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https://www.readbyqxmd.com/read/28095775/ara-peps-a-repository-of-putative-sorf-encoded-peptides-in-arabidopsis-thaliana
#1
Rashmi R Hazarika, Barbara De Coninck, Lidia R Yamamoto, Laura R Martin, Bruno P A Cammue, Vera van Noort
BACKGROUND: Many eukaryotic RNAs have been considered non-coding as they only contain short open reading frames (sORFs). However, there is increasing evidence for the translation of these sORFs into bioactive peptides with potent signaling, antimicrobial, developmental, antioxidant roles etc. Yet only a few peptides encoded by sORFs are annotated in the model organism Arabidopsis thaliana. RESULTS: To aid the functional annotation of these peptides, we have developed ARA-PEPs (available at http://www...
January 17, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28094103/characterization-of-particulate-matter-binding-peptides-screened-from-phage-display
#2
Aw Wei Liang Alvin, Masayoshi Tanaka, Mina Okochi
Particulate matter (PM), especially particulates with diameters of less than 2.5 μm, can penetrate the alveolar region and increase the risk of respiratory diseases. This has stimulated research efforts to develop detection methods so that counter measures can be taken. In this study, four PM binding peptides were obtained by phage display and binding characteristics of these peptides were investigated using the peptide array. The strongest binding peptide, WQDFGAVRSTRS, displayed a binding property, measured in terms of spot intensity, 11...
January 13, 2017: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/28092048/using-reciprocal-protein-peptide-array-screening-to-unravel-protein-interaction-networks
#3
Huadong Liu, Courtney Voss, Shawn S C Li
Protein-protein interactions (PPIs) play a central role in almost all cellular processes. Recent technological advances have enabled the elucidation of an incredibly complex PPI network within the cell. However, protein interactions driven by posttranslational modifications (PTMs) such as phosphorylation, which comprises a significant part of the PPI network, have proven difficult to decipher systematically. Herein, we describe a reciprocal protein-peptide array strategy to uncover PPIs mediated by tyrosine phosphorylation and the Src homology 2 (SH2) domain...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092043/characterizing-sh2-domain-specificity-and-network-interactions-using-spot-peptide-arrays
#4
Bernard A Liu
Src Homology 2 (SH2) domains are protein interaction modules that recognize and bind tyrosine phosphorylated ligands. Their ability to distinguish binding to over thousands of potential phosphotyrosine (pTyr) ligands within the cell is critical for the fidelity of receptor tyrosine kinase (RTK) signaling. Within humans there are over a hundred SH2 domains with more than several thousand potential ligands across many cell types and cell states. Therefore, defining the specificity of individual SH2 domains is critical for predicting and identifying their physiological ligands...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28092031/expression-and-production-of-sh2-domain-proteins
#5
Bernard A Liu, Mari Ogiue-Ikeda, Kazuya Machida
The Src Homology 2 (SH2) domain lies at the heart of phosphotyrosine signaling, coordinating signaling events downstream of receptor tyrosine kinases (RTKs), adaptors, and scaffolds. Over a hundred SH2 domains are present in mammals, each having a unique specificity which determines its interactions with multiple binding partners. One of the essential tools necessary for studying and determining the role of SH2 domains in phosphotyrosine signaling is a set of soluble recombinant SH2 proteins. Here we describe methods, based on a broad experience with purification of all SH2 domains, for the production of SH2 domain proteins needed for proteomic and biochemical-based studies such as peptide arrays, mass-spectrometry, protein microarrays, reverse-phase microarrays, and high-throughput fluorescence polarization (HTP-FP)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28076420/chaperone-mediated-autophagy-protein-bag3-negatively-regulates-ebola-and-marburg-vp40-mediated-egress
#6
Jingjing Liang, Cari A Sagum, Mark T Bedford, Sachdev S Sidhu, Marius Sudol, Ziying Han, Ronald N Harty
Ebola (EBOV) and Marburg (MARV) viruses are members of the Filoviridae family which cause outbreaks of hemorrhagic fever. The filovirus VP40 matrix protein is essential for virus assembly and budding, and its PPxY L-domain motif interacts with WW-domains of specific host proteins, such as Nedd4 and ITCH, to facilitate the late stage of virus-cell separation. To identify additional WW-domain-bearing host proteins that interact with VP40, we used an EBOV PPxY-containing peptide to screen an array of 115 mammalian WW-domain-bearing proteins...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28074089/antiviral-activity-of-animal-venom-peptides-and-related-compounds
#7
REVIEW
Élida Cleyse Gomes da Mata, Caroline Barbosa Farias Mourão, Marisa Rangel, Elisabeth Ferroni Schwartz
Viruses exhibit rapid mutational capacity to trick and infect host cells, sometimes assisted through virus-coded peptides that counteract host cellular immune defense. Although a large number of compounds have been identified as inhibiting various viral infections and disease progression, it is urgent to achieve the discovery of more effective agents. Furthermore, proportionally to the great variety of diseases caused by viruses, very few viral vaccines are available, and not all are efficient. Thus, new antiviral substances obtained from natural products have been prospected, including those derived from venomous animals...
