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Protein footprinting

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https://www.readbyqxmd.com/read/27913192/the-cellular-protein-nucleolin-preferentially-binds-long-looped-g-quadruplex-nucleic-acids
#1
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
#2
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...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27881650/mechanism-of-enhanced-hiv-restriction-by-virion-coencapsidated-cytidine-deaminases-apobec3f-and-apobec3g
#3
Anjuman Ara, Robin P Love, Tyson B Follack, Khawaja A Ahmed, Madison B Adolph, Linda Chelico
: The APOBEC3 (A3) enzymes, A3G and A3F, are coordinately expressed in CD4+ T cells and can become coencapsidated into HIV-1 virions, primarily in the absence of the viral infectivity factor (Vif). A3F and A3G are deoxycytidine deaminases that inhibit HIV-1 replication by inducing guanine to adenine hypermutation through deamination of cytosine to form uracil in (-)DNA. The effect of the simultaneous presence of both A3G and A3F on HIV-1 restriction ability is not clear. Here, we used a single cycle infectivity assay and biochemical analyses to determine if coencapsidated A3G and A3F differ in their restriction capacity than A3G or A3F alone...
November 23, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27875800/evaluation-of-tspo-pet-imaging-a-marker-of-glial-activation-to-study-the-neuroimmune-footprints-of-morphine-exposure-and-withdrawal
#4
Sylvain Auvity, Sébastien Goutal, Benoît Thézé, Catarina Chaves, Benoît Hosten, Bertrand Kuhnast, Wadad Saba, Raphaël Boisgard, Irène Buvat, Salvatore Cisternino, Nicolas Tournier
INTRODUCTION: A growing area of research suggests that neuroimmunity may impact the pharmacology of opioids. Microglia is a key component of the brain immunity. Preclinical and clinical studies have demonstrated that microglial modulators may improve morphine-induced analgesia and prevent the development of tolerance and dependence. Positron emission tomography (PET) using translocator protein 18kDa (TSPO) radioligand is a clinically validated strategy for the non-invasive detection of microglial activation...
November 8, 2016: Drug and Alcohol Dependence
https://www.readbyqxmd.com/read/27863083/promotion-of-neurological-recovery-in-rat-spinal-cord-injury-by-mesenchymal-stem-cells-loaded-on-nerve-guided-collagen-scaffold-through-increasing-alternatively-activated-macrophage-polarization
#5
Zhan Peng, Wei Gao, Bing Yue, Jie Jiang, Yong Gu, Jianwu Dai, Liang Chen, Qin Shi
Mesenchymal stem cells(MSCs)characterized by multi-differentiation potent and immunoregulatory have been used in the treatment of spinal cord injury (SCI), but the direct transplantation may limit its effectiveness due to quick diffusion. In addition, the role of macrophages in healing is being increasingly recognized because of the ability to polarize into pro- and anti-inflammatory phenotypes. In the present study, we developed the nerve-guide collagen scaffold (CS) and rat MSCs. After CS was confirmed to minimize MSCs distribution in vivo by the positron emission tomography (PET) imaging, the repair capacity of combined implantation of CS and MSCs and the effect on classically activated macrophage (M1)/alternatively activated macrophage (M2) polarization was assessed in a hemisected SCI rat model...
November 15, 2016: Journal of Tissue Engineering and Regenerative Medicine
https://www.readbyqxmd.com/read/27848959/carbene-footprinting-accurately-maps-binding-sites-in-protein-ligand-and-protein-protein-interactions
#6
Lucio Manzi, Andrew S Barrow, Daniel Scott, Robert Layfield, Timothy G Wright, John E Moses, Neil J Oldham
Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry...
