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REFERENCE LINKING PLATFORM OF KOREA S&T JOURNALS
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Journal of the Korean Magnetic Resonance Society
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Korean Magnetic Resonance Society
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Volume 20, Issue 2 - Jun 2016
Volume 20, Issue 1 - Mar 2016
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Secondary structure analysis of MRA1997 from Mycobacterium tuberculosis and characterization of DNA binding property
Kim, Hyo Jung ; Lee, Ki-Young ; Kim, Yena ; Kwon, Ae-Ran ; Lee, Bong-Jin ;
Journal of the Korean Magnetic Resonance Society, volume 20, issue 2, 2016, Pages 36~40
DOI : 10.6564/JKMRS.2016.20.2.036
MRA1997 is a highly conserved protein from mycobacterial strains. However, no structural and functional information is associated with it. Thus, to obtain details about structure and function of this protein, we have utilized NMR spectroscopy. The recombinant MRA1997 was highly purified and its DNA binding mode was characterized. The tertiary structure of MRA1997 was modeled on the basis of our NMR chemical shift data combined with the webserver CS23D. The binding of MRA1997 with DNA was first monitored by electrophoresis mobility shift assays. The residues involved in DNA binding are identified using NMR chemical shift perturbation experiments. Based on our study, we suggest that MRA1997 interacts with DNA and may play an important role in Mycobacterium tuberculosis physiology.
Bile acids from a Marine Sponge-Associated Fungus Penicillium sp.
Pil, Gam Bang ; Won, Ho Shik ; Shin, Hee Jae ;
Journal of the Korean Magnetic Resonance Society, volume 20, issue 2, 2016, Pages 41~45
DOI : 10.6564/JKMRS.2016.20.2.041
Chemical investigation of a marine-derived fungus, Penicillium sp. 108YD020, resulted in the discovery of six bile acid derivatives, glycocholic acid (1), glycocholic acid methyl ester (2), cholic acid (3), glycochenodeoxycholic acid (4), glycodeoxycholic acid methyl ester (5), and cholic acid methyl ester (6). The structures of six bile acid derivatives 1-6 were determined by the detailed analysis of 1D, 2D NMR and LC-MS data, along with chemical methods and literature data analysis.
Structural Characterization of pre-miRNA 155
Kim, Won-Je ; Shin, JiYeon ; Bang, Kyeongmi ; Song, Hyun Kyu ; Kim, Nak-Kyoon ;
Journal of the Korean Magnetic Resonance Society, volume 20, issue 2, 2016, Pages 46~49
DOI : 10.6564/JKMRS.2016.20.2.046
MiRNA-155, upregulated in various cancers, is one of the miRNAs that suppress apoptosis of human cancer. Thus, inhibition of the maturation of miRNA-155 could be an effective way to induce apoptotic cancer cell death. The apical stem-loop of the pre-miRNA-155 has been known as a Dicer biding site for RNA cleavage. Here, to understand the molecular basis of the tertiary interaction between pre-miRNA-155 with Dicer, we characterize the structure of the apical stem-loop of pre-miRNA-155 using NMR spectroscopy. The RNA has a stem-bulge-stem-loop-stem structure, which is consist of G-C Watson-Crick and G-U Wobble base pairs. The assignments of imino- protons were further confirmed by 2D
HSQC NMR spectrum. The NMR parameters obtained in this study can be further used to investigate the tertiary interaction between pre-miRNA-155 and other biomolecules such as protein, nucleic acids, or small chemicals which might be used to control the apoptosis of cancer.
Backbone assignment of the anticodon binding domain of human Glycyl-tRNA synthetase
Mushtaq, Ameeq Ul ; Cho, Hye Young ; Byun, Youngjoo ; Jeon, Young Ho ;
Journal of the Korean Magnetic Resonance Society, volume 20, issue 2, 2016, Pages 50~55
DOI : 10.6564/JKMRS.2016.20.2.050
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 [
]-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.
NMR Signal Assignments of Human Adenylate Kinase 1 (hAK1) and its R138A Mutant (hAK1R138A)
Kim, Gilhoon ; Chang, Hwanbong ; Won, Hoshik ;
Journal of the Korean Magnetic Resonance Society, volume 20, issue 2, 2016, Pages 56~60
DOI : 10.6564/JKMRS.2016.20.2.056
Adenylate kinase (AK) enzyme which acts as the catalyst of reversible high energy phosphorylation reaction between ATP and AMP which associate with energetic metabolism and nucleic acid synthesis and signal transmission. This enzyme has three distinct domains: Core, AMP binding domain (AMPbd) and Lid domain (LID). The primary role of AMPbd and LID is associated with conformational changes due to flexibility of two domains. Three dimensional structure of human AK1 has not been confirmed and various mutation experiments have been done to determine the active sites. In this study, AK1R138A which is changed arginine of LID domain with alanine was made and conducted with NMR experiments, backbone dynamics analysis and mo-lecular docking dynamic simulation to find the cause of structural change and substrate binding site. Synthetic human muscle type adenylate kinase 1 (hAK1) and its mutant (AK1R138A) were re-combinded with E. coli and expressed in M9 cell. Expressed proteins were purified and finally gained at 0.520 mM hAK1 and 0.252 mM AK1R138A. Multinuclear multidimensional NMR experiments including HNCA, HN(CO)CA, were conducted for amino acid sequence analysis and signal assignments of
HSQC spectrum. Our chemical shift perturbation data is shown LID domain residues and around alanine and per-turbation value(0.22ppm) of valine is consid-ered as inter-communication effect with LID domain and the structural change between hAK1 and AK1R138A.
An Investigation of the Sample Rotation Effects on Suppression of Convective Flows in PGSE Diffusion NMR Experiments
Kim, Minkyoung ; Chung, Kee-Choo ;
Journal of the Korean Magnetic Resonance Society, volume 20, issue 2, 2016, Pages 61~65
DOI : 10.6564/JKMRS.2016.20.2.061
Undesirable convective flow in an NMR tube inhibits the accurate measurement of diffusion coefficients by NMR spectroscopy. To minimize the convection effects, various methods have been suggested, and it has been known that the use of sample rotation can be useful. However, it has not been clearly examined that the convection suppressing effect of the sample rotation under the different spinning speeds. In this study, the relation between convective flow and the sample rotation was investigated using PGSE NMR diffusion experiments to reveal the feasibility for controlling the convective flow in an NMR tube by sample rotation itself. The viscosity effect was also examined using solvents with four different viscosities, acetone-
. The sample rotation showed apparent convection suppressing effects at all temperature range for the low viscosity solvents, acetone-
and chloroform-d, even at the faster than 5 Hz spinning rate. The similar patterns were also observed for pyridine-
, which have higher viscosity. This effect was observed even at high temperatures where convective flow arises conspicuously.