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https://www.readbyqxmd.com/read/29036638/the-basic-tilted-helix-bundle-domain-of-the-prolyl-isomerase-fkbp25-is-a-novel-double-stranded-rna-binding-module
#1
David Dilworth, Santosh K Upadhyay, Pierre Bonnafous, Amiirah Bibi Edoo, Sarah Bourbigot, Francy Pesek-Jardim, Geoff Gudavicius, Jason J Serpa, Evgeniy V Petrotchenko, Christoph H Borchers, Christopher J Nelson, Cameron D Mackereth
Prolyl isomerases are defined by a catalytic domain that facilitates the cis-trans interconversion of proline residues. In most cases, additional domains in these enzymes add important biological function, including recruitment to a set of protein substrates. Here, we report that the N-terminal basic tilted helix bundle (BTHB) domain of the human prolyl isomerase FKBP25 confers specific binding to double-stranded RNA (dsRNA). This binding is selective over DNA as well as single-stranded oligonucleotides. We find that FKBP25 RNA-association is required for its nucleolar localization and for the vast majority of its protein interactions, including those with 60S pre-ribosome and early ribosome biogenesis factors...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036596/delphiforce-web-server-electrostatic-forces-and-energy-calculations-and-visualization
#2
Lin Li, Zhe Jia, Yunhui Peng, Arghya Chakravorty, Lexuan Sun, Emil Alexov
Summary: Electrostatic force is an essential component of the total force acting between atoms and macromolecules. Therefore, accurate calculations of electrostatic forces are crucial for revealing the mechanisms of many biological processes. We developed a DelPhiForce web server to calculate and visualize the electrostatic forces at molecular level. DelPhiForce web server enables modeling of electrostatic forces on individual atoms, residues, domains and molecules, and generates an output that can be visualized by VMD software...
August 3, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036376/the-mechanism-and-high-free-energy-transition-state-of-lac-repressor-lac-operator-interaction
#3
Rituparna Sengupta, Michael W Capp, Irina A Shkel, M Thomas Record
Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)-lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29035510/crispri-and-crispra-screens-in-mammalian-cells-for-precision-biology-and-medicine
#4
Martin Kampmann
Next-generation DNA sequencing technologies have led to a massive accumulation of genomic and transcriptomic data from patients and healthy individuals. The major challenge ahead is to understand the functional significance of the elements of the human genome and transcriptome, and implications for diagnosis and treatment. Genetic screens in mammalian cells are a powerful approach to systematically elucidate gene function in health and disease states. In particular, recently developed CRISPR/Cas9-based screening approaches have enormous potential to uncover mechanisms and therapeutic strategies for human diseases...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29035199/structure-based-nuclear-import-mechanism-of-histones-h3-and-h4-mediated-by-kap123
#5
Sojin An, Jungmin Yoon, Hanseong Kim, Ji-Joon Song, Uhn-Soo Cho
Kap123, a major karyopherin protein of budding yeast, recognizes the nuclear localization signals (NLSs) of cytoplasmic histones H3 and H4 and translocates them into the nucleus during DNA replication. Mechanistic questions include H3- and H4-NLS redundancy toward Kap123 and the role of the conserved diacetylation of cytoplasmic H4 (K5ac and K12ac) in Kap123-mediated histone nuclear translocation. Here, we report crystal structures of full-length Kluyveromyces lactis Kap123 alone and in complex with H3- and H4-NLSs...
