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Binding site

Sandra Claes, Thomas D'huys, Anneleen Van Hout, Dominique Schols, Tom Van Loy
G protein-coupled receptors (GPCRs) are of great importance to the pharmaceutical industry as they are involved in many human diseases and include well-validated targets for therapeutic intervention. Discovery of lead compounds, including small synthetic molecules, that specifically inhibit the receptor's function, is an important initial step in drug development and relies on sensitive, specific, and robust cell-based assays. Here, we describe a kinetic cellular assay with a fluorescent readout primarily designed to identify receptor-specific antagonists that inhibit the intracellular Ca2+ release evoked upon the activation of the CXC chemokine receptor 4 (CXCR4) by its endogenous ligand, the CXC chemokine ligand 12 (CXCL12)...
February 20, 2018: Journal of Visualized Experiments: JoVE
Gizem Ertürk, Rolf Lood
The ability to detect and quantitate biomolecules in complex solutions has always been highly sought-after within natural science; being used for the detection of biomarkers, contaminants, and other molecules of interest. A commonly used technique for this purpose is the Enzyme-linked Immunosorbent Assay (ELISA), where often one antibody is directed towards a specific target molecule, and a second labeled antibody is used for the detection of the primary antibody, allowing for the absolute quantification of the biomolecule under study...
February 16, 2018: Journal of Visualized Experiments: JoVE
Carla Lloret-Fernández, Miren Maicas, Carlos Mora-Martínez, Alejandro Artacho, Angela Jimeno-Martín, Laura Chirivella, Peter Weinberg, Nuria Flames
Cell differentiation is controlled by individual transcription factors (TFs) that together activate a selection of enhancers in specific cell types. How these combinations of TFs identify and activate their target sequences remains poorly understood. Here, we identify the cis -regulatory transcriptional code that controls the differentiation of serotonergic HSN neurons in C. elegans . Activation of the HSN transcriptome is directly orchestrated by a collective of six TFs. Binding site clusters for this TF collective form a regulatory signature that is sufficient for de novo identification of HSN neuron functional enhancers...
March 19, 2018: ELife
Joana Isidro, Andrea Santos, Alexandra Nunes, Vítor Borges, Catarina Silva, Luís Vieira, Aristides L Mendes, Mónica Serrano, Adriano O Henriques, João Paulo Gomes, Mónica Oleastro
We describe imipenem-resistant and imipenem-susceptible clinical isolates of Clostridium difficile ribotype 017 in Portugal. All ribotype 017 isolates carried an extra penicillin-binding protein gene, pbp5, and the imipenem-resistant isolates had additional substitutions near the transpeptidase active sites of pbp1 and pbp3. These clones could disseminate and contribute to imipenem resistance.
April 2018: Emerging Infectious Diseases
Greg A Mutch, Sarah Shulda, Alan J McCue, Martin J Menart, Cristian V Ciobanu, Chilan Ngo, James A Anderson, Ryan M Richards, David Vega-Maza
Solid metal oxides for carbon capture exhibit reduced adsorption capacity following high temperature exposure, due to surface area reduction by sintering. Furthermore, only low coordinate corner/edge sites on the thermodynamically sta-ble (100) facet display favourable binding towards CO2 , providing inherently low capacity. The (111) facet however, exhibits a high concentration of low coordinate sites. In this work, MgO(111) nanosheets displayed high capacity for CO2 , as well as a ≈ 65% increase in capacity despite a ≈ 30% reduction in surface area following sintering (0...
March 19, 2018: Journal of the American Chemical Society
Daisuke Kondoh, Motoki Sasaki, Nobuo Kitamura
Receptor cells of the olfactory epithelium (OE) and vomeronasal organ (VNO) project axons to glomeruli in the main olfactory bulb (MOB) and accessory olfactory bulb (AOB), respectively and undergo continuous turnover throughout life. Alpha1-2 fucose (α1-2Fuc) glycan mediates neurite outgrowth and synaptic plasticity and plays important roles in the formation of the olfactory system during development. We previously confirmed the localization of α1-2Fuc glycan in the olfactory system of 3- to 4-month-old mice but whether such localization persists throughout life remains unknown...
March 19, 2018: Cell and Tissue Research
Bhavana V Mohite, Sunil H Koli, Satish V Patil
Currently, the heavy metal pollution is of grave concern, and the part of microorganism for metal bioremediation should take into account as an efficient and economic strategy. On this framework, the heavy metal stress consequences on exopolysaccharide (EPS)-producing agricultural isolate, Pantoea agglomerans, were studied. The EPS production is a protective response to stress to survive and grow in the metal-contaminated environment. P. agglomerans show tolerance and mucoid growth in the presence of heavy metals, i...
