• Bulletin of the Korean Chemical Society
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• 제33권2호
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• pp.583-588
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• 2012

Functional interaction between Drosophila orphan receptor FTZ-F1 (NR5A3) and a segmentation gene product fushi tarazu (FTZ) is crucial for regulating genes related to define the identities of alternate segmental regions in the Drosophila embryo. FTZ binding to the ligand-binding domain (LBD) of FTZ-F1 is of essence in activating its transcription process. We determined solution structures of the cofactor peptide ($FTZ^{PEP}$) derived from FTZ by NMR spectroscopy. The cofactor peptide showed a nascent helical conformation in aqueous solution, however, the helicity was increased in the presence of TFE. Furthermore, $FTZ^{PEP}$ formed ${\alpha}$-helical conformation upon FTZ-F1 binding, which provides a receptor bound structure of $FTZ^{PEP}$. The solution structure of $FTZ^{PEP}$ in the presence of FTZ-F1 displays a long stretch of the ${\alpha}$-helix with a bend in the middle of helix.

• Korea-Australia Rheology Journal
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• 제15권1호
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• pp.27-33
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• 2003

Associating polymers are hydrophilic long-chain molecules to which a small amount of hydrophobic groups (hydrophobes) is incorporated. In aqueous solution, the association interactions result in the formation of three-dimensional network through flowerlike micelles at high concentrations. In colloidal suspensions, the associating polymers act as flocculated by bridging mechanism. The rheological properties of suspensions flocculated by associating polymers end-capped with hydrophobes are studied in relation to the bridging conformation. At low polymer concentrations, the polymer chains effectively form bridges between particles by multichain association. The suspensions are highly flocculated and show typical viscoelastic responses. When the polymer concentration is increased above the absorbance at saturation, the excess polymer chains remaining in the solution phase build up three-dimensional network by associating interactions. Since the presence of particles does not significantly influence the network structures in the medium, the relative viscosity, which gives a measure of the degree of flocculation is decreased with increasing polymer concentration. The bridging conformation and flocculation level vary strongly depending on the polymer concentrations.

• Bulletin of the Korean Chemical Society
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• 제32권2호
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• pp.687-692
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• 2011

$^1H$ and $^{13}C$ NMR spectra of series of (E)-1-aryl-(2- and 3-thienyl)-2-propenones, that are aldol condensation products between 2- and 3-thiophenecarbaldehydes and m- and p-substituted acetophenones, were examined to make complete assignments of the chemical shifts. Long range couplings, $^4J$ and $^5J$, are observed in the $^1H-^1H$ COSY of both 2- and 3-thienyl compounds, which makes the elucidation of the conformation in solution possible. In contrast, the 2-furyl analogue shows the long range coupling phenomena, but the 3-furyl and phenyl analogues do not show similar phenomena.

• Bulletin of the Korean Chemical Society
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• 제11권2호
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• pp.144-149
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• 1990

Conformational free energy calculations using an empirical potential function (ECEPP/2) and the hydration shell model were carried out on the sulfonylurea herbicides of bensulfuron methyl (Londax) and metsulfuron methyl (Ally). The conformational energy was minimized from starting conformations which included possible combinations of torsion angles in the molecule. The conformational entropy of each conformation was computed using a harmonic approximation. To understand the hydration effect on the conformation of the molecule in aqueous solution, the hydration free energy of each group was calculated and compared each other. It was found that the low-free-energy conformations of two molecules in aqueous solution prefer the overall folded structure, in which an interaction between the carbonyl group of ester in aryl ring and the first amido group of urea bridge plays an important role. From the analysis of total free energy, the hydration and conformational entropy are known to be essential in stabilizing low-free-energy conformations of Londax, whereas the conformational energy is proved to be a major contribution to the total free energy of low-free-energy conformations of Ally.

• Bulletin of the Korean Chemical Society
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• 제20권3호
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• pp.301-306
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• 1999

Hepatitis C virus (HCV) has been known to be an enveloped virus with a positive strand RNA genome and the major agent of the vast majority of transfusion associated cases of hepatitis. For viral replication, HCV structural proteins are first processed by host cell signal peptidases and NS2/NS3 site of the nonstructural protein is cleaved by a zinc-dependent protease NS2 with N-terminal NS3. The four remaining junctions are cleaved by a separate NS3 protease. The solution conformations of NS4B/5A, NS5A/5B substrates and NS5A/5B inhibitor have been determined by two-dimensional nuclear magnetic resonance (NMR) spectroscopy. NMR data suggested that the both NS5A/5B substrate and inhibitor appeared to have a folded tum-like conformation not only between P1 and P6 position but also C-terminal region, whereas the NS4B/5A substrate exhibited mostly extended conformation. In addition, we have found that the conformation of the NS5A/5B inhibitor slightly differs from that of NS5A/5B substrate peptide, suggesting different binding mode for NS3 protease. These findings will be of importance for designing efficient inhibitor to suppress HCV processing.

