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https://www.readbyqxmd.com/read/27925667/tracking-the-activity-of-mtorc1-in-living-cells-using-genetically-encoded-fret-based-biosensor-torcar
#1
Xin Zhou, Simin Li, Jin Zhang
Mechanistic target of rapamycin complex 1 (mTORC1) is a highly conserved serine/threonine protein kinase that responds to multiple distinct signals (e.g., growth factors, amino acids, stress, and energy level) and coordinates cell growth and proliferation. The underlying molecular mechanisms by which these stimuli regulate the activity of mTORC1 are still not fully understood. The spatial compartmentalization of mTORC1 signaling has been suggested as an important mechanism for mTORC1 to achieve the signal specificity and efficiency...
December 7, 2016: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/27924569/measuring-erk-activity-dynamics-in-single-living-cells-using-fret-biosensors
#2
Yannick Blum, Rafael D Fritz, Hyunryul Ryu, Olivier Pertz
Fluorescence resonance energy transfer (FRET)-based biosensors are powerful tools for measuring spatio-temporal signaling dynamics in single living cells with subcellular resolution. There are quite a number of already existing sensors and this technology is increasingly used to obtain quantitative dynamic datasets. In this chapter, we describe the analysis of endogenous extracellular signal-regulated kinase (ERK) activity in living cells using the EKAR2G (ERK activity reporter second generation) probe. We focus on the generation of stable cell lines expressing the EKAR2G sensor as well as data acquisition and analysis...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924491/single-molecule-fluorescence-energy-transfer-assays-for-the-characterization-of-reaction-pathways-of-mirna-argonaute-complex
#3
Myung Hyun Jo, Sungchul Hohng
Argonaute proteins are key components of the microRNA-induced silencing complexes (miRISCs) that mediate the posttranscriptional gene silencing of microRNAs and small interfering RNA (siRNAs). The complex reaction mechanism of miRISC is expected to be characterized by tracing the reaction pathways of miRISC at the single-molecule level in real time. In this chapter, we describe single-molecule fluorescence resonance energy transfer (FRET) assays to observe the target binding and reaction pathways of miRISC composed of a recombinant Argonaute and a small RNA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924490/site-specific-fluorescent-labeling-of-argonaute-for-fret-based-bio-assays
#4
Sarah Willkomm, Adrian Zander, Dina Grohmann
Deciphering the molecular mechanisms of eukaryotic Argonaute proteins is crucial for the understanding of RNA interference (RNAi), a posttranscriptional gene silencing process. Fluorescence-based single-molecule studies like single-molecule Förster resonance energy transfer (FRET) between a donor and acceptor dye represent a versatile tool to gain a mechanistic understanding of the structural dynamics of a biomolecular complex. Until today it was not possible to site-specifically introduce fluorophores into eukaryotic Argonaute...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27924007/bridging-of-double-stranded-breaks-by-the-nonhomologous-end-joining-ligation-complex-is-modulated-by-dna-end-chemistry
#5
Dylan A Reid, Michael P Conlin, Yandong Yin, Howard H Chang, Go Watanabe, Michael R Lieber, Dale A Ramsden, Eli Rothenberg
The nonhomologous end-joining (NHEJ) pathway is the primary repair pathway for DNA double strand breaks (DSBs) in humans. Repair is mediated by a core complex of NHEJ factors that includes a ligase (DNA Ligase IV; L4) that relies on juxtaposition of 3' hydroxyl and 5' phosphate termini of the strand breaks for catalysis. However, chromosome breaks arising from biological sources often have different end chemistries, and how these different end chemistries impact the way in which the core complex directs the necessary transitions from end pairing to ligation is not known...
December 6, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27922011/detecting-stoichiometry-of-macromolecular-complexes-in-live-cells-using-fret
#6
Manu Ben-Johny, Daniel N Yue, David T Yue
The stoichiometry of macromolecular interactions is fundamental to cellular signalling yet challenging to detect from living cells. Fluorescence resonance energy transfer (FRET) is a powerful phenomenon for characterizing close-range interactions whereby a donor fluorophore transfers energy to a closely juxtaposed acceptor. Recognizing that FRET measured from the acceptor's perspective reports a related but distinct quantity versus the donor, we utilize the ratiometric comparison of the two to obtain the stoichiometry of a complex...
