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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 Q4 BIOCHEMICAL RESEARCH METHODS 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
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.
基于核磁共振的膜蛋白结构研究由于各种原因具有挑战性,主要包括核磁共振波谱分散窄、峰展宽严重以及缺乏远程noe。尽管膜蛋白的生物物理性质很差,但考虑到其在生物系统中的功能重要性,对膜蛋白的结构研究必须继续下去。在这篇综述中,我们提供了一个简单的概述,通常用于膜蛋白结构研究的技术,通过溶液核磁共振的实验例子,螺旋膜蛋白caveolin 3。洗涤剂筛选通常是第一步,选择合适的洗涤剂是成功接近膜蛋白的最重要的一步。然后,各种工具可以应用于溶液中的NMR专业技术,包括样品变质,氨基酸选择性同位素标记,残余偶极耦合和顺磁弛豫增强。
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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 Q4 BIOCHEMICAL RESEARCH METHODS 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
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.
从燕尾蝶(Papilio xuthus)中提取的Papiliocin对革兰氏阴性菌具有较高的细菌细胞选择性。最近,我们设计了一个从Lys 3到Ala 22, PapN的n端螺旋的22mer模拟物。对革兰氏阴性菌具有较强的抑菌活性,对哺乳动物细胞的毒性较低。在这项研究中,我们利用核磁共振光谱测定了300 mM DPC胶束中PapN的三维结构,并研究了PapN与DPC胶束之间的相互作用。结果表明,PapN具有从赖氨酸3到赖氨酸21的两亲性α-螺旋结构。STD-NMR和DOSY实验表明,该螺旋在与细菌细胞膜的结合中起重要作用。此外,我们测试了在盐存在下的抗菌活性,用于治疗应用。在生理条件下,PapN对钙和镁具有抗性,特别是对革兰氏阴性菌,这意味着它可能是一种强有力的候选肽抗生素。
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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 Q4 BIOCHEMICAL RESEARCH METHODS 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
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.
Syndesmos在局灶接触中与syndecan-4细胞质结构域(Syn4 cyto)共定位,与包括Syn4 cyto在内的多种细胞粘附衔接蛋白相互作用,控制细胞信号传导。Syndesmos由211个氨基酸组成,在溶液中以二聚体(44kDa)存在。最近,我们已经通过x射线晶体学确定了syndesmos的结构,然而,与syndecan结合相关的动力学仍然是难以捉摸的。在这篇报道中,我们进行了核磁共振实验来获取综合征的生化和结构信息。通过对13c / 15n / 2h标记蛋白进行三维三重共振实验,获得了分散均匀的核磁共振波谱。我们提出了syndesmos的序列特异性主链分配,并且分配的具有组合结构信息的NMR数据可以直接用于与Syn4细胞和其他结合分子相互作用的研究。
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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 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.067
Gilhoon Kim, S. Han, Hoshik Won
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.
微囊藻毒素是一种环七肽,来自于菌胞属蓝藻的代谢物,是富营养化的结果。众所周知,微囊藻毒素lr是蛋白磷酸酶-1 (PP-1)催化亚基的有效抑制剂,也是强大的肿瘤启动子。微囊藻毒素的活性位点实际上有两个金属离子fe2 + / zn2 +靠近pp -1-微囊藻毒素复合物的亲核部分。我们报道了从韩国忠清岛大兴大坝的蓝藻(蓝绿藻)中分离和纯化这种微囊藻毒素lr。用CN滤筒从固相萃取(SPE)样品制备中提取微囊藻毒素lr。采用高效液相色谱法纯化蓝藻提取物,得到微囊藻毒素lr,并采用液相色谱/质谱法进行鉴定。利用分子动力学方法对其进行了详细的结构研究,以阐明单价和二价金属离子在pp -1-微囊藻毒素络合中的可能作用。采用分子计算和平均力势(PMF)方法,利用自由能摄动法监测金属与配体结合过程中的构象变化。微囊藻毒素-金属结合PMF模拟结果表明,微囊藻毒素采用广义几何分布为0.5~4.5 Å的mg2 +离子,其结合自由能非常稳定,为-10.95 kcal/mol,且与其他一价碱金属离子相比,K +离子可以形成稳定的金属配合物。
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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 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.061
Mookyoung Han, J. Suh
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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 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.074
Yonghyun Song, Sunmi Kang, Sunghyouk Park
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.