November 16, 2016: Nature Communications
https://www.readbyqxmd.com/read/27847185/urban-consumption-of-meat-and-milk-and-its-green-and-blue-water-footprints-patterns-in-the-1980s-and-2000s-for-nairobi-kenya
#7
Caroline K Bosire, Mats Lannerstad, Jan de Leeuw, Maarten S Krol, Joseph O Ogutu, Pamela A Ochungo, Arjen Y Hoekstra
THE PROBLEM: Various studies show that the developing world experiences and will continue to experience a rise in consumption of animal proteins, particularly in cities, as a result of continued urbanization and income growth. Given the relatively large water footprint (WF) of animal products, this trend is likely to increase the pressure on already scarce water resources. AIM: We estimate, analyse and interpret the changes in consumption of meat and milk between the 1980s and 2000s for three income classes in Nairobi, the ratio of domestic production to imports, and the WF (the volume of freshwater consumed) to produce these commodities in Kenya and abroad...
November 12, 2016: Science of the Total Environment
https://www.readbyqxmd.com/read/27826761/kelch-motif-containing-acyl-coa-binding-proteins-atacbp4-and-atacbp5-are-differentially-expressed-and-function-in-floral-lipid-metabolism
#8
Zi-Wei Ye, Jie Xu, Jianxin Shi, Dabing Zhang, Mee-Len Chye
We herein demonstrated two of the Arabidopsis acyl-CoA-binding proteins (ACBPs), AtACBP4 and AtACBP5, both function in floral lipid metabolism and they may possibly play complementary roles in Arabidopsis microspore-to-pollen development. Histological analysis on transgenic Arabidopsis expressing β-glucuronidase driven from the AtACBP4 and AtACBP5 promoters, as well as, qRTPCR analysis revealed that AtACBP4 was expressed at stages 11-14 in the mature pollen, while AtACBP5 was expressed at stages 7-10 in the microspores and tapetal cells...
November 8, 2016: Plant Molecular Biology
https://www.readbyqxmd.com/read/27825385/neurogenomics-and-the-role-of-a-large-mutational-target-on-rapid-behavioral-change
#9
Craig E Stanley, Rob J Kulathinal
BACKGROUND: Behavior, while complex and dynamic, is among the most diverse, derived, and rapidly evolving traits in animals. The highly labile nature of heritable behavioral change is observed in such evolutionary phenomena as the emergence of converged behaviors in domesticated animals, the rapid evolution of preferences, and the routine development of ethological isolation between diverging populations and species. In fact, it is believed that nervous system development and its potential to evolve a seemingly infinite array of behavioral innovations played a major role in the successful diversification of metazoans, including our own human lineage...
November 8, 2016: Biology Direct
https://www.readbyqxmd.com/read/27819269/structural-basis-of-gm-csf-and-il-2-sequestration-by-the-viral-decoy-receptor-gif
#10
Jan Felix, Eaazhisai Kandiah, Steven De Munck, Yehudi Bloch, Gydo C P van Zundert, Kris Pauwels, Ann Dansercoer, Katka Novanska, Randy J Read, Alexandre M J J Bonvin, Bjorn Vergauwen, Kenneth Verstraete, Irina Gutsche, Savvas N Savvides
Subversion of the host immune system by viruses is often mediated by molecular decoys that sequester host proteins pivotal to mounting effective immune responses. The widespread mammalian pathogen parapox Orf virus deploys GIF, a member of the poxvirus immune evasion superfamily, to antagonize GM-CSF (granulocyte macrophage colony-stimulating factor) and IL-2 (interleukin-2), two pleiotropic cytokines of the mammalian immune system. However, structural and mechanistic insights into the unprecedented functional duality of GIF have remained elusive...
November 7, 2016: Nature Communications
https://www.readbyqxmd.com/read/27809763/mublastp-database-indexed-protein-sequence-search-on-multicore-cpus
#11
Jing Zhang, Sanchit Misra, Hao Wang, Wu-Chun Feng
BACKGROUND: The Basic Local Alignment Search Tool (BLAST) is a fundamental program in the life sciences that searches databases for sequences that are most similar to a query sequence. Currently, the BLAST algorithm utilizes a query-indexed approach. Although many approaches suggest that sequence search with a database index can achieve much higher throughput (e.g., BLAT, SSAHA, and CAFE), they cannot deliver the same level of sensitivity as the query-indexed BLAST, i.e., NCBI BLAST, or they can only support nucleotide sequence search, e...
