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Biomolecules

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https://www.readbyqxmd.com/read/28406433/diversity-of-amyloid-motifs-in-nlr-signaling-in-fungi
#1
REVIEW
Antoine Loquet, Sven J Saupe
Amyloid folds not only represent the underlying cause of a large class of human diseases but also display a variety of functional roles both in prokaryote and eukaryote organisms. Among these roles is a recently-described activity in signal transduction cascades functioning in host defense and programmed cell death and involving Nod-like receptors (NLRs). In different fungal species, prion amyloid folds convey activation signals from a receptor protein to an effector domain by an amyloid templating and propagation mechanism...
April 13, 2017: Biomolecules
https://www.readbyqxmd.com/read/28398221/amyloid-fibrils-from-hemoglobin
#2
Nadishka Jayawardena, Manmeet Kaur, Smitha Nair, Jenny Malmstrom, David Goldstone, Leonardo Negron, Juliet A Gerrard, Laura J Domigan
Amyloid fibrils are a class of insoluble protein nanofibers that are formed via the self-assembly of a wide range of peptides and proteins. They are increasingly exploited for a broad range of applications in bionanotechnology, such as biosensing and drug delivery, as nanowires, hydrogels, and thin films. Amyloid fibrils have been prepared from many proteins, but there has been no definitive characterization of amyloid fibrils from hemoglobin to date. Here, nanofiber formation was carried out under denaturing conditions using solutions of apo-hemoglobin extracted from bovine waste blood...
April 11, 2017: Biomolecules
https://www.readbyqxmd.com/read/28383498/quef-like-a-non-homologous-archaeosine-synthase-from-the-crenarchaeota
#3
Adriana Bon Ramos, Lide Bao, Ben Turner, Valérie de Crécy-Lagard, Dirk Iwata-Reuyl
Archaeosine (G⁺) is a structurally complex modified nucleoside ubiquitous to the Archaea, where it is found in the D-loop of virtually all archaeal transfer RNA (tRNA). Its unique structure, which includes a formamidine group that carries a formal positive charge, and location in the tRNA, led to the proposal that it serves a key role in stabilizing tRNA structure. Although G⁺ is limited to the Archaea, it is structurally related to the bacterial modified nucleoside queuosine, and the two share homologous enzymes for the early steps of their biosynthesis...
April 6, 2017: Biomolecules
https://www.readbyqxmd.com/read/28375166/trna-modifications-impact-on-structure-and-thermal-adaptation
#4
REVIEW
Christian Lorenz, Christina E Lünse, Mario Mörl
Transfer RNAs (tRNAs) are central players in translation, functioning as adapter molecules between the informational level of nucleic acids and the functional level of proteins. They show a highly conserved secondary and tertiary structure and the highest density of post-transcriptional modifications among all RNAs. These modifications concentrate in two hotspots-the anticodon loop and the tRNA core region, where the D- and T-loop interact with each other, stabilizing the overall structure of the molecule. These modifications can cause large rearrangements as well as local fine-tuning in the 3D structure of a tRNA...
April 4, 2017: Biomolecules
https://www.readbyqxmd.com/read/28346397/the-process-and-regulatory-components-of-inflammation-in-brain-oncogenesis
#5
REVIEW
A G M Mostofa, Surendra R Punganuru, Hanumantha Rao Madala, Mohammad Al-Obaide, Kalkunte S Srivenugopal
Central nervous system tumors comprising the primary cancers and brain metastases remain the most lethal neoplasms and challenging to treat. Substantial evidence points to a paramount role for inflammation in the pathology leading to gliomagenesis, malignant progression and tumor aggressiveness in the central nervous system (CNS) microenvironment. This review summarizes the salient contributions of oxidative stress, interleukins, tumor necrosis factor-α (TNF-α), cyclooxygenases, and transcription factors such as signal transducer and activator of transcription 3 (STAT3) and nuclear factor kappa-light-chain-enhancer of activated B-cells (NF-κB) and the associated cross-talks to the inflammatory signaling in CNS cancers...
March 27, 2017: Biomolecules
https://www.readbyqxmd.com/read/28327539/diverse-mechanisms-of-sulfur-decoration-in-bacterial-trna-and-their-cellular-functions
#6
REVIEW
Chenkang Zheng, Katherine A Black, Patricia C Dos Santos
Sulfur-containing transfer ribonucleic acids (tRNAs) are ubiquitous biomolecules found in all organisms that possess a variety of functions. For decades, their roles in processes such as translation, structural stability, and cellular protection have been elucidated and appreciated. These thionucleosides are found in all types of bacteria; however, their biosynthetic pathways are distinct among different groups of bacteria. Considering that many of the thio-tRNA biosynthetic enzymes are absent in Gram-positive bacteria, recent studies have addressed how sulfur trafficking is regulated in these prokaryotic species...
