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https://www.readbyqxmd.com/read/27926995/frozen-but-no-accident-why-the-20-standard-amino-acids-were-selected
#1
REVIEW
Andrew J Doig
The 20 standard amino acids encoded by the Genetic Code were adopted during the RNA World, around 4 billion years ago. This amino acid set could be regarded as a frozen accident, implying that other possible structures could equally well have been chosen to use in proteins. Amino acids were not primarily selected for their ability to support catalysis, since the RNA World already had highly effective cofactors to perform reactions, such as oxidation, reduction and transfer of small molecules. Rather, they were selected to enable the formation of soluble structures with close-packed cores, allowing the presence of ordered binding pockets...
December 7, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27926877/ptbp1-and-ptbp2-serve-both-specific-and-redundant-functions-in-neuronal-pre-mrna-splicing
#2
John K Vuong, Chia-Ho Lin, Min Zhang, Liang Chen, Douglas L Black, Sika Zheng
Families of alternative splicing regulators often contain multiple paralogs presumed to fulfill different functions. Polypyrimidine tract binding proteins PTBP1 and PTBP2 reprogram developmental pre-mRNA splicing in neurons, but how their regulatory networks differ is not understood. To compare their targeting, we generated a knockin allele that conditionally expresses PTBP1. Bred to a Ptbp2 knockout, the transgene allowed us to compare the developmental and molecular phenotypes of mice expressing only PTBP1, only PTBP2, or neither protein in the brain...
December 6, 2016: Cell Reports
https://www.readbyqxmd.com/read/27924258/chaperonin-groel-uses-asymmetric-and-symmetric-reaction-cycles-in-response-to-the-concentration-of-non-native-substrate-proteins
#3
REVIEW
Ryo Iizuka, Takashi Funatsu
The Escherichia coli chaperonin GroEL is an essential molecular chaperone that mediates protein folding in association with its cofactor, GroES. It is widely accepted that GroEL alternates the GroES-sealed folding-active rings during the reaction cycle. In other words, an asymmetric GroEL-GroES complex is formed during the cycle, whereas a symmetric GroEL-(GroES)2 complex is not formed. However, this conventional view has been challenged by the recent reports indicating that such symmetric complexes can be formed in the GroEL-GroES reaction cycle...
2016: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/27923990/regulation-of-prp43-mediated-disassembly-of-spliceosomes-by-its-cofactors-ntr1-and-ntr2
#4
Jean-Baptiste Fourmann, Marcel J Tauchert, Ralf Ficner, Patrizia Fabrizio, Reinhard Lührmann
The DEAH-box NTPase Prp43 disassembles spliceosomes in co-operation with the cofactors Ntr1/Spp382 and Ntr2, forming the NTR complex. How Prp43 is regulated by its cofactors to discard selectively only intron-lariat spliceosomes (ILS) and defective spliceosomes and to prevent disassembly of earlier and properly assembled/wild-type spliceosomes remains unclear. First, we show that Ntr1's G-patch motif (Ntr1GP) can be replaced by the GP motif of Pfa1/Sqs1, a Prp43's cofactor in ribosome biogenesis, demonstrating that the specific function of Ntr1GP is to activate Prp43 for spliceosome disassembly and not to guide Prp43 to its binding site in the spliceosome...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27923567/an-experimental-modeling-of-trinomial-bioengineering-crp-rdna-and-transporter-engineering-within-single-cell-factory-for-maximizing-two-phase-bioreduction
#5
Souvik Basak, Sumanta Kumar Ghosh, Vinay Deep Punetha, Ashish N Aphale, Prabir K Patra, Nanda Gopal Sahoo
A carbonyl reductase (cr) gene from Candida glabrata CBS138 has been heterologously expressed in cofactor regenerating E. coli host to convert Ethyl-4-chloro-3-oxobutanoate (COBE) into Ethyl-4-chloro-3-hydroxybutanoate (CHBE). The CR enzyme exhibited marked velocity at substrate concentration as high as 363mM with highest turnover number (112.77±3.95s(-1)). Solitary recombineering of such catalytic cell reproduced CHBE 161.04g/L per g of dry cell weight (DCW). Introduction of combinatorially engineered crp (crp*, F136I) into this heterologous E...
