• Journal of the Korean Magnetic Resonance Society
• /
• v.23 no.3
• /
• pp.61-66
• /
• 2019

RNAs exhibit distinct structural and dynamic features required for proper function. The hydrogen-bonded imino protons of RNAs are a probe of the conformational transition and dynamic feature. MicroRNAs originate from primary transcripts containing hairpin structures. The levels of mature miR156 influence the flowering time of plants. To understand the molecular mechanism of biological function of $miR156:miR156^*$ duplex, we performed hydrogen exchange study on the model RNAs mimicking two phenotypes of $miR156:miR156^*$, $miR156:miR156^*$ (m-miR156a) and $miR156:miR156^*$ (m-miR156g) duplexes. This study found that the internal bulge of m-miR156a destabilized the neighboring base-pairs, whereas the bulge structure of m-miR156g did not affect the thermal stabilities of the neighboring base-pairs.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.3
• /
• pp.848-854
• /
• 2012

We have studied the oligomerization of a fibril-forming segment of ${\alpha}$-Synulcein using a replica exchange molecular dynamics (REMD) simulation. The simulation was performed with trimers and tetramers of a 12 amino acid residue stretch (residues 71-82) of ${\alpha}$-Synulcein. From extensive REMD simulations, we observed the spontaneous formation of both trimer and tetramer, demonstrating the self-aggregating and fibril-forming properties of the peptides. Secondary structure profile and clustering analysis illustrated that antiparallel ${\beta}$-sheet structures are major species corresponding to the global free energy minimum. As the size of the oligomer increases from a dimer to a tetramer, conformational stability is increased. We examined the evolution of simple order parameters and their free energy profiles to identify the process of aggregation. It was found that the degree of aggregation increased as time passed. Tetramer formation was slower than trimer formation and a transition in order parameters was observed, indicating the full development of tetramer conformation which is more stable than that of the trimer. The shape of free energy surface and change of order parameter distributions indicate that the oligomer formation follows a dock-and-lock process.

• Journal of the Korean Magnetic Resonance Society
• /
• v.6 no.1
• /
• pp.1-11
• /
• 2002

Physical properties of PVB [Poly(vinyl butyral)] polymer are strongly correlated with water contents in the polymer. Thus dynamics of PVB containing 10~50(w/w) ％ of water were studied by $^{13}$ C CP/MAS/DD over the temperature range 293K -348K. From the Peak area, line width, chemical shift, and relaxation times ( $T_{1}$ $T_{1p}$) measured at 9.4 T, it was deduced that water facilitates molecular dynamics of the PVB molecules overall including conformational exchange of the racemic and meso butyaldehyde rings in the PVB. However, the influence of water was not linear to the amount of water in the PVB samples. It is suggested that water up to 30 w/w ％ of the sample is closely bound to the PVB polymer and water relatively free from the PVB polymer starts to appear when water is added more than 30 w/w ％.％.

• Journal of Photoscience
• /
• v.6 no.4
• /
• pp.157-158
• /
• 1999

The conformational studies of glycinemethylester have been carried out by the ab initio method. We have optimized the geometries of glycinemethylester at various levels of sophisticated for electron exchange and correlation within MP2 level. The scale factors of glycinemethylester were used to obtain the scaled ab initio force field of the minimum energy conformer of it, which was used to predict the vibrational frequencies and their potential energy distribution. The Raman spectra of the glycinemethylester were compared with the observed one and the other calculated with HF/6-3IG level.

• Journal of the Korean Magnetic Resonance Society
• /
• v.20 no.2
• /
• pp.50-55
• /
• 2016

Backbone $^1H$, $^{13}C$ and $^{15}N$ resonance assignments are presented for the anticodon binding domain (residues 557-674) of human glycyl-tRNA synthetase (GRS). Role of the anticodon binding domain (ABD) of GRS as an anticancer ligand has recently been reported and its role in other diseases like Charcot-Marie-Tooth (CMT) and polymyositis have increased its interest. NMR assignments were completed using the isotope [$^{13}C/^{15}N$]-enriched protein and chemical shifts based secondary structure analysis with TALOS+ demonstrate similar secondary structure as reported in X-ray structure PDB 2ZT8, except some C-terminal residues. NMR signals from the N-terminal residues 557 to 571 and 590 to 614 showed very weak or no signals exhibiting dynamics or conformational exchange in NMR timescale.

