Pub Date : 2014-12-20DOI: 10.6564/JKMRS.2014.18.2.074
Gilhoon Kim, Hoshik Won
The N2O2 tetradentate Schiff base ligand, N,N'-bis(salicylidene)pentane-1,3-diamine (Salpn), coupled with 1:2 concentration ratio of 1,3-diamino- pentane and salicylaldehyde was used to produce a series of macrocyclic Nikel(Ⅱ) complexes. In the metal complexation, it was observed that Salpn mac- rocyclic ligand can adopt more than a metal ion giv- ing an unique multinuclear metal complexes includ- ing Ni(II)Salpn and Ni(II)3(Salpn)2. Characteristic IR υ(M-O) peaks for Ni(II)Salpn and Ni(II)3(Salpn)2 were observed to be 1028cm -1 and 1024cm -1 , respec- tively. Characteristic UV-Vis absorption λmax peaks for Ni(II)3(Salpn)2 were observed to be 241nm and 401 nm. Structural characterization of Ni(II)3(Salpn)2 by NMR exhibits that the salicylidene ring moiety has two different resonance signals originated from the magnetically asymmetric diligand and trinuclear bis complex. Complete NMR signal assignments and characterizations elucidating structural features of Ni(II)3(Salpn)2 were described in detail.
{"title":"Spectroscopic characterization of N,N'-bis(salicylidene)pentane-1,3-diamine nickel(II) complex","authors":"Gilhoon Kim, Hoshik Won","doi":"10.6564/JKMRS.2014.18.2.074","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.2.074","url":null,"abstract":"The N2O2 tetradentate Schiff base ligand, N,N'-bis(salicylidene)pentane-1,3-diamine (Salpn), coupled with 1:2 concentration ratio of 1,3-diamino- pentane and salicylaldehyde was used to produce a series of macrocyclic Nikel(Ⅱ) complexes. In the metal complexation, it was observed that Salpn mac- rocyclic ligand can adopt more than a metal ion giv- ing an unique multinuclear metal complexes includ- ing Ni(II)Salpn and Ni(II)3(Salpn)2. Characteristic IR υ(M-O) peaks for Ni(II)Salpn and Ni(II)3(Salpn)2 were observed to be 1028cm -1 and 1024cm -1 , respec- tively. Characteristic UV-Vis absorption λmax peaks for Ni(II)3(Salpn)2 were observed to be 241nm and 401 nm. Structural characterization of Ni(II)3(Salpn)2 by NMR exhibits that the salicylidene ring moiety has two different resonance signals originated from the magnetically asymmetric diligand and trinuclear bis complex. Complete NMR signal assignments and characterizations elucidating structural features of Ni(II)3(Salpn)2 were described in detail.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"74-81"},"PeriodicalIF":0.3,"publicationDate":"2014-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-12-20DOI: 10.6564/JKMRS.2014.18.2.063
Youngil Lee, Ji-Yao An, Seul-A. Park, H. Song
Li nuclear magnetic resonance (NMR) spectra have been observed for LiMPO4 (M = Fe, Mn) samples, as a promising cathode material of lithium ion battery. Observed 7 Li shifts of LiFe1-xMnxPO4 (x = 0, 0.6, 0.8, and 1) synthesized with solid-state reaction are compared with calculated 7 Li shift ranges based on the supertranferred hyperfine interaction of Li–O–M. Ex situ 7 Li NMR study of LiFe0.4Mn0.6PO4 in different cut-off voltage for the first charge process is also performed to understand the relationship between 7 Li
{"title":"Ex-situ 7 Li MAS NMR Study of Olivine Structured Material for Cathode of Lithium Ion Battery","authors":"Youngil Lee, Ji-Yao An, Seul-A. Park, H. Song","doi":"10.6564/JKMRS.2014.18.2.063","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.2.063","url":null,"abstract":"Li nuclear magnetic resonance (NMR) spectra have been observed for LiMPO4 (M = Fe, Mn) samples, as a promising cathode material of lithium ion battery. Observed 7 Li shifts of LiFe1-xMnxPO4 (x = 0, 0.6, 0.8, and 1) synthesized with solid-state reaction are compared with calculated 7 Li shift ranges based on the supertranferred hyperfine interaction of Li–O–M. Ex situ 7 Li NMR study of LiFe0.4Mn0.6PO4 in different cut-off voltage for the first charge process is also performed to understand the relationship between 7 Li","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"63-68"},"PeriodicalIF":0.3,"publicationDate":"2014-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329233","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-12-20DOI: 10.6564/JKMRS.2014.18.2.058
Sung-Sub Choi, Ji-ho Jeong, Ji-sun Kim, Yongae Kim
{"title":"Structure Determination of Syndecan-4 Transmembrane Domain using PISA Wheel Pattern and Molecular Dynamics simulation","authors":"Sung-Sub Choi, Ji-ho Jeong, Ji-sun Kim, Yongae Kim","doi":"10.6564/JKMRS.2014.18.2.058","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.2.058","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"58-62"},"PeriodicalIF":0.3,"publicationDate":"2014-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-20DOI: 10.6564/JKMRS.2014.18.1.041
Jae Hun Choi, A. Lim
{"title":"Study on nuclear magnetic resonance of superionic conductor NH 4 HSeO 4 in rotating frame","authors":"Jae Hun Choi, A. Lim","doi":"10.6564/JKMRS.2014.18.1.041","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.1.041","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"41-46"},"PeriodicalIF":0.3,"publicationDate":"2014-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-20DOI: 10.6564/JKMRS.2014.18.1.010
Sub Hur, H. Lee, A. Shin, Sung Jean Park
Hsp90 is a good drug target molecule that is involved in regulating various signaling pathway in normal cell and the role of Hsp90 is highly emphasized especially in cancer cells. Thus, much efforts for discovery and development of Hsp90 inhibitor have been continued and a few Hsp90 inhibitors targeting the N-terminal ATP binding site are being tested in the clinical trials. There are no metabolic signature molecules that can be used to evaluate the effect of Hsp90 inhibition. We previously found a potential C-domain binder named PPC1 that is a synthetic small molecule. Here we report the metabolomics study to find signature metabolites upon treatment of PPC1 compound in lung cancer cell line, A549 and discuss the potentiality of metabolomic approach for evaluation of hit compounds.
