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Forster resonance energy transfer

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https://www.readbyqxmd.com/read/28424742/fret-from-single-to-multiplexed-signaling-events
#1
REVIEW
Gertrude Bunt, Fred S Wouters
Förster resonance energy transfer (FRET) is a powerful tool for the visualization of molecular signaling events such as protein activities and interactions in cells. In its different implementations, FRET microscopy has been mainly used for monitoring single events. Recently, there has been a trend of extending FRET imaging towards the simultaneous detection of multiple events and interactions. The concomitant increase in experimental complexity requires a deeper understanding of the biophysical background of FRET...
April 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28422208/encapsulation-into-complex-coacervate-core-micelles-promotes-egfp-dimerization
#2
A Nolles, N J E van Dongen, A H Westphal, A J W G Visser, J M Kleijn, W J H van Berkel, J W Borst
Complex coacervate core micelles (C3Ms) are colloidal structures useful for encapsulation of biomacromolecules. We previously demonstrated that enhanced green fluorescent protein (EGFP) can be encapsulated into C3Ms using the diblock copolymer poly(2-methyl-vinyl-pyridinium)41-b-poly(ethylene-oxide)205. This packaging resulted in deviating spectroscopic features of the encapsulated EGFP molecules. Here we show that for monomeric EGFP variant (mEGFP) micellar encapsulation affects the absorption and fluorescence properties to a much lesser extent, and that changes in circular dichroism characteristics are specific for encapsulated EGFP...
April 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28421739/an-ultra-efficient-cap-exchange-protocol-to-compact-biofunctional-quantum-dots-for-sensitive-ratiometric-biosensing-and-cell-imaging
#3
Weili Wang, Yuan Guo, Christian Tiede, Siyuan Chen, Michal Kopytynski, Yifei Kong, Alexander N Kulak, Darren Tomlinson, Rongjun Chen, Michael John McPherson, Dejian Zhou
An ultra-efficient cap-exchange protocol (UCEP) that can convert hydrophobic quantum dots (QDs) into stable, biocompatible and aggregation-free water-dispersed ones at a ligand:QD molar ratio (LQMR) as low as 500, some 20-200 fold less than most literature methods has been developed. The UCEP works conveniently with air-stable lipoic acid (LA)-based ligands by exploiting tris(2-carboxylethyl phosphine) based rapid in situ reduction. The resulting QDs are compact (hydrodynamic radius, Rh, <4.5 nm), bright (retaining >90% of original fluorescence), resist nonspecific adsorption of proteins and display good stability in biological buffers even with high salt content (e...
April 19, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28415028/the-dynamics-of-multimer-formation-of-the-amphiphilic-hydrophobin-protein-hfbii
#4
M S Grunér, A Paananen, G R Szilvay, M B Linder
Hydrophobins are surface-active proteins produced by filamentous fungi. They have amphiphilic structures and form multimers in aqueous solution to shield their hydrophobic regions. The proteins rearrange at interfaces and self-assemble into films that can show a very high degree of structural order. Little is known on dynamics of multimer interactions in solution and how this is affected by other components. In this work we examine the multimer dynamics by stopped-flow fluorescence measurements and Förster Resonance Energy Transfer (FRET) using the class II hydrophobin HFBII...
April 5, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28414462/pyrene-apelin-conjugation-modulates-fluorophore-and-peptide-micelle-interactions
#5
Robin E Patterson, Nathan Weatherbee-Martin, Jan K Rainey
Bioactive apelin peptide forms ranging in length from 12 to 55 amino acids bind to and activate the apelin receptor (AR or APJ), a class A G-protein coupled receptor. Apelin-12, -17, and -36 isoforms, named according to length, with an additional N-terminal cysteine residue allowed for regiospecific and efficient conjugation of pyrene-maleimide. Through steady-state fluorescence spectroscopy, the emission properties of pyrene in aqueous buffer were compared to those of the pyrene-apelin conjugates both without and with zwitterionic or anionic micelles...