2017: Journal of Venomous Animals and Toxins Including Tropical Diseases
https://www.readbyqxmd.com/read/28069948/genomic-targeting-of-epigenetic-probes-using-a-chemically-tailored-cas9-system
#8
Glen P Liszczak, Zachary Z Brown, Samuel H Kim, Rob C Oslund, Yael David, Tom W Muir
Recent advances in the field of programmable DNA-binding proteins have led to the development of facile methods for genomic localization of genetically encodable entities. Despite the extensive utility of these tools, locus-specific delivery of synthetic molecules remains limited by a lack of adequate technologies. Here we combine the flexibility of chemical synthesis with the specificity of a programmable DNA-binding protein by using protein trans-splicing to ligate synthetic elements to a nuclease-deficient Cas9 (dCas9) in vitro and subsequently deliver the dCas9 cargo to live cells...
January 9, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28062494/cellular-repressor-of-e1a-stimulated-genes-is-a-critical-determinant-of-vascular-remodeling-in-response-to-angiotensin-ii
#9
Li Yang, Liu Yanxia, Tian Xiaoxiang, Zhang Yan, Song Haixu, Liu Meili, Zhang Xiaolin, Liu Haiwei, Zhang Jian, Zhang Quanyu, Liu Dan, Peng Chengfei, Yan Chenghui, Han Yaling
OBJECTIVE: Cellular repressor of E1A-stimulated genes (CREG) is a lysosomal glycoprotein implicated in maintaining vascular homeostasis. Here, we have hypothesized that CREG is a critical target of intervention for the prevention of hypertensive vascular remodeling. APPROACH AND RESULTS: CREG gene expression was significantly decreased accompanied by an upregulated expression of angiotensin II (Ang II) in remodeled vascular tissues of high salt-induced Dahl salt-sensitive rats and Ang II-induced mice...
January 5, 2017: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28061765/mir-663a-regulates-growth-of-colon-cancer-cells-after-administration-of-antimicrobial-peptides-by-targeting-cxcr4-p21-pathway
#10
Kengo Kuroda, Tomokazu Fukuda, Marija Krstic-Demonacos, Constantinos Demonacos, Kazuhiko Okumura, Hiroshi Isogai, Miwa Hayashi, Kazuki Saito, Emiko Isogai
BACKGROUND: Antimicrobial peptides (AMPs) play important roles in the innate immune system of all life forms and recently have been characterized as multifunctional peptides that have a variety of biological roles such as anticancer agents. However, detailed mechanism of antimicrobial peptides on cancer cells is still largely unknown. METHODS: miRNA array and real-time qPCR were performed to reveal the behavior of miRNA in colon cancer HCT116 cells during the growth suppression induced by the AMPs...