March 22, 2017: Biomolecules
https://www.readbyqxmd.com/read/28335556/trm5-and-trmd-two-enzymes-from-distinct-origins-catalyze-the-identical-trna-modification-m%C3%A2-g37
#7
REVIEW
Sakurako Goto-Ito, Takuhiro Ito, Shigeyuki Yokoyama
The N¹-atom of guanosine at position 37 in transfer RNA (tRNA) is methylated by tRNA methyltransferase 5 (Trm5) in eukaryotes and archaea, and by tRNA methyltransferase D (TrmD) in bacteria. The resultant modified nucleotide m¹G37 positively regulates the aminoacylation of the tRNA, and simultaneously functions to prevent the +1 frameshift on the ribosome. Interestingly, Trm5 and TrmD have completely distinct origins, and therefore bear different tertiary folds. In this review, we describe the different strategies utilized by Trm5 and TrmD to recognize their substrate tRNAs, mainly based on their crystal structures complexed with substrate tRNAs...
March 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28335468/differential-degradation-and-detoxification-of-an-aromatic-pollutant-by-two-different-peroxidases
#8
Aysha Hamad Alneyadi, Iltaf Shah, Synan F AbuQamar, Syed Salman Ashraf
Enzymatic degradation of organic pollutants is a new and promising remediation approach. Peroxidases are one of the most commonly used classes of enzymes to degrade organic pollutants. However, it is generally assumed that all peroxidases behave similarly and produce similar degradation products. In this study, we conducted detailed studies of the degradation of a model aromatic pollutant, Sulforhodamine B dye (SRB dye), using two peroxidases-soybean peroxidase (SBP) and chloroperoxidase (CPO). Our results show that these two related enzymes had different optimum conditions (pH, temperature, H₂O₂ concentration, etc...
March 18, 2017: Biomolecules
https://www.readbyqxmd.com/read/28300792/chemical-and-conformational-diversity-of-modified-nucleosides-affects-trna-structure-and-function
#9
REVIEW
Ville Y P Väre, Emily R Eruysal, Amithi Narendran, Kathryn L Sarachan, Paul F Agris
RNAs are central to all gene expression through the control of protein synthesis. Four major nucleosides, adenosine, guanosine, cytidine and uridine, compose RNAs and provide sequence variation, but are limited in contributions to structural variation as well as distinct chemical properties. The ability of RNAs to play multiple roles in cellular metabolism is made possible by extensive variation in length, conformational dynamics, and the over 100 post-transcriptional modifications. There are several reviews of the biochemical pathways leading to RNA modification, but the physicochemical nature of modified nucleosides and how they facilitate RNA function is of keen interest, particularly with regard to the contributions of modified nucleosides...
March 16, 2017: Biomolecules
https://www.readbyqxmd.com/read/28300774/protection-of-the-queuosine-biosynthesis-enzyme-quef-from-irreversible-oxidation-by-a-conserved-intramolecular-disulfide
#10
Adeba Mohammad, Adriana Bon Ramos, Bobby W K Lee, Spencer W Cohen, Maryam K Kiani, Dirk Iwata-Reuyl, Boguslaw Stec, Manal A Swairjo
QueF enzymes catalyze the nicotinamide adenine dinucleotide phosphate (NADPH)-dependent reduction of the nitrile group of 7-cyano-7-deazaguanine (preQ₀) to 7-aminomethyl-7-deazaguanine (preQ₁) in the biosynthetic pathway to the tRNA modified nucleoside queuosine. The QueF-catalyzed reaction includes formation of a covalent thioimide intermediate with a conserved active site cysteine that is prone to oxidation in vivo. Here, we report the crystal structure of a mutant of Bacillus subtilis QueF, which reveals an unanticipated intramolecular disulfide formed between the catalytic Cys55 and a conserved Cys99 located near the active site...
March 16, 2017: Biomolecules
https://www.readbyqxmd.com/read/28294979/evaluation-of-stability-of-amylose-inclusion-complexes-depending-on-guest-polymers-and-their-application-to-supramolecular-polymeric-materials
#11
Tomonari Tanaka, Atsushi Tsutsui, Kazuya Tanaka, Kazuya Yamamoto, Jun-Ichi Kadokawa
This paper describes the evaluation of the stability of amylose-polymer inclusion complexes under solution state in dimethyl sulfoxide (DMSO) depending on guest polymers. The three complexes were prepared by the vine-twining polymerization method using polytetrahydrofuran (PTHF), poly(ε-caprolactone) (PCL), and poly(l-lactide) (PLLA) as guest polymers. The stability investigation was conducted at desired temperatures (25, 30, 40, 60 °C) in DMSO solutions of the complexes. Consequently, the amylose-PTHF inclusion complex was dissociated at 25 °C, while the other complexes were stable under the same conditions...
