Pub Date : 2018-01-01DOI: 10.6564/JKMRS.2018.22.4.132
Kwang-Ho Choi, Joon-Hwa Lee
The plucking season of green tea leaves is one of the important parameters that decide their metabolic quality. Here, we performed the identification and quantity analysis of the metabolites of the green tea using NMR spectroscopy. We assigned the 1H resonances for sixteen metabolites. This analysis found that four metabolites, gallic acid, quinic acid, theobromine and ECG, exhibited clear discrimination of green teas by the three different grades, Ujeon, Sejak and Jungjak. Our results suggest that these four metabolites could be used for diagnostics for quality control of green tea.
{"title":"Quantitative analysis of metabolites in Korean green tea using NMR","authors":"Kwang-Ho Choi, Joon-Hwa Lee","doi":"10.6564/JKMRS.2018.22.4.132","DOIUrl":"https://doi.org/10.6564/JKMRS.2018.22.4.132","url":null,"abstract":"The plucking season of green tea leaves is one of the important parameters that decide their metabolic quality. Here, we performed the identification and quantity analysis of the metabolites of the green tea using NMR spectroscopy. We assigned the 1H resonances for sixteen metabolites. This analysis found that four metabolites, gallic acid, quinic acid, theobromine and ECG, exhibited clear discrimination of green teas by the three different grades, Ujeon, Sejak and Jungjak. Our results suggest that these four metabolites could be used for diagnostics for quality control of green tea.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"22 1","pages":"132-138"},"PeriodicalIF":0.3,"publicationDate":"2018-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71330154","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 : 2017-09-20DOI: 10.6564/JKMRS.2017.21.3.085
Jong-Jae Yi, Won-Je Kim, J. Rhee, Jongsoo Lim, Bong‐Jin Lee, W. Son
Pyrazinamidase (PncA) from Mycobacterium tuberculosis is the hydrolytic enzyme (hydrolase) that can hydrolyze substrate PZA to active form pyrazoic acid (POA). To investigate hydrolytic reaction of M. tuberculosis PncA, 1D NMR spectra were monitored at various molar ratios of PncA and PZA. The line-width of PZA was changed as PncA was added into PZA with different molar ratios. These results suggested that determination of PncA enzymatic activity could potentially serve as an indirect measure of PZA susceptibility.
{"title":"Identification of Enzymatic Catalysis of PncA using 1H-NMR","authors":"Jong-Jae Yi, Won-Je Kim, J. Rhee, Jongsoo Lim, Bong‐Jin Lee, W. Son","doi":"10.6564/JKMRS.2017.21.3.085","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.3.085","url":null,"abstract":"Pyrazinamidase (PncA) from Mycobacterium tuberculosis is the hydrolytic enzyme (hydrolase) that can hydrolyze substrate PZA to active form pyrazoic acid (POA). To investigate hydrolytic reaction of M. tuberculosis PncA, 1D NMR spectra were monitored at various molar ratios of PncA and PZA. The line-width of PZA was changed as PncA was added into PZA with different molar ratios. These results suggested that determination of PncA enzymatic activity could potentially serve as an indirect measure of PZA susceptibility.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"85-89"},"PeriodicalIF":0.3,"publicationDate":"2017-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44978481","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 : 2017-09-20DOI: 10.6564/JKMRS.2017.21.3.109
J. Shin, Kyeong-Mi Bang, H. Song, Nak-Kyoon Kim
The hepatitis C virus (HCV) internal ribosome entry site (IRES) is an RNA structure located in the 5’-UTR of the HCV RNA genome. The HCV IRES consists of four domains I, II, III, and IV, where domains II - IV are recognized by 40S ribosomal subunit and the domain III is bound to eukaryotic initiation factor 3 (eIF3) for translation initiation. Here, we have characterized the tertiary interaction between an L-/K- rich peptide and the HCV IRES domain IV. To probe the peptide binding interface in RNA, we synthesized 13 C- and 15 N-double labeled RNA and the binding site was identified by using the chemical shift perturbation (CSP) NMR methods. Our results showed that the peptide binds to the upper stem of the IRES domain IV, indicating that the tertiary interaction between the IRES domain IV and the peptide would disrupt the initiation of translation of HCV mRNA by blocking the start codon exposure. This study will provide an insight into the new peptide-based anti-viral drug design targeting HCV IRES RNA.
