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Protein footprinting

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https://www.readbyqxmd.com/read/29672625/mechanistic-studies-of-depr-in-regulating-fk228-biosynthesis-in-chromobacterium-violaceum-no-968
#1
Yongjian Qiao, Tiantian Tong, Jiao Xue, Wenjing Lin, Zixin Deng, Yi-Qiang Cheng, Dongqing Zhu
DepR, a LysR-type transcriptional regulator encoded by the last gene of the putative min operon (orf21-20-19-depR) located at the downstream region of the anticancer agent FK228 biosynthetic gene cluster in Chromobacterium violaceum No. 968, positively regulates the biosynthesis of FK228. In this work, the mechanism underlining this positive regulation was probed by multiple approaches. Electrophoretic mobility shift assay (EMSA) and DNase I footprinting assay (DIFA) identified a conserved 35-nt DNA segment in the orf21-orf22 intergenic region where the purified recombinant DepR binds to...
2018: PloS One
https://www.readbyqxmd.com/read/29663323/single-pass-diafiltration-integrated-into-a-fully-continuous-mab-purification-process
#2
Joanna Rucker-Pezzini, Lindsay Arnold, Kevin Hill-Byrne, Tom Sharp, Maksim Avazhanskiy, Chris Forespring
The concept of continuous manufacturing has gained significant interest from the biopharmaceutical industry over the past several years. Benefits include increased manufacturing productivity, improved quality control, reduction in plant footprint, and more flexible management of facility capacity. There are several technologies currently available that enable continuous processing for chromatography and ultrafiltration. However, a single pass diafiltration design that meets the required small molecule clearance and has been integrated into a fully continuous monoclonal antibody purification process has not been previously published...
April 16, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29644623/single-pass-diafiltration-integrated-into-a-fully-continuous-mab-purification-process
#3
Joanna Rucker-Pezzini, Lindsay Arnold, Kevin Hill-Byrne, Tom Sharp, Maksim Avazhanskiy, Chris Forespring
The concept of continuous manufacturing has gained significant interest from the biopharmaceutical industry over the past several years. Benefits include increased manufacturing productivity, improved quality control, reduction in plant footprint, and more flexible management of facility capacity. There are several technologies currently available that enable continuous processing for chromatography and ultrafiltration. However, a single pass diafiltration design that meets the required small molecule clearance and has been integrated into a fully continuous monoclonal antibody purification process has not been previously published...
April 12, 2018: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/29643507/an-evolutionarily-conserved-ribosome-rescue-pathway-maintains-epidermal-homeostasis
#4
Kifayathullah Liakath-Ali, Eric W Mills, Inês Sequeira, Beate M Lichtenberger, Angela Oliveira Pisco, Kalle H Sipilä, Ajay Mishra, Harunori Yoshikawa, Colin Chih-Chien Wu, Tony Ly, Angus I Lamond, Ibrahim M Adham, Rachel Green, Fiona M Watt
Ribosome-associated mRNA quality control mechanisms ensure the fidelity of protein translation1,2 . Although these mechanisms have been extensively studied in yeast, little is known about their role in mammalian tissues, despite emerging evidence that stem cell fate is controlled by translational mechanisms3,4 . One evolutionarily conserved component of the quality control machinery, Dom34 (in higher eukaryotes known as Pelota (Pelo)), rescues stalled ribosomes 5 . Here we show that Pelo is required for mammalian epidermal homeostasis...
April 11, 2018: Nature
https://www.readbyqxmd.com/read/29624880/translation-initiation-by-cap-dependent-ribosome-recruitment-recent-insights-and-open-questions
#5
REVIEW
Nikolay E Shirokikh, Thomas Preiss
Gene expression universally relies on protein synthesis, where ribosomes recognize and decode the messenger RNA template by cycling through translation initiation, elongation, and termination phases. All aspects of translation have been studied for decades using the tools of biochemistry and molecular biology available at the time. Here, we focus on the mechanism of translation initiation in eukaryotes, which is remarkably more complex than prokaryotic initiation and is the target of multiple types of regulatory intervention...