November 4, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27808243/genomic-analysis-reveals-selection-in-chinese-native-black-pig
#12
Yuhua Fu, Cencen Li, Qianzi Tang, Shilin Tian, Long Jin, Jianhai Chen, Mingzhou Li, Changchun Li
Identification of genomic signatures that help reveal mechanisms underlying desirable traits in domesticated pigs is of significant biological, agricultural and medical importance. To identify the genomic footprints left by selection during domestication of the Enshi black pig, a typical native and meat-lard breed in China, we generated about 72-fold coverage of the pig genome using pools of genomic DNA representing three different populations of Enshi black pigs from three different locations. Combining this data with the available whole genomes of 13 Chinese wild boars, we identified 417 protein-coding genes embedded in the selected regions of Enshi black pigs...
November 3, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27807341/t-cell-receptor-recognition-of-cd1b-presenting-a-mycobacterial-glycolipid
#13
Stephanie Gras, Ildiko Van Rhijn, Adam Shahine, Tan-Yun Cheng, Mugdha Bhati, Li Lynn Tan, Hanim Halim, Kathryn D Tuttle, Laurent Gapin, Jérôme Le Nours, D Branch Moody, Jamie Rossjohn
CD1 proteins present microbial lipids to T cells. Germline-encoded mycolyl lipid-reactive (GEM) T cells with conserved αβ T cell receptors (TCRs) recognize CD1b presenting mycobacterial mycolates. As the molecular basis underpinning TCR recognition of CD1b remains unknown, here we determine the structure of a GEM TCR bound to CD1b presenting glucose-6-O-monomycolate (GMM). The GEM TCR docks centrally above CD1b, whereby the conserved TCR α-chain extensively contacts CD1b and GMM. Through mutagenesis and study of T cells from tuberculosis patients, we identify a consensus CD1b footprint of TCRs present among GEM T cells...
October 27, 2016: Nature Communications
https://www.readbyqxmd.com/read/27791167/super-resolution-ribosome-profiling-reveals-unannotated-translation-events-in-arabidopsis
#14
Polly Yingshan Hsu, Lorenzo Calviello, Hsin-Yen Larry Wu, Fay-Wei Li, Carl J Rothfels, Uwe Ohler, Philip N Benfey
Deep sequencing of ribosome footprints (ribosome profiling) maps and quantifies mRNA translation. Because ribosomes decode mRNA every 3 nt, the periodic property of ribosome footprints could be used to identify novel translated ORFs. However, due to the limited resolution of existing methods, the 3-nt periodicity is observed mostly in a global analysis, but not in individual transcripts. Here, we report a protocol applied to Arabidopsis that maps over 90% of the footprints to the main reading frame and thus offers super-resolution profiles for individual transcripts to precisely define translated regions...
October 21, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27780225/additive-promotion-of-viral-internal-ribosome-entry-site-mediated-translation-by-far-upstream-element-binding-protein-1-and-an-enterovirus-71-induced-cleavage-product
#15
Chuan-Tien Hung, Yu-An Kung, Mei-Ling Li, Gary Brewer, Kuo-Ming Lee, Shih-Tung Liu, Shin-Ru Shih
The 5' untranslated region (5' UTR) of the enterovirus 71 (EV71) RNA genome contains an internal ribosome entry site (IRES) that is indispensable for viral protein translation. Due to the limited coding capacity of their RNA genomes, EV71 and other picornaviruses typically recruit host factors, known as IRES trans-acting factors (ITAFs), to mediate IRES-dependent translation. Here, we show that EV71 viral proteinase 2A is capable of cleaving far upstream element-binding protein 1 (FBP1), a positive ITAF that directly binds to the EV71 5' UTR linker region to promote viral IRES-driven translation...
