• BMB Reports
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• v.44 no.2
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• pp.118-122
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• 2011

Most widely used secondary structure assignment methods such as DSSP identify structural elements based on N-H and C=O hydrogen bonding patterns from X-ray or NMR-determined coordinates. Secondary structure assignment algorithms using limited $C{\alpha}$ information have been under development as well, but their accuracy is only ~80% compared to DSSP. We have hereby developed SABA (Secondary Structure Assignment Program Based on only Alpha Carbons) with ~90% accuracy. SABA defines a novel geometrical parameter, termed a pseudo center, which is the midpoint of two continuous $C{\alpha}s$. SABA is capable of identifying $\alpha$-helices, $3_{10}$-helices, and $\beta$-strands with high accuracy by using cut-off criteria on distances and dihedral angles between two or more pseudo centers. In addition to assigning secondary structures to $C{\alpha}$-only structures, algorithms using limited $C{\alpha}$ information with high accuracy have the potential to enhance the speed of calculations for high capacity structure comparison.

• 한국생물공학회:학술대회논문집
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• 2005.10a
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• pp.945-945
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• 2005

• Journal of the Korean Magnetic Resonance Society
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• v.14 no.1
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• pp.45-54
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• 2010

HP1423 (Y1423_HELPY) is a conserved hypothetical protein from H. pylori strain 26695. However, Sequence Blast result indicates that HP1423 belongs to S4 (PF01479) superfamily. According to Pfam database, the S4 domain is a small domain consisting of 60-65 amino acid residues, that probably mediates binding to RNA. In this study, we report the sequence-specific backbone resonance assignment of HP1423, which has 84 amino acid residues. We could assign unambiguously about 88% of all $^{1}H_{N}$, $^{15}N$, $^{13}C_{\alpha}$, $^{13}C_{\beta}$ and $^{13}C=O$ resonances. We could not detect the resonances from residues 15-20, and disappearance of these peaks seems to be related with the intermediate-conformational exchange. These assigned NMR peaks of HP1423 can be used for studying the role of protein dynamics in millisecond timescale, and Protein-RNA binding.

• Journal of the Korean Magnetic Resonance Society
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• v.10 no.1
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• pp.115-125
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• 2006

Hippuryl-L-histidyl-L-leucine(HHL) is widely used as a substrate of angiotensin converting enzyme(ACE) cleaving the neurotransmitter angiotensin(I) to the octapeptide angiotensin(II). The structure of the substrate molecules should provide information regarding the geometric requirements of the ACE active site. For the purpose of determination of in vivo reaction, metallo(Cu, Zn)-HHL complexes were synthesized and the degree of complex formation were identified by MALDITOF, ESI mass spectrometric analysis. Tn addition, the pH-dependent species distribution curves were obtained by potentiometric titration. Nitrogen atoms of imidazole ring and oxygen atom of caboxylate groups in the peptide chain were observed to be participated in the metal complex formation. After purification of complexes further structural characterization were made by utilizing UV-Vis, electrochemical methods and NMR. Complete NMR signal assignments were carried out by using 2D-spectrum techniques COSY, TOCSY, NOESY, HETCOR. A complex that two imidazole and carboxylate groups are asymmetrically participating to coordination mode was predicted to the solution-state structure of $Cu(II)-HHL_2$ based on $^{13}C-NMR$ signal assignment and NOE information.

• Applied Biological Chemistry
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• v.38 no.2
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• pp.184-189
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• 1995

(20S)- and (20R)-Ginsenoside $Rh_2$ were prepared from crude ginseng saponin by chemical treatments. The $^1H-$ and $^{13}C-NMR$ signals of these compounds were fully assigned by various NMR techniques such as DEPT, $^1H-^1H$ COSY, HMQC, HMBC and NOESY.