April 6, 2018: Wiley Interdisciplinary Reviews. RNA
https://www.readbyqxmd.com/read/29624790/gene-therapy-for-glut1-deficient-mouse-using-an-adeno-associated-virus-vector-with-the-human-intrinsic-glut1-promoter
#6
Sachie Nakamura, Shin-Ichi Muramatsu, Naomi Takino, Mika Ito, Eriko F Jimbo, Kuniko Shimazaki, Tatsushi Onaka, Sumio Ohtsuki, Tetsuya Terasaki, Takanori Yamagata, Hitoshi Osaka
BACKGROUND: We generated an adeno-associated virus (AAV) vector in which the human SLC2A1 gene, encoding glucose transporter type 1 (GLUT1), was expressed under the human endogenous GLUT1 promoter (AAV-GLUT1). We examined whether AAV-GLUT1 administration could lead to functional improvement in GLUT1-deficient mice. METHODS: We extrapolated human endogenous GLUT1 promoter sequences from rat minimal Glut1 promoter sequences. We generated a tyrosine-mutant AAV9/3 vector in which human SLC2A1-myc-DDK was expressed under the human GLUT1 promoter (AAV-GLUT1)...
April 6, 2018: Journal of Gene Medicine
https://www.readbyqxmd.com/read/29600250/relaxase-mobm-induces-a-molecular-switch-at-its-cognate-origin-of-transfer
#7
Fabián Lorenzo-Díaz, Cris Fernández-López, Beatriz Guillén-Guío, Alicia Bravo, Manuel Espinosa
The MOBV1 family of relaxases is broadly distributed in plasmids and other mobile genetic elements isolated from staphylococci, enterococci, and streptococci. The prototype of this family is protein MobM encoded by the streptococcal promiscuous plasmid pMV158. MobM cleaves the phosphodiester bond of a specific dinucleotide within the origin of transfer ( oriT ) to initiate conjugative transfer. Differently from other relaxases, MobM and probably other members of the family, cleaves its target single-stranded DNA through a histidine residue rather than the commonly used tyrosine...
2018: Frontiers in Molecular Biosciences
https://www.readbyqxmd.com/read/29575296/modifications-generated-by-fast-photochemical-oxidation-of-proteins-reflect-the-native-conformations-of-proteins
#8
Emily E Chea, Lisa M Jones
Hydroxyl radical footprinting (HRF) is a nonspecific protein footprinting method that has been increasingly used in recent years to analyze protein structure. The method oxidatively modifies solvent accessible sites in proteins, which changes upon alterations in the protein such as ligand binding or a change in conformation. For HRF to provide accurate structural information, the method must probe the native structure of proteins. This requires careful experimental controls since an abundance of oxidative modifications can induce protein unfolding...
March 25, 2018: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/29570733/ribosome-profiling-reveals-changes-in-translational-status-of-soybean-transcripts-during-immature-cotyledon-development
#9
Md Shamimuzzaman, Lila Vodkin
To understand translational capacity on a genome-wide scale across three developmental stages of immature soybean seed cotyledons, ribosome profiling was performed in combination with RNA sequencing and cluster analysis. Transcripts representing 216 unique genes demonstrated a higher level of translational activity in at least one stage by exhibiting higher translational efficiencies (TEs) in which there were relatively more ribosome footprint sequence reads mapping to the transcript than were present in the control total RNA sample...
2018: PloS One
https://www.readbyqxmd.com/read/29562180/hidden-structural-modules-in-a-cooperative-rna-folding-transition
#10
Brant Gracia, Hashim M Al-Hashimi, Namita Bisaria, Rhiju Das, Daniel Herschlag, Rick Russell
Large-scale, cooperative rearrangements underlie the functions of RNA in RNA-protein machines and gene regulation. To understand how such rearrangements are orchestrated, we used high-throughput chemical footprinting to dissect a seemingly concerted rearrangement in P5abc RNA, a paradigm of RNA folding studies. With mutations that systematically disrupt or restore putative structural elements, we found that this transition reflects local folding of structural modules, with modest and incremental cooperativity that results in concerted behavior...
