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Protein footprinting

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https://www.readbyqxmd.com/read/28526559/a-single-nucleotide-polymorphism-of-cyclin-dependent-kinase-inhibitor-1b-p27-kip1-associated-with-human-vein-graft-failure-affects-growth-of-human-venous-adventitial-cells-but-not-smooth-muscle-cells
#1
Richard D Kenagy, Shinsuke Kikuchi, Lihua Chen, Errol S Wijelath, Andrew B Stergachis, John Stamatoyannopoulos, Gale L Tang, Alexander W Clowes, Michael Sobel
BACKGROUND: Cyclin-dependent kinase inhibitor 1B (p27(Kip1)) is a cell-cycle inhibitor whose -838C>A single nucleotide polymorphism (rs36228499; hereafter called p27 SNP) has been associated with the clinical failure of peripheral vein grafts, but the functional effects of this SNP have not been demonstrated. METHODS: Human saphenous vein adventitial cells and intimal/medial smooth muscle cells (SMCs) were derived from explants obtained at the time of lower extremity bypass operations...
May 16, 2017: Journal of Vascular Surgery
https://www.readbyqxmd.com/read/28525600/a-novel-double-kink-turn-module-in-euryarchaeal-rnase-p-rnas
#2
Lien B Lai, Akiko Tanimoto, Stella M Lai, Wen-Yi Chen, Ila A Marathe, Eric Westhof, Vicki H Wysocki, Venkat Gopalan
RNase P is primarily responsible for the 5΄ maturation of transfer RNAs (tRNAs) in all domains of life. Archaeal RNase P is a ribonucleoprotein made up of one catalytic RNA and five protein cofactors including L7Ae, which is known to bind the kink-turn (K-turn), an RNA structural element that causes axial bending. However, the number and location of K-turns in archaeal RNase P RNAs (RPRs) are unclear. As part of an integrated approach, we used native mass spectrometry to assess the number of L7Ae copies that bound the RPR and site-specific hydroxyl radical-mediated footprinting to localize the K-turns...
May 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28525347/sustainable-farming-of-the-mealworm-tenebrio-molitor-for-the-production-of-food-and-feed
#3
Thorben Grau, Andreas Vilcinskas, Gerrit Joop
The farming of edible insects is an alternative strategy for the production of protein-rich food and feed with a low ecological footprint. The industrial production of insect-derived protein is more cost-effective and energy-efficient than livestock farming or aquaculture. The mealworm Tenebrio molitor is economically among the most important species used for the large-scale conversion of plant biomass into protein. Here, we review the mass rearing of this species and its conversion into food and feed, focusing on challenges such as the contamination of food/feed products with bacteria from the insect gut and the risk of rapidly spreading pathogens and parasites...
May 17, 2017: Zeitschrift Für Naturforschung. C, A Journal of Biosciences
https://www.readbyqxmd.com/read/28516119/affinity-pulldown-of-biotinylated-rna-for-detection-of-protein-rna-complexes
#4
Amaresh C Panda, Jennifer L Martindale, Myriam Gorospe
RNA-binding proteins (RBPs) have recently emerged as crucial players in the regulation of gene expression. The interactions of RBPs with target mRNAs control the levels of gene products by altering different regulatory steps, including pre-mRNA splicing and maturation, nuclear mRNA export, and mRNA stability and translation (Glisovic et al., 2008). There are several methodologies available today to identify RNAs bound to specific RBPs; some detect only recombinant molecules in vitro, others detect recombinant and endogenous molecules, while others detect only endogenous molecules...
December 20, 2016: Bio-protocol
https://www.readbyqxmd.com/read/28514447/global-translational-reprogramming-is-a-fundamental-layer-of-immune-regulation-in-plants
#5
Guoyong Xu, George H Greene, Heejin Yoo, Lijing Liu, Jorge Marqués, Jonathan Motley, Xinnian Dong
In the absence of specialized immune cells, the need for plants to reprogram transcription to transition from growth-related activities to defence is well understood. However, little is known about translational changes that occur during immune induction. Using ribosome footprinting, here we perform global translatome profiling on Arabidopsis exposed to the microbe-associated molecular pattern elf18. We find that during this pattern-triggered immunity, translation is tightly regulated and poorly correlated with transcription...