March 15, 2017: Biomolecules
https://www.readbyqxmd.com/read/28287455/biosynthesis-of-sulfur-containing-trna-modifications-a-comparison-of-bacterial-archaeal-and-eukaryotic-pathways
#12
REVIEW
Mirela Čavužić, Yuchen Liu
Post-translational tRNA modifications have very broad diversity and are present in all domains of life. They are important for proper tRNA functions. In this review, we emphasize the recent advances on the biosynthesis of sulfur-containing tRNA nucleosides including the 2-thiouridine (s²U) derivatives, 4-thiouridine (s⁴U), 2-thiocytidine (s²C), and 2-methylthioadenosine (ms²A). Their biosynthetic pathways have two major types depending on the requirement of iron-sulfur (Fe-S) clusters. In all cases, the first step in bacteria and eukaryotes is to activate the sulfur atom of free l-cysteine by cysteine desulfurases, generating a persulfide (R-S-SH) group...
March 11, 2017: Biomolecules
https://www.readbyqxmd.com/read/28282871/factors%C3%A2-that%C3%A2-shape%C3%A2-eukaryotic%C3%A2-trnaomes-%C3%A2-processing-%C3%A2-modification%C3%A2-and%C3%A2-anticodon-codon%C3%A2-use
#13
REVIEW
Richard J Maraia, Aneeshkumar G Arimbasseri
Transfer RNAs (tRNAs) contain sequence diversity beyond their anticodons and the large variety of nucleotide modifications found in all kingdoms of life. Some modifications stabilize structure and fit in the ribosome whereas those to the anticodon loop modulate messenger RNA (mRNA) decoding activity more directly. The identities of tRNAs with some universal anticodon loop modifications vary among distant and parallel species, likely to accommodate fine tuning for their translation systems. This plasticity in positions 34 (wobble) and 37 is reflected in codon use bias...
March 8, 2017: Biomolecules
https://www.readbyqxmd.com/read/28272317/modulation%C3%A2-of%C3%A2-the%C3%A2-proteostasis%C3%A2-machinery%C3%A2-to%C3%A2-overcome%C3%A2-stress%C3%A2-caused%C3%A2-by%C3%A2-diminished%C3%A2-levels%C3%A2-of%C3%A2-t6a-modified%C3%A2-trnas%C3%A2-in%C3%A2-drosophila
#14
Diego Rojas-Benítez, Cristián Eggers, Alvaro Glavic
Transfer RNAs (tRNAs) harbor a subset of post-transcriptional modifications required for structural stability or decoding function. N6-threonylcarbamoyladenosine (t6A) is a universally conserved modification found at position 37 in tRNA that pair A-starting codons (ANN) and is required for proper translation initiation and to prevent frame shift during elongation. In its absence, the synthesis of aberrant proteins is likely, evidenced by the formation of protein aggregates. In this work, our aim was to study the relationship between t6A-modified tRNAs and protein synthesis homeostasis machinery using Drosophila melanogaster...
March 6, 2017: Biomolecules
https://www.readbyqxmd.com/read/28257121/dealing%C3%A2-with%C3%A2-an%C3%A2-unconventional%C3%A2-genetic%C3%A2-code%C3%A2-in%C3%A2-mitochondria-%C3%A2-the%C3%A2-biogenesis%C3%A2-and%C3%A2-pathogenic%C3%A2-defects%C3%A2-of%C3%A2-the%C3%A2-5-formylcytosine%C3%A2-modification%C3%A2-in%C3%A2-mitochondrial%C3%A2-trna-met
#15
REVIEW
Lindsey Van Haute, Christopher A Powell, Michal Minczuk
Human mitochondria contain their own genome, which uses an unconventional genetic code. In addition to the standard AUG methionine codon, the single mitochondrial tRNA Methionine (mt-tRNAMet) also recognises AUA during translation initiation and elongation. Post-transcriptional modifications of tRNAs are important for structure, stability, correct folding and aminoacylation as well as decoding. The unique 5-formylcytosine (f5C) modification of position 34 in mt-tRNAMet has been long postulated to be crucial for decoding of unconventional methionine codons and efficient mitochondrial translation...
