keyword
MENU ▼
Read by QxMD icon Read
search

Protein footprinting

keyword
https://www.readbyqxmd.com/read/28090586/holliday-junction-trap-shows-how-cells-use-recombination-and-a-junction-guardian-role-of-recq-helicase
#1
Jun Xia, Li-Tzu Chen, Qian Mei, Chien-Hui Ma, Jennifer A Halliday, Hsin-Yu Lin, David Magnan, John P Pribis, Devon M Fitzgerald, Holly M Hamilton, Megan Richters, Ralf B Nehring, Xi Shen, Lei Li, David Bates, P J Hastings, Christophe Herman, Makkuni Jayaram, Susan M Rosenberg
DNA repair by homologous recombination (HR) underpins cell survival and fuels genome instability, cancer, and evolution. However, the main kinds and sources of DNA damage repaired by HR in somatic cells and the roles of important HR proteins remain elusive. We present engineered proteins that trap, map, and quantify Holliday junctions (HJs), a central DNA intermediate in HR, based on catalytically deficient mutant RuvC protein of Escherichia coli. We use RuvCDefGFP (RDG) to map genomic footprints of HR at defined DNA breaks in E...
November 2016: Science Advances
https://www.readbyqxmd.com/read/28089819/lentivirus-mediated-silencing-of-the-ctgf-gene-suppresses-the-formation-of-glial-scar-tissue-in-a-rat-model-of-spinal-cord-injury
#2
Yuan Wang, Qin-Jie Kong, Jing-Chuan Sun, Yong Yang, Hai-Bo Wang, Qiang Zhang, Jian-Gang Shi
BACKGROUND CONTEXT: - One of the many reactive changes following an Spinal cord injury (SCI) is the formation of a glial scar, a reactive cellular process whereby glial cells accumulate and surround central nervous system (CNS) injury sites to seal in the wound. Thus the inhibition of glial scar is of great importance for SCI recovery. PURPOSE: - This study aimed to explore the effect of lentivirus-mediated silencing of the CTGF gene on the formation of glial scar tissue in a rat model of spinal cord injury (SCI)...
January 9, 2017: Spine Journal: Official Journal of the North American Spine Society
https://www.readbyqxmd.com/read/28069952/toxic-prn-poly-dipeptides-encoded-by-the-c9orf72-repeat-expansion-block-nuclear-import-and-export
#3
Kevin Y Shi, Eiichiro Mori, Zehra F Nizami, Yi Lin, Masato Kato, Siheng Xiang, Leeju C Wu, Ming Ding, Yonghao Yu, Joseph G Gall, Steven L McKnight
The toxic proline:arginine (PRn) poly-dipeptide encoded by the (GGGGCC)n repeat expansion in the C9orf72 form of heritable amyotrophic lateral sclerosis (ALS) binds to the central channel of the nuclear pore and inhibits the movement of macromolecules into and out of the nucleus. The PRn poly-dipeptide binds to polymeric forms of the phenylalanine:glycine (FG) repeat domain, which is shared by several proteins of the nuclear pore complex, including those in the central channel. A method of chemical footprinting was used to characterize labile, cross-β polymers formed from the FG domain of the Nup54 protein...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28060339/the-chip-exo-method-identifying-protein-dna-interactions-with-near-base-pair-precision
#4
Andrea A Perreault, Bryan J Venters
Chromatin immunoprecipitation (ChIP) is an indispensable tool in the fields of epigenetics and gene regulation that isolates specific protein-DNA interactions. ChIP coupled to high throughput sequencing (ChIP-seq) is commonly used to determine the genomic location of proteins that interact with chromatin. However, ChIP-seq is hampered by relatively low mapping resolution of several hundred base pairs and high background signal. The ChIP-exo method is a refined version of ChIP-seq that substantially improves upon both resolution and noise...