• Bulletin of the Korean Chemical Society
• /
• v.20 no.6
• /
• pp.683-688
• /
• 1999

In deuterium NMR spectra of phosphatidylethanolamine bilayers with an extremely high content of saturated fatty acids, each C1 deuteron of the glycerol backbone gave rise to a doublet. This suggests the presence of two backbone conformations, the exchange between which is slow on an NMR time scale. The origin of the two conformations has been investigated in this work using saturated 1,2-diacyl-sn-glycero-3-phosphoethanolamine specifically deuterated in the glycerol backbone. The results showed that the two conformations originate from different domains, which have different fatty acid compositions. The differential scanning calorimetry of the bilayers suggested that the size of the domain is not large enough to show an independent phase transition. Thus, the formation of microdomains in the phosphatidylethanolamine bilayers has been concluded. Conformational difference in different domains was shown to be restricted to the C1 position of the glycerol backbone. The microdomains of phosphatidylethanolamine were retained even in the presence of other phospholipids.

• Proceedings of the PSK Conference
• /
• 2002.10a
• /
• pp.346.3-346.3
• /
• 2002

The polyamine pathway represents a logical target for chemotherapeutic intervention, since depletion of polyamines results in the disruption of a variety of cellular functions, and may in specific cases result in cytotoxicity. Polyamine interaction with DNA has also long been thought to be an important function of the natural polyamines and as more is learned about the specific interactions and the resultant conformational changes which can be influenced by the polyamine binding to DNA the potential for regional and gene-specific changes are becoming more evident. We have prepraed the elaborate polyamines by the reaction of simpler polyamines with polyalkyating agents. Synthesized polyamines were separated and purified by metal complex formation and ion-exchange chromatography. They were characterized by X-ray crystal structure determinations of their metal complexes.

• Journal of Plant Biology
• /
• v.39 no.2
• /
• pp.85-92
• /
• 1996

Small GTP-binding proteins are divided into three major group: Ras, Rho and Ypt/Rab. They have the conserved regions designed G1 to G5 that are critical in GDP/GTP exchange, GTP-induced conformational change and GTP hydrolysis. We isolated and characterized genomic DNA or cDNAfragments encoding G1 to G3 domains of small GTP-binding protein Rab and Rho from several plant species using two different PCR-based cloning strategies. Seven rab DNA fragments were isolated from 4 different plants, mung-bean, tobacco, rice and pepper using two degenerate primers corresponding to the GTP-binding domain G1 and G3 in small GTP-binding proteins. The amino acid sequences among these rab DNA fragments and other known small GTP-binding proteins shows that they belong to the Ypt/Rab family. Six rho DNA fragments were isolated from 5 different plants, mung-bean, rice, Arabidopsis, Allium and Gonyaulax using the nested PCR method that involves four degenerate primers corresponding to the GTP-binding domain G1, G3 and G4. The rho DNA fragments cloned show more than 90% homology to each other. Sequence comparison between plant and other known Rho family genes suggests that they are closely related (67 to 82% amino acid identity). Sequence analysis and southern blot analysis of rab and rho in mung-bean suggest than thses genes are encoded by multigene family in mung-bean.

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

• Bulletin of the Korean Chemical Society
• /
• v.29 no.10
• /
• pp.1937-1940
• /
• 2008

The P1 duplex of Tetrahymena group I ribozyme is the important system for studying the conformational changes in folding of ribozyme. The formation of the P1 duplex between IGS and substrate RNA and the catalytic activity of ribozyme require a variety of metal ions such as $Mg^{2+}$ and $Mn^{2+}$. In order to investigate the effect of the $Mg^{2+}$ concentration on the conformation of the P1 duplex, the NMR study was performed as a function of $Mg^{2+}$ concentration. This study revealed that the less stable AU-rich region formed duplex at $50{^{\circ}C}$ under high $Mg^{2+}$ concentration condition but melts out under low $Mg^{2+}$ concentration condition. It was also found that in the active conformation under 10 mM $MgCl_2$ condition, the unstable central G${\cdot}$U wobble pair maintains the significant base pairing up to $50{^{\circ}C}$. This study provides the information of the unique feature of the P1 duplex structure and the roll of $Mg^{2+}$ ion on the formation of the active conformation.