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[Three dimensional structure of the dimeric gene-engineered variant of green fluorescent protein EGFP-K162Q in P6(1) crystal space group]. 【绿色荧光蛋白EGFP-K162Q二聚体基因工程变体P6(1)晶体空间群的三维结构】。
Pub Date : 2014-08-27 DOI: 10.2210/pdb4n3d/pdb
N. Pletneva, S. Pletnev, A. Bogdanov, E. Goriacheva, I. V. Artem’ev, E. A. Suslova, S. F. Arkhipova, V. Pletnev
The crystal structure of the dimeric green fluorescent protein EGFP-K162Q with C-terminal deletion MDELYK (EGFPv) has been determined in space group P6 at resolution 1.34 A. The obtained structure has been compared with that of the monomeric form of EGFP (green biomarker with enhanced photophysical properties) determined in other crystal space group P2(1)2(1)2(1) at resolution 1.50 and 1.35 A [1, 2]. Two subunits in the EGFPv structure are packed at 75 degrees with the contact surface approximately 800 A2. The dimeric structure is stabilized by six hydrogen bonds and the central hydrophobic core built of six residues. The RMSD value for Calpha atoms of 3-230 residues in the superimposed P61 and P2(1)2(1)2(1) structures is 0.55 A. The distinguishing feature of EGFPv- P6(1) structure, compared with that of EGFP-P2(1)2(1)2(1), is the noticeable difference in orientation of the Glu222 side chain and also new conformation of the loop fragment 155-159 with deviations among the Calpha atoms of superimposed structures reaching for Lys156 - 4.6 A and Lys158 - 5.5 A
在空间群P6中以1.34 A的分辨率测定了c端缺失MDELYK的二聚体绿色荧光蛋白EGFP-K162Q (EGFPv)的晶体结构。所获得的结构已与在其他晶体空间群P2(1)2(1)2(1)中以1.50和1.35 A分辨率测定的单体形式的EGFP(具有增强光物理性质的绿色生物标志物)进行了比较[1,2]。EGFPv结构中的两个亚单元以75度排列,接触面约为800a2。二聚体结构由六个氢键和六个残基组成的中心疏水核稳定。在P61和P2(1)2(1)2(1)叠加结构中,3-230残基的Calpha原子的RMSD值为0.55 A。与EGFP-P2(1)2(1)2(1)相比,EGFPv- P6(1)结构的显著特征是Glu222侧链取向的显著差异以及环路片段155-159的新构象,重叠结构的Calpha原子之间的偏差达到Lys156 - 4.6 A和Lys158 - 5.5 A
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引用次数: 0
[Identification of the protein partners of the human nucleolar protein SURF6 in HeLa cells by GST pull-down assay]. [用GST下拉法鉴定HeLa细胞中人核仁蛋白SURF6的蛋白伴侣]。
Pub Date : 2014-07-01
M Iu Kordiukova, M A Polzikov, K V Shishova, O V Zatsepina

The eukaryotic proteins comprising the SURF6 protein family are evolutionary conservative and housekeeping proteins however, functional roles of human SURF6 have not been studied so far. To shed light to this question in the present work we applied GST pull-down assay and used two proteins fused with GST, namely human GST-SURF6 and the conservative C-terminal domain of mouse Surf6 that has 85% homology with the C-terminus of the human SURF6 conservative domain (GST-Surf6-dom), to identify SURF6-interacting proteins in human HeLa cells. The results obtained showed that GST-SURF6 interacts with several key nucleolar RNA processing factors (B23/nucleophosmin, nucleolin, EBP2), and also with the specific cofactor of RNA polymerase I, protein UBE These results are the first experimental evidences in favor of participation of the human SURF6 protein in ribosome biogenesis, including transcription of rDNA and processing of rRNAs. The same results were obtained, when GST-Surf6-dom was used to pull-down proteins in HeLa cells. In addition, the panel of the GST-Surf6-dom protein partners, which were identified by mass-spectrometry, points to putative interactions of human SURF6 with a number of nuclear and nucleolar, proteins of other functional groups, i.e. to the protein plurifunctionality.