March 19, 2018: Applied Biochemistry and Biotechnology
Seeyoung Choi, Paul E Love
Oxidative inactivation of cysteine-dependent Protein Tyrosine Phosphatases (PTPs) by cellular reactive oxygen species (ROS) plays a critical role in regulating signal transduction in multiple cell types. The phosphatase activity of most PTPs depends upon a 'signature' cysteine residue within the catalytic domain that is maintained in the de-protonated state at physiological pH rendering it susceptible to ROS-mediated oxidation. Direct and indirect techniques for detection of PTP oxidation have been developed (Karisch and Neel, 2013)...
January 5, 2018: Bio-protocol
Ava Yuan Xue, Antonella Di Pizio, Anat Levit, Tali Yarnitzky, Osnat Penn, Tal Pupko, Masha Y Niv
The 25 human bitter taste receptors (hT2Rs) recognize thousands of structurally and chemically diverse bitter substances. The binding modes of human bitter taste receptors hT2R10 and hT2R46, which are responsible for strychnine recognition, were previously established using site-directed mutagenesis, functional assays, and molecular modeling. Here we construct a phylogenetic tree and reconstruct ancestral sequences of the T2R10 and T2R46 clades. We next analyze the binding sites in view of experimental data to predict their ability to recognize strychnine...
2018: Frontiers in Molecular Biosciences
Fangfang Tao, Xinxin Tian, Zhiqian Zhang
Long non-coding RNAs (lncRNAs) have been reported to be of great importance in the formation and progression of a wide range of human carcinomas including prostate cancer (PCa). Among them, PCAT3 and PCAT9 have been identified as two prostate tissue-specific lncRNAs and are up-regulated in PCa. However, their roles in the biological characteristics of PCa have not been fully elucidated. In the present study, our data revealed that knockdown of PCAT3 and PCAT9 suppressed cellular proliferation, invasion, migration, angiogenesis and stemness in androgen-dependent LNCaP and 22Rv1 cells...
February 23, 2018: Oncotarget
Mei-Yi Lu, Syuan-Shao Lu, Shiann-Luen Chang, Fang Liao
CCR6 is a G protein-coupled receptor (GPCR) that recognizes a single chemokine ligand, CCL20 and is primarily expressed by leukocytes. Upon ligand binding, CCR6 activates Gαi heterotrimeric G proteins to induce various potential cellular outcomes through context-specific cell signaling. It is well known that differential phosphorylation of Ser and Thr residues in the C-terminal domains or intracellular loops of GPCRs can generate barcodes that regulate GPCR function by regulating the recruitment of β-arrestins...
2018: Frontiers in Immunology
Andrej Steyer, Tilen Konte, Martin Sagadin, Marko Kolenc, Andrej Škoberne, Julija Germ, Tadeja Dovč-Drnovšek, Miha Arnol, Mateja Poljšak-Prijatelj
Noroviruses are the leading cause of acute gastroenteritis, and they can affect humans of all age groups. In immunocompromised patients, norovirus infections can develop into chronic diarrhea or show prolonged asymptomatic virus shedding. Chronic norovirus infections are frequently reported for solid organ transplant recipients, with rapid intrahost norovirus evolution seen. In this report, we describe a case of chronic norovirus infection in an immunocompromised patient who was followed up for over 5 years...
2018: Frontiers in Microbiology
Pin Yu, Qing-Ting Bu, Yi-Li Tang, Xu-Ming Mao, Yong-Quan Li
AdpA, an AraC/XylS family protein, had been proved as a key regulator for secondary metabolism and morphological differentiation in Streptomyces griseus . Here, we identify AdpAch , an ortholog of AdpA, as a "higher level" pleiotropic regulator of natamycin biosynthesis with bidirectional regulatory ability in Streptomyces chattanoogensis L10. DNase I footprinting revealed six AdpAch -binding sites in the scnRI - scnRII intergenic region. Further analysis using the xylE reporter gene fused to the scnRI - scnRII intergenic region of mutated binding sites demonstrated that the expression of scnRI and scnRII was under the control of AdpAch ...
2018: Frontiers in Microbiology
Eiichi Tokuda, Takao Nomura, Shinji Ohara, Seiji Watanabe, Koji Yamanaka, Yuta Morisaki, Hidemi Misawa, Yoshiaki Furukawa
Dominant mutations in the gene encoding copper and zinc-binding superoxide dismutase (SOD1) cause amyotrophic lateral sclerosis (ALS). Abnormal accumulation of misfolded SOD1 proteins in spinal motoneurons is a major pathological hallmark in SOD1-related ALS. Dissociation of copper and/or zinc ions from SOD1 has been shown to trigger the protein aggregation/oligomerization in vitro, but the pathological contribution of such metal dissociation to the SOD1 misfolding still remains obscure. Here, we tested the relevance of the metal-deficient SOD1 in the misfolding in vivo by developing a novel antibody (anti-apoSOD), which exclusively recognized mutant SOD1 deficient in metal ions at its copper-binding site...
