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https://www.readbyqxmd.com/read/29352744/crystal-structure-of-adp-dependent-glucokinase-from-methanocaldococcus-jannaschii-in-complex-with-5-iodotubercidin-reveals-phosphoryl-transfer-mechanism
#1
Piotr Tokarz, Magdalena Wiśniewska, Marcin M Kamiński, Grzegorz Dubin, Przemysław Grudnik
ADP-dependent glucokinase (ADPGK) is an alternative novel glucose phosphorylating enzyme in a modified glycolysis pathway of hyperthermophilic Archaea. In contrast to classical ATP-dependent hexokinases, ADPGK utilizes ADP as a phosphoryl group donor. Here we present a crystal structure of archaeal ADPGK from Methanocaldococcus jannaschii in complex with an inhibitor, 5-iodotubercidin, D-glucose, inorganic phosphate and a magnesium ion. Detailed analysis of the architecture of the active site allowed for confirmation of the previously proposed phosphorylation mechanism and the crucial role of the invariant arginine residue (Arg197)...
January 20, 2018: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29352739/determination-of-protein-oligomeric-structure-from-small-angle-x-ray-scattering
#2
REVIEW
David A Korasick, John J Tanner
Small-angle X-ray scattering (SAXS) is useful for determining the oligomeric states and quaternary structures of proteins in solution. The average molecular mass in solution can be calculated directly from a single SAXS curve collected on an arbitrary scale from a sample of unknown protein concentration, without the need for beamline calibration or protein standards. The quaternary structure in solution can be deduced by comparing the experimental SAXS curve to theoretical curves calculated from proposed models of the oligomer...
January 20, 2018: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29352107/mycolyltransferase-from-mycobacterium-tuberculosis-in-covalent-complex-with-tetrahydrolipstatin-provides-insights-into-antigen-85-catalysis
#3
Christopher M Goins, Steven Dajnowicz, Micholas D Smith, Jerry M Parks, Donald R Ronning
Mycobacterium tuberculosis Antigen 85 enzymes (Ag85s) catalyze the transfer of mycolic acid (MA) from trehalose monomycolate to produce the mycolyl arabinogalactan (mAG) or trehalose dimycolate (TDM). These lipids define the protective mycomembrane of Mycobacteria. The current model of substrate binding within the active sites of Ag85s for the production of TDM is not sterically and geometrically feasible; additionally, this model does not account for the production of mAG. Furthermore, this model does not address how Ag85s limit the hydrolysis of the acyl-enzyme intermediate while catalyzing acyl transfer...
January 19, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29352104/a-ph-like-domain-of-the-rab12-guanine-nucleotide-exchange-factor-dennd3-binds-actin-and-is-required-for-autophagy
#4
Jie Xu, Guennadi Kozlov, Peter S McPherson, Kalle Gehring
Rab GTPases are key regulators of membrane trafficking and many are activated by guanine nucleotide exchange factors bearing a <span style="text-decoration: underline;">d</span>ifferentially <span style="text-decoration: underline;">e</span>xpressed in <span style="text-decoration: underline;">n</span>ormal and <span style="text-decoration: underline;">n</span>eoplastic cells (DENN) domain. By activating the small GTPase Rab12, DENN domain-containing protein 3 (DENND3) functions in autophagy...
January 19, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29352089/cryptic-production-of-trans-3-hydroxyproline-in-echinocandin-b-biosynthesis
#5
Johanna Mattay, Stefanie Houwaart, Wolfgang Hüttel
Echinocandins are antifungal nonribosomal hexapeptides produced by fungi. Two of the amino acids are hydroxy-l-prolines: trans-4-hydroxy-l-proline and, in most echinocandin structures, (trans-2,3)-3-hydroxy-(trans-2,4)-4-methyl-l-proline. In the case of echinocandin biosynthesis by Glarea lozoyensis, both amino acids are found in pneumocandin A0, while in pneumocandin B0 the latter residue is substituted by trans-3- hydroxy-l-proline (3-Hyp). We have recently reported that all three amino acids are generated by the 2-oxoglutarate-dependent proline hydroxylase GloF...
