• BMB Reports
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• 제40권2호
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• pp.261-269
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• 2007

The structure and dynamics of a 37-residue antimicrobial peptide gaegurin 4 (GGN4) isolated from the skin of the native Korean frog, Rana rugosa, was determined in SDS micelles by NMR spectroscopy. The solution structure of the peptide in SDS micelles was determined from 352 NOE-derived distance constraints and 22 backbone torsion angle constraints. Dynamic properties for the amide backbone were characterized by $^1H-^{15}N $heteronuclear NOE experiments. The structural study revealed two amphipathic helices spanning residues 2-10 and 16-32 and that the helices were connected by a flexible loop. An intraresidue disulfide bridge was formed between residues Cys31 and Cys37 near the C-terminus. The loop region (11-15) connecting the two helices are were slightly more flexible than these helices themselves. From the fact that since there is no contact NOEs between two helices, it is implied that the GGN4 peptide shows an independent motion of both helices which has an angle of about $ 60^{\circ}-120^{\circ}$ from each other.

• 한국자기공명학회논문지
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• 제19권2호
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• pp.61-66
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• 2015

The plant hormone auxin is involved in all stages of plant development. Aux/IAAs are the transcriptional repressors that bind to the Auxin Response Factors (ARFs) to regulate the gene expression upon auxin release. Aux/IAA have highly conserved C-terminal domains (domains III-IV) that mediate both homotypic and heterotypic interactions between Aux/IAA and ARF family proteins. Recent studies revealed that the conserved domains III-IV share a common ${\beta}$-grasp fold that oligomerizes in a front-to-back manner. In particular, Aux/IAA contains a mobile insert helix in the domain III-IV, whereas ARFs do not. Here, we investigated the dynamics of the insert helix using paramagnetic NMR spectroscopy. The insert helix exhibited fast motions in the ps-ns time scale from $^{15}N$ relaxation data, but the amplitude of the motion is likely limited to the local neighborhood. Our result suggests that the motion of the helix may have functional implications in protein-protein interactions for transcriptional regulations.

• BMB Reports
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• 제49권8호
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• pp.431-436
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• 2016

Human papillomavirus (HPV) is the major cause of cervical cancer, a deadly threat to millions of females. The early oncogene product (E7) of the high-risk HPV16 is the primary agent associated with HPV-related cervical cancers. In order to understand how E7 contributes to the transforming activity, we investigated the structural features of the flexible N-terminal region (46 residues) of E7 by carrying out N-15 heteronuclear NMR experiments and replica exchange molecular dynamics simulations. Several NMR parameters as well as simulation ensemble structures indicate that this intrinsically disordered region of E7 contains two transient (10-20% populated) helical pre-structured motifs that overlap with important target binding moieties such as an E2F-mimic motif and a pRb-binding LXCXE segment. Presence of such target-binding motifs in HPV16 E7 provides a reasonable explanation for its promiscuous target-binding behavior associated with its transforming activity.

• Biomolecules & Therapeutics
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• 제24권2호
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• pp.191-198
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• 2016

The vitamin D receptor (VDR) is a member of the nuclear receptor (NR) superfamily. The VDR binds to active vitamin $D_3$ metabolites, which stimulates downstream transduction signaling involved in various physiological activities such as calcium homeostasis, bone mineralization, and cell differentiation. Quercetin is a widely distributed flavonoid in nature that is known to enhance transactivation of VDR target genes. However, the detailed molecular mechanism underlying VDR activation by quercetin is not well understood. We first demonstrated the interaction between quercetin and the VDR at the molecular level by using fluorescence quenching and saturation transfer difference (STD) NMR experiments. The dissociation constant ($K_d$) of quercetin and the VDR was $21.15{\pm}4.31{\mu}M$, and the mapping of quercetin subsites for VDR binding was performed using STD-NMR. The binding mode of quercetin was investigated by a docking study combined with molecular dynamics (MD) simulation. Quercetin might serve as a scaffold for the development of VDR modulators with selective biological activities.

