• Microbiology and Biotechnology Letters
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• v.40 no.4
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• pp.409-413
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• 2012

Indolicidin (ID) is a 13-residue Trp-rich antimicrobial peptide (AMP) isolated from bovine neutrophils. In addition to having a high antimicrobial potency, it is also toxic to mammalian cells. To develop novel ID-derived AMPs with shorter lengths and enhanced prokaryotic selectivities (meaning potent antimicrobial activity against bacterial cells without toxicity against mammalian cells) over the parental ID, several ID analogs were designed and synthesized. Finally, 10-residue ID analogs (SI, SI-PA, SI-WF and SI-WL) with much higher prokaryotic selectivity than the parental ID were developed. Our results suggest that the hydrophobic and aromatic amino acids at the central position of the analog SI with the highest prokaryotic selectivity are important for potent antimicrobial activity, but two Pro residues do not affect antimicrobial activity. The order of prokaryotic selectivity for ID and its designed analogs was SI > SI-PA > SI-WF > SI-WL > ID > SI-WA. Taken together, our designed short ID analogs could be developed as therapeutic agents for treating bacterial infections.

• Microbiology and Biotechnology Letters
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• v.24 no.6
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• pp.678-686
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• 1996

To improve the preservation of Kimchi, we isolated Lactobacillus plantarum lytic enzyme-producing strain from soil, and the enzyme was purified and characterized. From the observation of cultural and morpho- logical characteristics, the isolated strain was identified as Metarrisium anisopliae (Metschn.) Sorok. The enzyme was purified to 75-folds with 40% yields through affinity adsorption and CM-Sephadex C-50 column chromatog- raphy. The optimum pH and temperature for lytic activity are 4.0 and 40$\circ$C, respectively, and the enzyme acitvity is stable between pH 3.0 and 9.0, and up to 50$\circ$C. The enzyme is a monomeric protein with molecular weight of 40,000 daltons by SDS-PAGE and gel filtration. The enzyme is endopeptidase which breaks the peptide linkage of Lactobacillus plantarum peptidoglycan. The lytic action spectra confirmed that Leuconostoc mesenteroides, a useful strain for the fermentation of Kimchi, is not lysed by the enzyme. The enzyme activity is inhibited by N-bromosuccinimide (NBS), which probably indicates the involvement of tryptophan residue in active site of the enzyme, and also inhibited by Ag$^{+}$. The amino acid composition analysis showed that the enzyme contains more acidic amino acids than basic ones, and composition of alanine, glycine, proline and tyrosines was very high.

• Journal of the Korean Society of Food Science and Nutrition
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• v.28 no.6
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• pp.1332-1338
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• 1999

Intermolecular collagen cross links stabilize collagen fibrils and are necessary for normal tensile strength in collagen fibrils. Once the fibrils are aligned, hydroxyllysine, hydroxylysine derived aldehyde modified enzymatically, reacts with hydroxylysine to form the dehydrodihydroxylysinonorleucine (DHLNL), an immature crosslink. Pyridinoline, one of matured cross links is presumably formed nonenzymatically through condensation of DHLNL and hydroxylysine residue. It is widely distributed in hard connective tissues such as cartilage, bone and tendon. L ascorbic acid(AsA) is well known to be required for the enzymatic hydroxylation of proline and lysine in collagen fibrils. The purpose of this study is to clarify the role of AsA on the biosynthesis of DHLNL in vitro. We examined the effect of AsA on the formation of hydroxylysine and DHLNL in collagen. Pyridinoline and DHLNL were measured as a function of time. The contents of DHLNL was increased, reached maximum within 2 hr and was held until 24 hr, then it decreased slowly. On the contrary, pyridinoline increased gradually after 24 hr and continued to increase for 2 weeks. Moreover, the contents of DHLNL remarkably decreased at 60 min after incubation, the contents of DHLNL was decreased by addition of AsA or dehydroascorbic acid(DHA). These results suggest that the supplementation of AsA causes decrease in DHLNL formation and pyridinoline formed by nonenzymatic reaction of DHLNL.

• BMB Reports
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• v.38 no.5
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• pp.591-594
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• 2005

One of the small proteins from Helicobacter pylori, HP1242, was investigated by the solution nuclear magnetic resonance (NMR) spectroscopy. HP1242 is known as a 76-residue conserved hypothetical protein and its function cannot be identified based on sequence homology. Here, the results of the backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments of the HP1242 are reported using double- and triple-resonance techniques. About 95% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances that cover 75 non- Proline residues of the 76 residues are clarified through sequential- and specific- assignments. In addition, three helical regions were clearly identified on the basis of the resonance assignments.