January 19, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29351963/the-exon-junction-complex-structural-insights-into-a-faithful-companion-of-mammalian-mrnps
#6
REVIEW
Jennifer V Gerbracht, Niels H Gehring
During splicing, the exon junction complex (EJC) is deposited upstream of exon-exon boundaries. The EJC and its peripheral bound proteins play an essential role in mediating mRNA export, translation and turnover. However, the exact sequence of EJC assembly and the involved factors during splicing remain elusive. Recently published structures of the human C* spliceosome clarified the position of the EJC at this phase of splicing and have given insight into previously unidentified interactions between the EJC and spliceosomal proteins...
January 19, 2018: Biochemical Society Transactions
https://www.readbyqxmd.com/read/29351733/glutamate-synthases-from-conifers-gene-structure-and-phylogenetic-studies
#7
Ángel García-Gutiérrez, Francisco M Cánovas, Concepción Ávila
BACKGROUND: Plants synthesize glutamate from ammonium by the combined activity of the enzymes glutamine synthetase (GS) and glutamate synthase (GOGAT) through the glutamate synthase cycle. In plants, there are two forms of glutamate synthases that differ in their electron donors, NADH-GOGAT (EC 1.4.1.14) and Fd-GOGAT (EC 1.4.7.1), which have differential roles either in primary ammonia assimilation or in the reassimilation of ammonium from different catabolic processes. Glutamate synthases are complex iron-sulfur flavoproteins containing functional domains involved in the control and coordination of their catalytic activities in annual plants...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351731/a-chelicerate-specific-burst-of-nonclassical-dscam-diversity
#8
Guozheng Cao, Yang Shi, Jian Zhang, Hongru Ma, Shouqing Hou, Haiyang Dong, Weiling Hong, Shuo Chen, Hao Li, Yandan Wu, Pengjuan Guo, Xu Shao, Bingbing Xu, Feng Shi, Yijun Meng, Yongfeng Jin
BACKGROUND: The immunoglobulin (Ig) superfamily receptor Down syndrome cell adhesion molecule (Dscam) gene can generate tens of thousands of isoforms via alternative splicing, which is essential for both nervous and immune systems in insects. However, further information is required to develop a comprehensive view of Dscam diversification across the broad spectrum of Chelicerata clades, a basal branch of arthropods and the second largest group of terrestrial animals. RESULTS: In this study, a genome-wide comprehensive analysis of Dscam genes across Chelicerata species revealed a burst of nonclassical Dscams, categorised into four types-mDscam, sDscamα, sDscamβ, and sDscamγ-based on their size and structure...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351654/what-is-the-role-of-imaging-in-the-clinical-diagnosis-of-osteoarthritis-and-disease-management
#9
Xia Wang, Win Min Oo, James M Linklater
While OA is predominantly diagnosed on the basis of clinical criteria, imaging may aid with differential diagnosis in clinically suspected cases. While plain radiographs are traditionally the first choice of imaging modality, MRI and US also have a valuable role in assessing multiple pathologic features of OA, although each has particular advantages and disadvantages. Although modern imaging modalities provide the capability to detect a wide range of osseous and soft tissue (cartilage, menisci, ligaments, synovitis, effusion) OA-related structural damage, this extra information has not yet favourably influenced the clinical decision-making and management process...
January 16, 2018: Rheumatology
https://www.readbyqxmd.com/read/29351566/patterns-in-reef-fish-assemblages-insights-from-the-chagos-archipelago
#10
Melita Samoilys, Ronan Roche, Heather Koldewey, John Turner
Understanding the drivers of variability in the composition of fish assemblages across the Indo-Pacific region is crucial to support coral reef ecosystem resilience. Whilst numerous relationships and feedback mechanisms between the functional roles of coral reef fishes and reef benthic composition have been investigated, certain key groups, such as the herbivores, are widely suggested to maintain reefs in a coral-dominated state. Examining links between fishes and reef benthos is complicated by the interactions between natural processes, disturbance events and anthropogenic impacts, particularly fishing pressure...
2018: PloS One
https://www.readbyqxmd.com/read/29351397/acute-small-intestinal-inflammation-results-in-persistent-lymphatic-alterations
#11
Sonia Rehal, Matthew Stephens, Simon Roizes, Shan Liao, Pierre-Yves von der Weid
Inflammatory bowel disease (IBD) has a complex pathophysiology with limited treatments. Structural and functional changes in the intestinal lymphatic system have been associated with the disease, with increased risk of IBD occurrence linked to a history of acute intestinal injury. To examine the potential role of the lymphatic system in inflammation recurrence, we evaluated morphological and functional changes in mouse mucosal and mesenteric lymphatic vessels, and within the mesenteric lymph nodes during acute ileitis caused by a 7-day treatment with dextran sodium sulfate (DSS)...