January 7, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28056107/autophagy-is-an-innate-mechanism-associated-with-leprosy-polarization
#11
Bruno Jorge de Andrade Silva, Mayara Garcia de Mattos Barbosa, Priscila Ribeiro Andrade, Helen Ferreira, José Augusto da Costa Nery, Suzana Côrte-Real, Gilberto Marcelo Sperandio da Silva, Patricia Sammarco Rosa, Mario Fabri, Euzenir Nunes Sarno, Roberta Olmo Pinheiro
Leprosy is a chronic infectious disease that may present different clinical forms according to the immune response of the host. Levels of IFN-γ are significantly raised in paucibacillary tuberculoid (T-lep) when compared with multibacillary lepromatous (L-lep) patients. IFN-γ primes macrophages for inflammatory activation and induces the autophagy antimicrobial mechanism. The involvement of autophagy in the immune response against Mycobacterium leprae remains unexplored. Here, we demonstrated by different autophagic assays that LC3-positive autophagosomes were predominantly observed in T-lep when compared with L-lep lesions and skin-derived macrophages...
January 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28052595/lysine-based-%C3%AE-peptide-%C3%AE-peptoid-peptidomimetics-influence-of-hydrophobicity-fluorination-and-distribution-of-cationic-charge-on-antimicrobial-activity-and-cytotoxicity
#12
Natalia Molchanova, Paul Robert Hansen, Peter Damborg, Hanne Mørck Nielsen, Henrik Franzyk
Multidrug-resistant bacteria pose a serious threat to public health worldwide. Previously, α-peptide/β-peptoid hybrid oligomers were found to display activity against Gram-negative multidrug-resistant bacteria. In the present work, the influence of hydrophobicity, fluorination and distribution of cationic/hydrophobic residues on antimicrobial, hemolytic and cytotoxic properties of α-peptide/β-peptoid hybrids were investigated. An array of 22 peptidomimetics was tested. Analogues with enhanced hydrophobicity exhibited increased activity against Gram-positive bacteria...
January 4, 2017: ChemMedChem
https://www.readbyqxmd.com/read/28042044/consecutive-elongation-of-d-amino-acids-in-translation
#13
Takayuki Katoh, Kenya Tajima, Hiroaki Suga
Recent progress in the field of genetic code reprogramming using a reconstituted cell-free translation system has made it possible to incorporate a wide array of non-proteinogenic amino acids, including N-methyl-amino acids and D-amino acids. Despite the fact that up to ten N-methyl-amino acid residues can be continuously elongated, the successive incorporation of even two D-amino acids into a nascent peptide chain remains a formidable challenge, thus far being nearly impossible. Here we report achievement of continuous D-amino acid elongation by the use of engineered tRNAs and optimized concentrations of translation factors, enabling us to incorporate up to ten consecutive D-Ser residues into a nascent peptide chain...
December 13, 2016: Cell Chemical Biology
https://www.readbyqxmd.com/read/28035955/exon-shuffling-and-origin-of-scorpion-venom-biodiversity
#14
Xueli Wang, Bin Gao, Shunyi Zhu
Scorpion venom is a complex combinatorial library of peptides and proteins with multiple biological functions. A combination of transcriptomic and proteomic techniques has revealed its enormous molecular diversity, as identified by the presence of a large number of ion channel-targeted neurotoxins with different folds, membrane-active antimicrobial peptides, proteases, and protease inhibitors. Although the biodiversity of scorpion venom has long been known, how it arises remains unsolved. In this work, we analyzed the exon-intron structures of an array of scorpion venom protein-encoding genes and unexpectedly found that nearly all of these genes possess a phase-1 intron (one intron located between the first and second nucleotides of a codon) near the cleavage site of a signal sequence despite their mature peptides remarkably differ...
December 26, 2016: Toxins
https://www.readbyqxmd.com/read/28035012/deep-sequencing-of-phage-displayed-peptide-libraries-reveals-sequence-motif-that-detects-norovirus
#15
Amy M Hurwitz, Wanzhi Huang, Mary K Estes, Robert L Atmar, Timothy Palzkill
Norovirus infections are the leading cause of non-bacterial gastroenteritis and result in about 21 million new cases and $2 billion in costs per year in the United States. Existing diagnostics have limited feasibility for point-of-care applications, so there is a clear need for more reliable, rapid, and simple-to-use diagnostic tools in order to contain outbreaks and prevent inappropriate treatments. In this study, a combination of phage display technology, deep sequencing and computational analysis was used to identify 12-mer peptides with specific binding to norovirus genotype GI...