March 20, 2018: Cell Reports
https://www.readbyqxmd.com/read/29551998/bidirectional-regulation-of-adpa-ch-in-controlling-the-expression-of-scnri-and-scnrii-in-the-natamycin-biosynthesis-of-streptomyces-chattanoogensis-l10
#11
Pin Yu, Qing-Ting Bu, Yi-Li Tang, Xu-Ming Mao, Yong-Quan Li
AdpA, an AraC/XylS family protein, had been proved as a key regulator for secondary metabolism and morphological differentiation in Streptomyces griseus . Here, we identify AdpAch , an ortholog of AdpA, as a "higher level" pleiotropic regulator of natamycin biosynthesis with bidirectional regulatory ability in Streptomyces chattanoogensis L10. DNase I footprinting revealed six AdpAch -binding sites in the scnRI - scnRII intergenic region. Further analysis using the xylE reporter gene fused to the scnRI - scnRII intergenic region of mutated binding sites demonstrated that the expression of scnRI and scnRII was under the control of AdpAch ...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29544050/what-controls-the-limit-of-supercooling-and-superheating-of-pinned-ice-surfaces
#12
Pavithra Madhavi Naullage, Yuqing Qiu, Valeria Molinero
Cold-adapted organisms produce antifreeze proteins and glycoproteins to control the growth, melting and recrystallization of ice. It has been proposed that these molecules pin the crystal surface, creating a surface curvature that arrests its growth and melting. Here we use thermodynamic modeling and molecular simulations to elucidate how does the curvature of the metastable ice front depend on the temperature and distance between pinned molecules, and what determines the thermal hysteresis on melting and freezing, i...
March 15, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29539273/high-resolution-hydroxyl-radical-protein-footprinting-biophysics-tool-for-drug-discovery
#13
Janna Kiselar, Mark R Chance
Hydroxyl radical footprinting (HRF) of proteins with mass spectrometry (MS) is a widespread approach for assessing protein structure. Hydroxyl radicals react with a wide variety of protein side chains, and the ease with which radicals can be generated (by radiolysis or photolysis) has made the approach popular with many laboratories. As some side chains are less reactive and thus cannot be probed, additional specific and nonspecific labeling reagents have been introduced to extend the approach. At the same time, advances in liquid chromatography and MS approaches permit an examination of the labeling of individual residues, transforming the approach to high resolution...
March 14, 2018: Annual Review of Biophysics
https://www.readbyqxmd.com/read/29536665/innovative-optimization-of-ready-to-use-food-for-treatment-of-acute-malnutrition
#14
Garyk Brixi
Treatment of acute malnutrition typically requires the provision of ready-to-use food (RUF). Common RUF is effective but expensive, being manufactured from costly ingredients, and shipped worldwide from few global suppliers. I developed a linear programming tool to create RUF optimized for low cost using locally grown crops while maintaining necessary nutritional goals and other constraints. My tool utilizes a database of the nutritional value, price, and water efficiency of suitable ingredients and allows adjustment of constraints, including nutrients, flavour, and crop water efficiency...
March 14, 2018: Maternal & Child Nutrition
https://www.readbyqxmd.com/read/29529022/proteomic-analysis-of-corneal-endothelial-cell-descemet-membrane-tissues-reveals-influence-of-insulin-dependence-and-disease-severity-in-type-2-diabetes-mellitus
#15
Jessica M Skeie, Benjamin T Aldrich, Andrew S Goldstein, Gregory A Schmidt, Cynthia R Reed, Mark A Greiner
The objective of this study was to characterize the proteome of the corneal endothelial cell layer and its basement membrane (Descemet membrane) in humans with various severities of type II diabetes mellitus compared to controls, and identify differentially expressed proteins across a range of diabetic disease severities that may influence corneal endothelial cell health. Endothelium-Descemet membrane complex tissues were peeled from transplant suitable donor corneas. Protein fractions were isolated from each sample and subjected to multidimensional liquid chromatography and tandem mass spectrometry...
