• Journal of Microbiology
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• v.45 no.2
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• pp.179-184
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• 2007

Pasteurella multocida, a Gram-negative facultative anaerobic bacterium, is a causative animal pathogen in porcine atrophic rhinitis and avian fowl cholera. For the development of recombinant subunit vaccine against P. multocida, we cloned and analyzed the gene for outer membrane protein H (ompH) from a native strain of Pasteurella multocida in Korea. The OmpH had significant similarity in both primary and secondary structure with those of other serotypes. The full-length, and three short fragments of ompH were expressed in E. coli and the recombinant OmpH proteins were purified, respectively. The recombinant OmpH proteins were antigenic and detectable with antisera produced by either immunization of commercial vaccine for respiratory disease or formalin-killed cell. Antibodies raised against the full-length OmpH provided strong protection against P. multocida, however, three short fragments of recombinant OmpHs, respectively, showed slightly lower protection in mice challenge. The recombinant OmpH might be a useful vaccine candidate antigen for P. multocida.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.305-310
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• 2005

Internal motion of the protein has been described in many papers with C$_{\alpha}$ correlation coefficients to find motional correlation and functional characteristics. To describe the secondary structural motion and stability in protein, we have studied molecular dynamics (MD) simulations on FADD Death Domain and FADD Death Effector Domain which have a similar structure but have different functional characteristics. After 10ns MD simulations, the inter-helical motional correlations and the hydrogen bond ratios were compared between the two domains. From these data we could distinctly compare the internal motions of them and could explain the differences in experimental thermodynamic melting behaviors at molecular level.

• Proceedings of the Korean Society of Near Infrared Spectroscopy Conference
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• 2001.06a
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• pp.1628-1628
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• 2001

Near infrared (NIR) spectroscopy is a powerful technique for non-destructive analysis that can be obtained in a wide range of environments. Recently, NIR measurements have been utilized as probe for quantitative analysis in agricultural, industrial, and medical sciences. In addition, it is also possible to make practical application on NIR for molecular structural analysis. In this work, Fourier transform near infrared (FT-NIR) measurements were carried out to utilize extensively in the relative amounts of different secondary structures were employed, such as Iysozyme, concanavalin A, silk fibroin and so on. Several broad NIR bands due to the protein absorption were observed between 4000 and $5000\;^{-1}$. In order to obtain more structural information from these featureless bands, second derivative and Fourier-self-deconvolution procedures were performed. Significant band separation was observed near the feature at $4610\;^{-1}$ ,. Particularly the peak intensity at $4525\;^{-1}$ shows a characteristic change with thermal denaturation of fibroin. The structural information can be also obtained by mid-IR and CD spectral. Correlation of NIR spectra with protein structure is discussed.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.86-87
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• 2000

Protein folding is a fundamental problem in structural bioinformatics and so numerous studies have been devoted to the subject. As the most common regular secondary conformation in proteins, helix has been an important ingredient of the protein folding problem. In particular, alanine based polypeptides are widely studied to identify the helix folding process in that the aianine amino acid is known to have one of the highest helix propensities. In principle, intrinsic helix propensities can be obtained from gas-phase measurements where solvent effect is absent. Hudgins et al. studied alanine-based peptides in vacuo using high-resolution ion mobility measurement technique. It was reported that introduction of a single Iysine at the C terminus resulted in the formation of very stable, monomeric polyalanine helices. We also have investigated helix formation in vacuo with different terminal charge conditions; we have found a new type of helix motif, To the best of our knowledge, this type of helix conformation has not been characterized before and we name it as I-helix.

• Proceedings of the Korean Biophysical Society Conference
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• 1996.07a
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• pp.33-33
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• 1996

An ectodomain of gp41, the transmembrane fusion protein of HIV, without the fusion peptide region was expressed using pET system in E. coli. The expressed protein gp41core, was isolated as inclusion body and was purified by ion-exchange chromatography after solubilized in 6M urea. The purified denatured protein was renaturated and the folded domain of gp41core was identified by the presence of the proteolysis resistence domain and a high content of ${\alpha}$-helical secondary structure. (omitted)

• Journal of the Korean Magnetic Resonance Society
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• v.27 no.3
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• pp.17-22
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• 2023

Bloom syndrome protein (BLM) is a pivotal RecQ helicase necessary for genetic stability through DNA repair processes. Our investigation focuses on the N-terminal region of BLM, which has been considered as an intrinsically disordered region (IDR). This IDR plays a critical role in DNA metabolism by interacting with other proteins. In this study, we performed triple resonance experiments of BLM_220-300 and presented the backbone chemical shifts. The secondary structure prediction based on chemical shifts of the backbone atoms shows the region is disordered. Our data could help further interaction studies between BLM_220-300 and its binding partners using NMR.

