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TIRF microscopy can be used in conjunction with CFP/YFP FRET to detect movements of the cytoplasmic tails of GIRK channels (Riven et al., this issue of Neuron). This innovative combination of techniques allows molecular resolution of small motions underlying ion channel activation by G proteins and will likely find widespread use for study of membrane-associated molecules.
L-type Ca(2+) channels possess a Ca(2+)-dependent inactivation (CDI) mechanism, affording feedback in diverse neurobiological settings and serving as prototype for unconventional calmodulin (CaM) regulation emerging in many Ca(2+) channels. Crucial to such regulation is the preassociation of Ca(2+)-free CaM (apoCaM) to channels, facilitating rapid triggering of CDI as Ca(2+)/CaM shifts to a channel IQ site (IQ). Progress has been hindered by controversy over the preassociation site, as identified by in vitro assays. Most critical has been the failure to resolve a functional signature of preassociation. Here, we deploy novel FRET assays in live cells to identify a 73 aa channel segment, containing IQ, as the critical preassociation pocket. IQ mutations disrupting preassociation revealed accelerated voltage-dependent inactivation (VDI) as the functional hallmark of channels lacking preassociated CaM. Hence, the alpha(1C) IQ segment is multifunctional-serving as ligand for preassociation and as Ca(2+)/CaM effector site for CDI.
Many neurodegenerative diseases, including tauopathies, Parkinson's disease, amyotrophic lateral sclerosis, and the polyglutamine diseases, are characterized by intracellular aggregation of pathogenic proteins. It is difficult to study modifiers of this process in intact cells in a high-throughput and quantitative manner, although this could facilitate molecular insights into disease pathogenesis. Here we introduce a high-throughput assay to measure intracellular polyglutamine protein aggregation using fluorescence resonance energy transfer (FRET). We screened over 2800 biologically active small molecules for inhibitory activity and have characterized one lead compound in detail. Y-27632, an inhibitor of the Rho-associated kinase p160ROCK, diminished polyglutamine protein aggregation (EC(50) congruent with 5 microM) and reduced neurodegeneration in a Drosophila model of polyglutamine disease. This establishes a novel high-throughput approach to study protein misfolding and aggregation associated with neurodegenerative diseases and implicates a signaling pathway of previously unrecognized importance in polyglutamine protein processing.
Hexapeptides incorporating two fluorophores flanking a tripeptide sequence that binds Ni(II) and Cu(II) with high affinity have been synthesized. While Cu(II) quenches the fluorescence of the resulting peptides, coordination of Ni(II) enables enhanced FRET (fluorescent resonance energy transfer) from one fluorophore to the other.
The diverse effects of TCR agonists and antagonists on T cell activation are believed to be modified by the differential recruitment of CD4 or CD8 coreceptors to the TCR-MHCp complex. We used three-dimensional live cell imaging of fluorescence resonance energy transfer (FRET) between CD3zeta and CD4 fused to variants of the green fluorescent protein to investigate TCR-CD4 interactions during T cell activation. We demonstrate that recognition of agonist MHCp complexes triggers intermolecular interaction between CD4 and TCR, detectable across the T-hybridoma-APC contact area. This interaction is blocked by the presence of antagonist ligands without decreasing the recruitment of zeta and CD4 or preventing their partial colocalization in the immunological synapse.
Assay miniaturization applicable across a wide range of target classes, along with automation and process integration, are well-recognized goals for ultra-high-throughput screening on an industrial scale. This report summarizes the implementation of fluorescence resonance energy transfer (FRET)-based biochemical and cell-based assays in 3456-well NanoWelltrade mark assay plates using key components of Aurora's ultra-high-throughput screening system.
How the occupied KDEL receptor ERD2 is sorted into COPI vesicles for Golgi-to-ER transport is largely unknown. Here, interactions between proteins of the COPI transport machinery occurring during a "wave" of transport of a KDEL ligand were studied in living cells. FRET between CFP and YFP fusion proteins was measured by multifocal multiphoton microscopy and bulk-cell spectrofluorimetry. Ligand binding induces oligomerization of ERD2 and recruitment of ARFGAP to the Golgi, where the (ERD2)n/ARFGAP complex interacts with membrane-bound ARF1. During KDEL ligand transport, interactions of ERD2 with beta-COP and p23 decrease and the proteins segregate. Both p24a and p23 interact with ARF1, but only p24 interacts with ARFGAP. These findings suggest a model for how cargo-induced oligomerization of ERD2 regulates its sorting into COPI-coated buds.
In established methods for analyzing ribozyme kinetics, radiolabeled RNA substrates are primarily used. Each data point requires the cumbersome sampling, gel electrophoretic separation, and quantitation of reaction products, apart from the continuous loss of substrate by radioactive decay. We have used stable, double fluorescent end-labeled RNA substrates. Fluorescence of one fluorophore is quenched by intramolecular energy transfer (FRET). Upon substrate cleavage, both dyes become separated in two RNA products and fluorescence is restored. This can be followed in real time and ribozyme reactions can be analyzed under multiple (substrate excess) and under single (ribozyme excess) turnover conditions. A detailed comparison of unlabeled, single, and double fluorescent-labeled RNAs revealed moderate kinetic differences. Results with two systems, hammerhead ribozymes in I/II (small ribozyme, large substrate) and in I/III format (large ribozyme, small substrate), are reported.
