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https://www.readbyqxmd.com/read/27922213/quantitative-maldi-ms-binding-assays-an-alternative-to-radiolabeling
#1
Maxime Rossato, Guillaume Miralles, Céline M'Kadmi, Mathieu Maingot, Muriel Amblard, Bernard Mouillac, Didier Gagne, Jean Martinez, Gilles Subra, Christine Enjalbal, Sonia Cantel
Radiolabeling of ligands is still the gold standard in the study of high-affinity receptor-ligand interactions. In an effort toward safer and simpler alternatives to the use of radioisotopes, we developed a quantitative and highly sensitive matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) method that relies on the use of chemically tagged ligands designed to be specifically detectable when present as traces in complex biological mixtures such as cellular lysates. This innovative technology allows easy, sensitive detection and accurate quantification of analytes at the sub-nanomolar level...
December 6, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27922023/systematic-site-directed-mutagenesis-of-the-helicobacter-pylori-cagl-protein-of-the-cag-type-iv-secretion-system-identifies-novel-functional-domains
#2
Tobias Bönig, Patrick Olbermann, Simon H Bats, Wolfgang Fischer, Christine Josenhans
The Cag Type IV secretion system, which contributes to inflammation and cancerogenesis during chronic infection, is one of the major virulence factors of the bacterial gastric pathogen Helicobacter pylori. We have generated and characterized a series of non-marked site-directed chromosomal mutants in H. pylori to define domains of unknown function of the essential tip protein CagL of the Cag secretion system. Characterizing the CagL mutants, we determined that their function to activate cells and transport the effector CagA was reduced to different extents...
December 6, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27922015/cryoem-structure-of-the-methanospirillum-hungatei-archaellum-reveals-structural-features-distinct-from-the-bacterial-flagellum-and-type-iv-pili
#3
Nicole Poweleit, Peng Ge, Hong H Nguyen, Rachel R Ogorzalek Loo, Robert P Gunsalus, Z Hong Zhou
Archaea use flagella known as archaella-distinct both in protein composition and structure from bacterial flagella-to drive cell motility, but the structural basis of this function is unknown. Here, we report an atomic model of the archaella, based on the cryo electron microscopy (cryoEM) structure of the Methanospirillum hungatei archaellum at 3.4 Å resolution. Each archaellum contains ∼61,500 archaellin subunits organized into a curved helix with a diameter of 10 nm and average length of 10,000 nm...
December 5, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27922008/defining-functional-interactions-during-biogenesis-of-epithelial-junctions
#4
J C Erasmus, S Bruche, L Pizarro, N Maimari, T Pogglioli, C Tomlinson, J Lees, I Zalivina, A Wheeler, A Alberts, A Russo, V M M Braga
In spite of extensive recent progress, a comprehensive understanding of how actin cytoskeleton remodelling supports stable junctions remains to be established. Here we design a platform that integrates actin functions with optimized phenotypic clustering and identify new cytoskeletal proteins, their functional hierarchy and pathways that modulate E-cadherin adhesion. Depletion of EEF1A, an actin bundling protein, increases E-cadherin levels at junctions without a corresponding reinforcement of cell-cell contacts...
December 6, 2016: Nature Communications
https://www.readbyqxmd.com/read/27921997/comparative-molecular-dynamics-study-of-dimeric-and-monomeric-forms-of-hiv-1-protease-in-ligand-bound-and-unbound-state
#5
Monikaben Padariya, Umesh Kalathiya
Human immunodeficiency virus type 1 protease is a viral-encoded enzyme and it is essential for replication and assembly of the virus. Inactivation of HIV-1 protease causes production of immature, noninfectious viral particles and thus HIV-1 protease is an attractive target in anti-AIDS drug design. In our current work, we performed molecular dynamics (MD) calculations (500 ns) for two different ligands (COM5 - designed in our previous study, and Darunavir) and made effort to understand dynamics behaviour of our designed compound COM5...