• Journal of Microbiology
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• v.41 no.3
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• pp.239-247
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• 2003

The LRV1-4 capsid protein possesses an endoribonuclease activity that is responsible for the single site-specific cleavage in the 5' untranslated region (UTR) of its own viral RNA genome and the formation of a conserved stem-loop structure (stem-loop IV) in the UTR is essential for the accurate RNA cleavage by the capsid protein. To delineate the nucleotide sequences, which are essential for the correct formation of the stem-loop structure for the accurate RNA cleavage by the viral capsid protein, a wildtype minimal RNA transcript (RNA 5' 249-342) and several synthetic RNA transcripts encoding point-mutations in the stem-loop region were generated in an in vitro transcription system, and used as substrates for the RNA cleavage assay and RNase mapping studies. When the RNA 5' 249-342 transcript was subjected to RNase T1 and A mapping studies, the results showed that the predicted RNA secondary structure in the stem-loop region using FOLD analysis only existed in the presence of Mg$\^$2＋/ ions, suggesting that the metal ion stabilizes the stem-loop structure of the substrate RNA in solution. When point-mutated RNA substrates were used in the RNA cleavage assay and RNase T1 mapping study, the specific nucleotide sequences in the stem-loop region were not required for the accurate RNA cleavage by the viral capsid protein, but the formation of a stem-loop like structure in a region (nucleotides from 267 to 287) stabilized by Mg$\^$2＋/ ions was critical for the accurate RNA cleavage. The RNase T1 mapping and EMSA studies revealed that the Ca$\^$2＋/ and Mn$\^$2＋/ ions, among the reagents tested, could change the mobility of the substrate RNA 5' 249-342 on a gel similarly to that of Mg$\^$2＋/ ions, but only Ca$\^$2＋/ ions identically showed the stabilizing effect of Mg$\^$2＋/ ions on the stem-loop structure, suggesting that binding of the metal ions (Mg$\^$2＋/ or Ca$\^$2＋/) onto the RNA substrate in solution causes change and stabilization of the RNA stem-loop structure, and only the substrate RNA with a rigid stem-loop structure in the essential region can be accurately cleaved by the LRV1-4 viral capsid protein.

• The Korean Journal of Food And Nutrition
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• v.15 no.4
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• pp.331-336
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• 2002

Conformation of soymilk protein was examined to obtain basic information for improved calcium intolerence of soymilk protein partially hydrolyzed with protease. Surface hydrophobicities of three proteins showed the order of SMP(soymilk protein) < SPI(soy protein isolate) < PT-SMP(protease treated soymilk protein). Total thiol group contents of SMP and PT-SMP were similar but larger than that of SPI. Reducing rate of disulfide bond in PT-SMP after 2-mercaptoethanol treatment was laster than that in SMP. And so, this result indicates that PT-SMP may be less compacting due to protease treatement. From circular dichroism result, PT-SMP showed different pattern from SMP and SPI suggesting change of secondary structure by hydrolysis. And analysis of heat denaturating property by DSC showed that denaturation enthalpy of three proteins were all small. Especially enthalpy of PT-SMP was least, and this result suggested that PT-SMP was denatured easily by heating due to less compacting structure.

• Molecules and Cells
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• v.21 no.1
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• pp.63-75
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• 2006

The 5′-region of Potato virus X (PVX) RNA, which contains an AC-rich, single-stranded region and stem-loop structure 1 (SL1), affects RNA replication and assembly. Using Systemic Evolution of Ligands by EXponential enrichment (SELEX) and the electrophoretic mobility shift assay, we demonstrate that SL1 interacts specifically with tobacco protoplast protein extracts (S100). The 36 nucleotides that correspond to the top region of SL1, which comprises stem C, loop C, stem D, and the tetra loop (TL), were randomized and bound to the S100. Remarkably, the wild-type (wt) sequence was selected in the second round, and the number of wt sequences increased as selection proceeded. All of the selected clones from the fifth round contained the wt sequence. Secondary structure predictions (mFOLD) of the recovered sequences revealed relatively stable stem-loop structures that resembled SL1, although the nucleotide sequences therein were different. Moreover, many of the clones selected in the fourth round conserved the TL and C-C mismatch, which suggests the importance of these elements in host protein binding. The SELEX clone that closely resembled the wt SL1 structure with the TL and C-C mismatch was able to replicate and cause systemic symptoms in plants, while most of the other winners replicated poorly only on inoculated leaves. The RNA replication level on protoplasts was also similarly affected. Taken together, these results indicate that the SL1 of PVX interacts with host protein(s) that play important roles related to virus replication.

• Journal of the Korean Magnetic Resonance Society
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• v.20 no.3
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• pp.95-101
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• 2016

Apolipoprotein B-100 (Apo-B100) is a major component of low density lipoprotein (LDL). Apo B-100 protein has 4,536 amino acid sequence and these amino acids are classified into peptide groups A to G with subsequent 20 amino acids (P1-P302). The peptide groups were act as immunoglobulin (Ig) antigens which oxidized via malondialdehyde (MDA). The mimetic peptide P1 (EEEMLENVSLVCPKDAT RFK) out of D-group peptides carrying the highest value of IgG antigens were selected for structural studies that may provide antigen specificity. Circular Dichroism (CD) spectra were measured for peptide secondary structure in the range of 190-250 nm. Experimental results show that P1 exhibit partial of ${\beta}-sheet$ and random coil structure. Homonuclear (COSY, TOCSY, NOESY) 2D-NMR experiments were carried out for NMR signal assignments and structure determination for P1. On the basis of these completely assigned NMR spectra and distance data, distance geometry (DG) and Molecular dynamics (MD) were carried out to determine the structures of P1. The proposed structure was selected by comparisons between experimental NOE spectra and back calculated 2D NOE results from determined structure showing acceptable agreement. The total Root-Mean-Square-Deviation (RMSD) value of P1 obtained upon superposition of all atoms was in the range $0.33{\AA}$. The solution state P1 has mixed structure of ${\beta}-sheet$ (Glu[1] to Cys[12]) and random coil (Pro[13] to Lys[20]). These NMR results are well consistent with secondary structure from experimental results of circular dichroism. Structural studies based on NMR may contribute to the studies of atherosclerosis and observed conformational characteristics of apo B-100 in LDL using monoclonal antibodies.