• Journal of the Korean Chemical Society
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• v.40 no.6
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• pp.394-400
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• 1996

The conformational transitions of oligopeptide -(HPPHPPP)$_n$- (H: hydrophobic amino acid, P: polar amino acid) which becomes cross linked-dimer are detected at various temperatures, pHs, ionic strengths, and the concentrations of denaturant. In this study, the transitions of oligopeptide due to denaturant, and those due to temperature are theoretically studied. Oligopeptide 20R as chain-dimer and guanidum-HCl as denaturant are used(20R, which contains 10 interchain and /or 10 intrachain electrostatic repulsions). Alpha helix-coil transitions by denaturant are very steep. This shows that the denaturations have transition states of, presumably all helical forms and random coils. The transitions by temperature are smoother than those by the concentration of denaturant. At low temperature the oligopetides which contain long helices exist more than those which contain short helices. As temperature rises, the mole fractions of the partially denatured oligopeptides increase. So the partially denatured oligopeptides are widely distributed at the transition temperature.

• BMB Reports
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• v.40 no.2
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• pp.247-260
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• 2007

Cinnamate 4-hydroxylase (C4H) is a key enzyme of phenylpropanoid pathway, which synthesizes numerous secondary metabolites to participate in development and adaption. Two C4H isoforms, the 2192-bp BnC4H-1 and 2108-bp BnC4H-2, were cloned from oilseed rape (Brassica napus). They both have two introns and a 1518-bp open reading frame encoding a 505-amino-acid polypeptide. BnC4H-1 is 57.73 kDa with an isoelectric point of 9.11, while 57.75 kDa and 9.13 for BnC4H-2. They share only 80.6% identities on nucleotide level but 96.6% identities and 98.4% positives on protein level. Showing highest homologies to Arabidopsis thaliana C4H, they possess a conserved p450 domain and all P450-featured motifs, and are identical to typical C4Hs at substrate-recognition sites and active site residues. They are most probably associated with endoplasmic reticulum by one or both of the N- and C-terminal transmembrane helices. Phosphorylation may be a necessary post-translational modification. Their secondary structures are dominated by alpha helices and random coils. Most helices locate in the central region, while extended strands mainly distribute before and after this region. Southern blot indicated about 9 or more C4H paralogs in B. napus. In hypocotyl, cotyledon, stem, flower, bud, young- and middle-stage seed, they are co-dominantly expressed. In root and old seed, BnC4H-2 is dominant over BnC4H-1, with a reverse trend in leaf and pericarp. Paralogous C4H numbers in Brassicaceae genomes and possible roles of conserved motifs in 5' UTR and the 2nd intron are discussed.

• Journal of the Korean Magnetic Resonance Society
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• v.16 no.1
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• pp.22-33
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• 2012

Tid1, belonging to the Hsp40/DnaJ family of proteins, functions as a cochaperone of cytosolic and mitochondrial Hsp70 proteins. In particular, the N-terminal J-domain of Tid1 (Tid1-JD) constitutes the major binding sites for proteinprotein interactions with client proteins, including p53, as well as its partner chaperone, Hsp70. In the present study, soluble, recombinant protein of Tid1-JD could be obtained by using the pCold vector system, and backbone NMR assignments were completed using the isotope $[^{13}C/^{15}N]$-enriched protein. Far-UV CD result implied that Tid1-JD is an ${\alpha}$-helical protein and the secondary structure determined using chemical shift data sets indentified four ${\alpha}$-helices with a loop region containing the HPD (conserved tripeptide of His, Pro and Asp) motif. Additionally, NMR spectra under different conditions implied that the HPD motif, which is a critical region for protein-protein interactions of Tid1-JD, would possess dynamic properties.

• Journal of the Korean Magnetic Resonance Society
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• v.10 no.1
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• pp.96-104
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• 2006

The gene coding for APG8a (At4g21980), a protein from Arabidopsis thaliana, is involved in the autophagy process. The protein is an interesting candidate for structure determination by NMR spectroscopy. Toward this end, APG8a has been produced recombinantly in Escherichia coli and typical NMR experiments such as $^{15}N-HSQC$, HNCA, HN(CO)CA, CBCA(CO)NH, HCCH-TOCSY, HNCO were performed. The backbone resonances, HN, N, CA, CB, and C' were sequence-specifically assigned, and the secondary structures including 3 $\alpha$ helices and $4\beta$ strands were deduced based on the assignments. Due to the intrinsic flexibility or the effect of the denaturant, the backbone resonances were not fully observed. Since the structure calculation by NMR data was not possible, the 3-dimensional model was built based on the sequence homology, and compared with the NMR results. The overall structure of the model could explain and complement the NMR derived secondary structures.

• Bulletin of the Korean Chemical Society
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• v.35 no.12
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• pp.3632-3636
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• 2014

In this study we designed and synthesized several heptapeptides that are enforced to form an amphipathic helix using all-hydrocarbon stapling system and evaluated their antimicrobial and hemolytic activities. The antimicrobial activity showed clear structure-activity relationships, confirming the importance of helicity and amphipathicity. Some stapled heptapeptides displayed a moderate antimicrobial activity along with a low hemolytic activity. To our best knowledge, although not highly potent, these stapled peptides represent the shortest helical amphipathic antimicrobial peptides reported to date. The preliminary data obtained in this work would serve as a good starting point for further developing short analogs of amphipathic helical antimicrobial peptides.