December 28, 2016: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/28032751/synthesis-of-grb2-sh2-domain-proteins-for-mirror-image-screening-systems
#16
Taro Noguchi, Hiroyuki Ishiba, Kaori Honda, Yasumitsu Kondoh, Hiroyuki Osada, Hiroaki Ohno, Nobutaka Fujii, Shinya Oishi
Grb2 is an adaptor protein that mediates cellular signal transduction. Grb2 contains an SH2 domain that interacts with phosphotyrosine-containing sequences in EGFR and other signaling molecules, and it is a promising molecular target for anti-cancer agents. To identify novel inhibitors of the Grb2 SH2 domain from natural products and their mirror-image isomers, screening systems using both enantiomers of a synthetic Grb2 SH2 domain protein were established. Two synthetic procedures for the proteins were investigated: one employed a single native chemical ligation (NCL) of two segment peptides, and the other used the N-to-C-directed NCL of three segment peptides for easier preparation...
December 29, 2016: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28026090/the-mesenchymal-precursor-cell-marker-antibody-stro-1-binds-to-cell-surface-heat-shock-cognate-70
#17
Stephen Fitter, Stan Gronthos, Soo Siang Ooi, Andrew C W Zannettino
Since its discovery more than 25 years ago, the STRO-1 antibody has played a fundamental role in defining the hierarchical nature of mesenchymal precursor cells (MPC) and their progeny. STRO-1 antibody binding remains a hallmark of immature pluripotent MPC. Despite the significance of STRO-1 in the MPC field, the identity of the antigen has remained elusive. Using a combination of 2-dimensional gel electrophoresis, coupled with Western blotting and Tandem mass spectroscopy, we have identified the STRO-1 antigen as heat shock cognate 70 (HSC70;HSPA8)...
December 27, 2016: Stem Cells
https://www.readbyqxmd.com/read/28025877/new-insights-into-the-understanding-of-mhc-associations-with-immune-mediated-disorders
#18
REVIEW
S Caillat-Zucman
Recent advances in technologies such as high density array-based genotyping, DNA and RNA deep sequencing, expression quantitative-trait loci mapping, epigenome analyses, and new computational strategies, have introduced drastic shifts into our understanding of major histocompatibility complex (MHC) association with immune-mediated diseases. Here, we review the most exciting findings in this field. We show how the fine characterization of structural features and expression levels of MHC alleles, posttranslational or environmental modifications of HLA-bound peptides, and epistatic interactions with non-HLA genes, has made it possible not only to provide mechanistic explanations for MHC associations with immune-mediated diseases but also to help choose relevant therapeutic targets...
January 2017: HLA
https://www.readbyqxmd.com/read/28024914/topical-and-cutaneous-delivery-using-nanosystems
#19
REVIEW
M S Roberts, Y Mohammed, M N Pastore, S Namjoshi, S Yousef, A Alinaghi, I N Haridass, E Abd, V R Leite-Silva, Hae Benson, J E Grice
The goal of topical and cutaneous delivery is to deliver therapeutic and other substances to a desired target site in the skin at appropriate doses to achieve a safe and efficacious outcome. Normally, however, when the stratum corneum is intact and the skin barrier is uncompromised, this is limited to molecules that are relatively lipophilic, small and uncharged, thereby excluding many potentially useful therapeutic peptides, proteins, vaccines, gene fragments or drug-carrying particles. In this review we will describe how nanosystems are being increasingly exploited for topical and cutaneous delivery, particularly for these previously difficult substances...
December 23, 2016: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28011643/deciphering-key-residues-involved-in-the-virulence-promoting-interactions-between-streptococcus-pneumoniae-and-human-plasminogen
#20
Christophe Moreau, Rémi Terrasse, Nicole M Thielens, Thierry Vernet, Christine Gaboriaud, Anne Marie Di Guilmi
Bacterial pathogens recruit circulating proteins to their own surfaces, coopting the host protein functions as a mechanism of virulence. Particular attention has focused on the binding of plasminogen (Plg) to bacterial surfaces, as it has been shown that this interaction contributes to bacterial adhesion to host cells, invasion of host tissues and evasion of the immune system. Several bacterial proteins are known to serve as receptors for Plg including glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a cytoplasmic enzyme that appears on the cell surface in this moonlighting role...
December 23, 2016: Journal of Biological Chemistry
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