• BMB Reports
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• 제37권6호
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• pp.676-683
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• 2004

The conformational properties of hydrophobic core variant ubiquitin (Val26 to Ala mutation) in an acidic solution were studied. The intrinsic tryptophan fluorescence emission spectrum, far-UV and near-UV circular dichroic spectra, the fluorescence emission spectrum of 8-anilinonaphthalene-1-sulfonic acid in the presence of V26A ubiquitin, and urea-induced unfolding measurements indicate this variant ubiquitin to be in the partially folded molten globule conformation in solution at pH 2. The folding kinetics from molten globule to the native state was nearly identical to those from the unfolded state to the native state. This observation suggests that the equilibrium molten globule state of hydrophobic core variant ubiquitin is an on-pathway folding intermediate.

• Bulletin of the Korean Chemical Society
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• 제24권3호
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• pp.339-344
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• 2003

The conformation of synthetic oligosaccharide can be elucidated by employing molecular modeling and highfield proton NMR (nuclear magnetic resonance) spectroscopy. Information with respect to the composition and configuration of saccharide residues and the sequence and linkage positions of the oligosaccharide can be obtained by employing a variety of one- and two-dimensional NMR techniques and molecular modeling. These techniques are also useful in establishing the solution conformation of the oligosaccharide moiety. This study is focused on the elucidation of linkage positions of synthetic trisaccharides, Gal(β1-4)Glc(β1-3)Glc, Gal(β1-4)Glc(β1-4)Glc and Gal(β1-4)Glc(β1-6)Glc.

• Bulletin of the Korean Chemical Society
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• 제25권6호
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• pp.838-842
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• 2004

Amyloid peptide (A${\beta}$) is the major component of senile plaques found in the brain of patient of Alzheimer's disease. ${\beta}$-amyloid peptide (25-35) (A${\beta}$25-35) is biologically active fragment of A${\beta}$. The three-dimensional structure of A${\beta}$25-35 in aqueous solution with 50% (vol/vol) TFE determined by NMR spectroscopy previously adopts an ${\alpha}$-helical conformation from $Ala^{30}$ to $Met^{35}$. It has been proposed that A${\beta}$(25-35) exhibits pH- and concentration-dependent ${\alpha}-helix{\leftrightarrow}{\beta}$sheet transition. This conformational transition with concomitant peptide aggregation is a possible mechanism of plaque formation. Here, in order to gain more insight into the mechanism of ${\alpha}$-helix formation of A${\beta}$25-35 peptide by TFE, which particularly stabilizes ${\alpha}$-helical conformation, we studied the secondary-structural elements of A${\beta}$25-35 peptide by molecular dynamics simulations. Secondary structural elements determined from NMR spectroscopy in aqueous TFE solution are preserved during the MD simulation. TFE/water mixed solvent has reduced capacity for forming hydrogen bond to the peptide compared to pure water solvent. TFE allows A${\beta}$25-35 to form bifurcated hydrogen bonds to TFE as well as to residues in peptide itself. MD simulation in this study supports the notion that TFE can act as an ${\alpha}$-helical structure forming solvent.

• Bulletin of the Korean Chemical Society
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• 제19권1호
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• pp.57-62
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• 1998

We have synthesized a 17-residue peptide with the amino acid sequence RQMKEDAKGKSEEELAD corresponding to residues 84-100 of chicken skeletal troponin C. This stretch of the protein sequence is in the middle one-third of the 32-residue 9-turn α-helix that connects the two globular domains of the dumbell-shaped molecule and includes the D/E linker helix. We describe here the solution conformation of the helix linker as studied by circular dichroism (CD) and two-dimensional nuclear magnetic resonance (2-D NMR) spectroscopy. The NOE connectivities together with the vicinal $^3J_{N{\alpha}}$ coupling constants suggest that the peptide exists in a fast conformational equilibrium among several secondary structure: a nascent helix near the N-terminus, a helix, and a substational population of extended and random coil forms. In addition, two interresidue α-α NOEs are observed suggesting a bent structure with a bend that includes the single glycine in position 92. These results are consistent with the ideas that in neutral solution the D/E linker region of the central helix in troponin C can adopt a helical conformation and the central helix may have a segmental flexibility around Gly 92.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 1997년도 학술발표회
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• pp.42-42
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• 1997

Local conformation of helical peptides in TFE solution are studied by NMR spectroscopy. One is a helix containing proline and the other is its alanine derivative in which alanine is substituted for the proline. Chemical shift and temperature coefficient In NMR spectroscopy can be used preliminarily to determine secondary structure in proteins and peptides.(omitted)