October 16, 2017: ELife
https://www.readbyqxmd.com/read/29034217/evolution-of-salmonella-host-cell-interactions-through-a-dynamic-bacterial-genome
#6
REVIEW
Bushra Ilyas, Caressa N Tsai, Brian K Coombes
Salmonella Typhimurium has a broad arsenal of genes that are tightly regulated and coordinated to facilitate adaptation to the various host environments it colonizes. The genome of Salmonella Typhimurium has undergone multiple gene acquisition events and has accrued changes in non-coding DNA that have undergone selection by regulatory evolution. Together, at least 17 horizontally acquired pathogenicity islands (SPIs), prophage-associated genes, and changes in core genome regulation contribute to the virulence program of Salmonella...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29032547/genome-wide-mutagenesis-in-borrelia-burgdorferi
#7
Tao Lin, Lihui Gao
Signature-tagged mutagenesis (STM) is a functional genomics approach to identify bacterial virulence determinants and virulence factors by simultaneously screening multiple mutants in a single host animal, and has been utilized extensively for the study of bacterial pathogenesis, host-pathogen interactions, and spirochete and tick biology. The signature-tagged transposon mutagenesis has been developed to investigate virulence determinants and pathogenesis of Borrelia burgdorferi. Mutants in genes important in virulence are identified by negative selection in which the mutants fail to colonize or disseminate in the animal host and tick vector...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29032544/analysis-of-dna-and-rna-binding-properties-of-borrelia-burgdorferi-regulatory-proteins
#8
J Seshu, Trever C Smith, Ying-Han Lin, S L Rajasekhar Karna, Christine L Miller, Tricia Van Laar
Bioinformatic approaches and a large volume of prokaryotic genome sequences have enabled rapid identification of regulatory proteins with features to bind DNA or RNA in a given prokaryote. However, biological relevance of these regulatory proteins requires methods to rapidly purify and determine their binding properties within the physiological context or life style of the organism. Here, we describe the experimental approaches to determine the nucleic acid binding properties of regulatory proteins of Borrelia burgdorferi using Borrelia host-adaptation Re...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29032152/structure-function-characterization-of-the-ell-associated-factor-eaf-from-schizosaccharomyces-pombe
#9
Preeti Dabas, Kumari Sweta, Mary Ekka, Nimisha Sharma
EAF (ELL Associated Factor) proteins interact with the transcription elongation factor, ELL (Eleven nineteen Lysine rich Leukemia) and enhance its ability to stimulate RNA polymerase II-mediated transcriptional elongation in vitro. Schizosaccharomyces pombe contains a single homolog of EAF (SpEAF), which is not essential for survival of S. pombe in contrast to its essential higher eukaryotic homologs. The physiological role of SpEAF is not well understood. In this study, we show that S. pombe EAF is important in regulating growth of S...
October 12, 2017: Gene
https://www.readbyqxmd.com/read/29031818/camptothecin-and-its-analog-sn-38-the-active-metabolite-of-irinotecan-inhibit-binding-of-the-transcriptional-regulator-and-oncoprotein-fubp1-to-its-dna-target-sequence-fuse
#10
Sabrina Khageh Hosseini, Stefanie Kolterer, Marlene Steiner, Victoria von Manstein, Katharina Gerlach, Jörg Trojan, Oliver Waidmann, Stefan Zeuzem, Jörg O Schulze, Steffen Hahn, Dieter Steinhilber, Volker Gatterdam, Robert Tampé, Ricardo M Biondi, Ewgenij Proschak, Martin Zörnig
The transcriptional regulator FUSE Binding Protein 1 (FUBP1) is overexpressed in more than 80% of all human hepatocellular carcinomas (HCCs) and other solid tumor entities including prostate and colorectal carcinoma. FUBP1 expression is required for HCC tumor cell expansion, and it functions as an important pro-proliferative and anti-apoptotic oncoprotein that binds to the single-stranded DNA sequence FUSE to regulate the transcription of a variety of target genes. In this study, we screened an FDA-approved drug library and discovered that the Topoisomerase I (TOP1) inhibitor camptothecin (CPT) and its derivative 7-ethyl-10-hydroxycamptothecin (SN-38), the active irinotecan metabolite that is used in the clinics in combination with other chemotherapeutics to treat carcinoma, inhibit FUBP1 activity...
