• Bulletin of the Korean Chemical Society
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• v.25 no.2
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• pp.198-202
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• 2004

Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate.

• Analytical Science and Technology
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• v.17 no.5
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• pp.388-392
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• 2004

Structural studies of membrane proteins, importantly involving interpretation of genomics information, many signaling pathway and major drug target for drug discovery, are having difficulty in characterizing the function using conventional solution nmr spectroscopy and x-ray crystallography because phospholipid bilayers hindered fast tumbling and crystallization. Here, we studied the structure of the pf1 coat protein in oriented phospholipid bilayers by home-built solid-state NMR probe. Bacteriophage pf1 was purified from Paeudomonas Aeruginosa and coat protein of bacteriophage pf1 was isolated from DNA and other proteins.

• Applied Chemistry for Engineering
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• v.10 no.4
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• pp.628-634
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• 1999

The orientational binding of ${\omega}$-phenylakylammonium ions to the sodium dodecyl (SDS) micellar interface has been studied from $^{1}H\;NMR$ chemical shift data. The NMR resonaces of the methylene protons of SDS and aromatic protons embedded into the micellar interior have shown the upfield shift. The aromatic induced chemical shifts of the alkyl chain methylene protons of SDS demonstrate the deep penetration into the palisade layer by these organic salts. Alkylammonium groups have been considered to be oriented toward outside of the micellar interface. Aromatic rings have been thought to be oriented toward the micellar core. The depth of penetration by organic salts has been observed to increase with the length of alkyl chain.

• BMB Reports
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• v.35 no.3
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• pp.343-347
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• 2002

The human protein tyrosine kinase-6 (PTK6) polypeptide that is deduced from the cDNA sequence contains a Src homology (SH) 3 domain, SH2 domain, and catalytic domain of tyrosine kinase. We initiated biochemical and NMR characterization of PTK6 SH3 domain in order to correlate the structural role of the PTK6 using circular dichroism and heteronuclear NMR techniques. The circular dichroism data suggested that the secondary structural elements of the SH3 domain are mainly composed of $\beta$-sheet conformations. It is most stable when the pH is neutral based on the pH titration data. In addition, a number of cross peaks at the low-field area of the proton chemical shift of the NMR spectra indicated that the PTK6 SH3 domain retains a unique and folded conformation at the neutral pH condition. For other pH conditions, the SH3 domain became unstable and aggregated during NMR measurements, indicating that the structural stability is very sensitive to pH environments. Both the NMR and circular dichroism data indicate that the PTK6 SH3 domain experiences a conformational instability, even in an aqueous solution.

• Bulletin of the Korean Chemical Society
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• v.15 no.8
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• pp.673-679
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• 1994

$^1H$ NMR spectra of imidazole, 2-and 4(5)-methylimidazole, histamine, L-histidine, L-histidine methyl ester, N${\alpha}$-acetyl-L-histidine, and L-carnosine coordinated to the paramagnetic undecatungstocobalto(II)silicate ($SiW_{11}Co$) and undecatungstonickelo(II)silicate ($SiW_{11}Ni$) anions are reported. For these complexes the ligand exchange is slow on the NMR time scale and the pure resonance lines of the free ligand and the complexes have been observed separately at room temperature. Two different complexes are formed, depending upon which nitrogen atom of the imidazole ring is coordinated to the cobalt or nickel ion of $SiW_{11}M$. Thus the NMR spectrum of a $D_2O$ solution containing a ligand and $SiW_{11}M$ consists of three sets of lines originating from the free ligand and two complexes. All NMR lines of the $SiW_{11}Co$ complexes have been assigned unequivocally using the saturation transfer technique. The temperature dependence of some spectra are also reported. The NMR spectra of some complexes show that the internal rotation of the substituent on the imidazole ring is hampered by the heteropolyanion moiety even at room temperature.

• Journal of the Korean Magnetic Resonance Society
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• v.28 no.1
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• pp.1-5
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• 2024

IscU, the iron-sulfur (Fe-S) cluster scaffold protein, is an essential protein for biogenesis of Fe-S clusters. Previous studies showed that IscU manifests a metamorphic structural feature; at least two structural states, namely the structured state (S-state) and the disordered state (D-state), interconverting in a physiological condition, was observed. Moreover, subsequent studies demonstrated that the metamorphic flexibility of IscU is important for its Fe-S cluster assembly activity as well as for an efficient interaction with various partner proteins. Although solution nuclear magnetic resonance (NMR) spectroscopy has been a useful tool to investigate this protein, the detailed molecular mechanism that sustains the structural heterogeneity of IscU is still unclear. To tackle this issue, we applied a high-pressure NMR (HP-NMR) technique to the IscU variant, IscU(I8K), which shows an increased population of the S-state. We found that the equilibrium between the S- and D-state was significantly perturbed by pressure application, and the specific regions of IscU exhibited more sensitivity to pressure than the other regions. Our results provide novel insights to appreciate the dynamic behaviors of IscU and the related versatile functionality.

• Bulletin of the Korean Chemical Society
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• v.32 no.9
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• pp.3425-3428
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• 2011

Apolipoprotein A-I (Apo A-I) is a major component for high density lipoproteins (HDL). A number of mimetic peptides of Apo A-I were screened from the phase-displayed random peptide library by utilizing monoclonal antibodies (A12). Mimetic peptide for A12 epitope against Apo A-I was selected as CPFARLPVEHHDVVGL (pA1). From the BLAST search, the mimetic peptide pA1 had 40% homology with Apo A-I. As a result of the structural determination of this mimotope using homo/hetero nuclear 2D-NMR techniques and NMR-based distance geometry (DG)/molecular dynamic (MD) computations, DG structure had low penalty value of 0.3-0.7 ${\AA}^2$ and the total RMSD was 0.6-1.6 ${\AA}$. The mimotope pA1 exhibited characteristic conformation including a ${\beta}$-turn from Pro[7] to His[11].

• Bulletin of the Korean Chemical Society
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• v.24 no.3
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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.

• Korean Journal of Pharmacognosy
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• v.9 no.1
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• pp.1-9
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• 1978

The principle of Fourier Transform Nuclear Magnetic Resonance and its usefulness in the fields of pharmacy and biological sciences are described. 1. The $^1H\;and\;^{13}C$ NMR spectra of triostin A and its mixture with purine derivatives were taken. From the analysis of the spectra it has established that triostin A, which exists in two symmetric conformers in chloroform solution, forms complexes only with purine derivatives by the participation of one of the conformers. 2. Also, the $^{13}C$ NMR spectra of "intact" substances in the field of pharmacognosy were taken. From the spectra it was suggested that the method is very useful for natural product research in cooperation with the chemical method.

• Bulletin of the Korean Chemical Society
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• v.22 no.5
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• pp.507-513
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• 2001

Histones, nuclear proteins that interact with DNA to form nucleosomes, are essential for both the regulation of transcription and the packaging of DNA within chromosomes. The N-terminal domain of histone H4 which contains four acetylation sites at lysines, may play a separate role in chromatin structure from the remainder of the H4 chain. NMR data suggest that H4NTP peptide does have relating disordered structure at physiological pH, however, it has a defined structure at lower pH conditions. The solution structure calculated from NMR data shows a well structured region comprising residues of Val21-Asp24. In addition, our results suggest that the H4NTP prefers an extended backbone conformation at acetylation sites, however, it (especially Lys 12 ) became more defined structures after acetylation for its optimum function.