Pub Date : 2015-06-30DOI: 10.6564/JKMRS.2015.19.1.001
J. Jee
{"title":"Comparison of NMR structures refined under implicit and explicit solvents","authors":"J. Jee","doi":"10.6564/JKMRS.2015.19.1.001","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.1.001","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"14 1","pages":"1-10"},"PeriodicalIF":0.3,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329477","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 : 2015-06-30DOI: 10.6564/JKMRS.2015.19.1.011
J. Park, H. Cheong
{"title":"Electron Spin Resonance Line-widths of Carbon Nanotubes based on the Hyperfine Interaction","authors":"J. Park, H. Cheong","doi":"10.6564/JKMRS.2015.19.1.011","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.1.011","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"11-17"},"PeriodicalIF":0.3,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329487","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 : 2015-06-30DOI: 10.6564/JKMRS.2015.19.1.029
A. Lim, K. Lee
The microscopic dynamics of CsH2PO4, with two distinct hydrogen bond lengths, are studied by static nuclear magnetic resonance (NMR) and magic angle spinning (MAS) NMR. The proton dynamics of the two crystallographically inequivalent hydrogen sites were discussed in terms of the 1 H
{"title":"Ferroelectric-Paraelectric Phase Transition of CsH 2 PO 4 studied by Static NMR and MAS NMR","authors":"A. Lim, K. Lee","doi":"10.6564/JKMRS.2015.19.1.029","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.1.029","url":null,"abstract":"The microscopic dynamics of CsH2PO4, with two distinct hydrogen bond lengths, are studied by static nuclear magnetic resonance (NMR) and magic angle spinning (MAS) NMR. The proton dynamics of the two crystallographically inequivalent hydrogen sites were discussed in terms of the 1 H","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"29-35"},"PeriodicalIF":0.3,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329368","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 : 2015-06-30DOI: 10.6564/JKMRS.2015.19.1.049
Hyojung Kim, Yena Kim, Kiyoung Lee, Bong‐Jin Lee
MRA1997 is a 76-residue conserved hypothetical protein of Mycobacterium tuberculosis H37Ra, one of the most pathogenic bacterial species and the causative agent of tuberculosis. In this study, the sequence–specific backbone resonance assignment of MRA1997 was performed using NMR spectroscopy. Approximately 88.3% of the total resonances could be unambiguously assigned. By analyzing deviations of the Cα and Cβ chemical shift values, the secondary structure of MRA1997 was calculated. The result revealed that secondary structure of MRA 1997 consists of one α-helix and five β-sheets. Our structural study will be a footstone towards the characterization of the three-dimensional structure of MRA1997.
{"title":"Backbone assignments of1H,15N and13C resonances and secondary structure prediction of MRA1997 from Mycobacterium tuberculosis H37Rv","authors":"Hyojung Kim, Yena Kim, Kiyoung Lee, Bong‐Jin Lee","doi":"10.6564/JKMRS.2015.19.1.049","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.1.049","url":null,"abstract":"MRA1997 is a 76-residue conserved hypothetical protein of Mycobacterium tuberculosis H37Ra, one of the most pathogenic bacterial species and the causative agent of tuberculosis. In this study, the sequence–specific backbone resonance assignment of MRA1997 was performed using NMR spectroscopy. Approximately 88.3% of the total resonances could be unambiguously assigned. By analyzing deviations of the Cα and Cβ chemical shift values, the secondary structure of MRA1997 was calculated. The result revealed that secondary structure of MRA 1997 consists of one α-helix and five β-sheets. Our structural study will be a footstone towards the characterization of the three-dimensional structure of MRA1997.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"49-53"},"PeriodicalIF":0.3,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329423","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 : 2015-06-30DOI: 10.6564/JKMRS.2015.19.1.036
Yoo-Sup Lee, W. Yoon, I. Chung, K. Chung, H. Won, M. Seo
{"title":"Backbone NMR Assignments of an Uncharacterized Protein, SF1002 from Shigella flexneri 5a M90T","authors":"Yoo-Sup Lee, W. Yoon, I. Chung, K. Chung, H. Won, M. Seo","doi":"10.6564/JKMRS.2015.19.1.036","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.1.036","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"36-41"},"PeriodicalIF":0.3,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329381","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 : 2015-06-30DOI: 10.6564/JKMRS.2015.19.1.018