December 6, 2016: General Physiology and Biophysics
https://www.readbyqxmd.com/read/27921296/digest-selection-on-life-histories-drives-the-formation-of-functional-mitonuclear-associations1
#6
Edward McAssey
The relative importance of interactions between mitochondrial and nuclear genes on adaptation has gained increased attention (see Wolff et al., 2014), although experimental systems to make direct tests of its importance are scarce. Mitonuclear epistasis is when nuclear and mitochondrial genes interact, often at the protein level, and variation in these interactions may result in phenotypic differences (Paliwal et al., 2014). These interactions are often found in the mitochondria where the energy-generating electron transport chain (ETC) is located, and consists of both nuclear and mitochondrial proteins...
December 6, 2016: Evolution; International Journal of Organic Evolution
https://www.readbyqxmd.com/read/27921232/biological-function-and-mechanism-of-mir-33a-in-prostate-cancer-survival-and-metastasis-via-downregulating-engrailed-2
#7
Q Li, S Lu, X Li, G Hou, L Yan, W Zhang, B Qiao
OBJECTIVE: Recent studies have identified Engrailed-2 (EN-2), a homeobox-containing transcription factor, as a candidate oncogene in prostate cancer (PC). Therapeutic targeting on EN-2, however, is limited because the mechanism underlying EN-2 overexpression in prostatic cancer cells is unknown. This study was to investigate the potential regulatory role of miR-33a on EN-2 expression and explore this signaling axis in ability of prostate cancer survival and metastasis. METHODS: The relative expression of miR-33a and EN-2 in paired prostate cancer tissue and adjacent normal tissue as well as in prostate cancer cell lines, PC3 and DU145, was determined using quantitative real-time PCR or western blot, respectively...
December 5, 2016: Clinical & Translational Oncology
https://www.readbyqxmd.com/read/27921081/a-fungus-specific-protein-domain-is-essential-for-rasa-mediated-morphogenetic-signaling-in-aspergillus-fumigatus
#8
Qusai Al Abdallah, Tiffany S Norton, Amy M Hill, Lawrence L LeClaire, Jarrod R Fortwendel
Ras proteins function as conserved regulators of eukaryotic growth and differentiation and are essential signaling proteins orchestrating virulence in pathogenic fungi. Here, we report the identification of a novel N-terminal domain of the RasA protein in the filamentous fungus Aspergillus fumigatus. Whereas this domain is absent in Ras homologs of higher eukaryotes, the N-terminal extension is conserved among fungi and is characterized by a short string of two to eight amino acids terminating in an invariant arginine...
November 2016: MSphere
https://www.readbyqxmd.com/read/27921077/data-of-the-interacting-protein-networks-and-nucleotide-metabolism-pathways-related-to-ndk-and-nt5
#9
Dan Zhang, Wen Ma, Yu He, Gu He, Peng Zhang, Hongxia Zhu, Ningzhi Xu, Shufang Liang
The data presented in this article are related to the research article entitled "Antibacterial mechanism of daptomycin antibiotic against Staphylococcus aureus based on a quantitative bacterial proteome analysis" (Ma et al., 2016) [1]. Nucleoside diphosphate kinase (NDK) and 5'-nucleotidase (NT5) are two proteins related to bacterial growth. Here, a bioinformatics analysis was presented to explore NDK and NT5-invovled in the interacting protein network and purine metabolism.
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27921076/yeast-2-hybrid-data-file-showing-progranulin-interactions-in-human-fetal-brain-and-bone-marrow-libraries
#10
Irmgard Tegeder
Progranulin deficiency in humans is associated with neurodegeneration. Its mechanisms are not yet fully understood. We performed a Yeast-2-Hybrid screen using human full-length progranulin as bait to assess the interactions of progranulin. Progranulin was screened against human fetal brain and human bone marrow libraries using the standard Matchmaker technology (Clontech). This article contains the full Y2H data table, including blast results and sequences, a sorted table according to selection criteria for likely positive, putatively positive, likely false and false preys, and tables showing the gene ontology terms associated with the likely and putative preys of the brain and bone marrow libraries...
