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https://www.readbyqxmd.com/read/29908124/modifications-in-small-nuclear-rnas-and-their-roles-in-spliceosome-assembly-and-function
#1
Markus T Bohnsack, Katherine E Sloan
Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2'-O-methylated nucleotides, which are largely introduced by small Cajal body-specific-RNPs...
June 1, 2018: Biological Chemistry
https://www.readbyqxmd.com/read/29907568/structure-of-human-adp-ribosyl-acceptor-hydrolase-3-bound-to-adp-ribose-reveals-a-conformational-switch-that-enables-specific-substrate-recognition
#2
Yasin Pourfarjam, Jessica Ventura, Igor Kurinov, Ahra Cho, Joel Moss, In-Kwon Kim
ADP-ribosyl-acceptor hydrolase 3 (ARH3) plays important roles in regulation of poly(ADP-ribosy)lation, a reversible post-translational modification, and in maintenance of genomic integrity. ARH3 degrades poly(ADP-ribose) to protect cells from poly(ADP-ribose)-dependent cell death, reverses serine-mono(ADP-ribosy)lation, and hydrolyzes O -acetyl-ADP-ribose, a product of Sirtuin-catalyzed histone deacetylation. ARH3 preferentially hydrolyzes O-linkages attached to the anomeric C1″ of ADP-ribose; however, how ARH3 specifically recognizes and cleaves structurally diverse substrates remains unknown...
June 15, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29907311/daring-metabolic-designs-for-enhanced-plant-carbon-fixation
#3
Arren Bar-Even
Increasing agricultural productivity is one of the major challenges our society faces. While multiple strategies to enhance plant carbon fixation have been suggested, and partially implemented, most of them are restricted to relatively simple modifications of endogenous metabolism, i.e., "low hanging fruit". Here, I portray the next generation of metabolic solutions to increase carbon fixation rate and yield. These strategies involve major rewiring of central metabolism, including dividing Rubisco's catalysis between several enzymes, replacing Rubisco with a different carboxylation reaction, substituting the Calvin Cycle with alternative carbon fixation pathways, and engineering photorespiration bypass routes that do not release carbon...
August 2018: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/29906339/comparing-neutral-monometallic-and-anionic-bimetallic-aluminium-complexes-in-hydroboration-catalysis-influences-of-lithium-cooperation-and-ligand-set
#4
Robert E Mulvey, Victoria A Pollard, Maria Angeles Fuentes, Alan R Kennedy, Ross McLellan
Bimetallic lithium aluminates and neutral aluminium counterparts are compared as catalysts in hydroboration reactions with aldehydes, ketones, imines and alkynes. Possessing Li-Al cooperativity, ate catalysts are found to be generally superior. Catalytic activity is also influenced by the ligand set, alkyl and/or amido. Devoid of an Al-H bond, iBu2Al(TMP) operates as a masked hydride reducing benzophenone through β-H elimination. This catalyst library therefore provides an entry point into the future design of Al catalysts targeting substrate specific transformations...
June 15, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29906127/palladium-catalyzed-dimerization-of-bis-2-biphenylyl-acetylene-toward-sterically-hindered-acephenanthrylene
#5
Maximilian Ackermann, Jan Freudenberg, Daniel Jänsch, Frank Rominger, Uwe H F Bunz, Klaus Müllen
The reaction of 2,2''-(1,2-ethynediyl)bis-1,1'-biphenyl under homogeneous (heterogeneous) catalysis with Pd/C/TMS-Cl results in a dimerization and the additional formation of five- and six-membered rings. The steric demand of the acetylene prevents a [2 + 2 + 2] cycloaddition, but paves the way toward an alternative reaction. By the formation of an unexpected planar acephenanthrylene, the system avoids steric stain. The synthetic scope and requirements are explored, and a reaction mechanism is proposed.