• Journal of Applied Biological Chemistry
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• v.49 no.3
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• pp.110-113
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• 2006

Prolyl endopeptidase (PEP, EC 3.4.21.26, also referred to as prolyl oligopeptidase) degrades proline containing, biologically active neuropeptides such as vasopressin, substance P and thyrotropin-releasing hormone by cleaving peptide bonds on carboxyl side of prolyl residue within neuropeptides of less than 30 amino acids. Evaluation of PEP levels in postmortem brains of Alzheimer's disease patients revealed significant increases in PEP activity. Therefore, a specific PEP inhibitor can be a good candidate of drug against memory loss. Upon our examination for PEP inhibitory activity from micronutrients, ascorbic acid (vitamin C) showed small but significant PEP inhibition (13% PEP inhibition at $8{\mu}g{\cdot}ml^{-1}$). Palmitic acid showed almost no PEP inhibition. However, 6-O-palmitoyl ascorbic acid ($\underline{1}$) showed 70% PEP inhibition at $8{\mu}g{\cdot}ml^{-1}$ indicating that hydrophobic portion of the compound $\underline{1}$ may facilitate the inhibitory effect. $IC_{50}$ value of compound $\underline{1}$ was $12.6{\pm}0.2{\mu}M$. The primary and secondary Lineweaver Burk and Dixon plots for compound $\underline{1}$ indicated that it is a non-competitive inhibitor with inhibition constant (Ki) value of $23.7{\mu}M$.

• Proceedings of the Korea Crystallographic Association Conference
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• 2003.05a
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• pp.15-15
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• 2003

To discover new drugs more quickly and more efficiently, pharmaceutical companies and biotechnology firms are increasingly turning to the genomics and the structural proteomics technologies. Structural-proteomics can provide a foundation for this through the determination and analysis for protein structure on a genomics scale. Among many structures determined by CGI, we will present with the representative examples drawn from our work on novel structures or complex structures of the disease-related proteins. The alpha subunit of Hypoxia-inducible factor (HIF) is targeted for degradation under normoxic conditions by an ubiquitin-ligase complex that recognizes a hydroxylated proline residue in HIF. Hydroxylation is catalysed by HIF prolyl 4-hydroxylases (HIFPH) which are fe(II) and 2-oxoglutarate (2-OG) dependent oxygenases. Here, we discuss the first crystal structure of the catalytic domain of HIFPH in complexes, with the Fe(II)/2-OG at 1.8Å. These structures suggest that the Ll region (residues 236-253), which is also conserved in mammals, form a 'lid' that closes over the active site. The structural and mutagenesis analyses allow us to provide a focus for understanding cellular responses to hypoxia and a target for the therapeutic manipulation.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.28-28
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• 2003

To discover new drugs more quickly and more efficiently, pharmaceutical companies and biotechnology firms are increasingly turning to the genomics and the structural proteomics technologies. Structural-proteomics can provide a foundation for this through the determination and analysis for protein structure on a genomics scale. Among many structures determined by CGI, we will present with the representative examples drawn from our work on novel structures or complex structures of the disease-related proteins. The alpha subunit of Hypoxia-inducible factor (HIF) is targeted for degradation under normoxic conditions by an ubiquitin-ligase complex that recognizes a hydroxylated proline residue in HIF, Hydroxylation is catalysed by HIF prolyl 4-hydroxylases (HIFPH) which are Fe(II) and 2-oxoglutarate (2-OG) dependent oxygenases. Here, we discuss the first crystal structure of the catalytic domain of HIFPH in complexes, with the Fe(II)/2-OG at 1.8 ${\AA}$. These structures suggest that the L1 region (residues 236-253), which is also conserved in mammals, form a ‘lid’ that closes over the active site. The structural and mutagenesis analyses allow us to provide a focus for understanding cellular responses to hypoxia and a target for the therapeutic manipulation.