{"title":"Structural Studies of Peptide Binding Interaction of HCV IRES Domain IV","authors":"J. Shin, Kyeong-Mi Bang, H. Song, Nak-Kyoon Kim","doi":"10.6564/JKMRS.2017.21.3.109","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.3.109","url":null,"abstract":"The hepatitis C virus (HCV) internal ribosome entry site (IRES) is an RNA structure located in the 5’-UTR of the HCV RNA genome. The HCV IRES consists of four domains I, II, III, and IV, where domains II - IV are recognized by 40S ribosomal subunit and the domain III is bound to eukaryotic initiation factor 3 (eIF3) for translation initiation. Here, we have characterized the tertiary interaction between an L-/K- rich peptide and the HCV IRES domain IV. To probe the peptide binding interface in RNA, we synthesized 13 C- and 15 N-double labeled RNA and the binding site was identified by using the chemical shift perturbation (CSP) NMR methods. Our results showed that the peptide binds to the upper stem of the IRES domain IV, indicating that the tertiary interaction between the IRES domain IV and the peptide would disrupt the initiation of translation of HCV mRNA by blocking the start codon exposure. This study will provide an insight into the new peptide-based anti-viral drug design targeting HCV IRES RNA.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"109-113"},"PeriodicalIF":0.3,"publicationDate":"2017-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47795661","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 : 2017-09-20DOI: 10.6564/JKMRS.2017.21.3.078
Yeongjoon Lee, Dasom Jeon, Jin-Kyoung Kim, Yangmee Kim
Pseudin is a naturally occurring 24 amino-acid-residue antimicrobial peptide derived from the skin of paradoxical frog Pseud’s paradoxa . It shows potency against the bacteria and antibiotic-resistant bacteria strain, but has high cytotoxicity against mammalian cell. In our previous study, substitution of Pro 11 for Gly (Ps-P) increased bacterial cell selectivity but decreased the antibacterial activity of pseudin. In this study, we designed pseudin analogue, Ps-4K-P with increased cationicity up to +7 in Ps-P by substituting Glu14, Gln10, Gln24, and Leu18 with Lys. Ps-4K-P showed improved potent antibacterial activity with high bacterial cell selectivity. We determined the tertiary structure of Ps-4K-P in the presence of DPC micelles by NMR spectroscopy and it has a hinge structure at Pro 11 followed by three turn helices from Pro 11 to Val 23 at the C-terminus. Amphipathicity with increased cationicity as well as helix-hinge-helix structural motif provided by introduction of a Pro at position Gly 11 are the crucial factors which confer antibacterial activity with bacterial cell selectivity to Ps-4K-P.
{"title":"Structure-Activity Relationships of Peptide Antibiotics with Improved Bacterial Cell Selectivity of Pseudin","authors":"Yeongjoon Lee, Dasom Jeon, Jin-Kyoung Kim, Yangmee Kim","doi":"10.6564/JKMRS.2017.21.3.078","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.3.078","url":null,"abstract":"Pseudin is a naturally occurring 24 amino-acid-residue antimicrobial peptide derived from the skin of paradoxical frog Pseud’s paradoxa . It shows potency against the bacteria and antibiotic-resistant bacteria strain, but has high cytotoxicity against mammalian cell. In our previous study, substitution of Pro 11 for Gly (Ps-P) increased bacterial cell selectivity but decreased the antibacterial activity of pseudin. In this study, we designed pseudin analogue, Ps-4K-P with increased cationicity up to +7 in Ps-P by substituting Glu14, Gln10, Gln24, and Leu18 with Lys. Ps-4K-P showed improved potent antibacterial activity with high bacterial cell selectivity. We determined the tertiary structure of Ps-4K-P in the presence of DPC micelles by NMR spectroscopy and it has a hinge structure at Pro 11 followed by three turn helices from Pro 11 to Val 23 at the C-terminus. Amphipathicity with increased cationicity as well as helix-hinge-helix structural motif provided by introduction of a Pro at position Gly 11 are the crucial factors which confer antibacterial activity with bacterial cell selectivity to Ps-4K-P.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"78-84"},"PeriodicalIF":0.3,"publicationDate":"2017-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45257097","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 : 2017-09-20DOI: 10.6564/JKMRS.2017.21.3.096
Youngae Jung
Metabolomics is one of latest '-omics', which is to analyze metabolome in cells, tissues and biofluids and to study metabolisms. It has become increasingly popular since 1990. The first goal of metabolomics is to analyze metabolites in a technical aspect. The major two analytical platforms in metabolomics are NMR spectroscopy and mass spectrometry (MS). MS is superior to NMR for detecting many more metabolites. That is one of the most important factors in metabolomics. However, NMR also has several advantages over MS. In this review, I firstly introduced metabolomics by comparing NMR-based metabolomics and MS-based metabolomics. Second, I explored technical issues on sample preparation and NMR experiments for metabolite identification and quantification.