May 17, 2017: Nature
https://www.readbyqxmd.com/read/28512867/the-structural-basis-for-inhibition-of-the-classical-and-lectin-complement-pathways-by-s-aureus-extracellular-adherence-protein
#6
Jordan L Woehl, Kasra X Ramyar, Benjamin B Katz, John K Walker, Brian V Geisbrecht
The extracellular adherence protein (Eap) plays a crucial role in pathogenesis and survival of Staphylococcus aureus by inhibiting the classical and lectin pathways of complement. We have previously shown that Eap binds with nanomolar affinity to complement C4b and disrupts the initial interaction between C4b and C2, thereby inhibiting formation of the classical and lectin pathway C3 pro-convertase. Although an underlying mechanism has been identified, the structural basis for Eap binding to C4b is poorly understood...
May 16, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28512450/host-plant-compatibility-shapes-the-proteogenome-of-frankia-coriariae
#7
Amir Ktari, Abdellatif Gueddou, Imen Nouioui, Guylaine Miotello, Indrani Sarkar, Faten Ghodhbane-Gtari, Arnab Sen, Jean Armengaud, Maher Gtari
Molecular signaling networks in the actinorhizal rhizosphere select host-compatible Frankia strains, trigger the infection process and eventually the genesis of nitrogen-fixing nodules. The molecular triggers involved remain difficult to ascertain. Root exudates (RE) are highly dynamic substrates that play key roles in establishing the rhizosphere microbiome. RE are known to induce the secretion by rhizobia of Nod factors, polysaccharides, and other proteins in the case of legume symbiosis. Next-generation proteomic approach was here used to decipher the key bacterial signals matching the first-step recognition of host plant stimuli upon treatment of Frankia coriariae strain BMG5...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28505348/implication-of-the-box-c-d-snornp-assembly-factor-rsa1p-in-u3-snornp-assembly
#8
Benjamin Rothé, Xavier Manival, Nicolas Rolland, Christophe Charron, Véronique Senty-Ségault, Christiane Branlant, Bruno Charpentier
The U3 box C/D snoRNA is one key element of 90S pre-ribosome. It contains a 5΄ domain pairing with pre-rRNA and the U3B/C and U3C΄/D motifs for U3 packaging into a unique small nucleolar ribonucleoprotein particle (snoRNP). The RNA-binding protein Snu13/SNU13 nucleates on U3B/C the assembly of box C/D proteins Nop1p/FBL and Nop56p/NOP56, and the U3-specific protein Rrp9p/U3-55K. Snu13p/SNU13 has a much lower affinity for U3C΄/D but nevertheless forms on this motif an RNP with box C/D proteins Nop1p/FBL and Nop58p/NOP58...
May 13, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28505149/distinct-dna-binding-surfaces-in-the-atpase-and-linker-domains-of-mutl%C3%AE-determine-its-substrate-specificities-and-exert-separable-functions-in-meiotic-recombination-and-mismatch-repair
#9
Corentin Claeys Bouuaert, Scott Keeney
Mlh1-Mlh3 (MutLγ) is a mismatch repair factor with a central role in formation of meiotic crossovers, presumably through resolution of double Holliday junctions. MutLγ has DNA binding, nuclease, and ATPase activities, but how these relate to one another and to in vivo functions are unclear. Here, we combine biochemical and genetic analyses to characterize Saccharomyces cerevisiae MutLγ. Limited proteolysis and atomic force microscopy showed that purified recombinant MutLγ undergoes ATP-driven conformational changes...
May 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28494964/near-membrane-refractometry-using-supercritical-angle-fluorescence
#10
Maia Brunstein, Lopamudra Roy, Martin Oheim
Total internal reflection fluorescence (TIRF) microscopy and its variants are key technologies for visualizing the dynamics of single molecules or organelles in live cells. Yet truly quantitative TIRF remains problematic. One unknown hampering the interpretation of evanescent-wave excited fluorescence intensities is the undetermined cell refractive index (RI). Here, we use a combination of TIRF excitation and supercritical angle fluorescence emission detection to directly measure the average RI in the "footprint" region of the cell during image acquisition...