April 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28414112/binding-of-erucic-acid-with-human-serum-albumin-using-a-spectroscopic-and-molecular-docking-study
#6
Gulam Rabbani, Mohammad Hassan Baig, Arif Tasleem Jan, Eun Ju Lee, Mohsin Vahid Khan, Masihuz Zaman, Abd-ElAziem Farouk Gad, Rizwan Hasan Khan, Inho Choi
Erucic acid (EA) is one of the key fatty acids usually found in canola oil, mustard oil and rapeseed oil. Consumption of EA in primates was found to cause myocardial lipidosis and cardiac steatosis. To have an insight of the effect of EA in humans, we performed in vitro interaction studies of EA with the primary plasma protein, human serum albumin (HSA). Spectroscopic (UV-vis and fluorescence) analysis of the EA-HSA interaction revealed a static mode of quenching, with binding constant Kb ∼10(4) reflecting high affinity of EA for HSA...
April 13, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28411372/development-of-a-vivid-fret-system-based-on-a-highly-emissive-dg-dc-analogue-pair
#7
Seigi Yamamoto, Ji Hoon Han, Soyoung Park, Hiroshi Sugiyama
We report a new type of Förster Resonance Energy Transfer (FRET) system using highly emissive isomorphic nucleobase analogues. The FRET pair consists of 2- aminothieno[3,4-d]pyrimidine G-mimic deoxyribonucleoside (thdG) as an energy donor and 1,3-diaza-2-oxophenothiazine (tC) as an energy acceptor. We controlled the distance and orientation between donor and acceptor by systematic incorporation of thdG and tC into DNA sequences and investigated the FRET efficiencies. This is the first Watson-Crick base-pairable FRET pair to produce vivid colors...
April 15, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28407563/recent-advances-in-fret-for-the-study-of-protein-interactions-and-dynamics
#8
REVIEW
Kenji Okamoto, Yasushi Sako
Förster/fluorescence resonance energy transfer (FRET) has been extensively used to detect the binding state or conformation of biomolecules. In the past few decades, various in vitro and in vivo applications of FRET measurement have been developed, including FRET probes, in-cell measurements, single-molecule measurements, and combination with computer simulation. In this review, we describe recent advances in FRET methods for examining biomolecular interactions and dynamics: (i) phasor plot analysis for quantitative analysis of protein interactions, (ii) single-molecule FRET measurement for detecting conformational dynamics in live cells, and (iii) data assimilation using molecular dynamics simulation to evaluate conformation of the whole protein...
April 10, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28402880/sedimentation-of-reversibly-interacting-macromolecules-with-changes-in-fluorescence-quantum-yield
#9
Sumit K Chaturvedi, Huaying Zhao, Peter Schuck
Sedimentation velocity analytical ultracentrifugation with fluorescence detection has emerged as a powerful method for the study of interacting systems of macromolecules. It combines picomolar sensitivity with high hydrodynamic resolution, and can be carried out with photoswitchable fluorophores for multicomponent discrimination, to determine the stoichiometry, affinity, and shape of macromolecular complexes with dissociation equilibrium constants from picomolar to micromolar. A popular approach for data interpretation is the determination of the binding affinity by isotherms of weight-average sedimentation coefficients sw...
April 11, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28397914/improving-target-amino-acid-selectivity-in-a-permissive-aminoacyl-trna-synthetase-through-counter-selection
#10
Itthipol Sungwienwong, Zachary M Hostetler, Robert J Blizzard, Joseph J Porter, Camden M Driggers, Lea Z Mbengi, José A Villegas, Lee C Speight, Jeffery G Saven, John J Perona, Rahul M Kohli, Ryan A Mehl, E James Petersson
The amino acid acridon-2-ylalanine (Acd) can be a valuable probe of protein dynamics, either alone or as part of a Förster resonance energy transfer (FRET) or photo-induced electron transfer (eT) probe pair. We have previously reported the genetic incorporation of Acd by an aminoacyl tRNA synthetase (RS). However, this RS, developed from a library of permissive RSs, also incorporates N-phenyl-aminophenylalanine (Npf), a trace byproduct of one Acd synthetic route. We have performed negative selections in the presence of Npf and analyzed the selectivity of the resulting AcdRSs by in vivo protein expression and detailed kinetic analyses of the purified RSs...
April 11, 2017: Organic & Biomolecular Chemistry
https://www.readbyqxmd.com/read/28389201/optical-measurement-of-receptor-tyrosine-kinase-oligomerization-on-live-cells
#11
REVIEW
Inhee Chung
Receptor tyrosine kinases (RTK) are important cell surface receptors that transduce extracellular signals across the plasma membrane. The traditional view of how these receptors function is that ligand binding to the extracellular domains acts as a master-switch that enables receptor monomers to dimerize and subsequently trans-phosphorylate each other on their intracellular domains. However, a growing body of evidence suggests that receptor oligomerization is not merely a consequence of ligand binding, but is instead part of a complex process responsible for regulation of receptor activation...