包含SURF6蛋白家族的真核蛋白是进化保守和管家蛋白,但迄今为止尚未对人类SURF6的功能作用进行研究。为了阐明这一问题,本研究采用GST下拉法,并利用与GST融合的两种蛋白,即人类GST-Surf6和小鼠Surf6的保守c端结构域(GST-Surf6-dom),与人类Surf6保守结构域的c端具有85%的同源性,来鉴定人类HeLa细胞中Surf6的相互作用蛋白。结果表明,GST-SURF6与几个关键的核仁RNA加工因子(B23/nucleophosmin, nucleolin, EBP2)相互作用,并与RNA聚合酶I特异性辅因子UBE蛋白相互作用,这些结果是支持人类SURF6蛋白参与核糖体生物发生的第一个实验证据,包括rDNA的转录和rrna的加工。当使用GST-Surf6-dom拉下HeLa细胞中的蛋白质时,获得了相同的结果。此外,通过质谱鉴定的GST-Surf6-dom蛋白伴侣组指出,人类SURF6可能与许多其他功能基团的核和核核蛋白相互作用,即蛋白质的多功能性。
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引用次数: 0
[Immunization witha synthetic fragment 155-164 of neurotrophin receptor p75 prevents memory loss and decreases beta-amyloid level in mice with experimentally induced Alzheimer's disease]. [神经营养蛋白受体p75合成片段155-164免疫可预防实验性诱导阿尔茨海默病小鼠的记忆丧失并降低β -淀粉样蛋白水平]。
Pub Date : 2014-07-01
O M Vol'pina, N I Medvinskaia, A V Kamynina, Ia V Zaporozhskaia, I Iu Aleksandrova, D O Koroev, A N Samokhin, T D Volkova, A S Arsen'ev, N V Bobkova

Neurotoxic beta-amyloid peptide plays an important role in the pathology of Alzheimer's disease. In aggregated form it binds to several proteins on the surface of the brain cells leading to their death. p75 receptor in- volved in supporting of cell balance is one of the targets for toxic beta-amyloid. We proposed that induction of antibodies against potential binding sites of p75 with beta-amyloid can be a promising approach towards new drug development for Alzheimer's disease therapy. Four potentially immunoactive fragments of p75 were chosen and chemically synthesized. Investigation of immunoprotective effect of the peptide fragments carried out in mice with experimentally induced form of Alzheimer's disease helped to reveal two fragments effectively preserving murine memory from impairment. Results obtained by ELISA biochemical analysis showed that only immunization with fragment p75 155-164 led to significant decrease in beta-amyloid level in the brain of the experimental mice. Thus, immunization with both fragments of p75 receptor is believed to be an effective tool for the development of new drugs against Alzheimer's disease.

神经毒性β -淀粉样肽在阿尔茨海默病的病理中起重要作用。它以聚集的形式与脑细胞表面的几种蛋白质结合,导致脑细胞死亡。P75受体参与细胞平衡的支持,是毒性β -淀粉样蛋白的靶点之一。我们提出,诱导针对p75与β -淀粉样蛋白潜在结合位点的抗体可能是开发阿尔茨海默病治疗新药的一种有希望的方法。选择4个具有潜在免疫活性的p75片段进行化学合成。在实验诱导的阿尔茨海默病小鼠中进行的肽片段的免疫保护作用研究有助于揭示两个片段有效地保护小鼠记忆免受损害。ELISA生化分析结果显示,仅免疫片段p75 155-164可导致实验小鼠脑内β -淀粉样蛋白水平显著降低。因此,p75受体的两个片段的免疫被认为是开发抗阿尔茨海默病新药的有效工具。
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引用次数: 0
Synthesis and pharmacological studies of new pyrazole analogues of podophyllotoxin. 鬼臼毒素新型吡唑类化合物的合成及药理研究。
Pub Date : 2014-07-01
B Umesha, Y B Basavarajuk

The pyrazole analogues of podophyllotoxin were synthesized by the chalcone route. This route attracts the attention because of its simple operating conditions and easy availability ofthe chemicals. Initially, benzylide-neacetophenones (chalcones) were prepared in high yields by Claisen-Schmidt reaction of acetophenones with 4-(methylthio)benzaldehyde. The cyclopropyl ketones were prepared in good yields by the reaction of chalcones with trimethylsulfoxonium iodide. Tetralones were prepared in good yields by the Friedel-Craft's intramolecular cyclization reaction of cyclopropyle ketones in the presence of anhyd. stannic chloride and acetic anhydride. The tetralones on formylation to give substituted hydroxylmethylene tetralones. Condensation of substituted hydroxylmethylene tetralones with hydrazine hydrate afforded target compounds. The structures of the synthesized compounds were confirmed by IR, 'H-NMR and Mass spectral technique. The title compounds were screened for their antimitotic and antimicrobial activities. Among the synthesized compounds cyclopropyl ketones and pyrazole analogues of podophyllotoxin, compound 7-(Methytthio)-5-(4-(methylthio)phe- nyl)-4,5.-dihydro-2H-benzo[g]indazole is more active than 5-(4-(Methylthio)phenyl)-4,5-dihydro-2H-ben- zo[g]indazole, 7-Methyl-5-(4-(methylthio)phenyl)-4,5-dihydro-2H-benzo[g]indazole, 7-Methoxy-5-(4-(meth- ylthio)phenyl)-4,5-dihydro-2H-benzo[g]indazole and the key intermediate tetralones in 100, 200 and 400 ppm at 12, 18 and 24 hrs and also showed very good activity against screened bacteria and fungi compared to their standard.

