cupin protein from Escherichia coli has been suggested to be involved in a novel activity of pyrimidine/purine nucleoside phosphorylase (PPNP). In the present study, we achieved a complete backbone NMR assignments of YaiE, by a series of heteronuclear multidimensional NMR experiments on its [$^{13}C/^{15}N$]-enriched sample. Subsequently, secondary structure analysis using the assigned chemical shift values identified 10 obvious ${\beta}-strands$ and a tentative $3_{10}-helix$. Taken all together, the results constitute the first structural characterization of a putative PPNP cupin protein.

• Archives of Plastic Surgery
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• v.38 no.4
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• pp.490-493
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• 2011

Purpose: Basosquamous carcinoma is a rare malignancy, with features of both basal cell carcinoma and squamous cell carcinoma. It is considered as aggressive tumor with a high risk of recurrence and metastases. Authors report a case of basosquamous cell carcinoma. Methods: A 72 year-old man, who had an erythematous ulcer on his left auricle, described a slow growing lesion, starting at the posterior surface of the superior helix with a steady increase in size during the past 10 years. At operation, auricular cartilage was grossly invaded by the tumor and was, therefore, amputated with tumor-free margins. Results: Histopathologic examination was revealed a basosquamous cell carcinoma. On positron emission tomography/computed tomography (PET/CT) and neck CT were negative for signs of further nodal involvement or metastases to other organs. At follow-up 6 months later, his wounds were noted to be well healed, with no evidence of local recurrence or identifiable metastases. Conclusion: Because basosquamous cell carcinoma has a significant potential to recur and metastasize, surgical excision for this type of carcinoma should be more extensive than that performed for conventional basal cell carcinoma or squamous cell carcinoma. In addition, regional lymph nodes should be monitored and close follow-up should be carried out.

• ALGAE
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• v.35 no.1
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• pp.1-15
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• 2020

Two strains isolated from a subtropical region in China, were morphologically identified as a Nostoc-like species, but its taxonomic identity was unknown. In this study, these two strains were taxonomically and phylogenetically characterized based on polyphasic approach combining morphological and genetic characteristics. Though both were virtually indistinguishable from Nostoc in field and cultured material, these two strains were phylogenetically distinct from Nostoc based on 16S rRNA phylogeny. The 16S-23S internal transcribed spacer rRNA secondary structure of these strains showed the unique pattern of D1-D1', Box-B, and V3 helix, which distinguished them from other Nostoc-like heterocytous genera. A unique cluster separated from Nostoc sensu stricto supports the establishment of Violetonostoc gen. nov. with the type species as Violetonostoc minutum sp. nov.

• Proceedings of the Korean Society of Precision Engineering Conference
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• 2005.10a
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• pp.370-374
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• 2005

This study deals with the method of post-processing in the automatic tool path generation for 5-axis NC machining. The 5-axis NC machining cannot only cope with the manufacturing of complicated shapes, but also offers numerous advantages such as reasonable tool employment, great reduction of set-up process and so on. Thus 5-axis NC machining has been used fur aircraft parts, mold and die as well as for complicated shapes such as impeller, propeller and rotor. However, most of the present CAM systems for 5-axis NC machining have limited functions in terms of tool collision, machine limits and post-processing. Especially 5-axis machine configurations are various according to the method which the rotational axes are adapted with the table and spindle. For that reason, in many cases the optimal numerical control (NC) data cannot be obtained or considerable time is consumed. To solve this problem, we applied a general post-processor fur 5-axis NC machining. The validity of this post-processor should be experimentally confirmed by successfully milling to a helix shaped workpiece.

• Food Science and Biotechnology
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• v.15 no.3
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• pp.418-423
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• 2006

Egg white powders (EWPs) were produced after pH adjustment (PH 6-9) of fresh egg white, followed by spray-drying, and foaming and gelling properties of EWPs were examined. EWP produced after pH adjustment to 6.5 (EWP-6.5) resulted in significantly higher foaming ability and gel hardness than control and other pH-adjusted EWP. Significant increases in surface -SH content and surface hydrophobicity of EWP-6.5 coincided with improved foaming ability and gel hardness. Significantly higher consistency index for reconstituted EWP-6.5 indicates unfolding of egg white protein was substantially increased in EWP-6.5. Decreased a-helix content in EWP-6.5 was confirmed by circular dichroism spectral analysis. These results indicate pH adjustment prior to spray-drying leads to structural changes in egg white proteins, significantly affecting major functionalities of EWP.

• Journal of the Korean Magnetic Resonance Society
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• v.9 no.2
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• pp.74-92
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• 2005

The high resolution solution structure of MCP-3 was determined using multinuclear, multidimensional NMR spectroscopy with an expressed and $^{13}C-\;and\;^{15}N-labeled$ protein. The MCP-3 has a typical chemokine fold including 3 anti-parallel $\beta-sheets$, and a C-terminal helix, but it exists as a monomer in solution under the conditions where the structure was determined (2 mM, pH 5.1 at $30^{\circ}C$). Based on the structure and the amino acid sequence compared to other chemokines we propose that Ile20 and Leu25 in MCP-3 play key roles in the formation of N-loop (residues between the $2^{nd}$ cysteine and the I sheet) which has been implicated as a determinant of chemokine specificity. Additional receptor binding surface is supplied by the 40s loop (residues between the 2 and the 3 sheet) and the binding interface of the acidic N-terminal region of chemokine receptor to MCP-3 would resemble the dimerization interface of CC type dimer.