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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】。
Bioorganicheskaia khimiia 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
{"title":"[Three dimensional structure of the dimeric gene-engineered variant of green fluorescent protein EGFP-K162Q in P6(1) crystal space group].","authors":"N. Pletneva, S. Pletnev, A. Bogdanov, E. Goriacheva, I. V. Artem’ev, E. A. Suslova, S. F. Arkhipova, V. Pletnev","doi":"10.2210/pdb4n3d/pdb","DOIUrl":"https://doi.org/10.2210/pdb4n3d/pdb","url":null,"abstract":"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","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"9 1","pages":"414-20"},"PeriodicalIF":0.0,"publicationDate":"2014-08-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74275690","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
[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]。
Bioorganicheskaia khimiia Pub Date : 2014-07-01
M Iu Kordiukova, M A Polzikov, K V Shishova, O V Zatsepina
{"title":"[Identification of the protein partners of the human nucleolar protein SURF6 in HeLa cells by GST pull-down assay].","authors":"M Iu Kordiukova,&nbsp;M A Polzikov,&nbsp;K V Shishova,&nbsp;O V Zatsepina","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 4","pages":"421-32"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33238495","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
[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]。
Bioorganicheskaia khimiia 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
{"title":"[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].","authors":"O M Vol'pina,&nbsp;N I Medvinskaia,&nbsp;A V Kamynina,&nbsp;Ia V Zaporozhskaia,&nbsp;I Iu Aleksandrova,&nbsp;D O Koroev,&nbsp;A N Samokhin,&nbsp;T D Volkova,&nbsp;A S Arsen'ev,&nbsp;N V Bobkova","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 4","pages":"451-7"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33241010","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
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。
Bioorganicheskaia khimiia Pub Date : 2014-07-01
B Umesha, Y B Basavarajuk
{"title":"Synthesis and pharmacological studies of new pyrazole analogues of podophyllotoxin.","authors":"B Umesha,&nbsp;Y B Basavarajuk","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 4","pages":"503-12"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33114611","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
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。
Bioorganicheskaia khimiia Pub Date : 2014-07-01
Heng Wang, Wei Tong, Li Feng, Qian Jiao, Li Long, Rongjun Fang, Weiguo Zhao
{"title":"De novo transcriptome analysis of mulberry (Morus L.) under drought stress using RNA-seq technology.","authors":"Heng Wang,&nbsp;Wei Tong,&nbsp;Li Feng,&nbsp;Qian Jiao,&nbsp;Li Long,&nbsp;Rongjun Fang,&nbsp;Weiguo Zhao","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 4","pages":"458-67"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33241011","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 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]。
Bioorganicheskaia khimiia Pub Date : 2014-07-01
D Iu Riazantsev, P E Drobiazina, S V Hlgatian, S K Zavriev, E V Svirshchevskaia
{"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]。
Bioorganicheskaia khimiia 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
{"title":"[Fluorescent fusion proteins with 10th human fibronectin domain].","authors":"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","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 4","pages":"405-13"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33238494","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
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。
Bioorganicheskaia khimiia Pub Date : 2014-07-01
Mert Olgun Karatas, Bulent Alici, Engin Cetinkaya, Ciğdem Bilen, Nahit Gençer, Oktay Arslan
{"title":"Synthesis, characterization, and tyrosinase inhibitory properties of benzimidazole derivatives.","authors":"Mert Olgun Karatas,&nbsp;Bulent Alici,&nbsp;Engin Cetinkaya,&nbsp;Ciğdem Bilen,&nbsp;Nahit Gençer,&nbsp;Oktay Arslan","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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).</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 4","pages":"497-502"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33241013","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
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。
Bioorganicheskaia khimiia Pub Date : 2014-07-01
C S Shantharam, D M Suyoga Vardhan, R Suhas, D Channe Gowda
{"title":"Design and synthesis of amino acids-conjugated heterocycle derived ureas/thioureas as potent inhibitors of protein glycation.","authors":"C S Shantharam,&nbsp;D M Suyoga Vardhan,&nbsp;R Suhas,&nbsp;D Channe Gowda","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 4","pages":"479-90"},"PeriodicalIF":0.0,"publicationDate":"2014-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33241014","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
PiRNAs biogenesis and its functions. pirna的生物发生及其功能。
Bioorganicheskaia khimiia Pub Date : 2014-05-01
Yong Huang, Jun Yan Bai, Hong Tao Ren
{"title":"PiRNAs biogenesis and its functions.","authors":"Yong Huang,&nbsp;Jun Yan Bai,&nbsp;Hong Tao Ren","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":9325,"journal":{"name":"Bioorganicheskaia khimiia","volume":"40 3","pages":"320-6"},"PeriodicalIF":0.0,"publicationDate":"2014-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33239061","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
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