December 6, 2016: Nature Communications
https://www.readbyqxmd.com/read/27921010/structural-insights-into-substrate-recognition-by-clostridium-difficile-sortase
#7
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/27920157/two-serk-receptor-like-kinases-interact-with-the-receptor-like-kinase-ems1-in-anther-cell-fate-determination
#8
Zhiyong Li, Yao Wang, Jian Huang, Nagib Ahsan, Gabriel Biener, Joel Paprocki, Jay J Thelen, Valerica Raicu, Dazhong Zhao
Cell signaling pathways mediated by leucine-rich repeat receptor-like kinases (LRR-RLK) are essential for plant growth, development and defense. The EMS1 (EXCESS MICROSPOROCYTES1) LRR-RLK and its small protein ligand TPD1 (TAPETUM DETERMINANT1) play a fundamental role in somatic and reproductive cell differentiation during early anther development in Arabidopsis (Arabidopsis thaliana). However, it is unclear whether other cell surface molecules serve as co-regulators of EMS1. Here, we show that SERK1 (SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE1) and SERK2 LRR-RLKs act redundantly as co-regulatory and physical partners of EMS1...
December 5, 2016: Plant Physiology
https://www.readbyqxmd.com/read/27918994/importance-of-5-6-aryl-substitution-on-the-pharmacological-profile-of-4-2-propyl-1h-benzo-d-imidazol-1-yl-methyl-1-1-biphenyl-2-carboxylic-acid-derived-ppar%C3%AE-agonists
#9
Victoria Obermoser, Robert Mauersberger, Daniela Schuster, Monika Czifersky, Marina Lipova, Monika Siegl, Ulrich Kintscher, Ronald Gust
In this structure-activity relationship study, the influence of aryl substituents at position 5 or 6 on the pharmacological profile of the partial PPARγ agonist 4'-((2-propyl-1H-benzo[d]imidazol-1-yl)methyl)-[1,1'-biphenyl]-2-carboxylic acid was investigated. This lead was previously identified as the essential part of telmisartan to induce PPARγ activation. Para-OCH3-phenyl substitution strongly increased potency and efficacy independent of the position. Both compounds represent full agonists because of strong hydrophobic contacts with the amino acid Phe363 in the ligand binding domain...
November 25, 2016: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/27918541/multidomain-structure-and-correlated-dynamics-determined-by-self-consistent-fret-networks
#10
Björn Hellenkamp, Philipp Wortmann, Florian Kandzia, Martin Zacharias, Thorsten Hugel
We present an approach that enables us to simultaneously access structure and dynamics of a multidomain protein in solution. Dynamic domain arrangements are experimentally determined by combining self-consistent networks of distance distributions with known domain structures. Local structural dynamics are correlated with the global arrangements by analyzing networks of time-resolved single-molecule fluorescence parameters. The strength of this hybrid approach is shown by an application to the flexible multidomain protein Hsp90...
December 5, 2016: Nature Methods
https://www.readbyqxmd.com/read/27917615/design-synthesis-and-evaluation-of-2-9-bis-substituted-aminomethyl-phenyl-1-10-phenanthroline-derivatives-as-g-quadruplex-ligands
#11
Nassima Meriem Gueddouda, Miyanou Rosales Hurtado, Stéphane Moreau, Luisa Ronga, Rabindra Nath Das, Solène Savrimoutou, Sandra Rubio, Adrien Marchand, Oscar Mendoza, Mathieu Marchivie, Lilian Elmi, Albain Chansavang, Vanessa Desplat, Valérie Gabelica, Anne Bourdoncle, Jean-Louis Mergny, Jean Guillon
Genomic sequences able to form guanine quadruplexes (G4) are found in oncogene promoters, in telomeres and in 5' and 3' untranslated regions as well as introns of messenger RNAs. These regions are potential targets for drugs designed to treat cancer. In the present work, we present the design and syntheses of ten new phenantroline derivatives and characterization of their interactions with G4-forming oligonucleotides. We evaluated ligand-induced stabilization and specificity and selectivity of ligands for various G4 conformations using FRET-melting experiments...