Seung Jin Lee, A. Lim
【The structural geometry of $[N(CH_3)_4]_2CdCl_4$ in a hexagonal phase is studied by $^1H$ MAS NMR, $^{13}C$ CP/MAS NMR, and $^{14}N$ NMR. The changes in the chemical shifts for $^{13}C$ and $^{14}N$ in the hexagonal phase are explained by the structural geometry. In addition, the temperature dependencies of the spin-lattice relaxation time in the rotating frame $T_{1{rho}}$ for $^1H$ MAS NMR and $^{13}C$ CP/MAS NMR are measured.】
用$^1H$ MAS NMR、$^{13}C$ CP/MAS NMR和$^{14}N$ NMR研究了$[N(CH_3)_4]_2CdCl_4$在六方相中的结构几何。六方相中$^{13}C$和$^{14}N$的化学位移变化可以用结构几何来解释。此外，还测量了$^1H$ MAS NMR和$^{13}C$ CP/MAS NMR在旋转框架$T_{1{rho}}$中自旋晶格弛豫时间的温度依赖性。
{"title":"Structural characteristics of [N(CH 3 ) 4 ] 2 CdCl 4 determined by 1 H MAS NMR, 13 C CP/ MAS NMR, and 14 N NMR","authors":"Seung Jin Lee, A. Lim","doi":"10.6564/JKMRS.2015.19.1.018","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.1.018","url":null,"abstract":"【The structural geometry of $[N(CH_3)_4]_2CdCl_4$ in a hexagonal phase is studied by $^1H$ MAS NMR, $^{13}C$ CP/MAS NMR, and $^{14}N$ NMR. The changes in the chemical shifts for $^{13}C$ and $^{14}N$ in the hexagonal phase are explained by the structural geometry. In addition, the temperature dependencies of the spin-lattice relaxation time in the rotating frame $T_{1{rho}}$ for $^1H$ MAS NMR and $^{13}C$ CP/MAS NMR are measured.】","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"18-22"},"PeriodicalIF":0.3,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329495","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.2014.18.2.047
Sung Jean Park
Larger proteins (above molecular weight 50 kDa) usually show slow motional tumbling in solution, which facilitates the decay of NMR signal, resulting in poor signal-to-noise. In the past twenty years, researchers have tried to overcome this problem with higher molecular weight by improvement of hardware (higher magnetic field and cryoprobe), optimization of pulse sequences for lager molecules, and development of isotope-labeling techniques. Actually, GroEL/ES complex (≈ 900 kDa) was successfully studied using combination of above techniques. Among the techniques used in large molecular studies, the impact of isotope-labeling for large molecules study is summarized and discussed here.
{"title":"NMR Study of larger proteins using isotope labeling","authors":"Sung Jean Park","doi":"10.6564/JKMRS.2014.18.2.047","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.2.047","url":null,"abstract":"Larger proteins (above molecular weight 50 kDa) usually show slow motional tumbling in solution, which facilitates the decay of NMR signal, resulting in poor signal-to-noise. In the past twenty years, researchers have tried to overcome this problem with higher molecular weight by improvement of hardware (higher magnetic field and cryoprobe), optimization of pulse sequences for lager molecules, and development of isotope-labeling techniques. Actually, GroEL/ES complex (≈ 900 kDa) was successfully studied using combination of above techniques. Among the techniques used in large molecular studies, the impact of isotope-labeling for large molecules study is summarized and discussed here.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"9 1","pages":"47-51"},"PeriodicalIF":0.3,"publicationDate":"2014-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329061","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.2014.18.2.052
Hee-Eun Kim, Yong-Geun Choi, Ae-Ree Lee, Yeo-Jin Seo, Mun-Young Kwon, Joon-Hwa Lee
The TCP domain is a DNA-binding domain present in plant transcription factors and plays important roles in various biological functions. The hydrogen exchange rate constants of the imino protons were determined for the three DNA duplexes containing the DNA-binding sites for the TCP11, TCP15, and TCP20 transcription factors using NMR spectroscopy. The M11 duplex displays unique hydrogen exchange property of the five base pairs in the first binding site (5’-GTGGG-3’). However, the M15 and M20 duplexes lead to clear changes in thermal stabilities of these five base pairs. The unique dynamic features of the five base pairs in the first binding site might play crucial roles in the sequence-specific DNA binding of the class I TCP transcription factors.
