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Solution State Structure of P1, the Mimetic Peptide Derived from IgM Antigen Apo B-100 by NMR 来源于IgM抗原Apo B-100的模拟肽P1的溶液状态结构
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-09-20 DOI: 10.6564/JKMRS.2016.20.3.095
Gilhoon Kim, Hyuk-Pyo Lee, H. Oh, Hoshik Won
{"title":"Solution State Structure of P1, the Mimetic Peptide Derived from IgM Antigen Apo B-100 by NMR","authors":"Gilhoon Kim, Hyuk-Pyo Lee, H. Oh, Hoshik Won","doi":"10.6564/JKMRS.2016.20.3.095","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.3.095","url":null,"abstract":"Apolipoprotein B-100 (Apo-B100) is a major component of low density lipoprotein (LDL). Apo B-100 protein has 4,536 amino acid sequence and these amino acids are classified into peptide groups A to G with subsequent 20 amino acids (P1-P302). The peptide groups were act as immunoglobulin (Ig) antigens which oxidized via malondialdehyde (MDA). The mimetic peptide P1 (EEEMLENVSLVCPKDAT RFK) out of D-group peptides carrying the highest value of IgG antigens were selected for structural studies that may provide antigen specificity. Circular Dichroism (CD) spectra were measured for peptide secondary structure in the range of 190-250 nm. Experimental results show that P1 exhibit partial of β-sheet and random coil structure. Homonuclear (COSY, TOCSY, NOESY) 2DNMR experiments were carried out for NMR signal assignments and structure determination for P1. On the basis of these completely assigned NMR spectra and distance data, distance geometry (DG) and Molecular dynamics (MD) were carried out to determine the structures of P1. The proposed structure was selected by comparisons between experimental NOE spectra and back calculated 2D NOE results from determined structure showing acceptable agreement. The total Root-Mean-Square-Deviation (RMSD) value of P1 obtained upon superposition of all atoms was in the range 0.33Å. The solution state P1 has mixed structure of β-sheet (Glu[1] to Cys[12]) and random coil (Pro[13] to Lys[20]). These NMR results are well consistent with secondary structure from experimental results of circular dichroism. Structural studies based on NMR may contribute to the studies of atherosclerosis and observed conformational characteristics of apo B-100 in LDL using monoclonal antibodies.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"95-101"},"PeriodicalIF":0.3,"publicationDate":"2016-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329886","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}
引用次数: 0
An Investigation of the Sample Rotation Effects on Suppression of Convective Flows in PGSE Diffusion NMR Experiments PGSE扩散核磁共振实验中样品旋转对对流抑制效应的研究
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-06-20 DOI: 10.6564/JKMRS.2016.20.2.061
Minkyoung Kim, Kee-Choo Chung
{"title":"An Investigation of the Sample Rotation Effects on Suppression of Convective Flows in PGSE Diffusion NMR Experiments","authors":"Minkyoung Kim, Kee-Choo Chung","doi":"10.6564/JKMRS.2016.20.2.061","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.2.061","url":null,"abstract":"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-d6 chloroform-d, pyridine-d5, and D2O. The sample rotation showed apparent convection suppressing effects at all temperature range for the low viscosity solvents, acetone-d6 and chloroform-d, even at the faster than 5 Hz spinning rate. The similar patterns were also observed for pyridine-d5 and D2O, which have higher viscosity. This effect was observed even at high temperatures where convective flow arises conspicuously.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"61-65"},"PeriodicalIF":0.3,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329772","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}
引用次数: 0
Backbone assignment of the anticodon binding domain of human Glycyl-tRNA synthetase 人glyyl - trna合成酶反密码子结合域的主链分配
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-06-20 DOI: 10.6564/JKMRS.2016.20.2.050
A. U. Mushtaq, H. Cho, Youngjoo Byun, Y. Jeon
{"title":"Backbone assignment of the anticodon binding domain of human Glycyl-tRNA synthetase","authors":"A. U. Mushtaq, H. Cho, Youngjoo Byun, Y. Jeon","doi":"10.6564/JKMRS.2016.20.2.050","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.2.050","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"50-55"},"PeriodicalIF":0.3,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329685","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}
引用次数: 0
Secondary structure analysis of MRA1997 from Mycobacterium tuberculosis and characterization of DNA binding property 结核分枝杆菌MRA1997二级结构分析及DNA结合特性分析