December 3, 2016: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/27923244/-improvement-of-psychosomatic-rehabilitation-after-prestationary-intervention
#6
K Sander, G Winkler, N Hofer, S Hunatschek, R Doerr
Aim of the study: Improvement of psychosomatic rehabilitation efforts with prestationary intervention. Method: The study is designed as a prospective and randomisized interventon study including 317 in patients. Result: Most of the patients were women (69.4 %), the mean age was 50.2 years. As measured with the BDI-II patients with prestationary intervention improved more than patients without intervention. The motivation has not been changed significantly in both treatment arms. Various independent cofactors like long duration of unemployment, disablement and patients who apply to pension were identified...
December 2016: Die Rehabilitation
https://www.readbyqxmd.com/read/27923069/characterization-in-helicobacter-pylori-of-a-nickel-transporter-essential-for-colonization-that-was-acquired-during-evolution-by-gastric-helicobacter-species
#7
Frédéric Fischer, Marie Robbe-Saule, Evelyne Turlin, Francesco Mancuso, Valérie Michel, Pierre Richaud, Frédéric J Veyrier, Hilde De Reuse, Daniel Vinella
Metal acquisition is crucial for all cells and for the virulence of many bacterial pathogens. In particular, nickel is a virulence determinant for the human gastric pathogen Helicobacter pylori as it is the cofactor of two enzymes essential for in vivo colonization, urease and a [NiFe] hydrogenase. To import nickel despite its scarcity in the human body, H. pylori requires efficient uptake mechanisms that are only partially defined. Indeed, alternative ways of nickel entry were predicted to exist in addition to the well-described NixA permease...
December 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27922496/metabolic-myopathies
#8
Mark A Tarnopolsky
PURPOSE OF REVIEW: Metabolic myopathies are genetic disorders that impair intermediary metabolism in skeletal muscle. Impairments in glycolysis/glycogenolysis (glycogen-storage disease), fatty acid transport and oxidation (fatty acid oxidation defects), and the mitochondrial respiratory chain (mitochondrial myopathies) represent the majority of known defects. The purpose of this review is to develop a diagnostic and treatment algorithm for the metabolic myopathies. RECENT FINDINGS: The metabolic myopathies can present in the neonatal and infant period as part of more systemic involvement with hypotonia, hypoglycemia, and encephalopathy; however, most cases present in childhood or in adulthood with exercise intolerance (often with rhabdomyolysis) and weakness...
December 2016: Continuum: Lifelong Learning in Neurology
https://www.readbyqxmd.com/read/27921179/activation-of-dioxygen-by-copper-metalloproteins-and-insights-from-model-complexes
#9
REVIEW
David A Quist, Daniel E Diaz, Jeffrey J Liu, Kenneth D Karlin
Nature uses dioxygen as a key oxidant in the transformation of biomolecules. Among the enzymes that are utilized for these reactions are copper-containing metalloenzymes, which are responsible for important biological functions such as the regulation of neurotransmitters, dioxygen transport, and cellular respiration. Enzymatic and model system studies work in tandem in order to gain an understanding of the fundamental reductive activation of dioxygen by copper complexes. This review covers the most recent advancements in the structures, spectroscopy, and reaction mechanisms for dioxygen-activating copper proteins and relevant synthetic models thereof...
December 5, 2016: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/27920295/a-novel-transcriptional-regulator-related-to-thiamine-phosphate-synthase-controls-thiamine-metabolism-genes-in-archaea
#10
Dmitry A Rodionov, Semen A Leyn, Xiaoqing Li, Irina A Rodionova
: Thiamine (vitamin B1) is a precursor of thiamine pyrophosphate (TPP), an essential coenzyme in the central metabolism of all living organisms. Bacterial thiamin biosynthesis and salvage genes are controlled at the RNA level by TPP-responsive riboswitches. In Archaea, TPP riboswitches are restricted to the Thermoplasmatales order. Mechanisms of transcriptional control of thiamine genes in other archaeal lineages remain unknown. Using the comparative genomics approach, we identified a novel family of transcriptional regulators (named ThiR) controlling thiamine biosynthesis and transport genes in diverse lineages from the Crenarchaeota phylum, as well as in the Halobacteria and Thermococci classes of the Euryarchaeota ThiR regulators are composed of an N-terminal DNA-binding domain and a C-terminal ligand-binding domain that is similar to the archaeal thiamin phosphate synthase ThiN...