Ryanodine receptor (RyR)是细胞内ca2 +储存库膜上的两个主要ca2 +通道之一,存在于肌浆网(SR)、内质网(ER)中。RyR1也是肌浆网膜上主要的钙调素结合蛋白。RyR1多肽链中4064 ~ 4210残基与calmodulin (CaM)具有相似的初级序列,被命名为CaM样结构域(CaMLD)。在先前的研究中,CaMLD在表达后表现出几种类似cam的特性。尽管如此,以前对CaMLD的研究主要集中在蛋白质之间的相互作用上,而不是其本身的性质。在此,我们研究了CaMLD及其对应于CaM各叶的亚结构域在大肠杆菌中的表达。虽然CaMLD具有α -螺旋二级结构,但经尿素增溶、核磁共振、圆二色性、凝胶过滤等实验证明,CaMLD以非特异性聚集体的形式存在。相比之下,CaMLD (R4061-4141)的前半部分可以通过硫氧还蛋白融合得到天然可溶性蛋白。去除融合标签后,核磁共振和圆二色性实验显示其具有折叠和螺旋性质。其低聚状态与CaMLD不同,在溶液中以二聚体形式存在。然而,无论融合标签如何,蛋白的后半部分都不能作为可溶性蛋白获得。基于这些结果,我们认为CaMLD虽然在序列上与CaM相似,但具有完全不同的物理化学性质,并且蛋白质的后半部分使其具有聚集性。
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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 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2015-10-10 DOI: 10.6564/JKMRS.2015.19.2.088
Hyun-Hwi Kim, H. Song, Bong‐Jin Lee, Sung Jean Park
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.
Bub1是纺锤体检查点蛋白之一,在向着丝点募集相关蛋白中起作用。本文利用圆二色性(CD)和核磁共振(NMR)研究了进化上保守的n端160个氨基酸区域(hBub1 CD1)的结构特征。我们的CD结果表明,hBub1 CD1是一种高度螺旋状的蛋白,其结构受pH的影响:当pH升高到碱性pH时,螺旋倾向增加。这可能与hbub1cd1的表面电荷有关。然而,盐浓度对结构变化的影响不大,但热稳定性略有提高。之前的NMR分析显示hBub1 CD1采用8个螺旋结构,这与CD的结果一致。我们的研究结果将有助于评价hBub1 - CD1和蛋白-蛋白相互作用的分子机制。
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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 Q4 BIOCHEMICAL RESEARCH METHODS 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
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.
逆回转酶是一种嗜热性极强的特异性蛋白质,它将正超螺旋引入DNA分子中。反旋酶由n端类解旋酶结构域和c端拓扑异构酶结构域组成。解旋酶样结构域与两个串联的reca折叠域(H1和H2)共享三维结构,其中子结构域H2被锁存结构域(H3)中断。为了了解这种超嗜热特异性蛋白的物理性质,我们将两个亚结构域af_H1和af_H23克隆到大肠杆菌表达载体pET28a中。表达并纯化了n标记的af_H1和af_H23蛋白,用于异核磁共振研究。af_H1蛋白在其H/N-HSQC光谱中表现出酰胺信号的良好分散,因此进一步的核磁共振研究仍在继续进行。
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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 Q4 BIOCHEMICAL RESEARCH METHODS Pub Date : 2015-06-30 DOI: 10.6564/JKMRS.2015.19.1.023
K. Lee, J. Rho
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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 Q4 BIOCHEMICAL RESEARCH METHODS 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
期刊
Journal of the Korean magnetic resonance society
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