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-06-20 DOI: 10.6564/JKMRS.2016.20.2.036
Hyo Jung Kim, Kiyoung Lee, Yena Kim, A. Kwon, Bong‐Jin Lee
{"title":"Secondary structure analysis of MRA1997 from Mycobacterium tuberculosis and characterization of DNA binding property","authors":"Hyo Jung Kim, Kiyoung Lee, Yena Kim, A. Kwon, Bong‐Jin Lee","doi":"10.6564/JKMRS.2016.20.2.036","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.2.036","url":null,"abstract":"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.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"36-40"},"PeriodicalIF":0.3,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329623","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}
引用次数: 0
NMR Signal Assignments of Human Adenylate Kinase 1 (hAK1) and its R138A Mutant (hAK1R138A) 人腺苷酸激酶1 (hAK1)及其突变体R138A的核磁共振信号定位
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-06-20 DOI: 10.6564/JKMRS.2016.20.2.056
Gilhoon Kim, Hwanbong Chang, Hoshik Won
{"title":"NMR Signal Assignments of Human Adenylate Kinase 1 (hAK1) and its R138A Mutant (hAK1R138A)","authors":"Gilhoon Kim, Hwanbong Chang, Hoshik Won","doi":"10.6564/JKMRS.2016.20.2.056","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.2.056","url":null,"abstract":"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[138] of LID domain with alanine[138] 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[138] and per-turbation value(0.22ppm) of valine[179] is consid-ered as inter-communication effect with LID domain and the structural change between hAK1 and AK1R138A.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"56-60"},"PeriodicalIF":0.3,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329747","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}
引用次数: 0
Structural Characterization of pre-miRNA 155 pre-miRNA的结构表征
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-06-20 DOI: 10.6564/JKMRS.2016.20.2.046
Won-Je Kim, J. Shin, Kyeong-Mi Bang, H. Song, Nak-Kyoon Kim
{"title":"Structural Characterization of pre-miRNA 155","authors":"Won-Je Kim, J. Shin, Kyeong-Mi Bang, H. Song, Nak-Kyoon Kim","doi":"10.6564/JKMRS.2016.20.2.046","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.2.046","url":null,"abstract":"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 15 N- 1 H 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.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"46-49"},"PeriodicalIF":0.3,"publicationDate":"2016-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329663","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}
引用次数: 0
Expression and Preparation of Periostin FAS1 Domains for NMR Structure Determination 用于核磁共振结构测定的Periostin FAS1结构域的表达和制备
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-03-20 DOI: 10.6564/JKMRS.2016.20.1.017
Hyosuk Yun, J. Kim, C. Lee
{"title":"Expression and Preparation of Periostin FAS1 Domains for NMR Structure Determination","authors":"Hyosuk Yun, J. Kim, C. Lee","doi":"10.6564/JKMRS.2016.20.1.017","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.1.017","url":null,"abstract":"Periostin, a component of extracellular matrix (ECM) protein, is produced and secreted by the fibroblasts that are involved in chronic allergic inflammation diseases and various types of human cancers. Periostin protein is composed of multiple domains including four FAS1 domains which play important roles in cell adhesion and tumor metastasis by interacting with integrins. In spite of their important biological role, the structural information of periosin FAS1 domains was not revealed yet. Recently we systemically prepared various constructs of the FAS1 domains and tried to express them in E. coli. Of them, only single FAS1-II and -IV domains were highly soluble. Circular dichroism (CD) and nuclear magnetic resonance (NMR) studies revealed that the FAS1-IV domain might be suitable for three-dimensional structure determination using NMR spectroscopy.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"17-21"},"PeriodicalIF":0.3,"publicationDate":"2016-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329530","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}
引用次数: 3
Expression, Purification and Characterization of the BLM binding region of human Fanconi Anemia Group J Protein 人Fanconi贫血J组蛋白BLM结合区的表达、纯化及特性研究
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-03-20 DOI: 10.6564/JKMRS.2016.20.1.022
Kyu-Hyeon Yeom, Chin-Ju Park