December 4, 2016: ChemMedChem
https://www.readbyqxmd.com/read/27916881/optimization-of-cyanine-dye-stability-and-analysis-of-fret-interaction-on-dna-microarrays
#12
Marcel von der Haar, Christopher Heuer, Martin Pähler, Kathrin von der Haar, Patrick Lindner, Thomas Scheper, Frank Stahl
The application of DNA microarrays for high throughput analysis of genetic regulation is often limited by the fluorophores used as markers. The implementation of multi-scan techniques is limited by the fluorophores' susceptibility to photobleaching when exposed to the scanner laser light. This paper presents combined mechanical and chemical strategies which enhance the photostability of cyanine 3 and cyanine 5 as part of solid state DNA microarrays. These strategies are based on scanning the microarrays while the hybridized DNA is still in an aqueous solution with the presence of a reductive/oxidative system (ROXS)...
November 30, 2016: Biology
https://www.readbyqxmd.com/read/27916123/a-mitochondria-targeted-fluorescence-probe-for-ratiometric-detection-of-endogenous-hypochlorite-in-the-living-cells
#13
Wen-Li Wu, Xuan Zhao, Long-Long Xi, Miao-Fei Huang, Wen-Hui Zeng, Jun-Ying Miao, Bao-Xiang Zhao
A mitochondria-targeted fluorescence probe (CPBT) for ratiometric detection of endogenous hypochlorite in the living cells was developed. CPBT could detect hypochlorite with high selectivity and sensitivity in a ratiometric manner based on FRET mechanism. In absence of hypochlorite, when CPBT was excited with absorption maximum wavelength of the donor moiety, it showed the emission of acceptor moiety because of FRET process. However, in the presence of hypochlorite, the reaction of CC double bond with hypochlorite interrupted the conjugation system resulting in the inhibition of FRET process and the emission of the donor moiety...
January 15, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/27914369/dna-tetrahedral-scaffolds-based-platform-for-the-construction-of-electrochemiluminescence-biosensor
#14
Qiu-Mei Feng, Zhen Zhou, Mei-Xing Li, Wei Zhao, Jing-Juan Xu, Hong-Yuan Chen
Proximal metallic nanoparticles (NPs) could quench the electrochemiluminescence (ECL) emission of semiconductor quantum dots (QDs) due to Förster energy transfer (FRET), but at a certain distance, the coupling of light-emission with surface plasmon resonance (SPR) result in enhanced ECL. Thus, the modification strategies and distances control between QDs and metallic NPs are critical for the ECL intensity of QDs. In this strategy, a SPR enhanced ECL sensor based on DNA tetrahedral scaffolds modified platform was reported for the detection of telomerase activity...
November 27, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27914079/assessing-vacuolar-escape-of-listeria-monocytogenes
#15
Juan J Quereda, Martin Sachse, Damien Balestrino, Théodore Grenier, Jennifer Fredlund, Anne Danckaert, Nathalie Aulner, Spencer Shorte, Jost Enninga, Pascale Cossart, Javier Pizarro-Cerdá
Listeria monocytogenes is a bacterial pathogen which invades and multiplies within non-professional phagocytes. Signaling cascades involved in cellular entry have been extensively analyzed, but the events leading to vacuolar escape remain less clear. In this chapter, we detail a microscopy FRET-based assay which allows quantitatively measuring L. monocytogenes infection and escape from its internalization vacuole, as well as a correlative light/electron microscopy method to investigate the morphological features of the vacuolar compartments containing L...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913177/effect-of-trunnion-roughness-and-length-on-the-modular-taper-junction-strength-under-typical-intraoperative-assembly-forces
#16
S Y Jauch-Matt, A W Miles, H S Gill
Modular hip implants are at risk of fretting-induced postoperative complications most likely initiated by micromotion between adjacent implant components. A stable fixation between ball head and stem-neck taper is critical to avoid excessive interface motions. Therefore, the aim of this study was to identify the effect of trunnion roughness and length on the modular taper strength under typical intraoperative assembly forces. Custom-made Titanium trunnions (standard/mini taper, smooth/grooved surface finish) were assembled with modular Cobalt-chromium heads by impaction with peak forces ranging from 2kN to 6kN...