March 15, 2018: Biochimica et Biophysica Acta
Breann L Brown, Julia R Kardon, Robert T Sauer, Tania A Baker
5-Aminolevulinic acid synthase (ALAS) catalyzes the first step in heme biosynthesis. We present the crystal structure of a eukaryotic ALAS from Saccharomyces cerevisiae. In this homodimeric structure, one ALAS subunit contains covalently bound cofactor, pyridoxal 5'-phosphate (PLP), whereas the second is PLP free. Comparison between the subunits reveals PLP-coupled reordering of the active site and of additional regions to achieve the active conformation of the enzyme. The eukaryotic C-terminal extension, a region altered in multiple human disease alleles, wraps around the dimer and contacts active-site-proximal residues...
March 5, 2018: Structure
Anthony M Mustoe, Steven Busan, Greggory M Rice, Christine E Hajdin, Brant K Peterson, Vera M Ruda, Neil Kubica, Razvan Nutiu, Jeremy L Baryza, Kevin M Weeks
mRNAs can fold into complex structures that regulate gene expression. Resolving such structures de novo has remained challenging and has limited our understanding of the prevalence and functions of mRNA structure. We use SHAPE-MaP experiments in living E. coli cells to derive quantitative, nucleotide-resolution structure models for 194 endogenous transcripts encompassing approximately 400 genes. Individual mRNAs have exceptionally diverse architectures, and most contain well-defined structures. Active translation destabilizes mRNA structure in cells...
March 13, 2018: Cell
Justin Weinberg, Shaojie Zhang, Gillian Crews, Giorgio Carta, Todd Przybycien
Chemical modification of Protein A (ProA) chromatography ligands with polyethylene glycol (PEGylation) has been proposed as a strategy to increase the process selectivity and resin robustness by providing the ligand with a steric repulsion barrier against non-specific binding. This article comprises a comprehensive study of IgG adsorption and transport in Repligen CaptivA PriMAB resin with PEGylated ProA ligands that are modified using 5.2 and 21.5 kDa PEG chains. We studied the impact of the molecular weight of the PEG as well as the extent of PEGylation for the 5...
March 9, 2018: Journal of Chromatography. A
Davar Abedini, Sajad Rashidi Monfared
A primary mechanism for controlling the development of multicellular organisms is transcriptional regulation, which carried out by transcription factors (TFs) that recognize and bind to their binding sites on promoter region. The distance from translation start site, order, orientation, and spacing between cis elements are key factors in the concentration of active nuclear TFs and transcriptional regulation of target genes. In this study, overrepresented motifs in cold and pathogenesis responsive genes were scanned via Gibbs sampling method, this method is based on detection of overrepresented motifs by means of a stochastic optimization strategy that searches for all possible sets of short DNA segments...
March 17, 2018: Molecular Biology Reports
Wei Chen, Suhong Pan, Hao Cheng, Andrew J Sweetman, Hao Zhang, Kevin C Jones
A passive water sampler based on the diffusive gradients in thin-films (DGT) technique was developed and tested for 3 groups of endocrine disrupting chemicals (EDCs, including oestrogens, alkyl-phenols and bisphenols). Three different resins (hydrophilic-lipophilic-balanced (HLB), XAD18 and Strata-XL-A (SXLA)) were investigated for their suitability as the binding phase for DGT devices. Laboratory tests across a range of pH (3.5-9.5), ionic strength (0.001-0.5 M) and dissolved organic matter concentration (0-20 mg L-1 ) showed HLB and XAD18-DGT devices were more stable compared to SXLA-DGT...
March 12, 2018: Water Research
Chong Chen, Nengjie Feng, Qirui Guo, Zhong Li, Xue Li, Jing Ding, Lei Wang, Hui Wan, Guofeng Guan
Targeting CO2 capture application, a new strategy for building multiple adsorption sites in metal-organic framework MIL-101(Cr) was constructed through the incorporation of diethylenetriamine-based ionic liquid (DETA-Ac) via a post-synthetic modification approach. The DETA-Ac, with multi-amine-tethered cation and acetate anion, could not only provide additional binding sites, but also enhance the affinity of framework surfaces toward CO2 . Simultaneously, the high surface area and large cage size of MIL-101(Cr) ensured the better dispersion of IL, thus exposing more active sites for CO2 adsorption...
March 12, 2018: Journal of Colloid and Interface Science
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