December 23, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28057466/expression-of-the-alae-gene-is-positively-regulated-by-the-global-regulator-lrp-in-response-to-intracellular-accumulation-of-l-alanine-in-escherichia-coli
#5
Kohei Ihara, Kazuki Sato, Hatsuhiro Hori, Yumiko Makino, Shuji Sigenobu, Tasuke Ando, Emiko Isogai, Hiroshi Yoneyama
The alaE gene in Escherichia coli encodes an l-alanine exporter that catalyzes the active export of l-alanine using proton electrochemical potential. In our previous study, alaE expression was shown to increase in the presence of l-alanyl-l-alanine (Ala-Ala). In this study, the global regulator leucine-responsive regulatory protein (Lrp) was identified as an activator of the alaE gene. A promoter less β-galactosidase gene was fused to an alaE upstream region (240 nucleotides). Cells that were lacZ-deficient and harbored this reporter plasmid showed significant induction of β-galactosidase activity (approximately 17-fold) in the presence of 6 mM l-alanine, l-leucine, and Ala-Ala...
January 2, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28052104/insertional-mutagenesis-by-crispr-cas9-ribonucleoprotein-gene-editing-in-cells-targeted-for-point-mutation-repair-directed-by-short-single-stranded-dna-oligonucleotides
#6
Natalia Rivera-Torres, Kelly Banas, Pawel Bialk, Kevin M Bloh, Eric B Kmiec
CRISPR/Cas9 and single-stranded DNA oligonucleotides (ssODNs) have been used to direct the repair of a single base mutation in human genes. Here, we examine a method designed to increase the precision of RNA guided genome editing in human cells by utilizing a CRISPR/Cas9 ribonucleoprotein (RNP) complex to initiate DNA cleavage. The RNP is assembled in vitro and induces a double stranded break at a specific site surrounding the mutant base designated for correction by the ssODN. We use an integrated mutant eGFP gene, bearing a single base change rendering the expressed protein nonfunctional, as a single copy target in HCT 116 cells...
2017: PloS One
https://www.readbyqxmd.com/read/28031034/uqlust-combining-profile-hashing-with-linear-time-ranking-for-efficient-clustering-and-analysis-of-big-macromolecular-data
#7
Rafal Adamczak, Jarek Meller
BACKGROUND: Advances in computing have enabled current protein and RNA structure prediction and molecular simulation methods to dramatically increase their sampling of conformational spaces. The quickly growing number of experimentally resolved structures, and databases such as the Protein Data Bank, also implies large scale structural similarity analyses to retrieve and classify macromolecular data. Consequently, the computational cost of structure comparison and clustering for large sets of macromolecular structures has become a bottleneck that necessitates further algorithmic improvements and development of efficient software solutions...
December 28, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28029108/a-zno-nanowire-bio-hybrid-solar-cell
#8
Houman Yaghoubi, Michael Schaefer, Shayan Yaghoubi, Daniel Jun, Rudy Schlaf, J Thomas Beatty, Arash Takshi
Harvesting solar energy as a carbon free source can be a promising solution to the energy crisis and environmental pollution. Biophotovoltaics seek to mimic photosynthesis to harvest solar energy and to take advantage of the low material costs, negative carbon footprint, and material abundance. In the current study, we report on a combination of zinc oxide (ZnO) nanowires with monolayers of photosynthetic reaction centers which are self-assembled, via a cytochrome c linker, as photoactive electrode. In a three-probe biophotovoltaics cell, a photocurrent density of 5...
February 3, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28028173/human-mitochondrial-transcription-factor-b2-is-required-for-promoter-melting-during-initiation-of-transcription
#9
Viktor Posse, Claes M Gustafsson
The mitochondrial transcription initiation machinery in humans consists of three proteins, the RNA polymerase (POLRMT) and two accessory factors; transcription factors A and B2 (TFAM and TFB2M respectively). This machinery is required for the expression of mitochondrial DNA and the biogenesis of the oxidative phosphorylation system. Previous experiments suggested that TFB2M is required for promoter melting, but conclusive experimental proof for this effect has not been presented. Moreover, the role of TFB2M in promoter unwinding has not been discriminated from that of TFAM...
December 27, 2016: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28027957/site-directed-chemical-probing-to-map-transient-rna-protein-interactions
#10
Mélodie Duval, Alessandra Marenna, Clément Chevalier, Stefano Marzi
RNA-protein interactions are at the bases of many biological processes, forming either tight and stable functional ribonucleoprotein (RNP) complexes (i.e. the ribosome) or transitory ones, such as the complexes involving RNA chaperone proteins. To localize the sites where a protein interacts on an RNA molecule, a common simple and inexpensive biochemical method is the footprinting technique. The protein leaves its footprint on the RNA acting as a shield to protect the regions of interaction from chemical modification or cleavages obtained with chemical or enzymatic nucleases...