{"title":"Practical Guide to NMR-based Metabolomics - I : Introduction and Experiments","authors":"Youngae Jung","doi":"10.6564/JKMRS.2017.21.3.096","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.3.096","url":null,"abstract":"Metabolomics is one of latest '-omics', which is to analyze metabolome in cells, tissues and biofluids and to study metabolisms. It has become increasingly popular since 1990. The first goal of metabolomics is to analyze metabolites in a technical aspect. The major two analytical platforms in metabolomics are NMR spectroscopy and mass spectrometry (MS). MS is superior to NMR for detecting many more metabolites. That is one of the most important factors in metabolomics. However, NMR also has several advantages over MS. In this review, I firstly introduced metabolomics by comparing NMR-based metabolomics and MS-based metabolomics. Second, I explored technical issues on sample preparation and NMR experiments for metabolite identification and quantification.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"96-101"},"PeriodicalIF":0.3,"publicationDate":"2017-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48596097","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 : 2017-09-20DOI: 10.6564/JKMRS.2017.21.3.102
Y. Chae, Seol Hyun Kim
{"title":"Stress Adaptation of Escherichia coli as Monitored via Metabolites by Using Two-Dimensional NMR Spectroscopy","authors":"Y. Chae, Seol Hyun Kim","doi":"10.6564/JKMRS.2017.21.3.102","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.3.102","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"102-108"},"PeriodicalIF":0.3,"publicationDate":"2017-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45109779","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 : 2017-09-20DOI: 10.6564/JKMRS.2017.21.3.090
Ae-Ree Lee, Seo-Ree Choi, Yeo-Jin Seo, Joon-Hwa Lee
The Z-DNA domain of human ADAR1 (Zα ADAR1 ) produces B-Z junction DNA through preferential binding to the CG-repeat segment and destabilizing the neighboring AT-rich region. 9 However, this study could not answer the question of how many base-pairs in AT-rich region are destabilized by binding of Zα ADAR1 . Thus, we have performed NMR experiments of Zα ADAR1 to the longer DNA duplex containing an 8-base-paired (8-bp) CG-repeat segment and a 12-bp AT-rich region. This study revealed that Zα ADAR1 preferentially binds to the CG-repeat segment rather than AT-rich region in a long DNA and then destabilizes at least 6 base-pairs in the neighboring AT-rich region for efficient B-Z transition of the CG-repeat segment.