采用查尔酮法合成了鬼臼毒素的吡唑类类似物。这条路线因其操作条件简单,化学品容易获得而引起人们的注意。以苯乙酮与4-(甲基硫代)苯甲醛为原料,采用Claisen-Schmidt反应制备了苄基-邻苯乙酮(查尔酮)。以查尔酮和碘化三甲基亚砜为原料,以较好的收率制备了环丙基酮。采用环丙基酮在无糖存在下的Friedel-Craft分子内环化反应制备了四酮类化合物。氯化亚锡和乙酸酐。甲酰基化生成取代羟基亚甲基四酮。取代羟基亚甲基四酮与水合肼缩合得到目标化合物。合成的化合物的结构经IR、H-NMR和质谱确证。对标题化合物的抗有丝分裂和抗菌活性进行了筛选。在合成的鬼臼毒素环丙基酮类和吡唑类化合物中,化合物7-(甲硫氧基)-5-(4-(甲硫氧基)苯基)-4,5。-二氢- 2h -苯并[g]茚唑在100ppm、200ppm、12h、18h和24h时的活性均高于5-(4-(甲基硫)苯基)-4,5-(4-(甲基硫)苯基)-4,5-二氢- 2h -苯并[g]茚唑、7-甲氧基-5-(4-(甲基硫)苯基)-4,5-二氢- 2h -苯并[g]茚唑和关键中间体四酮类化合物,对筛选的细菌和真菌也表现出较好的抑菌活性。
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引用次数: 0
De novo transcriptome analysis of mulberry (Morus L.) under drought stress using RNA-seq technology. 利用RNA-seq技术对干旱胁迫下桑树从头转录组进行分析。
Pub Date : 2014-07-01
Heng Wang, Wei Tong, Li Feng, Qian Jiao, Li Long, Rongjun Fang, Weiguo Zhao

A large-scale RNA sequencing (RNA-seq) of mulberry (Morus L.) was carried out between two samples in regular and drought stress condition. In this research, de novo assembly was performed, and totally 54736 contigs were obtained from the reads, including the scaffolded regions. 1051 genes were identified that were significantly differently expressed between the two samples. As determined by Gene Ontology (GO) annotation and the Kyoto Encyclopedia of Genes and Genomes pathway mapping, 10110 GO terms and 247 pathways were assigned and then analyzed. Thousands of SSR markers produced in this study will enable genetic linkage mapping construction and gene-based association studies. Seven unique genes showing different expression level in control and drought stress groups were subsequently analyzed and identified by real-time PCR. For lack of mulberry whole genome information, transcriptome and de novo analysis from the two samples will provide important and useful information for later research and help genetic breeding of mulberry.

对桑树(Morus L.)在正常胁迫和干旱胁迫条件下进行了大规模RNA测序(RNA-seq)。在本研究中,我们进行了从头组装,共从reads中获得了54736个contigs,包括支架区域。鉴定出1051个基因在两种样品中表达有显著差异。通过基因本体(Gene Ontology, GO)标注和京都基因与基因组百科全书(Kyoto Encyclopedia of Genes and Genomes)路径作图确定,共分配10110个GO术语和247条路径并进行分析。本研究产生的数千个SSR标记将为遗传连锁图谱的构建和基于基因的关联研究提供支持。随后,通过实时荧光定量PCR分析和鉴定了7个在对照和干旱胁迫组中表达水平不同的独特基因。在桑树全基因组信息缺乏的情况下,对两份样品的转录组和从头分析将为桑树的后续研究和遗传育种提供重要和有用的信息。
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引用次数: 0
[[Expression of house dust mite allergens Der f1 and Der f2 in Nicotiana benthamiana leaves]. [家尘螨过敏原 Der f1 和 Der f2 在烟叶中的表达]。
Pub Date : 2014-07-01
D Iu Riazantsev, P E Drobiazina, S V Hlgatian, S K Zavriev, E V Svirshchevskaia