December 24, 2016: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/28012227/widespread-selective-sweeps-throughout-the-genome-of-model-plant-pathogenic-fungi-and-identification-of-effector-candidates
#11
H Badouin, P Gladieux, J Gouzy, S Siguenza, G Aguileta, A Snirc, S Le Prieur, C Jeziorski, A Branca, T Giraud
Identifying the genes underlying adaptation, their distribution in genomes, and the evolutionary forces shaping genomic diversity, are key challenges in evolutionary biology. Very few studies have investigated the abundance and distribution of selective sweeps in species with high-quality reference genomes, outside of a handful of model species. Pathogenic fungi are tractable eukaryote models for investigating the genomics of adaptation. By sequencing 53 genomes of two species of anther-smut fungi and mapping them against a high-quality reference genome, we showed that selective sweeps were abundant and scattered throughout the genome in one species, affecting near 17% of the genome, but much less numerous and in different genomic regions in its sister species, where they left footprints in only 1% of the genome...
December 24, 2016: Molecular Ecology
https://www.readbyqxmd.com/read/28011633/the-pentatricopeptide-repeat-protein-emb2654-is-essential-for-trans-splicing-of-a-chloroplast-small-ribosomal-subunit-transcript
#12
Nader Aryamanesh, Hannes Ruwe, Lilian Vincis Pereira Sanglard, Leila Eshraghi, John Desmond Bussell, Katharine A Howell, Catherine Colas des Francs-Small, Ian D Small
We report the partial complementation and subsequent comparative molecular analysis of two non-viable mutants impaired in chloroplast translation, one (emb2394) lacking the RPL6 protein, and the other (emb2654) carrying a mutation in a gene encoding a P-class pentatricopeptide repeat protein. We show that EMB2654 is required for the trans-splicing of the plastid rps12 transcript, and that therefore the emb2654 mutant lacks Rps12 protein and fails to assemble the small subunit of the plastid ribosome, explaining the loss of plastid translation and consequent embryo-lethal phenotype...
December 23, 2016: Plant Physiology
https://www.readbyqxmd.com/read/28009009/bacteriophage-t5-gene-d10-encodes-a-branch-migration-protein
#13
Io Nam Wong, Jon R Sayers, Cyril M Sanders
Helicases catalyze the unwinding of double-stranded nucleic acids where structure and phosphate backbone contacts, rather than nucleobase sequence, usually determines substrate specificity. We have expressed and purified a putative helicase encoded by the D10 gene of bacteriophage T5. Here we report that this hitherto uncharacterized protein possesses branch migration and DNA unwinding activity. The initiation of substrate unwinding showed some sequence dependency, while DNA binding and DNA-dependent ATPase activity did not...
December 23, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27977908/integrated-continuous-processing-of-proteins-expressed-as-inclusion-bodies-gcsf-as-a-case-study
#14
Nikhil Kateja, Harshit Agarwal, Vishwanath Hebbi, Anurag S Rathore
Affordability of biopharmaceuticals continues to be a challenge, particularly in developing economies. This has fuelled advancements in manufacturing that can offer higher productivity and better economics without sacrificing product quality in the form of an integrated continuous manufacturing platform. While platform processes for monoclonal antibodies have existed for more than a decade, development of an integrated continuous manufacturing process for bacterial proteins has received relatively scant attention...
December 15, 2016: Biotechnology Progress
https://www.readbyqxmd.com/read/27974629/throughput-optimization-of-continuous-biopharmaceutical-manufacturing-facilities
#15
Fernando Antonio Garcia, Michael W Vandiver
In order to operate profitably under different product demand scenarios, biopharmaceutical companies must design their facilities with mass output flexibility in mind. Traditional biologics manufacturing technologies pose operational challenges in this regard due to their high costs and slow equipment turnaround times, restricting the types of products and mass quantities that can be processed. Modern plant design, however, has facilitated the development of lean and efficient bioprocessing facilities through footprint reduction, and adoption of disposable and continuous manufacturing technologies...