December 14, 2017: American Journal of Physiology. Gastrointestinal and Liver Physiology
https://www.readbyqxmd.com/read/29351317/hafts-are-novel-lncrna-transcripts-from-aflatoxin-exposure
#12
B Alex Merrick, Justin S Chang, Dhiral P Phadke, Meredith A Bostrom, Ruchir R Shah, Xinguo Wang, Oksana Gordon, Garron M Wright
The transcriptome can reveal insights into precancer biology. We recently conducted RNA-Seq analysis on liver RNA from male rats exposed to the carcinogen, aflatoxin B1 (AFB1), for 90 days prior to liver tumor onset. Among >1,000 differentially expressed transcripts, several novel, unannotated Cufflinks-assembled transcripts, or HAfTs (Hepatic Aflatoxin Transcripts) were found. We hypothesized PCR-cloning and RACE (rapid amplification of cDNA ends) could further HAfT identification. Sanger data was obtained for 6 transcripts by PCR and 16 transcripts by 5'- and 3'-RACE...
2018: PloS One
https://www.readbyqxmd.com/read/29351204/mtor-cross-talk-in-cancer-and-potential-for-combination-therapy
#13
REVIEW
Fabiana Conciatori, Ludovica Ciuffreda, Chiara Bazzichetto, Italia Falcone, Sara Pilotto, Emilio Bria, Francesco Cognetti, Michele Milella
The mammalian Target of Rapamycin (mTOR) pathway plays an essential role in sensing and integrating a variety of exogenous cues to regulate cellular growth and metabolism, in both physiological and pathological conditions. mTOR functions through two functionally and structurally distinct multi-component complexes, mTORC1 and mTORC2, which interact with each other and with several elements of other signaling pathways. In the past few years, many new insights into mTOR function and regulation have been gained and extensive genetic and pharmacological studies in mice have enhanced our understanding of how mTOR dysfunction contributes to several diseases, including cancer...
January 19, 2018: Cancers
https://www.readbyqxmd.com/read/29350910/highly-asymmetric-phase-behaviors-of-polyhedral-oligomeric-silsesquioxanes-based-multi-headed-giant-surfactants
#14
Mingjun Huang, Kan Yue, Jiahao Huang, Chang Liu, Zhe Zhou, Jing Wang, Kan Wu, Wenpeng Shan, An-Chang Shi, Stephen Z D Cheng
This work reports the molecular design, synthesis, and systematic study on the bulk self-assembly behaviors of three series of polyhedral oligomeric silsesquioxanes (POSS)-based multi-headed giant surfactants XDPOSS-PSn (X = 2, 3 and 4), which are composed of two, three or four hydrophilic hydroxyl-group functionalized DPOSS cages attached via one junction point to a hydrophobic polystyrene (PS) chain. These series of hybrid polymeric amphiphiles with precisely defined chemical structure and controllable molecular architecture are synthesized by the sequential usage of "click" reactions...
January 19, 2018: ACS Nano
https://www.readbyqxmd.com/read/29350725/effects-of-chemically-heterogeneous-nanoparticles-on-polymer-dynamics-insights-from-molecular-dynamics-simulations
#15
Zijian Zheng, Fanzhu Li, Jun Liu, Raffaele Pastore, Guido Raos, Youping Wu, Liqun Zhang
The dispersion of solid nanoparticles within polymeric materials is widely used to enhance their performance. Many scientific and technological aspects of the resulting polymer nanocomposites have been studied, but the role of the structural and chemical heterogeneity of the nanoparticles has just started to be appreciated. For example, simulations of polymer films on planar heterogeneous surfaces revealed unexpected, non-monotonic activation energy to diffusion on varying the surface composition. Motivated by these intriguing results, here we simulate via molecular dynamics a different, fully three-dimensional system, in which the heterogeneous nanoparticles are incorporated in a polymer melt...