{"title":"Expression, Purification and Characterization of the BLM binding region of human Fanconi Anemia Group J Protein","authors":"Kyu-Hyeon Yeom, Chin-Ju Park","doi":"10.6564/JKMRS.2016.20.1.022","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.1.022","url":null,"abstract":"【FANCJ is a DNA helicase which contributes genome stability by resolving G-quadruplex DNA from 5' to 3' direction. In addition to main ATPase helicase core, FANCJ has the protein binding region at its C-terminal part. BRCA1 and BLM are the binding partner of FANCJ and these protein-protein interactions contribute genomic stability and the proper response to replication stress. As the first attempt for studying FANCJ-BLM interaction, we prepared BLM binding region of FANCJ and characterized with CD and NMR spectroscopy. FANCJ (881-941) with N-ter 6xHis was purified as the oligomer. Secondary structure prediction based on CD data revealed that FANCJ (881-941) composed with ${beta}$ sheet, turn and coils. $^1H-^{15}N$ HSQC spectra showed nonhomogeneous peak intensities with less number of peaks comparing than the number of amino acids in the construct. It indicated that optimization should be necessary for detailed further structural studies.】","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"22-26"},"PeriodicalIF":0.3,"publicationDate":"2016-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329584","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}
引用次数: 0
Recent NMR developments for pharmaceutical research 核磁共振在药物研究中的最新进展
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-03-20 DOI: 10.6564/JKMRS.2016.20.1.027
Kwang-Sik Lee
{"title":"Recent NMR developments for pharmaceutical research","authors":"Kwang-Sik Lee","doi":"10.6564/JKMRS.2016.20.1.027","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.1.027","url":null,"abstract":"NMR spectrometer has been regarded as essential tool for structure elucidation in variable scientific field as like organic synthesis, natural product and macro protein research. Also NMR can be applied for defining dynamic behavior like ligand and receptor binding. One of advantage of research with NMR is that to be great confident to confirm structure and the measured sample could be recovered. Nevertheless NMR also has a weak points than other spectroscopic methods that require a lot of time for interpreting acquired spectrum and running time due to low sensitivity. For last two decade Bruker has developed hardware and software solution for overcome those weak points. In order to overcome low sensitivity Bruker introduced Cryo and Micro diameter probe head technology. And researcher can reduce the time for routine spectrum processing and interpretation works due to lots of introductions in software solutions for quantification, identification and statistics analysis. With four examples, this article describing those new hardware and software solutions in field of recent pharmaceutical research as follows. - New Horizons for NMR in the Biopharmaceutical Industry","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"27-35"},"PeriodicalIF":0.3,"publicationDate":"2016-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329614","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}
引用次数: 1
The difference of metabolic profile between male and female zebrafish 雌雄斑马鱼代谢谱的差异
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2016-03-20 DOI: 10.6564/JKMRS.2016.20.1.013
Dahye Yoon, J. Choi, Hyeonsoo Choi, Suhkmann Kim
{"title":"The difference of metabolic profile between male and female zebrafish","authors":"Dahye Yoon, J. Choi, Hyeonsoo Choi, Suhkmann Kim","doi":"10.6564/JKMRS.2016.20.1.013","DOIUrl":"https://doi.org/10.6564/JKMRS.2016.20.1.013","url":null,"abstract":"Various experiments using zebrafish have been highlighted recently in the scientific community. Because it is possible to conduct practical experiment from various neurological research to area of genetic study or toxicity experiment. However, gender difference effects are nearly not considered. If the gender differences of zebrafish are considered it is possible to obtain more accurate data. In this study, zebrafish which have different genders were compared each other with NMR-based metabolomics. The extracts of male and female zebrafish were measured by 600 MHz NMR spectrometer. Statistical analysis and target profiling were conducted. As a result, muscle related metabolites were observed in male zebrafish and nerve related metabolites were observed in female zebrafish.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"20 1","pages":"13-16"},"PeriodicalIF":0.3,"publicationDate":"2016-03-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329519","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}
引用次数: 2
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