• Natural Product Sciences
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• v.2 no.2
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• pp.106-114
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• 1996

Four polymethoxyfavones were isolated from the leaves of Citrus deliciosa, three of which (nobiletin, 5-O-demethylnobiletin, and tangeritin) are bioactive. The fourth (7,4'-dihydroxy-5,6,8,3'-tetramethoxyflavone) is reported for the first time in the genus Citrus and is a potential chemotaxonomic marker. The structures of these flavones were confirmed by analysing their spectral data and comparison with similar compounds. The previously reported $^{13}C$ NMR assignment of 5-O-demethylnobiletin has been revised on the basis of 2D NMR experiments (HETCOR, COSY, and COLOC). The chemotaxonomic value of the present finding is verified.

• BMB Reports
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• v.30 no.6
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• pp.421-425
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• 1997

The 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT) has been used as intercalating DNA binding drugs in the photo-chemotherapy of skin diseases. The conformation and stability of DNA octamer duplex, $d(GGGTACCC)_2$, cross-linked with AMT has been studied by NMR spectroscopy. All the proton resonances of the psoralen cross-linked octamer were assigned and meting temperature studies were carried out based on the assignment of the proton resonances. The aromatic proton chemical shift data suggest that the conformation of the helix cross-linked with psoralen is destabilized more to furanside of the psoralen. possibly due to the protrusion of the aminomethyl side chain of the psoralen.

• Korean Journal of Pharmacognosy
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• v.44 no.1
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• pp.6-9
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• 2013

Two fraxinellone-based hydrogenated derivatives were prepared from fraxinellone, a well-known degraded limonin, via catalytic hydrogenation in the presence of $PtO_2$ in HOAc. Their structures were confirmed as (3S,3aR,3'R)-3a,7-dimethyl-3-(tetrahydrofuran-3-yl)-3a,4,5,6-tetrahydroisobenzofuran-1(3H)-one and (3S,3aR,2'R)-3-((R)-1-hydroxybutan-2-yl)-3a,7-dimethyl-3a,4,5,6-tetrahydroisobenzofuran-1(3H)-one on the basis of 2D NMR assignments. The $^{13}C$ NMR assignments of two quaternary carbons in the ${\alpha}$,${\beta}$-unsaturated carbonyl moiety of ${\gamma}$-butyrolactone core of fraxinellone should be revised.

• Journal of the Korean Magnetic Resonance Society
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• v.4 no.2
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• pp.125-132
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• 2000

The detailed $^1$H and $^{13}$ C NMR assignments of a novel sucrose isovaleryl ester isolated from the seed of Euphorbia Lathyris L., were achieved by one-and two-dimensional techniques. The new sucrose ester was characterized as an $\alpha$-D-glucopyranoside, 3,4,6-tris-O-(3-methyl-1-oxobutyl)-$\beta$-D-fructofuranosyl, 2,6-bis(3-methylbutanoate); sucrose 4,7,8,11,12-pentaisovalerate by MS and NMR experiments.

• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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• pp.59-66
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• 2013

BldD, a developmental transcription factor from Streptomyces coelicolor, is a homodimeric, DNA-binding protein with 167 amino acids in each subunit. Each monomer consists of two structurally distinct domains, the N-terminal domain (BldD-NTD) responsible for DNA-binding and dimerization and the C-terminal domain (BldD-CTD). In contrast to the BldD-NTD, of which crystal structure has been solved, the BldD-CTD has been characterized neither in structure nor in function. Thus, in terms of structural genomics, structural study of the BldD-CTD has been conducted in solution, and in the present work, mainchain NMR assignments of the recombinant BldD-CTD (residues 80-167 of BldD) could be achieved by a series of heteronuclear multidimensional NMR experiments on a [$^{13}C/^{15}N$]-enriched protein sample. Finally, the secondary structure prediction by CSI and TALOS+ analysis using the assigned chemical shifts data identified a ${\beta}-{\alpha}-{\alpha}-{\beta}-{\alpha}-{\alpha}-{\alpha}$ topology of the domain. The results will provide the most fundamental data for more detailed approach to the atomic structure of the BldD-CTD, which would be essential for entire understanding of the molecular function of BldD.