October 12, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/29031576/acute-and-long-term-effects-of-trophic-exposure-to-silver-nanospheres-in-the-central-nervous-system-of-a-neotropical-fish-hoplias-intermedius
#11
T Klingelfus, J R Lirola, L F Oya Silva, G R Disner, M Vicentini, M J B Nadaline, J C Z Robles, L M Trein, C L Voigt, H C Silva de Assis, M Mela, D M Leme, M M Cestari
Nanotechnologies are at the center of societal interest, due to their broad spectrum of application in different industrial products. The current concern about nanomaterials (NMs) is the potential risks they carry for human health and the environment. Considering that NMs can reach bodies of water, there is a need for studying the toxic effects of NMs on aquatic organisms. Among the NMs' toxic effects on fish, the interactions between NMs and the nervous system are yet to be understood. For this reason, our goal was to assess the neurotoxicity of polyvinylpyrrolidone coated silver nanospheres [AgNS (PVP coated)] and compare their effects in relation to silver ions (Ag(+)) in carnivorous Hoplias intermedius fish after acute and subchronic trophic exposure through the analysis of morphological (retina), biochemical (brain) and genetic biomarkers (brain and blood)...
October 11, 2017: Neurotoxicology
https://www.readbyqxmd.com/read/29031033/an-arabidopsis-divergent-pumilio-protein-apum24-is-essential-for-embryogenesis-and-required-for-faithful-pre-rrna-processing
#12
Thiruvenkadam Shanmugam, Nazia Abbasi, Hyung-Sae Kim, Ho Bang Kim, Nam-Il Park, Guen Tae Park, Sung Aeong Oh, Soon Ki Park, Douglas G Muench, Yeonhee Choi, Youn-Il Park, Sang-Bong Choi
Pumilio RNA-binding proteins are largely involved in mRNA degradation and translation repression. However, a few evolutionarily divergent Pumilios are also responsible for proper pre-rRNA processing in human and yeast. Here, we describe an essential Arabidopsis nucleolar Pumilio, APUM24, that is expressed in tissues undergoing rapid proliferation and cell division. A T-DNA insertion for APUM24 did not affect the male and female gametogenesis, but instead resulted in a negative female gametophytic effect on zygotic cell division immediately after fertilization...
October 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29030827/genome-wide-identification-of-transcription-factor-binding-sites-in-quiescent-adult-neural-stem-cells
#13
Shradha Mukherjee, Jenny Hsieh
Transcription factors bind to specific DNA sequences and control the transcription rate of nearby genes in the genome. This activation or repression of gene expression is further potentiated by epigenetic modifications of histones with active and silent marks, respectively. Resident adult stem cells in the hematopoietic system, skin, and brain exist in a non-proliferative quiescent resting state. When quiescent stem cells become activated and transition to dividing progenitors and distinct cell types, they can replenish and repair tissue...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29029743/advances-of-vibrational-circular-dichroism-vcd-in-bioanalytical-chemistry-a-review
#14
REVIEW
Dmitry Kurouski
Vibrational Circular Dichroism (VCD) is a unique and relatively new spectroscopic technique that is capable of determining an absolute configuration of chiral molecules. VCD can be also used to determine structure of large macromolecules. This review highlights the most recent advances of VCD in bioanalytical chemistry. It shows that VCD is capable of unraveling supramolecular organization of peptides, proteins, saccharides, glycerophospholipids, polypeptide microcrystals, as well as amyloid fibrils and DNA...
October 16, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29029697/the-identification-of-transcriptional-regulation-related-gene-of-laccase-poxc-through-yeast-one-hybrid-screening-from-pleurotus-ostreatus
#15
Yuancheng Qi, Chao Liu, Xiankai Sun, Liyou Qiu, Jinwen Shen
Pleurotus ostreatus laccase gene poxc is transcriptionally induced by copper, and several putative MREs have been found and confirmed in its promoter region. However, the related transcription factors mediating copper response via MREs have not been reported. To isolate MRE binding proteins, we carried out yeast one-hybrid screens. Reporter genes containing two trimers of the cMRE2 and cMRE3 element were prepared and introduced into a yeast strain. The yeast was transformed with library cDNA that represents RNA isolated from CuSO4-treated fungi of P...