December 5, 2016: Journal of Bacteriology
https://www.readbyqxmd.com/read/27919744/co-infections-with-liver-fluke-and-helicobacter-species-a-paradigm-change-in-pathogenesis-of-opisthorchiasis-and-cholangiocarcinoma
#11
REVIEW
Banchob Sripa, Raksawan Deenonpoe, Paul J Brindley
Infection with the fish-borne liver fluke Opisthorchis viverrini is classified by the International Agency for Research on Cancer as a Group 1 carcinogen: definitely carcinogenic in humans. Cofactors likely contribute to bile duct cancer (cholangiocarcinoma) caused by this infection. Here we review recent findings that address the role of liver fluke associated H. pylori in hepatobiliary disease and malignancy. We hypothesize that co-infection by O. viverrini and the bacillus Helicobacter pylori is central of liver fluke infection associated cholangiocarcinoma...
December 2, 2016: Parasitology International
https://www.readbyqxmd.com/read/27919686/structural-and-functional-study-of-chuy-from-escherichia-coli-strain-cft073
#12
Hun Kim, Akhilesh Kumar Chaurasia, Truc Kim, Jongkeun Choi, Sung Chul Ha, Doyoun Kim, Kyeong Kyu Kim
The uropathogenic Escherichia coli strain CFT073 contains multiple iron and heme transport systems, which facilitate infection of the host urinary tract. To elucidate the molecular and cellular function of ChuY, a hypothetical gene in the heme degradation/utilization pathway, we solved the crystal structure of ChuY at 2.4 Å resolution. ChuY has high structural homology with human biliverdin and flavin reductase. We confirmed that ChuY has flavin mononucleotide (FMN) reductase activity, using NAD(P)H as a cofactor, and shows porphyrin ring binding affinity...
December 2, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27919260/a-frameshift-mutation-in-mocos-is-associated-with-familial-renal-syndrome-xanthinuria-in-tyrolean-grey-cattle
#13
Leonardo Murgiano, Vidhya Jagannathan, Christian Piffer, Inmaculada Diez-Prieto, Marilena Bolcato, Arcangelo Gentile, Cord Drögemüller
BACKGROUND: Renal syndromes are occasionally reported in domestic animals. Two identical twin Tyrolean Grey calves exhibited weight loss, skeletal abnormalities and delayed development associated with kidney abnormalities and formation of uroliths. These signs resembled inherited renal tubular dysplasia found in Japanese Black cattle which is associated with mutations in the claudin 16 gene. Despite demonstrating striking phenotypic similarities, no obvious presence of pathogenic variants of this candidate gene were found...
December 5, 2016: BMC Veterinary Research
https://www.readbyqxmd.com/read/27919108/biocatalytic-synthesis-of-flavonoid-esters-by-lipases-and-their-biological-benefits
#14
Maria Elisa M B de Araújo, Yollanda E M Franco, Marcia C F Messias, Giovanna B Longato, João A Pamphile, Patricia de O Carvalho
Several studies have described important biological activities of flavonoids such as coronary heart disease prevention, hepatoprotective, anti-inflammatory and anticancer activities, enzyme inhibition activity, and antibacterial, antifungal, and antiviral activities. Flavonoids show promising activity as natural plant-based antioxidants due to their antioxidant and free radical scavenging properties. However, their primary applications as antioxidants in the pharmaceutical, cosmetic, and food industries are limited because of their moderately hydrophilic nature...
December 5, 2016: Planta Medica
https://www.readbyqxmd.com/read/27917880/actin-activates-pseudomonas-aeruginosa-exoy-nucleotidyl-cyclase-toxin-and-exoy-like-effector-domains-from-martx-toxins
#15
Alexander Belyy, Dorothée Raoux-Barbot, Cosmin Saveanu, Abdelkader Namane, Vasily Ogryzko, Lina Worpenberg, Violaine David, Veronique Henriot, Souad Fellous, Christien Merrifield, Elodie Assayag, Daniel Ladant, Louis Renault, Undine Mechold
The nucleotidyl cyclase toxin ExoY is one of the virulence factors injected by the Pseudomonas aeruginosa type III secretion system into host cells. Inside cells, it is activated by an unknown eukaryotic cofactor to synthesize various cyclic nucleotide monophosphates. ExoY-like adenylate cyclases are also found in Multifunctional-Autoprocessing Repeats-in-ToXin (MARTX) toxins produced by various Gram-negative pathogens. Here we demonstrate that filamentous actin (F-actin) is the hitherto unknown cofactor of ExoY...