{"title":"Temperature dependent hydrogen exchange study of DNA duplexes containing binding sites for Arabidopsis TCP transcription factors","authors":"Hee-Eun Kim, Yong-Geun Choi, Ae-Ree Lee, Yeo-Jin Seo, Mun-Young Kwon, Joon-Hwa Lee","doi":"10.6564/JKMRS.2014.18.2.052","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.2.052","url":null,"abstract":"The TCP domain is a DNA-binding domain present in plant transcription factors and plays important roles in various biological functions. The hydrogen exchange rate constants of the imino protons were determined for the three DNA duplexes containing the DNA-binding sites for the TCP11, TCP15, and TCP20 transcription factors using NMR spectroscopy. The M11 duplex displays unique hydrogen exchange property of the five base pairs in the first binding site (5’-GTGGG-3’). However, the M15 and M20 duplexes lead to clear changes in thermal stabilities of these five base pairs. The unique dynamic features of the five base pairs in the first binding site might play crucial roles in the sequence-specific DNA binding of the class I TCP transcription factors.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"83 1","pages":"52-57"},"PeriodicalIF":0.3,"publicationDate":"2014-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329073","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.2014.18.2.082
J. Rho
Three bicyclic and one monocyclic sesquiterpenoids were isolated from the marine sponge Topsentia species. Their planar structures were completely determined from a combination of extensive 1D and 2D NMR experiments, and also the relative stereochemistry on the chiral centers were established by the ROESY experiment. Compound 1 was determined as a new stereoisomer. Furthermore, the NMR spectral data for compounds 2 and 4, of which have not been reported, were listed. Four compounds did not show any cytotoxicity, instead compound 4 exhibited moderate antifungal activity against Candida albicans.
{"title":"Four sesquiterpenes isolated from a Marine Sponge Topsentia species","authors":"J. Rho","doi":"10.6564/JKMRS.2014.18.2.082","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.2.082","url":null,"abstract":"Three bicyclic and one monocyclic sesquiterpenoids were isolated from the marine sponge Topsentia species. Their planar structures were completely determined from a combination of extensive 1D and 2D NMR experiments, and also the relative stereochemistry on the chiral centers were established by the ROESY experiment. Compound 1 was determined as a new stereoisomer. Furthermore, the NMR spectral data for compounds 2 and 4, of which have not been reported, were listed. Four compounds did not show any cytotoxicity, instead compound 4 exhibited moderate antifungal activity against Candida albicans.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"82-88"},"PeriodicalIF":0.3,"publicationDate":"2014-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329317","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.2014.18.2.069
J. Jee
For performing a search of conformational spaces using a suitable algorithmic or software method, these methods must meet the experimental restraints as well as force field that defines the physical energies between atoms.Traditional software for NMR structure calculation use simplified force fields compared to atomistic molecular dynamics (MD) simulation to enhance the search efficiency of conformational space.
{"title":"Letter to Editor: Accelerating atomistic refinement of NMR structures using Graphics Processing Unit","authors":"J. Jee","doi":"10.6564/JKMRS.2014.18.2.069","DOIUrl":"https://doi.org/10.6564/JKMRS.2014.18.2.069","url":null,"abstract":"For performing a search of conformational spaces using a suitable algorithmic or software method, these methods must meet the experimental restraints as well as force field that defines the physical energies between atoms.Traditional software for NMR structure calculation use simplified force fields compared to atomistic molecular dynamics (MD) simulation to enhance the search efficiency of conformational space.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"18 1","pages":"69-73"},"PeriodicalIF":0.3,"publicationDate":"2014-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329250","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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