• Proceedings of the PSK Conference
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• 2002.10a
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• pp.330.2-330.2
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• 2002

The conformational study on cyclic Ac-Cys-Pro-Xaa-Cys-NHMe (Ac-CPXC-NHMe: X = Ala, Val. Leu. Aib. Gly. His. Phe, Tyr. Asn. and Ser) peptides has been carried out using the ECEPP/3 force field and the hydration shell model in the unhydrated and hydrated states. This work has been undertaken to investigate structural implications of the CPXC sequence as the chain reversal for the initiation of protein folding and as the motif for active site of disulfide oxidoreductases. The backbone conformation DAAA is in common the most feasible for cyclic CPXC peptides in the hydrated state. which has a type 1${\beta}$-turn at the Pro-Xaa sequence. The proline residue and the hydrogen bond between backbones of two cystines appear to play a role in stabilizing this preferred conformation of cycilc CPXC peptides. However. the distributions of backbone conformations and ${\beta}$-turns may indicate that the cyclic CPXC peptide seems to exist as an ensemble of ${\beta}$-turns and coiled conformations. The intirnsic stability of the cyclic CPXC motif itself the active conformation appears to play a role in determining electrochemical properties of disulfide oxidoreductases.

• Applied Biological Chemistry
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• v.36 no.3
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• pp.163-171
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• 1993

The collagens from filefish (Novoden modestus) and cod (Gadus macrocephalus Tilesius) skin were isolated and their physicochemical properties were investigated. Glutamic acid, hydroxyproline, valine and phenylalanine in the filefish skin collagen (FSC) were presented at higher levels than those of cod skin collagen (CSC), but the contents of glycine, proline and serine were contrary. The content of essential amino acids of FSC (265 residues/1000 residues) was higher than CSC (229 residues). The solubilities of both collagens were the lowest at pH 7.0, but precipitously increased at acid zone(below pH 5.0). FSC has lower viscosity than CSC. Furthermore, while the viscosities of both collagens were the lowest at pH 7.0, the viscosities of FSC and CSC were the highest at pH 4.0 and pH 2.0, respectively. The denaturation temperature of $FS(25^{\circ}C)$ was higher than $CSD\;(17^{\circ}C)$. The free hydrophobic residue contents of FSC and CSC tended to increase till $60^{\circ}C,\;and\;50^{\circ}C$ respectively, and to decrease thereafter. Hydration capacities of both collagens were the lowest at pH 7.0, and CSC had the superior hydration capacity to FSC. In addition, emulsifying and emulsifying stability of CSC was also superior to FSC.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.325-330
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• 2005

We are generally interested in the analysis, detection and prediction of structural motifs in proteins, in order to infer compatibility of amino acid sequence to structure in proteins of known three-dimensional structure available in the Protein Data Bank. In this context, we are analyzing some of the well-characterized structural motifs in proteins. We have analyzed simple structural motifs, such as, ${\beta}$-turns and ${\gamma}$-turns by evaluating the statistically significant type-dependent amino acid positional preferences in enlarged representative protein datasets and revised the amino acid preferences. In doing so, we identified a number of ‘unexpected’ isolated ${\beta}$-turns with a proline amino acid residue at the (i+2) position. We extended our study to the identification of multiple turns, continuous turns and to peptides that correspond to the combinations of individual ${\beta}$ and ${\gamma}$-turns in proteins and examined the hydrogen-bond interactions likely to stabilize these peptides. This led us to develop a database of structural motifs in proteins (DSMP) that would primarily allow us to make queries based on the various fields in the database for some well-characterized structural motifs, such as, helices, ${\beta}$-strands, turns, ${\beta}$-hairpins, ${\beta}$-${\alpha}$-${\beta}$, ${\psi}$-loops, ${\beta}$-sheets, disulphide bridges. We have recently implemented this information for all entries in the current PDB in a relational database called ODSMP using Oracle9i that is easy to update and maintain and added few additional structural motifs. We have also developed another relational database corresponding to amino acid sequences and their associated secondary structure for representative proteins in the PDB called PSSARD. This database allows flexible queries to be made on the compatibility of amino acid sequences in the PDB to ‘user-defined’ super-secondary structure conformation and vice-versa. Currently, we have extended this database to include nearly 23,000 protein crystal structures available in the PDB. Further, we have analyzed the ‘structural plasticity’ associated with the ${\beta}$-propeller structural motif We have developed a method to automatically detect ${\beta}$-propellers from the PDB codes. We evaluated the accuracy and consistency of predicting ${\beta}$ and ${\gamma}$-turns in proteins using the residue-coupled model. I will discuss results of our work and describe databases and software applications that have been developed.