2018: PloS One
https://www.readbyqxmd.com/read/29520342/control-of-hmu-heme-uptake-genes-in-yersinia-pseudotuberculosis-in-response-to-iron-sources
#16
Leah Schwiesow, Erin Mettert, Yahan Wei, Halie K Miller, Natalia G Herrera, David Balderas, Patricia J Kiley, Victoria Auerbuch
Despite the mammalian host actively sequestering iron to limit pathogenicity, heme (or hemin when oxidized) and hemoproteins serve as important sources of iron for many bloodborne pathogens. The HmuRSTUV hemin uptake system allows Yersinia species to uptake and utilize hemin and hemoproteins as iron sources. HmuR is a TonB-dependent outer membrane receptor for hemin and hemoproteins. HmuTUV comprise a inner membrane ABC transporter that transports hemin and hemoproteins from the periplasmic space into the bacterial cytoplasm, where it is degraded by HmuS...
2018: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/29512051/characterization-of-elisa-antibody-antigen-interaction-using-footprinting-mass-spectrometry-and-negative-staining-transmission-electron-microscopy
#17
Margaret Lin, Denise Krawitz, Matthew D Callahan, Galahad Deperalta, Aaron T Wecksler
We describe epitope mapping data using multiple covalent labeling footprinting-mass spectrometry (MS) techniques coupled with negative stain transmission electron microscopy (TEM) data to analyze the antibody-antigen interactions in a sandwich enzyme-linked immunosorbant assay (ELISA). Our hydroxyl radical footprinting-MS data using fast photochemical oxidation of proteins (FPOP) indicates suppression of labeling across the antigen upon binding either of the monoclonal antibodies (mAbs) utilized in the ELISA...
March 6, 2018: Journal of the American Society for Mass Spectrometry
https://www.readbyqxmd.com/read/29510247/mass-spectrometry-enabled-structural-biology-of-membrane-proteins
#18
REVIEW
Antonio N Calabrese, Sheena E Radford
The last ∼25 years has seen mass spectrometry (MS) emerge as an integral method in the structural biology toolkit. In particular, MS has enabled the structural characterization of proteins and protein assemblies that have been intractable by other methods, especially those that are large, heterogeneous or transient, providing experimental evidence for their structural organization in support of, and in advance of, high resolution methods. The most recent frontier conquered in the field of MS-based structural biology has been the application of established methods for studying water soluble proteins to the more challenging targets of integral membrane proteins...
March 3, 2018: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/29505248/sulfur-isotope-fractionation-by-sulfate-reducing-microbes-can-reflect-past-physiology
#19
Andre Pellerin, Christine Wenk, Itay Halevy, Boswell Wing
Sulfur (S) isotope fractionation by sulfate-reducing microorganisms is a direct manifestation of their respiratory metabolism. This fractionation is apparent in the substrate (sulfate) and waste (sulfide) produced. The sulfate-reducing metabolism responds to variability in the local environment, with the response determined by the underlying genotype, resulting in the expression of an 'isotope phenotype'. Sulfur isotope phenotypes have been used as a diagnostic tool for the metabolic activity of sulfate-reducing microorganisms in the environment...
March 5, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29493878/developing-a-piggybac-transposon-system-and-compatible-selection-markers-for-insertional-mutagenesis-and-genome-engineering-in-yarrowia-lipolytica
#20
James M Wagner, Eden V Williams, Hal S Alper
Yarrowia lipolytica is a non-conventional yeast of interest to the biotechnology industry. However, the physiology, metabolism, and genetic regulation of Y. lipolytica diverge significantly from more well-studied and characterized yeasts such as Saccharomyces cerevisiae. To develop additional genetic tools for this industrially relevant host, we adapt the piggyBac transposon system to enable efficient generation of genome-wide insertional mutagenesis libraries and introduction of scarless, footprint-free genomic modifications in Y...
March 1, 2018: Biotechnology Journal
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