June 15, 2018: Organic Letters
https://www.readbyqxmd.com/read/29906109/modular-ipso-ortho-difunctionalization-of-aryl-bromides-via-palladium-norbornene-cooperative-catalysis
#6
Zhe Dong, Gang Lu, Jianchun Wang, Peng Liu, Guangbin Dong
Palladium/norbornene (Pd/NBE) cooperative catalysis has emerged as a useful tool for preparing poly-substituted arenes; however, its substrate scope has been largely restricted to aryl iodides. While aryl bromides are considered as standard substrates for Pd-catalyzed cross coupling reactions, their use in Pd/NBE catalysis remains elusive. Here we describe the development of general approaches for aryl bromide-mediated Pd/NBE cooperative catalysis. Through careful tuning the phosphine ligands and quenching nucleophiles, ortho amination, acylation and alkylation of aryl bromides have been realized in good efficiency...
June 15, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29905753/porous-co-3-o-4-sno-2-quantum-dot-qd-heterostructures-with-abundant-oxygen-vacancies-and-co-2-ions-for-highly-efficient-gas-sensing-and-oxygen-evolution-reaction
#7
Xing Wang, Meizhen Gao
Porous Co3O4/SnO2 quantum dot (QD) heterojunctions with a strong synergistic effect are successfully synthesized in this paper. Owing to the strong synergistic effect between Co3O4 and SnO2QDs, Co3O4/SnO2QD heterostructures possess more Co2+ ions for a faster Co2+/Co0 redox reaction in the process of sensing of reducing gases and electrochemical reactions, and more oxygen vacancies for more active sites and reduced charge transfer resistance on the surface. These advantages are demonstrated to significantly enhance the gas sensitivity to xylene and greatly improve the catalysis for the oxygen evolution reaction (OER)...
June 15, 2018: Nanoscale
https://www.readbyqxmd.com/read/29904908/role-of-an-isoform-specific-residue-at-the-calmodulin-heme-no-synthase-interface-in-the-fmn-heme-electron-transfer
#8
Jinghui Li, Huayu Zheng, Wei Wang, Yubin Miao, Yinghong Sheng, Changjian Feng
The interface between calmodulin (CaM) and the NO synthase (NOS) heme domain is the least characterized interprotein interface that the NOS isoforms must traverse through during catalysis. Our previous simulations predicted a salt bridge between K497 in the human inducible NOS (iNOS) heme domain and D118(CaM). Herein, the FMN - heme interdomain electron transfer (IET) rate was found to be notably decreased by charge-reversal mutation, while the IET in the iNOS K497D mutant is significantly restored by the CaM D118K mutation...
June 15, 2018: FEBS Letters
https://www.readbyqxmd.com/read/29904084/signature-of-pareto-optimization-in-the-escherichia-coli-proteome
#9
Loren Koçillari, Piero Fariselli, Antonio Trovato, Flavio Seno, Amos Maritan
Proteins have coevolved with cellular environments to improve or preserve their functions, maintaining at the same time the degree of hydrophobicity necessary to fold correctly and enough solubility to perform their biological roles. Here, we study the Escherichia coli proteome using a Pareto front analysis in the solubility-hydrophobicity space. The results indicate the existence of a Pareto optimal front, a triangle whose vertices correspond to archetypal proteins specialized in distinct tasks, such as regulatory processes, membrane transport, outer-membrane pore formation, catalysis, and binding...
June 14, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29903723/long-read-sequencing-of-nascent-rna-reveals-coupling-among-rna-processing-events
#10
Lydia Herzel, Korinna Straube, Karla M Neugebauer
Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates...
June 14, 2018: Genome Research
https://www.readbyqxmd.com/read/29901984/modulating-enzyme-activity-by-altering-protein-dynamics-with-solvent
#11
Michael R Duff, Jose M Borreguero, Matthew Cuneo, Arvind Ramanathan, Junhong He, Ganesh Kamath, Chakra S Chennubhotla, Flora Meilleur, Elizabeth E Howell, Kenneth W Herwig, Dean A A Myles, Pratul K Agarwal
Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized, however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from Escherichia coli in aqueous mixtures of isopropanol (IPA) with water will decrease by ~3 fold at 20% (v/v) IPA concentration...