{"title":"Metabolic perturbation of an Hsp90 C-domain inhibitor in a lung cancer cell line, A549 studied by NMR-based chemometric analysis","authors":"Sub Hur, H. Lee, A. Shin, Sung Jean Park","doi":"10.6564/JKMRS.2014.18.1.010","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.1.010","url":null,"abstract":"Hsp90 is a good drug target molecule that is involved in regulating various signaling pathway in normal cell and the role of Hsp90 is highly emphasized especially in cancer cells. Thus, much efforts for discovery and development of Hsp90 inhibitor have been continued and a few Hsp90 inhibitors targeting the N-terminal ATP binding site are being tested in the clinical trials. There are no metabolic signature molecules that can be used to evaluate the effect of Hsp90 inhibition. We previously found a potential C-domain binder named PPC1 that is a synthetic small molecule. Here we report the metabolomics study to find signature metabolites upon treatment of PPC1 compound in lung cancer cell line, A549 and discuss the potentiality of metabolomic approach for evaluation of hit compounds.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"10-14"},"PeriodicalIF":0.3,"publicationDate":"2014-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-20DOI: 10.6564/JKMRS.2014.18.1.015
Jae Hun Choi, N. Kim, A. Lim
The structural properties and relaxation processes of MCsSO4 (M = Na, K, or Rb) crystals were investigated by measuring the NMR spectra and spin–lattice relaxation rates 1/T1 of their Na, K, Rb, and Cs nuclei. According to the NMR spectra, the MCsSO4 crystals contain two crystallographically inequivalent sites each for the M and Cs ions. Further, the relaxation rates of all these nuclei do not change significantly over the investigated temperature range, indicating that no phase transitions occur in these crystals in this range. The variations in the 1/T1 values of the Na, K, Rb, and Cs nuclei in these three crystals with increasing temperature are approximately proportional to T, indicating that Raman processes may be responsible for the relaxation. Therefore, for nuclear quadrupole relaxation of the Na, K, Rb, and Cs nuclei, Raman processes with n = 2 are more effective than direct processes.
{"title":"Nucleus-phonon interactions of MCsSO4 (M = Na, K, or Rb) single crystals studied using spin-lattice relaxation time","authors":"Jae Hun Choi, N. Kim, A. Lim","doi":"10.6564/JKMRS.2014.18.1.015","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.1.015","url":null,"abstract":"The structural properties and relaxation processes of MCsSO4 (M = Na, K, or Rb) crystals were investigated by measuring the NMR spectra and spin–lattice relaxation rates 1/T1 of their Na, K, Rb, and Cs nuclei. According to the NMR spectra, the MCsSO4 crystals contain two crystallographically inequivalent sites each for the M and Cs ions. Further, the relaxation rates of all these nuclei do not change significantly over the investigated temperature range, indicating that no phase transitions occur in these crystals in this range. The variations in the 1/T1 values of the Na, K, Rb, and Cs nuclei in these three crystals with increasing temperature are approximately proportional to T, indicating that Raman processes may be responsible for the relaxation. Therefore, for nuclear quadrupole relaxation of the Na, K, Rb, and Cs nuclei, Raman processes with n = 2 are more effective than direct processes.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"73 1","pages":"15-23"},"PeriodicalIF":0.3,"publicationDate":"2014-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-20DOI: 10.6564/JKMRS.2014.18.1.036
Won-Je Kim, J. Rhee, Jong-Jae Yi, Bong‐Jin Lee, W. Son
Predicting secondary structure of protein through assigned backbone chemical shifts has been used widely because of its convenience and flexibility. In spite of its usefulness, chemical shift based analysis has some defects including isotopic shifts and solvent interaction. Here, it is shown that corrected chemical shift analysis for secondary structure of protein. It is included chemical shift correction through consideration of deuterium isotopic effect and calculate chemical shift index using probability-based methods. Enhanced method was applied successfully to one of the proteins from Mycobacterium tuberculosis. It is suggested that correction of chemical shift analysis could increase accuracy of secondary structure prediction of protein and small molecule in solution.
