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A simple guide to the structural study on membrane proteins in detergents using solution NMR 用溶液核磁共振研究洗涤剂中膜蛋白结构的简单指南
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-12-20 DOI: 10.6564/JKMRS.2015.19.3.137
D. Sim, Yoo-Sup Lee, M. Seo, H. Won, Ji-Hun Kim
{"title":"A simple guide to the structural study on membrane proteins in detergents using solution NMR","authors":"D. Sim, Yoo-Sup Lee, M. Seo, H. Won, Ji-Hun Kim","doi":"10.6564/JKMRS.2015.19.3.137","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.3.137","url":null,"abstract":"Abstract NMR-based structural studies on membrane proteins are appreciated quite challenging due to various reasons, generally including the narrow dispersion of NMR spectra, the severe peak broadening, and the lack of long range NOEs. In spite of the poor biophysical properties, structural studies on membrane proteins have got to go on ,considering their functional importance in biological systems. In this review, we provide a simple overview of the techniques generally used in structural studies of membrane proteins by solution NMR, with experimental examples of a helical membrane protein, caveolin 3. Detergent screening is usually employed as the first step and the selection of appropriate detergent is the most important for successful approach to membrane proteins. Various tools can then be applied as NMR specializedtechniques in solution that include sample deteuration, amino-acid selective isotope labeling, residual dipolar coupling, and paramagnetic relaxation enhancement.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"137-142"},"PeriodicalIF":0.3,"publicationDate":"2015-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329891","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
Structure-Activity Relationship of the N-terminal Helix Analog of Papiliocin, PapN Papiliocin n端螺旋类似物的构效关系
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.054
Dasom Jeon, Min-Cheol Jeong, Jin-Kyoung Kim, K. Jeong, Yoon-Joo Ko, Yangmee Kim
{"title":"Structure-Activity Relationship of the N-terminal Helix Analog of Papiliocin, PapN","authors":"Dasom Jeon, Min-Cheol Jeong, Jin-Kyoung Kim, K. Jeong, Yoon-Joo Ko, Yangmee Kim","doi":"10.6564/JKMRS.2015.19.2.054","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.2.054","url":null,"abstract":"Papiliocin, from the swallowtail butterfly, Papilio xuthus, shows high bacterial cell selectivity against Gram-negative bacteria. Recently, we designed a 22mer analog with N-terminal helix from Lys 3 to Ala 22 , PapN. It shows outstanding antimicrobial activity against Gram-negative bacteria with low toxicity against mammalian cells. In this study, we determined the 3-D structure of PapN in 300 mM DPC micelle using NMR spectroscopy and investigated the interactions between PapN and DPC micelles. The results showed that PapN has an amphipathic α- helical structure from Lys 3 to Lys 21 . STD-NMR and DOSY experiment showed that this helix is important in binding to the bacterial cell membrane. Furthermore, we tested antibacterial activities of PapN in the presence of salt for therapeutic application. PapN was calcium- and magnesium-resistant in a physiological condition, especially against Gram-negative bacteria, implying that it can be a potent candidate as peptide antibiotics.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"54-60"},"PeriodicalIF":0.3,"publicationDate":"2015-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329426","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
Heteronuclear NMR studies on 44 kDa dimer, syndesmos 44 kDa二聚体的异核磁共振研究
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.083
Heeyoun Kim, Inhwan Lee, Jeongmin T. Han, H. Cheong, Eunhee Kim, Weontae Lee
{"title":"Heteronuclear NMR studies on 44 kDa dimer, syndesmos","authors":"Heeyoun Kim, Inhwan Lee, Jeongmin T. Han, H. Cheong, Eunhee Kim, Weontae Lee","doi":"10.6564/JKMRS.2015.19.2.083","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.2.083","url":null,"abstract":"Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain (Syn4 cyto ) in focal contacts, interacts with various cell adhesion adaptor proteins including Syn4 cyto to control cell signaling. Syndesmos consists of 211 amino acids and it exists as a dimer (44kDa) in solution. Recently, we have determined the structure of syndesmos by x-ray crystallography, however, dynamics related to syndecan binding still remain elusive. In this report, we performed NMR experiments to acquire biochemical and structural information of syndesmos. Based on a series of three-dimensional triple resonance experiments on a 13 C/ 15 N/ 2 H labeled protein, NMR spectra were obtained with well dispersed and homogeneous NMR data. We present the sequence specific backbone assignment of syndesmos and assigned NMR data with combination structural information can be directly used for the studies on interaction with Syn4 cyto and other binding molecules.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"83-87"},"PeriodicalIF":0.3,"publicationDate":"2015-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329049","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