May 9, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28491057/identification-of-genes-controlled-by-the-essential-yycfg-two-component-system-reveals-a-role-for-biofilm-modulation-in-staphylococcus-epidermidis
#11
Tao Xu, Yang Wu, Zhiwei Lin, Ralph Bertram, Friedrich Götz, Ying Zhang, Di Qu
Biofilms play a crucial role in the pathogenicity of Staphylococcus epidermidis, while little is known about whether the essential YycFG two-component signal transduction system (TCS) is involved in biofilm formation. We used antisense RNA (asRNA) to silence the yycFG TCS in order to study its regulatory functions in S. epidermidis. Strain 1457 expressing asRNA yycF exhibited a significant delay (~4-5 h) in entry to log phase, which was partially complemented by overexpressing ssaA. The expression of asRNA yycF and asRNA yycG resulted in a 68 and 50% decrease in biofilm formation at 6 h, respectively, while they had no significant inhibitory effect on 12 h biofilm formation...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28475873/structure-and-dynamics-of-a-197%C3%A2-bp-nucleosome-in-complex-with-linker-histone-h1
#12
Jan Bednar, Isabel Garcia-Saez, Ramachandran Boopathi, Amber R Cutter, Gabor Papai, Anna Reymer, Sajad H Syed, Imtiaz Nisar Lone, Ognyan Tonchev, Corinne Crucifix, Hervé Menoni, Christophe Papin, Dimitrios A Skoufias, Hitoshi Kurumizaka, Richard Lavery, Ali Hamiche, Jeffrey J Hayes, Patrick Schultz, Dimitar Angelov, Carlo Petosa, Stefan Dimitrov
Linker histones associate with nucleosomes to promote the formation of higher-order chromatin structure, but the underlying molecular details are unclear. We investigated the structure of a 197 bp nucleosome bearing symmetric 25 bp linker DNA arms in complex with vertebrate linker histone H1. We determined electron cryo-microscopy (cryo-EM) and crystal structures of unbound and H1-bound nucleosomes and validated these structures by site-directed protein cross-linking and hydroxyl radical footprinting experiments...
May 4, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28467855/use-of-ice-nucleating-proteins-to-improve-the-performance-of-freeze-thaw-valves-in-microfluidic-devices
#13
Joseph C Gaiteri, W Hampton Henley, Nathan A Siegfried, Thomas H Linz, J Michael Ramsey
Currently, reliable valving on integrated microfluidic devices fabricated from rigid materials is confined to expensive and complex methods. Freeze-thaw valves (FTVs) can provide a low cost, low complexity valving mechanism, but reliable implementation of them has been greatly hindered by the lack of ice nucleation sites within the valve body's small volume. Work to date has required very low temperatures (on the order of -40 °C or colder) to induce freezing without nucleation sites, making FTVs impractical due to instrument engineering challenges...
May 11, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28461460/maize-defective-kernel-mutant-generated-by-insertion-of-a-ds-element-in-a-gene-encoding-a-highly-conserved-tti2-cochaperone
#14
Nelson Garcia, Yubin Li, Hugo K Dooner, Joachim Messing
We have used the newly engineered transposable element Dsg to tag a gene that gives rise to a defective kernel (dek) phenotype. Dsg requires the autonomous element Ac for transposition. Upon excision, it leaves a short DNA footprint that can create in-frame and frameshift insertions in coding sequences. Therefore, we could create alleles of the tagged gene that confirmed causation of the dek phenotype by the Dsg insertion. The mutation, designated dek38-Dsg, is embryonic lethal, has a defective basal endosperm transfer (BETL) layer, and results in a smaller seed with highly underdeveloped endosperm...
May 1, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28457705/inhibition-of-eukaryotic-translation-by-the-antitumor-natural-product-agelastatin-a
#15
Brandon McClary, Boris Zinshteyn, Mélanie Meyer, Morgan Jouanneau, Simone Pellegrino, Gulnara Yusupova, Anthony Schuller, Jeremy Chris P Reyes, Junyan Lu, Zufeng Guo, Safiat Ayinde, Cheng Luo, Yongjun Dang, Daniel Romo, Marat Yusupov, Rachel Green, Jun O Liu
Protein synthesis plays an essential role in cell proliferation, differentiation, and survival. Inhibitors of eukaryotic translation have entered the clinic, establishing the translation machinery as a promising target for chemotherapy. A recently discovered, structurally unique marine sponge-derived brominated alkaloid, (-)-agelastatin A (AglA), possesses potent antitumor activity. Its underlying mechanism of action, however, has remained unknown. Using a systematic top-down approach, we show that AglA selectively inhibits protein synthesis...
