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Biochemical and Structural Characterization of HP1423 (Y1423_HELPY) from Helicobacter pylori
Kim, Ji-Hun,Lee, Ki-Young,Park, Sung-Jean,Lee, Bong-Jin Korean Magnetic Resonance Society 2010 Journal of the Korean Magnetic Resonance Society Vol.14 No.1
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.
Krishna, N.Rama,Jayalakshmi, V. Korean Magnetic Resonance Society 2002 Journal of the Korean Magnetic Resonance Society Vol.6 No.2
An interesting recent application of intermolecular NOE experiment is the saturation transfer difference NMR(STD-NMR) method that is useful in screening compound libraries to identify bio-active ligands. This technique also identifies the group epitopes of the bound ligand in a reversibly forming protein-ligand complex. We present here a complete relaxation and conformational exchange matrix (CORCEMA) theory (Moseley et al., J. Magn. Reson. B, 108, 243-261 (1995)) applicable for the STD-NMR experiment. Using some ideal model systems we have analyzed the factors that influence the STD intensity changes in the ligand proton NMR spectrum when the resonances from some protons on the receptor protein are saturated. These factors will be discussed and some examples of its application in some model systems will be presented. This CORCEMA theory for STD-NMR and the associated algorithm are useful in a quantitative interpretation of the STD-NMR effects, and are likely to be useful in structure-based drug design efforts. They are also useful in a quantitative characterization of protein-protein (or protein-nucleic acid) contact surfaces from an intermolecular cross-saturation NMR experiment.
Chung Kee-Choo,Ahn Sang-Doo Korean Magnetic Resonance Society 2006 Journal of the Korean Magnetic Resonance Society Vol.10 No.1
With a simple pulse sequence ($\pi/2$-{gradient, duration T}-acquisition) in solution NMR, detected signal has slowly grown up to percents of the equilibrium magnetization. The source of this unusual resurrection of dephased magnetization after a crushed gradient is cross-correlated effects of radiation damping and the distant dipolar field, which has been demonstrated by a numerical simulation and theoretical analysis.
NOISE Spectroscopy: Applications to Solid State NMR
Yang, Doo-Kyung,Zax, D.B. Korean Magnetic Resonance Society 2002 Journal of the Korean Magnetic Resonance Society Vol.6 No.2
One of the oldest, still unsolved, and often ignored problems in magnetic resonance remains the issue of how to observe undistorted, normal one-dimensional spectra where the frequencies and their relative intensities represent faithfully the distribution of spins and sites in the sample within the magnet. Often distortions in these parameters are accepted, as the price of sensitivity enhancement, or because it is unclear just how these distortions might be avoided. Surprisingly enough, the problem is exacerbated by the use of modern techniques of pulsed Fourier transform NMR. Noise spectroscopy is an approach to solving the problem of distorted NMR spectra, which is largely under appreciated; it promises virtually "unlimited" distortionless bandwidths without costly hardware investments. Nonetheless, its exploitation remains limited. We will discuss why noise spectroscopy belongs in the arsenal of tricks spectroscopists should be aware of, show examples where its use is essential if accurate, quantitative NMR is to be expected, and discuss some recent approaches which extend its applicability yet further, particularly in solid state NMR and in applications to quadrupolar nuclear spins.
Comparison of Spectral Data of Metabolites Collected from Bruker and Varian 600 MHz Spectrometers
Kang, Woo-Young,Chae, Young-Kee Korean Magnetic Resonance Society 2009 Journal of the Korean Magnetic Resonance Society Vol.13 No.1
The spectral data were collected from the two 600 MHz spectrometers from the two major manufacturers, Broker and Varian. The samples were prepared to create standard curves for quantitative measurements of metabolite concentrations. Instead of employing one-dimensional $^1H$ experiments, the two-dimensional $^1H-^{13}C$ HSQC experiments were performed for better separation of resonances. For some resonances, the high salt condition hindered the linear correlation between the intensity and actual metabolite concentration. Excluding overlapped ones, most resonances showed good linearity. Although the Varian spectrometer showed better linearity, both spectrometers were able to generate acceptable standard curves. From this data, we could identify resonances that could be used to better quantify the concentrations of the particular metabolites. With these standard curves, the quantitative measurements of the metabolites from the real samples will be facilitated.