• BMB Reports
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• v.37 no.5
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• pp.565-573
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• 2004

Orexin-A and orexin-B (hypocretin-1 and hypocretin-2, respectively) are important hypothalamic neuro-peptides, which are encoded by a single mRNA transcript and stimulate food intake as well as regulate wakefulness. Here we determined the solution structure of orexin-A by NMR spectroscopy and by simulated-annealing calculation. The structural features of orexin-A involve two $\alpha$-helices, with the hydrophobic residues disposed to on one side of helix, and hydrophilic residues to the other. A hydrophilic turn induced by two disulfide bonds provides the key difference between orexin-A and -B. With previous mutagenic studies, the derived structure of orexin-A provides us with a structure-functional view for novel drug design.

• Proceedings of the Korean Biophysical Society Conference
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• 2001.06a
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• pp.21-21
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• 2001

PDZ domains are molecular-recognition elements that mediate protein-protein interactions. The PDZ domain was discovered originally as a common motif present in three structurally related proteins： PSD-95 (postsynaptic density protein), Dlg (discs-large protein) and ZQ-1 (zonula occludens-1). The PDZ domain is globular domain, containing about 80-100 amino acids, and a conserved motif with two alpha helices and six beta strands. Most of them bind selectively to the C-termini of the interacting proteins at the complexes of signaling molecules and membrane associated receptors.(omitted)

• Journal of the Korean Magnetic Resonance Society
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• v.19 no.1
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• pp.42-48
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• 2015

The mannitol transporter Enzyme $II^{Mtl}$ of the bacterial phosphotransferase system has two cytoplasmic phosphoryl transfer domains $IIA^{Mtl}$ and $IIB^{Mtl}$. The two domains are linked by a flexible peptide linker in mesophilic bacterial strains, whereas they are expressed as separated domains in thermophilic strains. Here, we carried out backbone assignment of $IIA^{Mtl}$ from thermophilic Thermoanaerobacter Tencongensis using a suite of heteronuclear triple resonance NMR spectroscopy. We have completed 94% of the backbone assignment, and obtained secondary structural information based on torsion angles derived from the chemical shifts. $IIA^{Mtl}$ of Thermoanaerobacter Tencongensis is predicted to have six ${\beta}$ strands and six ${\alpha}$ helices, which is analogous to $IIA^{Mtl}$ of Escherichia coli.

• Molecules and Cells
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• v.26 no.2
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• pp.206-211
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• 2008

HI0381 of Haemophilus influenzae was investigated by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy. HI0381 is a 153-residue peptidoglycan-associated outer membrane lipoprotein, and a part of the larger Tol/Pal network. Here, we report its backbone $^1H$, $^{15}N$, and $^{13}C$ resonance assignments, and secondary structure predictions. About 97% of all of the $^1HN$, $^{15}N$, $^{13}CO$, $^{13}C{\alpha}$, and $^{13}C{\beta}$ resonances covering 131 non-proline residues of the 134 residue, mature protein, were clarified by sequential and specific assignments. CSI and TALOS analyses revealed that HI0381 contains five ${\alpha}$-helices and five ${\beta}$-strands. To characterize the structure of HI0381, the effects of pH and salt concentration were investigated by CD. In addition, the structural changes occurring when HI0381 was in a membranous environment were investigated by comparing its HSQC spectra and CD data in buffer and in DPC micelles; the results showed that helix ${\alpha}4$ and strand ${\beta}4$ became aligned with the membrane. We conclude that the conformation of HI0381 is affected by the membrane environment, implying that its folded state is directly related to its function.

• Journal of the Korean Magnetic Resonance Society
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• v.6 no.1
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• pp.54-68
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• 2002

PEBP2/CBF (Polyomavirus Enhancer-core Binding Protein 2/Core Binding Factor), represents a new family of heterodimeric transcription factor. Those members play important roles in hematopoiesis and osteogenesis in mouse and human. PEBP2/CBF is a sequence-specific DNA binding protein. Each member of the PEBP2/CBF family of transcription factors is composed of two subunits, ${\alpha}$ and ${\beta}$. The evolutionarily conserved 128 amino acid region in ${\alpha}$ subunit has been called the Runt domain, which harbors two different activities, the ability to bind DNA and interact with the ${\beta}$ subunit. Recently, cDNA clones encoding the C. elegans Runt domain were isolated by screening a cDNA library. This gene was referred to run (Runt homologous gene). In this study, the basic experiments for the structural characterization of RUN protein were performed using spectroscopic methods. We have identified the structural properties of RUN using bioinformatics, CD and NMR. The limit temperature of the structural stability was up to 60$^{\circ}C$ with irreversible thermal process, and the structure of RUN seems to adopt ${\alpha}$ helices and one or more ${\beta}$ sheet or turn. The degree of NMR peak dispersion and intensity was increased by addition of glycine. Therefore, glycine could be used to alleviate the aggregation property of RUN in NMR experiment.