{"title":"Enhanced Chemical Shift Analysis for Secondary Structure prediction of protein","authors":"Won-Je Kim, J. Rhee, Jong-Jae Yi, Bong‐Jin Lee, W. Son","doi":"10.6564/JKMRS.2014.18.1.036","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.1.036","url":null,"abstract":"Predicting secondary structure of protein through assigned backbone chemical shifts has been used widely because of its convenience and flexibility. In spite of its usefulness, chemical shift based analysis has some defects including isotopic shifts and solvent interaction. Here, it is shown that corrected chemical shift analysis for secondary structure of protein. It is included chemical shift correction through consideration of deuterium isotopic effect and calculate chemical shift index using probability-based methods. Enhanced method was applied successfully to one of the proteins from Mycobacterium tuberculosis. It is suggested that correction of chemical shift analysis could increase accuracy of secondary structure prediction of protein and small molecule in solution.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"36-40"},"PeriodicalIF":0.3,"publicationDate":"2014-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329010","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-20DOI: 10.6564/JKMRS.2014.18.1.001
J. Suh, Taekyung Yu, Young‐Joo Yun, Ko On Lee
It is generally understood that protein− protein interactions proceed via transient encounter complexes that rapidly evolve into the functional stereospecific complex. Direct detection and characterization of the encounter complexes, however, been difficult due to their low population and short lifetimes. Recent application of NMR paramagnetic relaxation enhancement first visualized the structures of the encounter complex ensemble, and allowed the characterization of their physicochemical properties. Further, rational protein mutations that perturbed the encounter complex formation provided a clue to the target search pathway during protein−protein association. Understanding the structure and dynamics of encounter complexes will provide useful information on the mechanism of protein association
{"title":"NMR Studies on Transient Protein Complexes: Perspectives","authors":"J. Suh, Taekyung Yu, Young‐Joo Yun, Ko On Lee","doi":"10.6564/JKMRS.2014.18.1.001","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.1.001","url":null,"abstract":"It is generally understood that protein− protein interactions proceed via transient encounter complexes that rapidly evolve into the functional stereospecific complex. Direct detection and characterization of the encounter complexes, however, been difficult due to their low population and short lifetimes. Recent application of NMR paramagnetic relaxation enhancement first visualized the structures of the encounter complex ensemble, and allowed the characterization of their physicochemical properties. Further, rational protein mutations that perturbed the encounter complex formation provided a clue to the target search pathway during protein−protein association. Understanding the structure and dynamics of encounter complexes will provide useful information on the mechanism of protein association","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"1-4"},"PeriodicalIF":0.3,"publicationDate":"2014-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329325","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-20DOI: 10.6564/JKMRS.2014.18.1.024
J. Jee
Abstract Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stagewith experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, the we compared qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fieldsff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.
{"title":"Effects of force fields for refining protein NMR structures with atomistic force fields and generalized-Born implicit solvent model","authors":"J. Jee","doi":"10.6564/JKMRS.2014.18.1.024","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.1.024","url":null,"abstract":"Abstract Atomistic molecular dynamics (MD) simulation has become mature enabling close approximation of the real behaviors of biomolecules. In biomolecular NMR field, atomistic MD simulation coupled with generalized implicit solvent model (GBIS) has contributed to improving the qualities of NMR structures in the refinement stagewith experimental restraints. Here all-atom force fields play important roles in defining the optimal positions between atoms and angles, resulting in more precise and accurate structures. Despite successful applications in refining NMR structure, however, the research that has studied the influence of force fields in GBIS is limited. In this study, the we compared qualities of NMR structures of two model proteins, ubiquitin and GB1, under a series of AMBER force fieldsff99SB, ff99SB-ILDN, ff99SB-NMR, ff12SB, and ff13with experimental restraints. The root mean square deviations of backbone atoms and packing scores that reflect the apparent structural qualities were almost indistinguishable except ff13. Qualitative comparison of parameters, however, indicates that ff99SB-ILDN is more recommendable, at least in the cases of ubiquitin and GB1.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"24-29"},"PeriodicalIF":0.3,"publicationDate":"2014-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329395","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2014-06-20DOI: 10.6564/JKMRS.2014.18.1.005
Nak-Kyoon Kim, Y. Nam, Kang‐Bong Lee
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.
{"title":"NMR methods for structural analysis of RNA: a Review","authors":"Nak-Kyoon Kim, Y. Nam, Kang‐Bong Lee","doi":"10.6564/JKMRS.2014.18.1.005","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.1.005","url":null,"abstract":"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.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"5-9"},"PeriodicalIF":0.3,"publicationDate":"2014-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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