• 한국초전도학회:학술대회논문집
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• 한국초전도학회 2000년도 High Temperature Superconductivity Vol.X
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• pp.107-110
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• 2000

($^{11}$B NMR measurements have been performed on single crystals of LuNi$_2$B$_2$C superconductor to investigate vortex lattice structures and dynamical behavior. The spectrum in the superconducting state is significantly broadened by local field inhomogeneity due to the vortex lattice and the peak point of the spectrum shifts toward low magnetic field due to the imperfect field penetration. The linewidth of the spectrum reflecting local field variation is much smaller than expected for conventional vortex lattices and shows peculiar increase at low temperature. Furthermore, the transverse relaxation rate, 1/T$_2$, probing the slow motion of vortices, exhibits a single peak as temperature decreases. These prominent results highlight significant fluctuation of vortices even for this low T$_c$, and nearly isotropic 3D superconductor.

• 한국자기공명학회논문지
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• 제18권1호
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• pp.5-9
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• 2014

In last three decades, RNA molecules have been revealed to play the central roles in many cellular processes. Structural understanding of RNA molecules is essential to interpret their functions, and many biophysical techniques have been adopted for this purpose. NMR spectroscopy is a powerful tool to study structures and dynamics of RNA molecules, and it has been further applied to study tertiary interactions between RNA molecules, RNA-protein, and RNA-small molecules. This short article accounts for the general methods for NMR sample preparations, and also partially covers the resonance assignments of structured RNA molecules.

• 한국자기공명학회논문지
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• 제15권2호
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• pp.104-114
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• 2011

Rapid exchange and hydrolysis of the tubulin-bound guanine nucleotides have been known to govern the dynamics of microtubules. However, the instability and low concentration have made it difficult for the microtubule-bound GTP to be observed directly. In this study, we circumvent these problems by lyophilization and using cross-polarization techniques. $^{31}P$ NMR signals were detected from the tubulin-bound GTP in microtubules for the first time. Analysis of the $^{31}P$ CPMAS NMR spectrum indicates that GTP hydrolysis was delayed by the presence of taxol.

• Bulletin of the Korean Chemical Society
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• 제19권5호
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• pp.519-524
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• 1998

In this work, we applied the 1D 11B nutation NMR method for the analysis of the local structural environments in powdered borosilicates (SiO2-B2O3). Spin dynamics during a rf irradiation for spin I=3/2 was analytically calculated with a density matrix formalism. Spectral simulation programs were written in MATLAB on a PC. Two borosilicates prepared by the sol-gel process at different stabilization temperature were used for the 1D 11B nutation NMR experiment. The 11B NMR parameters, quadrupole coupling constants (e2qQ/h) and asymmetry parameters (η), for each borosilicate were extracted from the nonlinear least-squares fitting. The effects of heat treatments on the local structures of boron sites in borosilicates were discussed.

• 한국자기공명학회논문지
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• 제1권2호
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• pp.79-94
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• 1997

The solution structure of bovine pancreatic trypsin inhibitor(BPTI) has been refined by NMR chemical shift data of C${\alpha}$H using classical molecular dynamics simulation. The structure dependent part of the observable chemical shift was modeled by ring current effect, magnetic anisotropy effect from the nearby groups, whereas the structure independent part was replaced with the random coil shift. A new harmonic function derived from the differences between the observed and calculated chemical shifts was added into physical force field as an pseudo potential energy term with force constant of 250 kJmol-1 ppm-2. During the 1.5 ns molecular dynamics simulation with chemical shift restraints BPTI has accessed different conformation space compared to crystal and NOE driven structure.

• 한국고분자학회:학술대회논문집
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• 한국고분자학회 2006년도 IUPAC International Symposium on Advanced Polymers for Emerging Technologies
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• pp.305-305
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• 2006

The molecular structure and dynamics of inclusion compounds (ICs) consisting of n-perfluoroalkane (PFA) guests and ${\Box}-cyclodextrin$ (${\Box}-CD$) host were investigated using $^{19}F$ magic angle spinning (MAS) and $^{1}H{\to}^{19}F$ cross polarization (CP) / MAS NMR spectroscopy with the aid of thermal analyses, FT-IR spectroscopy, X-ray diffraction, and $^{1}H{\to}^{19}F$ CP/MAS technique revealed that $C_{9}F_{20}$ molecules included in ${\Box}-CD$ undergo vigorous molecular motion and partly come out of the ${\Box}-CD$ channel above $80^{\circ}C$. In case of $C_{20}F_{42}/{\Box}-CD$, an exothermic peak is observed by differential scanning calorimetry (DSC) at ca. $40^{\circ}C$ which suggests that ${\Box}-CD$ molecules become mobile and commence rearrangements that form more ordered structures at higher temperatures.