December 14, 2016: PDA Journal of Pharmaceutical Science and Technology
https://www.readbyqxmd.com/read/27940950/a-gc-rich-sequence-feature-in-the-3-utr-directs-upf1-dependent-mrna-decay-in-mammalian-cells
#16
Naoto Imamachi, Kazi Abdus Salam, Yutaka Suzuki, Nobuyoshi Akimitsu
Up-frameshift protein 1 (UPF1) is an ATP-dependent RNA helicase that has essential roles in RNA surveillance and in post-transcriptional gene regulation by promoting the degradation of mRNAs. Previous studies revealed that UPF1 is associated with the 3' untranslated region (UTR) of target mRNAs via as-yet-unknown sequence features. Herein, we aimed to identify characteristic sequence features of UPF1 targets. We identified 246 UPF1 targets by measuring RNA stabilization upon UPF1 depletion and by identifying mRNAs that associate with UPF1...
December 9, 2016: Genome Research
https://www.readbyqxmd.com/read/27929747/localized-conformational-interrogation-of-antibody-and-antibody-drug-conjugates-by-site-specific-carboxyl-group-footprinting
#17
Lucy Yan Pan, Oscar Salas-Solano, John F Valliere-Douglass
Establishing and maintaining conformational integrity of monoclonal antibodies (mAbs) and antibody-drug conjugates (ADCs) during development and manufacturing is critical for ensuring their clinical efficacy. As presented here, we applied site-specific carboxyl group footprinting (CGF) for localized conformational interrogation of mAbs. The approach relies on covalent labeling that introduces glycine ethyl ester tags onto solvent-accessible side chains of protein carboxylates. Peptide mapping is used to monitor the labeling kinetics of carboxyl residues and the labeling kinetics reflects the conformation or solvent-accessibility of side chains...
December 8, 2016: MAbs
https://www.readbyqxmd.com/read/27924019/a-ribosome-profiling-study-of-mrna-cleavage-by-the-endonuclease-rele
#18
Jae-Yeon Hwang, Allen R Buskirk
Implicated in persistence and stress response pathways in bacteria, RelE shuts down protein synthesis by cleaving mRNA within the ribosomal A site. Structural and biochemical studies have shown that RelE cuts with some sequence specificity, which we further characterize here, and that it shows no activity outside the context of the ribosome. We obtained a global view of the effect of RelE on translation by ribosome profiling, observing that ribosomes accumulate on the 5'-end of genes through dynamic cycles of mRNA cleavage, ribosome rescue and initiation...
October 18, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27913192/the-cellular-protein-nucleolin-preferentially-binds-long-looped-g-quadruplex-nucleic-acids
#19
Sara Lago, Elena Tosoni, Matteo Nadai, Manlio Palumbo, Sara N Richter
BACKGROUND: G-quadruplexes (G4s) are four-stranded nucleic acid structures that form in G-rich sequences. Nucleolin (NCL) is a cellular protein reported for its functions upon G4 recognition, such as induction of neurodegenerative diseases, tumor and virus mechanisms activation. We here aimed at defining NCL/G4 binding determinants. METHODS: Electrophoresis mobility shift assay was used to detect NCL/G4 binding; circular dichroism to assess G4 folding, topology and stability; dimethylsulfate footprinting to detect G bases involved in G4 folding...
November 30, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27899674/cdd-sparcle-functional-classification-of-proteins-via-subfamily-domain-architectures
#20
Aron Marchler-Bauer, Yu Bo, Lianyi Han, Jane He, Christopher J Lanczycki, Shennan Lu, Farideh Chitsaz, Myra K Derbyshire, Renata C Geer, Noreen R Gonzales, Marc Gwadz, David I Hurwitz, Fu Lu, Gabriele H Marchler, James S Song, Narmada Thanki, Zhouxi Wang, Roxanne A Yamashita, Dachuan Zhang, Chanjuan Zheng, Lewis Y Geer, Stephen H Bryant
NCBI's Conserved Domain Database (CDD) aims at annotating biomolecular sequences with the location of evolutionarily conserved protein domain footprints, and functional sites inferred from such footprints. An archive of pre-computed domain annotation is maintained for proteins tracked by NCBI's Entrez database, and live search services are offered as well. CDD curation staff supplements a comprehensive collection of protein domain and protein family models, which have been imported from external providers, with representations of selected domain families that are curated in-house and organized into hierarchical classifications of functionally distinct families and sub-families...
January 4, 2017: Nucleic Acids Research
keyword
keyword
56239
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"