June 14, 2018: Biochemistry
https://www.readbyqxmd.com/read/29901864/organocatalytic-asymmetric-cascade-aerobic-oxidation-and-semipinacol-rearrangement-reaction-a-visible-light-induced-approach-to-access-chiral-2-2-disubstituted-indolin-3-ones
#12
Liwei Bu, Jiangtao Li, Yanli Yin, Baokun Qiao, Guobi Chai, Xiaowei Zhao, Zhiyong Jiang
An enantioselective cascade aerobic oxidation and semipinacol rearrangement reaction of 2-aryl-3-alkyl-substituted indoles via visible-light-driven cooperative organophotoredox and H-bonding catalysis is reported. The current method provides an expedient and sustainable approach to furnish a variety of valuable chiral 2-aryl-2-alkyl-substituted indolin-3-ones in 64-90 % yield with 58-94 % ee. Preliminary control experiments present important insights into the stereochemistry.
June 14, 2018: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/29901244/polymer-meets-frustrated-lewis-pair-second-generation-co2-responsive-nanosystem-for-sustainable-co2-conversion
#13
Qiang Yan, Liang Chen, Renjie Liu
Frustrated Lewis pair (FLP), as a couple of sterically encumbered Lewis acid and Lewis base, can offer latent reactivity for activating inert gas molecules. However, their use as a platform for fabricating gas-responsive materials has yet developed. Merging FLP concept and polymers, we report a new generation of CO2-responsive system, differing from the first-generation ones based on acid-base equilibrium mechanism. Two complementary Lewis acidic and basic block copolymers, installing bulky borane- and phosphine-containing blocks, were built as the macromolecular FLP...
June 14, 2018: Angewandte Chemie
https://www.readbyqxmd.com/read/29901066/diastereo-and-enantioselective-mannich-cyclization-cascade-reaction-of-isocyanoacetates-with-cyclic-sulfamide-ketimines-by-cinchona-alkaloid-squaramide-agoac-cooperative-catalysis
#14
Mei-Xin Zhao, Zhi-Wen Dong, Guang-Yu Zhu, Xiao-Li Zhao, Min Shi
We have developed an efficient diastereo- and enantioselective Mannich/cyclization cascade reaction of α-substituted isocyanoacetates with 4-aryl-3-carbonyl-1,2,5-thiadiazole-1,1-dioxide type cyclic sulfamide ketimines cooperatively catalyzed by cinchona alkaloid-derived squaramide and AgOAc. The corresponding optically active 2,3,3a,4-tetrahydroimidazo[1,5-b][1,2,5]thiadiazole-1,1-dioxide derivatives were obtained in excellent yields (up to 99%) and good to excellent stereoselectivities (up to >20 : 1 dr, up to 94% ee)...
June 14, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29900699/nhc-organocatalyzed-kinetic-resolutions-dynamic-kinetic-resolutions-and-desymmetrizations
#15
Zhongyao Wang, Dingwu Pan, Tingting Li, Zhichao Jin
The last couple of decades have witnessed tremendous development within N-heterocyclic carbene (abbreviated as NHC) organocatalysis. NHCs have been used as powerful organic catalysts in asymmetric synthesis. Although great achievements have been made in the asymmetric NHC catalysis, their applications in the kinetic resolution (abbreviated as KR), dynamic kinetic resolution (abbreviated as DKR) and desymmetrization processes have been relatively less developed. Moreover, limited activation modes have been involved in these processes...