Jang, Sun-Bok,Ma, Chao,Chandan, Pathak Chinar,Kim, Do-Hee,Lee, Bong-Jin Korean Magnetic Resonance Society 2011 Journal of the Korean Magnetic Resonance Society Vol.15 No.1
HP0827 has two RNP motif which is a very common protein domain involved in recognition of a wide range of ssRNA/DNA.We acquired 3D NMR spectra of HP0827 which shows well dispersed and homogeneous signals which allows us to assign 98% of all $^1H_N$, $^{15}N$, $^{13}C_{\alpha}$, $^{13}C_{\beta}$ and $^{13}C$=O resonances and 90% of all sidechain resonances. The sequence-specific backbone resonance assignment of HP0827 can be used to gain deeper insights into the nucleic acids binding specificity of HP0827 in the future study. Here, we report secondary structure prediction of HP0827 derived from NMR data. Additionally, ssRNA/DNA binding assay studies was also conducted. This study might provide a clue for exact function of HP0827 based on structure and sequence.
Kim, Do-Hee,Jang, Sun-Bok,Lee, Bong-Jin Korean Magnetic Resonance Society 2012 Journal of the Korean Magnetic Resonance Society Vol.16 No.2
SAV2228 has an OB (Oligomer-Binding)-motif which is frequently used for nucleic acid recognition. To characterize the activity of translation initiation factor-1 (IF-1) from Staphylococcus aureus, SAV2228 was expressed and purified in Escherichia coli. We acquired 3D NMR spectra showing well dispersed and homogeneous signals which allow us to assign 94.4% of all $^1HN$, $^{15}N$, $^{13}C{\alpha}$, $^{13}C{\beta}$ and $^{13}CO$ resonances. We could predict a secondary structure of SAV2228 using TALOS and CSI from NMR data. SAV2228 was consisted of one ${\alpha}$-helix and five ${\beta}$-sheets. The predicted secondary structure, ${\beta}-{\beta}-{\beta}-{\alpha}-{\beta}-{\beta}$, was similar to other bacterial IF-1, but it was not completely same to the eukaryotic one. Assigned NMR peaks and secondary structre prediction can be used for the study on interaction with nucleic acid in the future.
Yoon, Hyo In,Lim, Ae Ran Korean Magnetic Resonance Society 2015 Journal of the Korean Magnetic Resonance Society Vol.19 No.3
The thermodynamic properties and structural geometry of $KMgCl_3{\cdot}6H_2O$ were investigated using thermogravimetric analysis, differential scanning calorimetry, and nuclear magnetic resonance. The initial mass loss occurs around 351 K ($=T_d$), which is interpreted as the onset of partial thermal decomposition. Phase transition temperatures were found at 435 K ($=T_{C1}$) and 481 K ($=T_{C2}$). The temperature dependences of the spin-lattice relaxation time $T_1$ for the $^1H$ nucleus changes abruptly near $T_{C1}$. These changes are associated with changes in the geometry of the arrangement of octahedral water molecules.
Overhauser dynamic nuclear polarization for benchtop NMR system using a permanent magnet of 1.56 T
Lee, Yeon-seong,Lim, Duk-Young,Shim, Jeong Hyun Korean Magnetic Resonance Society 2019 Journal of the Korean Magnetic Resonance Society Vol.23 No.3
Overhauser dynamic nuclear polarization (O-DNP) has been an efficient method to boost the thermal nuclear polarization in liquids at room temperature. However, O-DNP for a benchtop NMR using a permanent magnet has remained unexplored yet. In this work, we report the development of an O-DNP system adopting a permanent magnet of 1.6 T. Q-band (~43 GHz) high-power amplifier produced 6 W microwave for saturation. Instead of resonator, we used an open-type antenna for the microwave irradiation. For several representative small molecules, we measured the concentration and frequency dependences of the enhancement factor. This work paves the way for the development of a benchtop DNP-NMR system overcoming its disadvantage of low quality signal when using a permanent magnet.
Park, Jung-Il,Sug, Joung-Young Korean Magnetic Resonance Society 2020 Journal of the Korean Magnetic Resonance Society Vol.24 No.1
Based on quantum transport theory, we investigated theoretically the magnetic field dependence of the quantum optical transition of quasi 2-dimensional Landau splitting system, in CdS and ZnO Through the analysis of the current work, we found the increasing properties of the cyclotron resonance line-profiles (CRLPs) which show the absorption power and the cyclotron resonance line-widths (CRLWs) with the magnetic field in CdS and ZnO We also found that that CRLWs, γ<sub>total</sub>(B) of CdS < γ<sub>total</sub>(B) of ZnO in the magnetic field region B < 15 Tesla.