Isolation of Microcystin-LR and Its Potential Function of Ionophore 微囊藻毒素- lr的分离及其离子载体的潜在功能
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.067
Gilhoon Kim, S. Han, Hoshik Won
{"title":"Isolation of Microcystin-LR and Its Potential Function of Ionophore","authors":"Gilhoon Kim, S. Han, Hoshik Won","doi":"10.6564/JKMRS.2015.19.2.067","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.2.067","url":null,"abstract":"The microcystin is a cyclic heptapeptide from metabolites of cyanobacteria in the genera mycrocystis, anabaeba as a result of eutrophication. It has been known that microcystin-LR is a potent inhibitor of the catalytic subunits of protein phosphatase-1 (PP-1) as well as powerful tumor promoter. The active site of microcystin actually has two metal ions Fe 2+ /Zn 2+ close to the nucleophilic portion of PP-1-microcystin complex. We report the isolation and purification of this microcystin-LR from cyanobacteria (blue-green algae) obtained from Daechung Dam in Chung-cheong Do, Korea. Microcystin-LR was extracted from solid-phase extraction (SPE) sample preparation using a CN cartridge. The cyanobacteria extract was purified to obtain microcystin-LR by HPLC method and identified by LC/MS. The detail structural studies that can elucidate the possible role of monovalent and divalent metal ions in PP-1-microcystin complexation were carried out by utilizing molecular dynamics. Conformational changes in metal binding for ligands were monitored by molecular computation and potential of mean force (PMF) using the method of the free energy perturbation. The microcystin-metal binding PMF simulation results exhibit that microcystin can have very stable binding free energy of -10.95 kcal/mol by adopting the Mg 2+ ion at broad geometrical distribution of 0.5~4.5 Å , and show that the K + ion can form a stable metal complex rather than other monovalent alkali metal ions.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"67-73"},"PeriodicalIF":0.3,"publicationDate":"2015-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329027","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
Dynamics of the mobile insert helix in the domain III-IV of Aux/IAA17 probed by site-directed spin labeling and paramagnetic NMR spectroscopy 利用定向自旋标记和顺磁共振波谱技术研究了Aux/IAA17结构域III-IV中可移动插入螺旋的动力学
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.061
Mookyoung Han, J. Suh
{"title":"Dynamics of the mobile insert helix in the domain III-IV of Aux/IAA17 probed by site-directed spin labeling and paramagnetic NMR spectroscopy","authors":"Mookyoung Han, J. Suh","doi":"10.6564/JKMRS.2015.19.2.061","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.2.061","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"61-66"},"PeriodicalIF":0.3,"publicationDate":"2015-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329436","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
Structural characterization of calmodulin like domain of ryanodine receptor type 1 ryanodine受体1型钙调蛋白样结构域的结构表征
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.074
Yonghyun Song, Sunmi Kang, Sunghyouk Park
{"title":"Structural characterization of calmodulin like domain of ryanodine receptor type 1","authors":"Yonghyun Song, Sunmi Kang, Sunghyouk Park","doi":"10.6564/JKMRS.2015.19.2.074","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.2.074","url":null,"abstract":"Ryanodine receptor (RyR) is one of the two major Ca 2+ channels in membranes of intracellular Ca 2+ stores and is found in sarcoplasmic reticulum (SR), endoplasmic reticulum (ER). RyR1 is also the major calmodulin-binding protein of sarcoplasmic reticulum membranes. Residues 4064-4210 in the RyR1 polypeptide chain has similar primary sequence with calmodulin (CaM) and was designated as CaM-like domain (CaMLD). When expressed CaMLD showed several CaM-like properties in previous studies. Still, previous studies of CaMLD were focused on protein-protein interactions rather than its own properties. Here, we studied the expression of CaMLD and its sub-domains corresponding to each lobe of CaM in Escherichia coli. CaMLD could be obtained only as inclusion body, and it was refolded using urea solubilization followed by such as NMR, circular dichroism, gel filtration that the refolded CaMLD exists as nonspecific aggregate, even though it has alpha helical secondary structure. In comparison, the first half of CaMLD (R4061-4141) could be obtained as natively soluble protein with thioredoxin fusion. After the removal of the fusion tag, it exhibited folded and helical properties as shown by NMR and circular dichroism experiments. Its oligomeric status was different from CaMLD, existing as dimeric form in solution. However, the second half of the protein could not be obtained as soluble protein regardless of fusion tag. Based on these results, we believe that CaMLD, although similar to CaM in sequence, has quite different physicochemical properties and that the second half of the protein renders it the aggregative properties.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"74-82"},"PeriodicalIF":0.3,"publicationDate":"2015-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329036","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