June 13, 2018: Chemistry, An Asian Journal
https://www.readbyqxmd.com/read/29900660/a-sensitive-sers-quantitative-analysis-method-for-ni-2-by-the-dimethylglyoxime-reaction-regulating-a-graphene-oxide-nanoribbon-catalytic-gold-nanoreaction
#16
Aihui Liang, Xin Li, Xinghui Zhang, Guiqing Wen, Zhiliang Jiang
The nanogold reaction between HAuCl4 and trisodium citrate (TCA) proceeded very slowly at 60°C in a water bath. The as-prepared graphene oxide nanoribbons (GONRs) exhibited strong catalysis during the reaction to form gold nanoparticles (Au NPs) and appeared as a strong surface-enhanced Raman scattering (SERS) peak at 1616 cm-1 in the presence of the molecular probe Victoria blue 4R (VB4r). With increase in GONR concentration, the SERS peak increased due to increased formation of Au NPs. Upon addition of dimethylglyoxime (DMG) ligand, which was adsorbed onto the GONR surface to inhibit GONR catalysis, the SERS peak decreased...
June 13, 2018: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/29900498/nucleoprotein-intermediates-in-hiv-1-dna-integration-structure-and-function-of-hiv-1-intasomes
#17
Robert Craigie
Integration of a DNA copy of the viral genome into host DNA is an essential step in the replication cycle of HIV-1 and other retroviruses and is an important therapeutic target for drugs. DNA integration is catalyzed by the viral integrase protein and proceeds through a series of stable nucleoprotein complexes of integrase, viral DNA ends and target DNA. These nucleoprotein complexes are collectively called intasomes. Retroviral intasomes undergo a series of transitions between initial formation and catalysis of the DNA cutting and joining steps of DNA integration...
2018: Sub-cellular Biochemistry
https://www.readbyqxmd.com/read/29900463/visible-light-mediated-desilylative-c-sp-2-c-sp-2-cross-coupling-reactions-of-arylsilanes-with-aryldiazonium-salts-under-au-i-au-iii-catalysis
#18
Indradweep Chakrabarty, Manjur O Akram, Suprakash Biswas, Nitin T Patil
Desilylative C(sp2)-C(sp2) cross-coupling reactions of arylsilanes with aryldiazonium salts under Au(i)/photoredox catalysis have been reported. The addition of Cu-salts as catalysts was found to be crucial for the success of this transformation.
June 14, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29900460/oxidation-of-%C3%AE-trifluoromethyl-and-non-fluorinated-alcohols-via-the-merger-of-oxoammonium-cations-and-photoredox-catalysis
#19
Vincent A Pistritto, Joshua M Paolillo, Kathryn A Bisset, Nicholas E Leadbeater
We present an alcohol oxidation strategy to access α-trifluoromethyl ketones (TFMKs) merging catalytic oxoammonium cation oxidation with visible-light photoredox catalysis. This work uses 4-acetamido-(2,2,6,6-tetramethyl-piperidin-1-yl)oxyl as an organic oxidant capable of generating TFMKs in good yields. The methodology serves as an improvement over previous reports of an analogous oxidation strategy requiring superstoichiometric quantities of oxidant. Both primary and secondary non-fluorinated alcohols can also be oxidised in good yields...
June 14, 2018: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/29899950/non-competitive-cyclic-peptides-for-targeting-enzyme-substrate-complexes
#20
T E McAllister, T-L Yeh, M I Abboud, I K H Leung, E S Hookway, O N F King, B Bhushan, S T Williams, R J Hopkinson, M Münzel, N D Loik, R Chowdhury, U Oppermann, T D W Claridge, Y Goto, H Suga, C J Schofield, A Kawamura
Affinity reagents are of central importance for selectively identifying proteins and investigating their interactions. We report on the development and use of cyclic peptides, identified by mRNA display-based RaPID methodology, that are selective for, and tight binders of, the human hypoxia inducible factor prolyl hydroxylases (PHDs) - enzymes crucial in hypoxia sensing. Biophysical analyses reveal the cyclic peptides to bind in a distinct site, away from the enzyme active site pocket, enabling conservation of substrate binding and catalysis...
May 28, 2018: Chemical Science
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