December 2016: Data in Brief
https://www.readbyqxmd.com/read/27921011/mechanisms-of-infectivity-and-evasion-derived-from-microvesicles-cargo-produced-by-trypanosoma-cruzi
#11
REVIEW
Bruna C Borges, Isadora A Uehara, Laysa O S Dias, Paula C Brígido, Claudio V da Silva, Marcelo J B Silva
Cell invasion by the intracellular protozoans requires interaction of proteins from both the host and the parasite. Many parasites establish chronic infections, showing they have the potential to escape the immune system; for example, Trypanosoma cruzi is an intracellular parasite that causes Chagas disease. Parasite internalization into host cell requires secreted and surface molecules, such as microvesicles. The release of microvesicles and other vesicles, such as exosomes, by different eukaryotic organisms was first observed in the late twentieth century...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27921010/structural-insights-into-substrate-recognition-by-clostridium-difficile-sortase
#12
Jui-Chieh Yin, Chun-Hsien Fei, Yen-Chen Lo, Yu-Yuan Hsiao, Jyun-Cyuan Chang, Jay C Nix, Yuan-Yu Chang, Lee-Wei Yang, I-Hsiu Huang, Shuying Wang
Sortases function as cysteine transpeptidases that catalyze the covalent attachment of virulence-associated surface proteins into the cell wall peptidoglycan in Gram-positive bacteria. The substrate proteins targeted by sortase enzymes have a cell wall sorting signal (CWSS) located at the C-terminus. Up to date, it is still not well understood how sortases with structural resemblance among different classes and diverse species of bacteria achieve substrate specificity. In this study, we focus on elucidating the molecular basis for specific recognition of peptide substrate PPKTG by Clostridium difficile sortase B (Cd-SrtB)...
2016: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/27920798/evolutionary-and-functional-features-of-copy-number-variation-in-the-cattle-genome
#13
Brittney N Keel, Amanda K Lindholm-Perry, Warren M Snelling
Genomic structural variations are an important source of genetic diversity. Copy number variations (CNVs), gains and losses of large regions of genomic sequence between individuals of a species, have been associated with a wide variety of phenotypic traits. However, in cattle, as well as many other species, relatively little is understood about CNV, including frequency of CNVs in the genome, sizes, and locations, chromosomal properties, and evolutionary processes acting to shape CNV. In this work, we focused on copy number variation in the bovine genome, with the aim to detect CNVs in Bos taurus coding sequence and explore potential evolutionary mechanisms shaping these CNV...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27920769/transcriptional-profiling-of-type-ii-toxin-antitoxin-genes-of-helicobacter-pylori-under-different-environmental-conditions-identification-of-hp0967-hp0968-system
#14
María G Cárdenas-Mondragón, Miguel A Ares, Leonardo G Panunzi, Sabino Pacheco, Margarita Camorlinga-Ponce, Jorge A Girón, Javier Torres, Miguel A De la Cruz
Helicobacter pylori is a Gram-negative bacterium that colonizes the human gastric mucosa and is responsible for causing peptic ulcers and gastric carcinoma. The expression of virulence factors allows the persistence of H. pylori in the stomach, which results in a chronic, sometimes uncontrolled inflammatory response. Type II toxin-antitoxin (TA) systems have emerged as important virulence factors in many pathogenic bacteria. Three type II TA systems have previously been identified in the genome of H. pylori 26695: HP0315-HP0316, HP0892-HP0893, and HP0894-HP0895...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920755/finding-potential-therapeutic-targets-against-shigella-flexneri-through-proteome-exploration
#15
Mohammad Uzzal Hossain, Md Arif Khan, Abu Hashem, Md Monirul Islam, Mohammad Neaz Morshed, Chaman Ara Keya, Md Salimullah
Background:Shigella flexneri is a gram negative bacteria that causes the infectious disease "shigellosis." S. flexneri is responsible for developing diarrhea, fever, and stomach cramps in human. Antibiotics are mostly given to patients infected with shigella. Resistance to antibiotics can hinder its treatment significantly. Upon identification of essential therapeutic targets, vaccine and drug could be effective therapy for the treatment of shigellosis. Methods: The study was designed for the identification and qualitative characterization for potential drug targets from S...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27920664/investigation-of-snp-rs2060546-immediately-upstream-to-ntn4-in-a-danish-gilles-de-la-tourette-syndrome-cohort
#16
Shanmukha S Padmanabhuni, Rayan Houssari, Ann-Louise Esserlind, Jes Olesen, Thomas M Werge, Thomas F Hansen, Birgitte Bertelsen, Fotis Tsetsos, Peristera Paschou, Zeynep Tümer
Gilles de la Tourette syndrome (GTS) is a neuropsychiatric disorder characterized by multiple motor and vocal tics. GTS is a complex disorder, with environmental factors and several genes involved. Although variations within a few genes such as AADAC, NRXN1, SLITRK1, HDC, and IMMP2L have been tentatively associated with GTS (in a small number of patients), the causative genes underlying GTS pathophysiology remain unknown. In a previous genome-wide association study (GWAS) a single nucleotide polymorphism (SNP, rs2060546) near the Netrin-4 (NTN4 - MIM 610401) gene was shown to be associated with GTS [odds ratio (OR) = 1...