April 4, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28386636/dynamic-monitoring-of-gi-o-protein-mediated-decreases-of-intracellular-camp-by-fret-based-epac-sensors
#12
Ursula Storch, Julie Straub, Serap Erdogmus, Thomas Gudermann, Michael Mederos Y Schnitzler
Analysis of G-protein-coupled receptor (GPCR) signaling, in particular of the second messenger cAMP that is tightly controlled by Gs- and Gi/o-proteins, is a central issue in biomedical research. The classical biochemical method to monitor increases in intracellular cAMP concentrations consists of a radioactive multicellular assay, which is well established, highly sensitive, and reproducible, but precludes continuous spatial and temporal assessment of cAMP levels in single living cells. For this purpose, Förster resonance energy transfer (FRET)-based Epac cAMP sensors are well suitable...
April 6, 2017: Pflügers Archiv: European Journal of Physiology
https://www.readbyqxmd.com/read/28381539/transient-tissue-priming-via-rock-inhibition-uncouples-pancreatic-cancer-progression-sensitivity-to-chemotherapy-and-metastasis
#13
Claire Vennin, Venessa T Chin, Sean C Warren, Morghan C Lucas, David Herrmann, Astrid Magenau, Pauline Melenec, Stacey N Walters, Gonzalo Del Monte-Nieto, James R W Conway, Max Nobis, Amr H Allam, Rachael A McCloy, Nicola Currey, Mark Pinese, Alice Boulghourjian, Anaiis Zaratzian, Arne A S Adam, Celine Heu, Adnan M Nagrial, Angela Chou, Angela Steinmann, Alison Drury, Danielle Froio, Marc Giry-Laterriere, Nathanial L E Harris, Tri Phan, Rohit Jain, Wolfgang Weninger, Ewan J McGhee, Renee Whan, Amber L Johns, Jaswinder S Samra, Lorraine Chantrill, Anthony J Gill, Maija Kohonen-Corish, Richard P Harvey, Andrew V Biankin, T R Jeffry Evans, Kurt I Anderson, Shane T Grey, Christopher J Ormandy, David Gallego-Ortega, Yingxiao Wang, Michael S Samuel, Owen J Sansom, Andrew Burgess, Thomas R Cox, Jennifer P Morton, Marina Pajic, Paul Timpson
The emerging standard of care for patients with inoperable pancreatic cancer is a combination of cytotoxic drugs gemcitabine and Abraxane, but patient response remains moderate. Pancreatic cancer development and metastasis occur in complex settings, with reciprocal feedback from microenvironmental cues influencing both disease progression and drug response. Little is known about how sequential dual targeting of tumor tissue tension and vasculature before chemotherapy can affect tumor response. We used intravital imaging to assess how transient manipulation of the tumor tissue, or "priming," using the pharmaceutical Rho kinase inhibitor Fasudil affects response to chemotherapy...
April 5, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28380300/biophysical-study-on-the-interaction-between-eperisone-hydrochloride-and-human-serum-albumin-using-spectroscopic-calorimetric-and-molecular-docking-analysis
#14
Gulam Rabbani, Mohammad Hassan Baig, Eun Ju Lee, Won Kyung Cho, Jin Yeul Ma, Inho Choi
Eperisone hydrochloride (EH) is a widely used as a muscle relaxant for patients with muscular contracture, low back pain, or spasticity. Human serum albumin (HSA), a highly soluble negatively charged, endogenous and abundant plasma protein ascribed with the ligand binding and transport properties. The current study was undertaken to explore the interaction between EH and the serum transport protein, HSA. Study of the interaction between HSA and EH was carried by UV-vis, fluorescence quenching, circular dichroism (CD) spectroscopy, FRET, and ITC...
April 5, 2017: Molecular Pharmaceutics
https://www.readbyqxmd.com/read/28379444/a-dead-box-protein-acts-through-rna-to-promote-hiv-1-rev-rre-assembly
#15
Rajan Lamichhane, John A Hammond, Raymond F Pauszek, Rae M Anderson, Ingemar Pedron, Edwin van der Schans, James R Williamson, David P Millar
The HIV-1 Rev protein activates nuclear export of unspliced and partially spliced viral RNA transcripts, which encode the viral genome and the genes encoding viral structural proteins, by binding to and oligomerizing on the Rev Response Element (RRE). The human DEAD-box protein 1 (DDX1) enhances the RNA export activity of Rev through an unknown mechanism. Using a single-molecule assembly assay and various DDX1 mutants, we show that DDX1 acts through the RRE RNA to specifically accelerate the nucleation step of the Rev-RRE assembly process...