The class E immunoglobulins (IgE) is known to recognize conformational epitopes and therefore the native conformation of recombinant allergens is essential for their using in test-systems. Recombinant Dermatophagoides farinae house dust mite (HDM) allergens Der f1 and Der f2 were expressed in bacteria Escherichia coli and Nicotiana benthamiana plants. It has been shown that IgE in sera from children allergic to HDM recognizes Der f2 expressed both in E. coli and N. benthamiana. Mature form of Der f1 expressed in E. coli does not interact with IgE while the protein purified from N. benthamiana is able to recognize IgE as a native allergen.

众所周知,E类免疫球蛋白(IgE)能识别构象表位,因此重组过敏原的原生构象对其在测试系统中的应用至关重要。重组 Dermatophagoides farinae 屋尘螨(HDM)过敏原 Der f1 和 Der f2 是在大肠杆菌和烟草植物中表达的。研究表明,对 HDM 过敏的儿童血清中的 IgE 可识别在大肠杆菌和烟草中表达的 Der f2。在大肠杆菌中表达的成熟形式的 Der f1 与 IgE 没有相互作用,而从 N. benthamiana 中纯化的蛋白质能够识别作为本地过敏原的 IgE。
{"title":"[[Expression of house dust mite allergens Der f1 and Der f2 in Nicotiana benthamiana leaves].","authors":"D Iu Riazantsev, P E Drobiazina, S V Hlgatian, S K Zavriev, E V Svirshchevskaia","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The class E immunoglobulins (IgE) is known to recognize conformational epitopes and therefore the native conformation of recombinant allergens is essential for their using in test-systems. Recombinant Dermatophagoides farinae house dust mite (HDM) allergens Der f1 and Der f2 were expressed in bacteria Escherichia coli and Nicotiana benthamiana plants. It has been shown that IgE in sera from children allergic to HDM recognizes Der f2 expressed both in E. coli and N. benthamiana. Mature form of Der f1 expressed in E. coli does not interact with IgE while the protein purified from N. benthamiana is able to recognize IgE as a native allergen.</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 4","pages":"468-78"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33241012","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
[Fluorescent fusion proteins with 10th human fibronectin domain]. [具有第 10 个人类纤连蛋白结构域的荧光融合蛋白]。
Pub Date : 2014-07-01
L E Petrovskaia, S Sh Gapizov, L N Shingarova, E A Kriukova, E F Boldyreva, S A Iakimov, E V Svirshchevskaia, E P Lukashev, D A Dolgikh, M P Kirpichnikov

In the current paper we describe a new type of hybrid molecules including red fluorescent protein mCherry and 10th type III human fibronectin domain (10Fn3) - one of the alternative scaffold proteins which can be used for the construction of antibody mimics with various binding specificity. We have constructed different gene variants encoding for the hybrid fluorescent protein and studied their expression in Escherichia coli cells. It was shown that N-terminal position of mCherry and modification of its N-terminal amino acid sequence promotes efficientbacterial expression of the hybrid protein in the soluble form. On the basis of the proposed construction we have obtained the hybrid fluorescent protein ChIBF, containing alphaVbeta3-integrin binding vari- ant of 10Fn3, and demonstrated the possibility of its utilization for the visualization of alphaVbeta3-integrin at the surface of MDCK epithelial cells by confocal microscopy.

本文描述了一种新型杂交分子,包括红色荧光蛋白 mCherry 和第 10 个 III 型人类纤连蛋白结构域(10Fn3)--一种可用于构建具有不同结合特异性的抗体模拟物的替代支架蛋白。我们构建了编码混合荧光蛋白的不同基因变体,并研究了它们在大肠杆菌细胞中的表达情况。结果表明,mCherry 的 N 端位置和对其 N 端氨基酸序列的修改可促进可溶性混合蛋白的高效细菌表达。在此基础上,我们获得了含有 10Fn3 的 alphaVbeta3 整合素结合变体的杂交荧光蛋白 ChIBF,并证明了用共聚焦显微镜观察 MDCK 上皮细胞表面 alphaVbeta3 整合素的可能性。
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引用次数: 0
Synthesis, characterization, and tyrosinase inhibitory properties of benzimidazole derivatives. 苯并咪唑衍生物的合成、表征及酪氨酸酶抑制性能。
Pub Date : 2014-07-01
Mert Olgun Karatas, Bulent Alici, Engin Cetinkaya, Ciğdem Bilen, Nahit Gençer, Oktay Arslan