2016: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/27920522/incorporation-of-heparin-binding-proteins-into-preformed-dextran-sulfate-chitosan-nanoparticles
#17
Paula Zaman, Julia Wang, Adam Blau, Weiping Wang, Tina Li, Daniel S Kohane, Joseph Loscalzo, Ying-Yi Zhang
Incorporation of proteins into dextran sulfate (DS)-chitosan (CS) nanoparticles (DSCS NPs) is commonly performed using entrapment procedures, in which protein molecules are mixed with DS and CS until particle formation occurs. As DS is an analog of heparin, the authors examined whether proteins could be directly incorporated into preformed DSCS NPs through a heparin binding domain-mediated interaction. The authors formulated negatively-charged DSCS NPs, and quantified the amount of charged DS in the outer shell of the particles...
2016: International Journal of Nanomedicine
https://www.readbyqxmd.com/read/27920426/crystal-structure-based-discovery-of-a-novel-synthesized-parp1-inhibitor-ol-1-with-apoptosis-inducing-mechanisms-in-triple-negative-breast-cancer
#18
Leilei Fu, Shuya Wang, Xuan Wang, Peiqi Wang, Yaxin Zheng, Dahong Yao, Mingrui Guo, Lan Zhang, Liang Ouyang
Poly (ADP-ribose) polymerase-1 (PARP1) is a highly conserved enzyme focused on the self-repair of cellular DNA damage. Until now, numbers of PARP inhibitors have been reported and used for breast cancer therapy in recent years, especially in TNBC. However, developing a new type PARP inhibitor with distinctive skeleton is alternatively promising strategy for TNBC therapy. In this study, based on co-crystallization studies and pharmacophore-docking-based virtual screening, we discovered a series of dihydrodibenzo[b,e]-oxepin compounds as PARP1 inhibitors...
December 2016: Scientific Reports
https://www.readbyqxmd.com/read/27920344/smad3-4-binding-to-promoter-ii-of-p450arom-so-as-to-regulate-aromatase-expression-in-endometriosis
#19
Juan Qu, Yuanyuan Zhu, Xiadi Wu, Juan Zheng, Zhen Hou, Yugui Cui, Yundong Mao, Jiayin Liu
Activin A can stimulate aromatase P450 (P450arom) expression in eutopic endometrial stromal cells (ESCs) of endometriosis by activin type I receptor-Smad pathway. In order to identify Smad3/4 binding to P450arom promoter II that mediates activin A response in ESCs, polymerase chain reaction (PCR) products of a serial truncated deletion of the P450arom promoter II region between -904 and +87 bp were inserted into the pGL3-basic vector to generate the promoter reporter plasmids. Luciferase reporter plasmids were cotransfected into cells with or without activin A (25 ng/mL)...
December 5, 2016: Reproductive Sciences
https://www.readbyqxmd.com/read/27920299/the-type-iii-secretion-system-effector-sptp-of-salmonella-enterica-serovar-typhi
#20
Rebecca Johnson, Alexander Byrne, Cedric N Berger, Elizabeth Klemm, Valerie F Crepin, Gordon Dougan, Gad Frankel
: Salmonella enterica serovars causes gastroenteritis or typhoid fever in humans, with virulence depending on the action of two type III secretion systems (SPI-1 and SPI-2). SptP is a Salmonella SPI-1 effector, involved in mediating recovery of the host cytoskeleton post-infection. SptP requires a chaperone, SicP, for stability and secretion. SptP has 94% identity between S Typhimurium and S Typhi; direct comparison of the protein sequences revealed that S Typhi SptP has numerous amino acid changes within its chaperone-binding domain...
December 5, 2016: Journal of Bacteriology
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