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Crystal structure and substrate specificity of plant adenylate isopentenyltransferase from Humulus lupulus: distinctive binding affinity for purine and pyrimidine nucleotides
No full textUnderstanding the pivotal step in cytokinin synthesis: crystal structure, substrate specificity and catalytic mechanism of adenylate isopentenyltransferase from H. lupulus
No full text細胞分裂素是重要的植物賀爾蒙，其生物合成最開始是從二甲烯丙烯基焦磷酸（dimethylallyl pyrophosphate, DMAPP)上的異戊烯基，轉移到腺嘌呤的氨基N6上，藉著腺苷酸異戊二烯基轉移酵素(adenylate isopentenyltransferase, AIPT)或轉移核醣核酸異戊二烯基轉移酵素(tRNA-IPT)。植物腺苷酸異戊二烯基轉移酵素使用三磷酸腺苷(ATP)或二磷酸腺苷(ADP)作為異戊二烯基接受者，而細菌和轉移核醣核酸的異戊二烯基轉移酵素則分別以單磷酸腺苷和轉移核醣核酸的特定位置作為接受者。在這裡，解析出來自啤酒花的腺苷酸異戊二烯基轉移酵素和三磷酸腺苷 (AIPT-ATP)複合體結晶結構，此結構類似於先前所發表的農桿菌的腺苷酸異戊二烯基轉移酵素和酵母菌的轉移核醣核酸異戊二烯基轉移酵素。這個酵素與NTP結合激素(NTP-binding kinase)有結構同源的關係，但是它會額外形成一個反應通道來讓兩個受質三磷酸腺苷(ATP)與二甲烯丙烯基焦磷酸(DMAPP)結合。利用等溫滴定微量熱法(ITC)去測量不同核苷酸與酵素的結合能力，得到了以下的關係ATP>dATP~ADP>GTP>CTP>UTP。然而當進一步測量這些不同核苷酸與酵素的活性時，發現它們的活性大小為ATP>ADP>dATP>CTP>>GTP≈UTP≈0，不同於之前結合能力的關係。此外除了二甲烯丙烯基焦磷酸(DMAPP(C5))，這個酵素也展現出對二異戊二烯基焦磷酸(Geranyl pyrophosphate, GPP(C10))有活性，表示其可以把它當作轉移反應的供給者。在結構中，兩個鹼性的胺基酸側鏈Lys275和Lys220會與三磷酸腺苷(ATP)的Cytokinins are important plant hormones, and their biosynthesis most begins with the transfer of isopentenyl group from dimethylallyl diphosphate (DMAPP) to the N6-amino group of adenine by either adenylate isopentenyltransferase (AIPT) or tRNA-IPT. Plant AIPTs use ATP/ADP as an isopentenyl acceptor and bacterial AIPTs prefer AMP, whereas tRNA-IPTs act on specific sites of tRNA. The crystal structure of an AIPT-ATP complex from Humulus lupulus (HlAIPT) presented here is similar to the previous structures of Agrobacterium AIPT and yeast tRNA-IPT. The enzyme is structurally homologous to the NTP-binding kinase family of proteins but forms a solvent-accessible channel that binds to the donor substrate DMAPP, which is directed toward the acceptor substrate ATP/ADP. When measured with isothermal titration calorimetry, some nucleotides displayed different binding affinities to HlAIPT with an order of ATP > dATP ~ ADP > GTP > CTP > UTP. However, further measurements of activity using these nucleotides showed that the order becomes ATP > ADP > dATP > CTP >> GTP ≈ UTP ≈ 0. In addition to DMAPP (C5), HlAIPT also showed remarkable activity for GPP (C10) as the donor substrate. Two basic residues Lys275 and Lys220 in HlAIPT interact with the β and γ-phosphate of ATP. By contrast, the interactions are absent in Agrobacterium AIPT because they are replaced by the acidic residues Asp221 and Asp171. Despite its structural similarity to the yeast tRNA-IPT, HlAIPT has evolved with a different binding strategy for adenylate. Finally, by screening a series of dinucleotide polyphosphates, it was found, surprisingly, that the binding affinities of some diadenosine polyphosphates (A(p)4A, A(p)5A and A(p)6A) are even higher than those of the original substrates (ATP and ADP). These results may imply that novel substrates of HlAIPT have been found in plant
Binding and catalysis of Humulus lupulus adenylate isopentenyltransferase for the synthesis of isopentenylated diadenosine polyphosphates
No full textStructures of the hyperthermophilic chromosomal protein Sac7d in complex with DNA decamers
No full textPreliminary X-ray diffraction analysis of octaprenyl pyrophosphate synthase crystals from Thermotoga maritima and Escherichia coli
No full text
Cysteine S-Nitrosylation Protects Protein-tyrosine Phosphatase 1B against Oxidation-induced Permanent Inactivation
No full textGoing Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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