Structural stability of CD1 domain of human mitotic checkpoint serine/threonine-protein kinase, Bub1 人有丝分裂检查点丝氨酸/苏氨酸蛋白激酶(Bub1) CD1结构域的结构稳定性
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.088
Hyun-Hwi Kim, H. Song, Bong‐Jin Lee, Sung Jean Park
{"title":"Structural stability of CD1 domain of human mitotic checkpoint serine/threonine-protein kinase, Bub1","authors":"Hyun-Hwi Kim, H. Song, Bong‐Jin Lee, Sung Jean Park","doi":"10.6564/JKMRS.2015.19.2.088","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.2.088","url":null,"abstract":"Bub1 is one of the spindle checkpoint proteins and plays a role in recruitment of the related proteins to kinetochore. Here, we studied the structural characteristic of the evolutionarily conserved 160 amino acid region in the N-terminus (hBub1 CD1), using Circular Dichroism (CD) and NMR. Our CD results showed that hBub1 CD1 is a highly helical protein and its structure was affected by pH: as pH was elevated to basic pH, the helical propensity increased. This could be related to the surface charge of the hBub1 CD1. However, the structural change did not largely depend on the salt concentration, though the thermal stability a little increased. The previous NMR analysis revealed that the hBub1 CD1 adopts eight helices, which is consistent with the CD result. Our result would be helpful for evaluating the molecular mechanism of the hBub1 CD1 and protein-protein interactions.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"88-94"},"PeriodicalIF":0.3,"publicationDate":"2015-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329088","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
Expression and Purification of the Helicase-like Subdomains, H1 and H23, of Reverse Gyrase from A. fulgidus for Heteronuclear NMR study 黄颡鱼反旋酶解旋酶样亚结构域H1和H23的表达和纯化及其异核磁共振研究
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.095
Mun-Young Kwon, Yeo-Jin Seo, Yeon-Mi Lee, Ae-Ree Lee, Joon-Hwa Lee
{"title":"Expression and Purification of the Helicase-like Subdomains, H1 and H23, of Reverse Gyrase from A. fulgidus for Heteronuclear NMR study","authors":"Mun-Young Kwon, Yeo-Jin Seo, Yeon-Mi Lee, Ae-Ree Lee, Joon-Hwa Lee","doi":"10.6564/JKMRS.2015.19.2.095","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.2.095","url":null,"abstract":"Reverse gyrase is a hyperthermophile specific protein which introduces positive supercoils into DNA molecules. Reverse gyrase consists of an N-terminal helicase-like domain and a C-terminal topoisomerase domain. The helicase-like domain shares the three-dimensional structure with two tandem RecA-folds (H1 and H2), in which the subdomain H2 is interrupted by the latch domain (H3). To understand the physical property of the hyperthermophile-specific protein, two subdomains af_H1 and af_H23 have been cloned into E. coli expression vector, pET28a. The N-labeled af_H1 and af_H23 proteins were expressed and purified for heteronuclear NMR study. The af_H1 protein exhibits the well-dispersion of amide signals in its H/N-HSQC spectra and thus further NMR study continues to be progressed.","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"95-98"},"PeriodicalIF":0.3,"publicationDate":"2015-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329721","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
A new sesterterpenoid showing anti-inflammatory effect from the Marine Sponge Haliclona species 一种新的具有抗炎作用的海绵酯萜类化合物
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-06-30 DOI: 10.6564/JKMRS.2015.19.1.023
K. Lee, J. Rho
{"title":"A new sesterterpenoid showing anti-inflammatory effect from the Marine Sponge Haliclona species","authors":"K. Lee, J. Rho","doi":"10.6564/JKMRS.2015.19.1.023","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.1.023","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"23-28"},"PeriodicalIF":0.3,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329358","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
1 H, 15 N, and 13 C backbone assignments and secondary structure of the cytoplasmic domain A of mannitol trasporter II Mannitol from Thermoanaerobacter Tencongensis phosphotransferase system 热厌氧菌Tencongensis磷酸转移酶系统甘露醇转运体II的1 H、15 N和13 C骨架分配和胞质结构域A的二级结构
IF 0.3
Journal of the Korean magnetic resonance society Pub Date : 2015-06-30 DOI: 10.6564/JKMRS.2015.19.1.042
Ko On Lee, J. Suh
{"title":"1 H, 15 N, and 13 C backbone assignments and secondary structure of the cytoplasmic domain A of mannitol trasporter II Mannitol from Thermoanaerobacter Tencongensis phosphotransferase system","authors":"Ko On Lee, J. Suh","doi":"10.6564/JKMRS.2015.19.1.042","DOIUrl":"https://doi.org/10.6564/JKMRS.2015.19.1.042","url":null,"abstract":"","PeriodicalId":17414,"journal":{"name":"Journal of the Korean magnetic resonance society","volume":"19 1","pages":"42-48"},"PeriodicalIF":0.3,"publicationDate":"2015-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71329411","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: 4
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