January 19, 2018: Soft Matter
https://www.readbyqxmd.com/read/29350562/enzymes-in-lipid-modification
#16
Uwe T Bornscheuer
This article reviews the application of enzymes in lipid modification. Lipases are the most established biocatalysts used for the synthesis of structured triacylglycerols, fats, and margarine for the release of flavoring fatty acids for food applications. In addition, the various enzymes, such as P450 monooxygenases, hydratases, lipoxygenases, and certain lyases, used for oxyfunctionalization and the phospholipases used for degumming are covered. Basic aspects of enzyme catalysis and the modern tools used for their discovery and improvement by protein engineering provide insight into how suitable biocatalysts can be identified and optimized for an application...
January 18, 2018: Annual Review of Food Science and Technology
https://www.readbyqxmd.com/read/29350531/on-the-electronic-structure-of-cu-chlorophyllin-and-its-breakdown-products-a-carbon-k-edge-x-ray-absorption-spectroscopy-study
#17
Katharina Witte, Ioanna Mantouvalou, Rocío Sánchez-de-Armas, Heiko Lokstein, Janina Lebendig-Kuhla, Adrian Jonas, Friedrich Roth, Birgit Kanngiesser, Holger Stiel
Using Near-Edge X-ray Absorption Fine Structure Spectroscopy (NEXAFS) the carbon backbone of sodium copper chlorophyllin (SCC), a widely used chlorophyll derivative, and its breakdown products are analyzed to elucidate their electronic structure and physicochemical properties. Using various sample preparation methods and complementary spectroscopic methods (including UV/VIS, X-ray Photoelectron Spectroscopy), a comprehensive insight into the SCC breakdown process is presented. The experimental results are supported by Density Functional Theory (DFT) calculations allowing a detailed assignment of characteristic NEXAFS-features to specific C-bonds...
January 19, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29350283/epigenetic-regulation-of-neuroblastoma-development
#18
REVIEW
Durinck Kaat, Speleman Frank
In recent years, technological advances have enabled a detailed landscaping of the epigenome and the mechanisms of epigenetic regulation that drive normal cell function, development and cancer. Rather than merely a structural entity to support genome compaction, we now look at chromatin as a very dynamic and essential constellation that is actively participating in the tight orchestration of transcriptional regulation as well as DNA replication and repair. The unique feature of chromatin flexibility enabling fast switches towards more or less restricted epigenetic cellular states is, not surprisingly, intimately connected to cancer development and treatment resistance, and the central role of epigenetic alterations in cancer is illustrated by the finding that up to 50% of all mutations across cancer entities affect proteins controlling the chromatin status...
January 19, 2018: Cell and Tissue Research
https://www.readbyqxmd.com/read/29350280/selective-precipitation-and-characterization-of-lignin-carbohydrate-complexes-lccs-from-eucalyptus
#19
Bao-Cheng Zhao, Ji-Dong Xu, Bo-Yang Chen, Xue-Fei Cao, Tong-Qi Yuan, Shuang-Fei Wang, Adam Charlton, Run-Cang Sun
Six types of lignin-carbohydrate complex (LCC) fractions were isolated from Eucalyptus. The acidic dioxane treatment applied significantly improved the yield of LCCs. The extraction conditions had a limited impact on the LCC structures and linkages. Characterization of the lignin-carbohydrate complex (LCC) structures and linkages promises to offer insight on plant cell wall chemistry. In this case, Eucalyptus LCCs were extracted by aqueous dioxane, and then precipitated sequentially by 70% ethanol, 100% ethanol, and acidic water (pH = 2)...
January 19, 2018: Planta
https://www.readbyqxmd.com/read/29350188/accurate-identification-of-layer-number-for-few-layer-ws2-and-wse2-via-spectroscopic-study
#20
Yuanzheng Li, Xinshu Li, Tong Yu, Guochun Yang, Heyu Chen, Cen Zhang, Qiushi Feng, Jiangang Ma, Weizhen Liu, Haiyang Xu, Yichun Liu, Xinfeng Liu
Transition metal dichalcogenides (TMDs) with typical layered structure are highly sensitive to their layer number in optical and electronic properties. Seeking a simple and effective method for layer number identification is very important to low-dimensional TMDs samples. Herein, a rapid and accurate layer number identification of few-layer WS2 and WSe2 is proposed via locking their photoluminescence (PL) peak-positions. As the layer number of WS2/WSe2 increases, it is found that indirect transition emission is more thickness-sensitive than direct transition emission, and the PL peak-position differences between the indirect and direct transitions can be regarded as fingerprints to identify their layer number...
January 19, 2018: Nanotechnology
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