1-Alkylbenzimidazole and 1,3-dialkyl benzimidazolium salts were synthesized and characterized by the data of IR, 1H NMR, 13C NMR spectra and elemental analyses. These compounds were investigated as tyrosinase inhibitors. Tyrosinase has been purified from banana by affinity chromatography on a Sepharose 4B gel conjugated with L-tyrosine-p-aminobenzoic acid. All the synthesized compounds inhibited the tyrosinase activity. Among the compounds studied, 1,4-di(1H-benzo[d]imidazol-1-yl)butane was found to be the most active tyrosinase inhibitor (IC50 0.31 mM).

合成了1-烷基苯并咪唑和1,3-二烷基苯并咪唑盐,并通过IR、1H NMR、13C NMR和元素分析对其进行了表征。这些化合物作为酪氨酸酶抑制剂进行了研究。用l -酪氨酸-对氨基苯甲酸偶联的Sepharose 4B凝胶亲和层析纯化了香蕉中的酪氨酸酶。所有合成的化合物均抑制酪氨酸酶活性。在所研究的化合物中,1,4-二(1h -苯并咪唑-1-基)丁烷是最具活性的酪氨酸酶抑制剂(IC50为0.31 mM)。
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引用次数: 0
Design and synthesis of amino acids-conjugated heterocycle derived ureas/thioureas as potent inhibitors of protein glycation. 设计和合成氨基酸共轭杂环衍生脲/硫脲作为蛋白质糖基化的有效抑制剂。
Pub Date : 2014-07-01
C S Shantharam, D M Suyoga Vardhan, R Suhas, D Channe Gowda

Protein glycation is believed to play an important role in the development of long-term disorders associated with diabetic complications. In view of the wide occurrence of advanced glycation end products (AGE's) and the oxidative stress derived from them in a variety of diabetic complications, it would be of great interest to identify and develop AGE inhibitors. In this study, synthesis and in vitro antiglycation activity of a small library of forty urea/thiourea derivatives of Phe/Tyr/Glu/Lys-benzisoxazole hybrids are reported. Structures of the compounds were confirmed by IR, NMR, mass spectrometry, and elemental analysis. Most of the title compounds exhibited promising activity. Best antiglycation activity was found for Tyr analogue with methoxy group as a substituent particularly at the para position with IC50 value of 1.9 microM against the positive control, Rutin, with IC50 = 41.9 microM. Thus, the title compounds represent novel class of potent antiglycating agents.

蛋白质糖化被认为在糖尿病并发症相关的长期疾病的发展中起重要作用。鉴于晚期糖基化终产物(AGE’s)及其引起的氧化应激在各种糖尿病并发症中的广泛发生,鉴定和开发AGE抑制剂将是非常有意义的。本研究报道了40个苯并异唑衍生物的合成及其体外抗糖基化活性。化合物的结构经红外、核磁共振、质谱和元素分析证实。大多数标题化合物显示出良好的活性。以甲氧基为取代基的Tyr类似物的抗糖化活性最好,特别是在对位,IC50值为1.9微米,而阳性对照芦丁的IC50值为41.9微米。因此,标题化合物代表了一类新的有效的抗糖化药物。
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引用次数: 0
PiRNAs biogenesis and its functions. pirna的生物发生及其功能。
Pub Date : 2014-05-01
Yong Huang, Jun Yan Bai, Hong Tao Ren

piRNAs (piwi-interacting RNA) are a novel class of non-coding small single-stranded RNAs with the length of 26-33 nt. The piRNAs play important biological role through the specific interaction with the piwi proteins of the Argonaute family. piRNA function in embryonic development, maintenance of germline DNA integrity, silencing of transposon transcription, suppressionof translation, formation of heterochromatin, and epigenetic regulation of sex determination. This review summarizes recent research and progress on biogenesis and function of piRNA in eukaryotic species.

pirna (piwi-interacting RNA)是一类长度为26- 33nt的新型非编码小单链RNA。pirna通过与Argonaute家族的piwi蛋白特异性相互作用发挥重要的生物学作用。piRNA在胚胎发育、维持种系DNA完整性、转座子转录沉默、翻译抑制、异染色质形成和性别决定的表观遗传调控中发挥作用。本文综述了piRNA在真核生物中的生物发生和功能方面的研究进展。
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引用次数: 0
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Bioorganicheskaia khimiia
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