March 2, 2017: Biomolecules
https://www.readbyqxmd.com/read/28257077/functional-regulation-of-the-plasma-protein-histidine-rich-glycoprotein-by-zn-2-in-settings-of-tissue-injury
#16
REVIEW
Kristin M Priebatsch, Marc Kvansakul, Ivan K H Poon, Mark D Hulett
Divalent metal ions are essential nutrients for all living organisms and are commonly protein-bound where they perform important roles in protein structure and function. This regulatory control from metals is observed in the relatively abundant plasma protein histidine-rich glycoprotein (HRG), which displays preferential binding to the second most abundant transition element in human systems, Zinc (Zn(2+)). HRG has been proposed to interact with a large number of protein ligands and has been implicated in the regulation of various physiological and pathological processes including the formation of immune complexes, apoptotic/necrotic and pathogen clearance, cell adhesion, antimicrobial activity, angiogenesis, coagulation and fibrinolysis...
March 2, 2017: Biomolecules
https://www.readbyqxmd.com/read/28264529/transfer%C3%A2-rna%C3%A2-methyltransferases%C3%A2-with%C3%A2-a%C3%A2-spou-trmd%C3%A2-spout-%C3%A2-fold%C3%A2-and%C3%A2-their%C3%A2-modified%C3%A2-nucleosides%C3%A2-in%C3%A2-trna
#17
REVIEW
Hiroyuki Hori
The existence of SpoU-TrmD (SPOUT) RNA methyltransferase superfamily was first predicted by bioinformatics. SpoU is the previous name of TrmH, which catalyzes the 2'-Omethylation of ribose of G18 in tRNA; TrmD catalyzes the formation of N1-methylguanosine at position 37 in tRNA. Although SpoU (TrmH) and TrmD were originally considered to be unrelated, the bioinformatics study suggested that they might share a common evolution origin and form a single superfamily. The common feature of SPOUT RNA methyltransferases is the formation of a deep trefoil knot in the catalytic domain...
February 28, 2017: Biomolecules
https://www.readbyqxmd.com/read/28241457/mapping%C3%A2-post-transcriptional%C3%A2-modifications%C3%A2-onto%C3%A2-transfer%C3%A2-ribonucleic%C3%A2-acid%C3%A2-sequences%C3%A2-by%C3%A2-liquid%C3%A2-chromatography%C3%A2-tandem%C3%A2-mass%C3%A2-spectrometry
#18
REVIEW
Robert L Ross, Xiaoyu Cao, Patrick A Limbach
Liquid chromatography, coupled with tandem mass spectrometry, has become one of the most popular methods for the analysis of post-transcriptionally modified transfer ribonucleic acids (tRNAs). Given that the information collected using this platform is entirely determined by the mass of the analyte, it has proven to be the gold standard for accurately assigning nucleobases to the sequence. For the past few decades many labs have worked to improve the analysis, contiguous to instrumentation manufacturers developing faster and more sensitive instruments...
February 22, 2017: Biomolecules
https://www.readbyqxmd.com/read/28230817/common%C3%A2-chemical%C3%A2-inductors%C3%A2-of%C3%A2-replication%C3%A2-stress-%C3%A2-focus%C3%A2-on%C3%A2-cell-based%C3%A2-studies
#19
REVIEW
Eva Vesela, Katarina Chroma, Zsofia Turi, Martin Mistrik
DNA replication is a highly demanding process regarding the energy and material supply and must be precisely regulated, involving multiple cellular feedbacks. The slowing down or stalling of DNA synthesis and/or replication forks is referred to as replication stress (RS). Owing to the complexity and requirements of replication, a plethora of factors may interfere and challenge the genome stability, cell survival or affect the whole organism. This review outlines chemical compounds that are known inducers of RS and commonly used in laboratory research...
February 21, 2017: Biomolecules
https://www.readbyqxmd.com/read/28230814/m1a%C3%A2-post-transcriptional%C3%A2-modification%C3%A2-in%C3%A2-trnas
#20
REVIEW
Stephanie Oerum, Clément Dégut, Pierre Barraud, Carine Tisné
To date, about 90 post-transcriptional modifications have been reported in tRNA expanding their chemical and functional diversity. Methylation is the most frequent post-transcriptional tRNA modification that can occur on almost all nitrogen sites of the nucleobases, on the C5 atom of pyrimidines, on the C2 and C8 atoms of adenosine and, additionally, on the oxygen of the ribose 2'-OH. The methylation on the N1 atom of adenosine to form 1-methyladenosine (m1A) has been identified at nucleotide position 9, 14, 22, 57, and 58 in different tRNAs...
February 21, 2017: Biomolecules
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