October 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27768872/chromatin-kinases-act-on-transcription-factors-and-histone-tails-in-regulation-of-inducible-transcription
#16
Steven Z Josefowicz, Miho Shimada, Anja Armache, Charles H Li, Rand M Miller, Shu Lin, Aerin Yang, Brian D Dill, Henrik Molina, Hee-Sung Park, Benjamin A Garcia, Jack Taunton, Robert G Roeder, C David Allis
The inflammatory response requires coordinated activation of both transcription factors and chromatin to induce transcription for defense against pathogens and environmental insults. We sought to elucidate the connections between inflammatory signaling pathways and chromatin through genomic footprinting of kinase activity and unbiased identification of prominent histone phosphorylation events. We identified H3 serine 28 phosphorylation (H3S28ph) as the principal stimulation-dependent histone modification and observed its enrichment at induced genes in mouse macrophages stimulated with bacterial lipopolysaccharide...
October 20, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27761706/aerodynamic-droplet-stream-expansion-for-the-production-of-spray-freeze-dried-powders
#17
Stefan Wanning, Richard Süverkrüp, Alf Lamprecht
In spray freeze-srying (SFD), a solution is sprayed into a refrigerant medium, frozen, and subsequently sublimation dried, which allows the production of flowable lyophilized powders. SFD allows commonly freeze-dried active pharmaceutical ingredients (e.g., proteins and peptides) to be delivered using new applications such as needle-free injection and nasal or pulmonary drug delivery. In this study, a droplet stream was injected into a vortex of cold gas in order to reduce the risk of droplet collisions and therefore droplet growth before congelation, which adversely affects the particle size distribution...
October 19, 2016: AAPS PharmSciTech
https://www.readbyqxmd.com/read/27758749/-an-intimate-look-at-the-viral-replication-cycle-through-ribosome-profiling
#18
Juliana Blin, Emiliano P Ricci
Next Generation Sequencing (NGS) techniques have revolutionized most biomedical research fields over the past decade by allowing a broader vision on biological processes that occur at the molecular level. Among these, ribosome profiling or footprinting is a powerful tool to study mRNA translation in a transcriptome-wide manner. Ribosome profiling has been used to study the impact of translational control of gene expression under many different cellular conditions including viral infections. Indeed, translation is a critical step during the viral replication cycle in which the infected cell is embezzled to produce viral proteins...
October 2016: Médecine Sciences: M/S
https://www.readbyqxmd.com/read/27755531/protein-dynamics-conformational-footprints
#19
Buyong Ma, Ruth Nussinov
No abstract text is available yet for this article.
October 18, 2016: Nature Chemical Biology
https://www.readbyqxmd.com/read/27750031/modulation-of-topoisomerase-ii%C3%AE-expression-and-chemosensitivity-through-targeted-inhibition-of-nf-y-dna-binding-by-a-diamino-p-anisyl-benzimidazole-hx-polyamide
#20
Luke Pett, Konstantinos Kiakos, Vijay Satam, Pravin Patil, Sarah Laughlin-Toth, Matthew Gregory, Michael Bowerman, Kevin Olson, Mia Savagian, Megan Lee, Moses Lee, W David Wilson, Daniel Hochhauser, John A Hartley
BACKGROUND: Sequence specific polyamide HxIP 1, targeted to the inverted CCAAT Box 2 (ICB2) on the topoisomerase IIα (topo IIα) promoter can inhibit NF-Y binding, re-induce gene expression and increase sensitivity to etoposide. To enhance biological activity, diamino-containing derivatives (HxI*P 2 and HxIP* 3) were synthesised incorporating an alkyl amino group at the N1-heterocyclic position of the imidazole/pyrrole. METHODS: DNase I footprinting was used to evaluate DNA binding of the diamino Hx-polyamides, and their ability to disrupt the NF-Y:ICB2 interaction assessed using EMSAs...
October 24, 2016: Biochimica et Biophysica Acta
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