March 31, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28378790/fast-collisional-lipid-transfer-among-polymer-bounded-nanodiscs
#16
Rodrigo Cuevas Arenas, Bartholomäus Danielczak, Anne Martel, Lionel Porcar, Cécile Breyton, Christine Ebel, Sandro Keller
Some styrene/maleic acid (SMA) copolymers solubilise membrane lipids and proteins to form polymer-bounded nanodiscs termed SMA/lipid particles (SMALPs). Although SMALPs preserve a lipid-bilayer core, they appear to be more dynamic than other membrane mimics. We used time-resolved Förster resonance energy transfer and small-angle neutron scattering to determine the kinetics and the mechanisms of phospholipid transfer among SMALPs. In contrast with vesicles or protein-bounded nanodiscs, SMALPs exchange lipids not only by monomer diffusion but also by fast collisional transfer...
April 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28378399/osmolyte-effects-on-the-conformational-dynamics-of-a-dna-hairpin-at-ambient-and-extreme-environmental-conditions
#17
Satyajit Patra, Christian Anders, Nelli Erwin, Roland Winter
The structural dynamics of a DNA hairpin (Hp) are studied in the absence and presence of the two natural osmolytes trimethylamine-N-oxide (TMAO) and urea at ambient and extreme environmental conditions, including high pressures and high temperatures, by using single-molecule Förster resonance energy transfer and fluorescence correlation spectroscopy. The effect of pressure on the conformational dynamics of the DNA Hp is investigated on a single-molecule level, providing novel mechanistic insights into its conformational conversions...
April 5, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28371153/multiplexed-nucleic-acid-hybridization-assays-using-single-fret-pair-distance-tuning
#18
Xue Qiu, Jiajia Guo, Zongwen Jin, Igor L Medintz, Niko Hildebrandt
Multiplexed photoluminescence (PL) detection plays an important role in chemical and biological sensing. Here, it is shown that time-gated (TG) detection of a single terbium-donor-based Förster resonance energy transfer (FRET) pair can be used to selectively quantify low nanomolar concentrations of multiple DNAs or microRNAs in a single sample. This study demonstrates the applicability of single-TG-FRET-pair multiplexing for molecular (Tb-to-dye) and nanoparticle (Tb-to-quantum-dot) biosensing. Both systems use acceptor-sensitization and donor-quenching for quantifying biomolecular recognition and modification of the donor-acceptor distance for tuning the PL decays...
April 3, 2017: Small
https://www.readbyqxmd.com/read/28369626/orientation-dependent-fret-system-reveals-differences-in-structures-and-flexibilities-of-nicked-and-gapped-dna-duplexes
#19
Hiromu Kashida, Ayako Kurihara, Hayato Kawai, Hiroyuki Asanuma
Differences in structures and flexibilities of DNA duplexes play important roles on recognition by DNA-binding proteins. We herein describe a novel method for structural analyses of DNA duplexes by using orientation dependence of Förster resonance energy transfer (FRET). We first analyzed canonical B-form duplex and correct structural parameters were obtained. The experimental FRET efficiencies were in excellent agreement with values theoretically calculated by using determined parameters. We then investigated DNA duplexes with nick and gaps, which are key intermediates in DNA repair systems...
March 23, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28362086/caging-and-photoactivation-in-single-molecule-f%C3%A3-rster-resonance-energy-transfer-experiments
#20
Atieh Aminian Jazi, Evelyn Ploetz, Muhamad Arizki, Balasubramaniam Dhandayuthapani, Izabela Waclawska, Reinhard Krämer, Christine Ziegler, Thorben Cordes
Caged organic fluorophores are established tools for localization-based super-resolution imaging. Their use relies on reversible deactivation of standard organic fluorophores by chemical reduction or commercially available caged dyes with ON switching of the fluorescent signal by ultraviolet (UV) light. Here, we establish caging of cyanine fluorophores and caged rhodamine dyes, i.e., chemical deactivation of fluorescence, for single-molecule Förster resonance energy transfer (smFRET) experiments with freely diffusing molecules...
April 11, 2017: Biochemistry
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