December 5, 2016: Nature Communications
https://www.readbyqxmd.com/read/27916823/vitamin-b12-among-vegetarians-status-assessment-and-supplementation
#16
REVIEW
Gianluca Rizzo, Antonio Simone Laganà, Agnese Maria Chiara Rapisarda, Gioacchina Maria Grazia La Ferrera, Massimo Buscema, Paola Rossetti, Angela Nigro, Vincenzo Muscia, Gaetano Valenti, Fabrizio Sapia, Giuseppe Sarpietro, Micol Zigarelli, Salvatore Giovanni Vitale
Cobalamin is an essential molecule for humans. It acts as a cofactor in one-carbon transfers through methylation and molecular rearrangement. These functions take place in fatty acid, amino acid and nucleic acid metabolic pathways. The deficiency of vitamin B12 is clinically manifested in the blood and nervous system where the cobalamin plays a key role in cell replication and in fatty acid metabolism. Hypovitaminosis arises from inadequate absorption, from genetic defects that alter transport through the body, or from inadequate intake as a result of diet...
November 29, 2016: Nutrients
https://www.readbyqxmd.com/read/27915377/crystal-structure-and-characterization-of-esterase-est25-mutants-reveal-improved-enantioselectivity-toward-s-ketoprofen-ethyl-ester
#17
Jinyeong Kim, Seung-Hyeon Seok, Eunsoo Hong, Tae Hyeon Yoo, Min-Duk Seo, Yeonwoo Ryu
Esterases comprise a group of enzymes that catalyze the cleavage and synthesis of ester bonds. They are important in biotechnological applications owing to their enantioselectivity, regioselectivity, broad substrate specificity, and the fact that they do not require cofactors. In a previous study, we isolated the esterase Est25 from a metagenomic library. Est25 showed catalytic activity toward the (R,S)-ketoprofen ethyl ester but had low enantioselectivity toward the (S)-ketoprofen ethyl ester. Because (S)-ketoprofen has stronger anti-inflammatory effects and fewer side effects than (R)-ketoprofen, enantioselectivity of this esterase is important...
December 3, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/27914869/glycolysis-without-pyruvate-kinase-in-clostridium-thermocellum
#18
Daniel G Olson, Manuel Hörl, Tobias Fuhrer, Jingxuan Cui, Jilai Zhou, Marybeth I Maloney, Daniel Amador-Noguez, Liang Tian, Uwe Sauer, Lee R Lynd
The metabolism of Clostridium thermocellum is notable in that it assimilates sugar via the EMP pathway but does not possess a pyruvate kinase enzyme. In the wild type organism, there are three proposed pathways for conversion of phosphoenolpyruvate (PEP) to pyruvate, which differ in their cofactor usage. One path uses pyruvate phosphate dikinase (PPDK), another pathway uses the combined activities of PEP carboxykinase (PEPCK) and oxaloacetate decarboxylase (ODC). Yet another pathway, the malate shunt, uses the combined activities of PEPCK, malate dehydrogenase and malic enzyme...
November 30, 2016: Metabolic Engineering
https://www.readbyqxmd.com/read/27913952/association-of-interleukin-18-and-asthma
#19
REVIEW
Ming-Hui Xu, Feng-Lai Yuan, Shu-Jing Wang, Hui-Ying Xu, Cheng-Wan Li, Xiao Tong
Cytokine-mediated immunity plays a dominant role in the pathogenesis of various immune diseases, including asthma. The recent identification of the family interleukin (IL)-1-related cytokine IL-18 now contributes to our understanding of the fine-tuning of cellular immunity. IL-18 can act as a cofactor for Th2 cell development and IgE production and also plays an important role in the differentiation of Th1 cells. Recent work identified an IL-18 association with the pathogenesis of asthma, wherein increased IL-18 expression was found in the serum of patients...
December 2, 2016: Inflammation
https://www.readbyqxmd.com/read/27913740/a-%C3%AE-ketoacyl-coa-synthase-is-involved-in-rice-leaf-cuticular-wax-synthesis-and-requires-a-cer2-like-protein-as-a-cofactor
#20
Xiaochen Wang, Yuanyuan Guan, Du Zhang, Xiangbai Dong, Lihong Tian, Le Qing Qu
Cuticular waxes are complex mixtures of very-long-chain fatty acids (VLCFAs) and their derivatives, forming a natural barrier on aerial surfaces of terrestrial plants against biotic and abiotic stresses. In VLCFA biosynthesis, β-ketoacyl-CoA synthase (KCS) is the key enzyme, catalyzing the first reaction in fatty acid elongation and determining substrate specificity. We isolated a rice (Oryza sativa L.) wax crystal-sparse leaf 4 (WSL4) gene using a map-based cloning strategy. WSL4 is predicted to encode a KCS, a homolog of Arabidopsis CER6...
December 2, 2016: Plant Physiology
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