November 29, 2016: Medical Engineering & Physics
https://www.readbyqxmd.com/read/27911813/spatiotemporal-imaging-of-small-gtpases-activity-in-live-cells
#17
Stephanie Voss, Dennis M Krüger, Oliver Koch, Yao-Wen Wu
Ras-like small GTPases function as molecular switches and regulate diverse cellular events. To examine the dynamics of signaling requires spatiotemporal visualization of their activity in the cell. Current small GTPase sensors rely on specific effector domains that are available for only a small number of GTPases and compete for endogenous regulator/effector binding. Here, we describe versatile conformational sensors for GTPase activity (COSGAs) based on the conserved GTPase fold. Conformational changes upon GDP/GTP exchange were directly observed in solution, on beads, and in live cells by Förster resonance energy transfer (FRET)...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27910732/binding-of-anti-cardiovascular-drug-to-serum-albumin-an-insight-in-the-light-of-spectroscopic-and-computational-approaches
#18
Tajalli Ilm Chandel, Gulam Rabbani, MohsinVahid Khan, Masihuz Zaman, Parvez Alam, Yasser Shahein, Rizwan Hasan Khan
Isoprenaline hydrochloride is a potential cardiovascular drug helps in the smooth functioning of the heart muscles. So, we have performed the binding study of ISO with BSA. This study was investigated by UV absorption, fluorescence, synchronous fluorescence, circular dichroism etc. The analysis of intrinsic fluorescence data showed the low binding affinity of ISO. The binding constant Kb was 2.8×103 M-1 and binding stoichiometry (n) was approximately one and the Gibb's free energy change at 310 K was determined to be -8...
December 2, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27909803/evolutionary-origin-of-endochondral-ossification-the-transdifferentiation-hypothesis
#19
REVIEW
Fret Cervantes-Diaz, Pedro Contreras, Sylvain Marcellini
The vertebrate endoskeleton results from the piecemeal assembly of bone and cartilage as well as additional types of calcified extracellular matrices produced by seemingly hybrid cell types of intermediate phenotypes between osteoblasts and chondrocytes. Hence, shedding light on the emergence and subsequent diversification of skeletal tissues represents a major challenge in vertebrate evolutionary developmental biology. A 150-year-old debate in the field was recently solved by lineage tracing experiments demonstrating that, during mouse endochondral bone development, a subset of chondrocytes evades apoptosis and transdifferentiate into osteoblasts at the chondro-osseous junction...
December 1, 2016: Development Genes and Evolution
https://www.readbyqxmd.com/read/27908723/oxidation-inhibits-pth-receptor-signaling-and-trafficking
#20
Juan A Ardura, Verónica Alonso, Pedro Esbrit, Peter A Friedman
Reactive Oxygen Species (ROS) increase during aging, potentially affecting many tissues including brain, heart, and bone. ROS alter signaling pathways and constitute potential therapeutic targets to limit oxidative damaging effects in aging-associated diseases. Parathyroid hormone receptors (PTHR) are widely expressed and PTH is the only anabolic therapy for osteoporosis. The effects of oxidative stress on PTHR signaling and trafficking have not been elucidated. Here, we used Fluorescence Resonance Energy Transfer (FRET)-based cAMP, ERK, and calcium fluorescent biosensors to analyze the effects of ROS on PTHR signaling and trafficking by live-cell imaging...
November 28, 2016: Biochemical and Biophysical Research Communications
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