{"title":"NMR Study on the Preferential Binding of the Zα Domain of Human ADAR1 to CG-repeat DNA Duplex","authors":"Ae-Ree Lee, Seo-Ree Choi, Yeo-Jin Seo, Joon-Hwa Lee","doi":"10.6564/JKMRS.2017.21.3.090","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.3.090","url":null,"abstract":"The Z-DNA domain of human ADAR1 (Zα ADAR1 ) produces B-Z junction DNA through preferential binding to the CG-repeat segment and destabilizing the neighboring AT-rich region. 9 However, this study could not answer the question of how many base-pairs in AT-rich region are destabilized by binding of Zα ADAR1 . Thus, we have performed NMR experiments of Zα ADAR1 to the longer DNA duplex containing an 8-base-paired (8-bp) CG-repeat segment and a 12-bp AT-rich region. This study revealed that Zα ADAR1 preferentially binds to the CG-repeat segment rather than AT-rich region in a long DNA and then destabilizes at least 6 base-pairs in the neighboring AT-rich region for efficient B-Z transition of the CG-repeat segment.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"90-95"},"PeriodicalIF":0.3,"publicationDate":"2017-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46325493","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 : 2017-06-20DOI: 10.6564/JKMRS.2017.21.2.050
Sung-Hee Lee, D. Sim, Eun-hee Kim, Ji-Hun Kim, H. Won
Cupin-superfamily proteins represent the most functionally diverse groups of proteins and include a huge number of functionally uncharacterized proteins. Recently, YaiE, a cupin protein from Escherichia coli has been suggested to be involved in a novel activity of pyrimidine/purine nucleoside phosphorylase (PPNP). In the present study, we achieved a complete backbone NMR assignments of YaiE, by a series of heteronuclear multidimensional NMR experiments on its [ 13 C/ 15 N]-enriched sample. Subsequently, secondary structure analysis using the assigned chemical shift values identified 10 obvious β-strands and a tentative 3 10 -helix. Taken all together, the results constitute the first structural characterization of a putative PPNP cupin protein.
{"title":"Backbone NMR Assignments and Secondary Structure Determination of a Cupin-family Protein YaiE from Escherichia coli","authors":"Sung-Hee Lee, D. Sim, Eun-hee Kim, Ji-Hun Kim, H. Won","doi":"10.6564/JKMRS.2017.21.2.050","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.2.050","url":null,"abstract":"Cupin-superfamily proteins represent the most functionally diverse groups of proteins and include a huge number of functionally uncharacterized proteins. Recently, YaiE, a cupin protein from Escherichia coli has been suggested to be involved in a novel activity of pyrimidine/purine nucleoside phosphorylase (PPNP). In the present study, we achieved a complete backbone NMR assignments of YaiE, by a series of heteronuclear multidimensional NMR experiments on its [ 13 C/ 15 N]-enriched sample. Subsequently, secondary structure analysis using the assigned chemical shift values identified 10 obvious β-strands and a tentative 3 10 -helix. Taken all together, the results constitute the first structural characterization of a putative PPNP cupin protein.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"50-54"},"PeriodicalIF":0.3,"publicationDate":"2017-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44170625","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 : 2017-06-20DOI: 10.6564/JKMRS.2017.21.2.055
Janghyun Lee, Byong-Seok Choi
It is now well established that RNAs exhibit fundamental roles in regulating cellular processes. Many of these RNAs do not exist in a single conformation. Rather, they undergo dynamic transitions among many different conformations to mediate critical interactions with other biomolecules such as proteins, RNAs, DNAs, or small molecules. Here, we briefly review NMR techniques that describe the dynamic behavior of RNA by determining structural, kinetic, and thermodynamic properties.
{"title":"NMR Tools to Decipher Dynamic Structure of RNA","authors":"Janghyun Lee, Byong-Seok Choi","doi":"10.6564/JKMRS.2017.21.2.055","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.2.055","url":null,"abstract":"It is now well established that RNAs exhibit fundamental roles in regulating cellular processes. Many of these RNAs do not exist in a single conformation. Rather, they undergo dynamic transitions among many different conformations to mediate critical interactions with other biomolecules such as proteins, RNAs, DNAs, or small molecules. Here, we briefly review NMR techniques that describe the dynamic behavior of RNA by determining structural, kinetic, and thermodynamic properties.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"55-62"},"PeriodicalIF":0.3,"publicationDate":"2017-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47654661","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 : 2017-06-20DOI: 10.6564/JKMRS.2017.21.2.044
W. Choi, Yong Woo In, Hyun Hwi Kim, Ja-shil Hyun, Sung Jean Park
{"title":"Metabolic Features of Coffee Beans Depending on Planted Areas","authors":"W. Choi, Yong Woo In, Hyun Hwi Kim, Ja-shil Hyun, Sung Jean Park","doi":"10.6564/JKMRS.2017.21.2.044","DOIUrl":"https://doi.org/10.6564/JKMRS.2017.21.2.044","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"21 1","pages":"44-49"},"PeriodicalIF":0.3,"publicationDate":"2017-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48237945","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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