November 2017: Fungal Biology
https://www.readbyqxmd.com/read/29028954/1-benzyl-indole-3-carbinol-is-a-highly-potent-new-small-molecule-inhibitor-of-wnt-%C3%AE-catenin-signaling-in-melanoma-cells-that-coordinately-inhibits-cell-proliferation-and-disrupts-expression-of-microphthalmia-associated-transcription-factor-isoform-m
#16
Aishwarya Kundu, Michelle G Khouri, Sheila Aryana, Gary L Firestone
1-Benzyl-indole-3-carbinol (1-benzyl-I3C), a synthetic analogue of the crucifer derived natural phytochemical I3C, displayed significantly wider sensitivity and anti-proliferative potency in melanoma cells than the natural compound. Unlike I3C, which targets mainly oncogenic BRAF-expressing cells, 1-benzyl I3C effectively inhibited proliferation of melanoma cells with a more extensive range of mutational profiles, including those expressing wild type BRAF. In both cultured melanoma cell lines and in vivo in melanoma cell-derived tumor xenografts, 1-benzyl-I3C disrupted canonical Wnt/β-catenin signaling that resulted in the down regulation of β-catenin protein levels with a concomitant increase in levels of the β-catenin destruction complex components GSK3β and Axin...
September 23, 2017: Carcinogenesis
https://www.readbyqxmd.com/read/29028926/structure-based-prediction-of-protein-peptide-binding-regions-using-random-forest
#17
Ghazaleh Taherzadeh, Yaoqi Zhou, Alan Wee-Chung Liew, Yuedong Yang
Motivation: Protein-peptide interactions are one of the most important biological interactions and play crucial role in many diseases including cancer. Therefore, knowledge of these interactions provides invaluable insights into all cellular processes, functional mechanisms, and drug discovery. Protein-peptide interactions can be analyzed by studying the structures of protein-peptide complexes. However, only a small portion has known complex structures and experimental determination of protein-peptide interaction is costly and inefficient...
September 26, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028882/enzymatic-methods-for-genome-wide-profiling-of-protein-binding-sites
#18
Robert A Policastro, Gabriel E Zentner
Genome-wide mapping of protein-DNA interactions is a staple approach in many areas of modern molecular biology. Genome-wide profiles of protein-binding sites are most commonly generated by chromatin immunoprecipitation and high-throughput sequencing (ChIP-seq). Although ChIP-seq has played a central role in studying genome-wide protein binding, recent work has highlighted systematic biases in the technique that warrant technical and interpretive caution and underscore the need for orthogonal techniques to both confirm the results of ChIP-seq studies and uncover new insights not accessible to ChIP...
October 6, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29027446/-interactions-of-aminoglycosides-with-rnas-and-proteins-via-carbohydrate-microarray
#19
Xueyu Wang, Xiaoli Wang, Beilei Zhang, Jing Hu, Jian Yin
Aminoglycosides are broad-spectrum antibacterials to treat bacterial infections, especially gram-negative bacteria infections. However, aminoglycosides are losing efficacy because of the increase in antibiotic resistance and their inherent toxicity, attracting more interests in developing new aminoglycosides. Several clinically used aminoglycosides are mainly exerted by inhibition of protein synthesis through binding to bacterial rRNA. The bacterial ribosome RNA is the most currently exploited RNA drug target...
October 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29027175/multiplexed-chip-seq-using-direct-nucleosome-barcoding-a-tool-for-high-throughput-chromatin-analysis
#20
Christophe D Chabbert, Sophie H Adjalley, Lars M Steinmetz, Vicent Pelechano
Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) or microarray hybridization (ChIP-on-chip) are standard methods for the study of transcription factor binding sites and histone chemical modifications. However, these approaches only allow profiling of a single factor or protein modification at a time.In this chapter, we present Bar-ChIP, a higher throughput version of ChIP-Seq that relies on the direct ligation of molecular barcodes to chromatin fragments. Bar-ChIP enables the concurrent profiling of multiple DNA-protein interactions and is therefore amenable to experimental scale-up, without the need for any robotic instrumentation...
2018: Methods in Molecular Biology
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