May 18, 2017: Cell Chemical Biology
https://www.readbyqxmd.com/read/28454561/a-comprehensive-multi-omics-approach-uncovers-adaptations-for-growth-and-survival-of-pseudomonas-aeruginosa-on-n-alkanes
#16
Sarah L Grady, Stephanie A Malfatti, Thusitha S Gunasekera, Brian K Dalley, Matt G Lyman, Richard C Striebich, Michael B Mayhew, Carol L Zhou, Oscar N Ruiz, Larry C Dugan
BACKGROUND: Examination of complex biological systems has long been achieved through methodical investigation of the system's individual components. While informative, this strategy often leads to inappropriate conclusions about the system as a whole. With the advent of high-throughput "omic" technologies, however, researchers can now simultaneously analyze an entire system at the level of molecule (DNA, RNA, protein, metabolite) and process (transcription, translation, enzyme catalysis)...
April 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28452748/soleil-shining-on-the-solution-state-structure-of-biomacromolecules-by-synchrotron-x-ray-footprinting-at-the-metrology-beamline
#17
A Baud, L Aymé, F Gonnet, I Salard, Y Gohon, P Jolivet, K Brodolin, P Da Silva, A Giuliani, B Sclavi, T Chardot, P Mercère, P Roblin, R Daniel
Synchrotron X-ray footprinting complements the techniques commonly used to define the structure of molecules such as crystallography, small-angle X-ray scattering and nuclear magnetic resonance. It is remarkably useful in probing the structure and interactions of proteins with lipids, nucleic acids or with other proteins in solution, often better reflecting the in vivo state dynamics. To date, most X-ray footprinting studies have been carried out at the National Synchrotron Light Source, USA, and at the European Synchrotron Radiation Facility in Grenoble, France...
May 1, 2017: Journal of Synchrotron Radiation
https://www.readbyqxmd.com/read/28452222/application-of-nanosecond-laser-photolysis-protein-footprinting-to-study-the-egfr-activation-by-egf-in-cell
#18
Yi Zhu, Aida Serra, Tiannan Guo, Jung Eun Park, Qing Zhong, Siu Kwan Sze
Mass spectrometry based protein footprinting emerged as a useful technology to understand protein ligand interactions in vitro. We have previously demonstrated the application of footprinting in live E. coli cells. Here we further optimized an ultrafast laser photolysis hydroxyl radical footprinting method and applied it to study the interaction of EGF and EGFR in live mammalian cells. This method used a nanosecond laser to photochemically generate a burst of hydroxyl radicals in situ in cell suspension to oxidize the amino acids on the protein surface...
April 28, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28439033/genome-wide-identification-of-resd-nsrr-and-fur-binding-in-bacillus-subtilis-during-anaerobic-fermentative-growth-by-in-vivo-footprinting
#19
Onuma Chumsakul, Divya P Anantsri, Tai Quirke, Taku Oshima, Kensuke Nakamura, Shu Ishikawa, Michiko M Nakano
Upon oxygen limitation, the Bacillus subtilis ResE sensor kinase and its cognate ResD response regulator play primary roles in transcriptional activation of genes functioning in anaerobic respiration. The nitric oxide (NO)-sensitive NsrR repressor controls transcription to support nitrate respiration. In addition, the ferric uptake repressor (Fur) can modulate transcription under anaerobic conditions. However, whether these controls are direct or indirect has been investigated only in a gene-specific manner...
April 24, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28437684/fibrillar-disruption-by-ac-electric-field-induced-oscillation-a-case-study-with-human-serum-albumin
#20
Shubhatam Sen, Monojit Chakraborty, Snigdha Goley, Swagata Dasgupta, Sunando DasGupta
The effect of oscillation induced by a frequency-dependent alternating current (AC) electric field to dissociate preformed amyloid fibrils has been investigated. An electrowetting-on-dielectric type setup has been used to apply the AC field of varying frequencies on preformed fibrils of human serum albumin (HSA). The disintegration potency has been monitored by a combination of spectroscopic and microscopic techniques. The experimental results suggest that the frequency of the applied AC field plays a crucial role in the disruption of preformed HSA fibrils...
April 13, 2017: Biophysical Chemistry
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