Site-directed mutagenesis provides a straightforward means of creating specific targets for chemical modifications of proteins. This capability enhanced the applications of spectroscopic methods adapted for addressing specific structural questions such as the characterization of partially folded and transient intermediate structures of globular proteins. Some applications such as the steady state or time-resolved fluorescence resonance energy transfer (FRET) detection of the kinetics of protein folding require relatively large quantities (approximately 10-100 mg) of site-specific doubly labeled protein samples. Engineered cysteine residues are common targets for labeling of proteins. The challenge here is to develop methods for selective modification of one of two reactive sulfhydryl groups in a protein molecule. A general systematic procedure for selective labeling of each of two cysteine residues in a protein molecule was developed, using Escherichia coli adenylate kinase (AKe) as a model protein. Potential sites for insertion of cysteine residues were selected by examination of the crystal structure of the protein. A series of single-cysteine mutants was prepared, and the rates of the reaction of each engineered cysteine residue with a reference reagent [5,5'-dithiobis(2-nitrobenzoic acid) (DTNB)] were determined. Two-cysteine mutants were prepared by selection of pairs of sites for which the ratio of this reaction rate constant was high (>80). The conditions for the selective labeling reaction were optimized. In a first cycle of labeling, the more reactive cysteine residue was labeled with a fluorescent probe (donor). The second probe was attached to the less reactive site under unfolding conditions in the second cycle of labeling. The doubly and singly labeled mutants retained full enzymatic activity and the capacity for a reversible folding-unfolding transition. High yields (70-90%) of the preparation of the pure, site-specific doubly labeled AK mutant were obtained. The procedure described herein is a general outline of procedures, which can meet the double challenge of both site specificity and large-scale preparation of doubly labeled proteins.
Phosphoinositides are important signal transduction intermediates in cell growth, survival, and motility. We have invented a fluorescence sensor for polyphosphorylated phosphoinositides based on a peptide derived from the Listeria protein ActA that undergoes a random coil to helix transition upon lipid binding. The sensor, termed CAY, is a fusion protein of cyan and yellow fluorescent proteins flanking the peptide at its N- and C-termini, respectively. CAY displays fluorescence resonance energy transfer in vitro in the absence of phosphorylated phosphoinositides, and this energy transfer is lost upon interaction with these phospholipids. These results demonstrate that a short peptide undergoing a coil to helix transition can be sufficient for the engineering of a FRET-based biosensor. CAY is predominantly localized to the cytoplasm in fibroblasts expressing the sensor but shows loss of fluorescence resonance energy transfer in regions of active actin dynamics such as ruffles that have previously been demonstrated to contain high levels of phosphoinositides.
An inhibition assay method was developed based on the modulation in the FRET efficiency between quantum dots (QDs) and gold nanoparticles (AuNPs) in the presence of the molecules which inhibit the interactions between QD- and AuNP-conjugated biomolecules. For the functionalization, AuNPs were first stabilized by chemisorption of n-alkanethiols and then capped with the first generation polyamidoamine (G1 PAMAM) dendrimers. By employing a streptavidin-biotin couple as a model system, avidin was quantitatively analyzed as an inhibitor by sensing the change in photoluminescence (PL) quenching of SA-QDs by biotin-AuNPs. The detection limit for avidin was about 10 nM. It is anticipated that the PL quenching-based sensing system can be used for the quantitative analysis and high throughput screening of molecules which inhibit the specific biomolecular interactions.
Optical-based distance measurements are essential for tracking biomolecular conformational changes, drug discovery, and cell biology. Traditional Forster resonance energy transfer (FRET) is efficient for separation distances up to 100 A. We report the first successful application of a dipole-surface type energy transfer from a molecular dipole to a nanometal surface that more than doubles the traditional Forster range (220 A) and follows a 1/R(4) distance dependence. We appended a 1.4 nm Au cluster to the 5' end of one DNA strand as the energy acceptor and a fluorescein (FAM) to the 5' end of the complementary strand as the energy donor. Analysis of the energy transfer on DNA lengths (15, 20, 30, 60bp), complemented by protein-induced DNA bending, provides the basis for fully mapping the extent of this dipole surface type mechanism over its entire usable range (50-250 A). Further, protein function is fully compatible with these nanometal-DNA constructs. Significantly extending the range of optical based methods in molecular rulers is an important leap forward for biophysics.
Control over supramolecular assemblies of donor and acceptor arrays in nanoscale dimension that facilitate efficient energy transfer resulting in tunable emission is an outstanding challenge. In pursuit of this goal, we have designed a supramolecular donor-acceptor organogel with tunable emission from green to red through controlled energy transfer by simply varying the acceptor concentration. Temperature-dependent UV/vis absorption, XRD, and AFM studies of the coassembly of 1 (donor) and 2 (acceptor) revealed the intercalation of 2 within the self-assembly of 1. Upon excitation of the decane gels of 1 with 0-2 mol % of 2, quenching of the emission of the former at 509 nm with the formation of the monomer emission of the latter at 555 nm is observed. Upon further addition of 2 (2-20 mol %), the emission was continuously red-shifted to 610 nm, which corresponds to the aggregate emission of 2. Consequently, a 98% quenching of the donor emission was observed at 509 nm. Fluorescence microscopic studies provided visual evidence for the color tuning of the FRET emission. Thus efficient trapping of excitons by "isolated" or "aggregated" acceptors through a subtle control of the self-assembly and the photophysical properties of the donor-acceptor building blocks allowed a continuous shifting of the emission color anywhere between green and red (lambdamax, 509-610 nm) in a supramolecular light harvesting system.
We have developed fluoro-substituted versions of the biarsenical-tetracysteine label FlAsH, exhibiting significant improvements in important properties over the original fluorescein derivative. In complexes with tetracysteine targets, F2FlAsH exhibits 50 times improved photostability, lower pH sensitivity, higher absorbance and quantum yield than FlAsH, and F4FlAsH adds a new color to the palette of biarsenical dyes. The two probes also provide a new FRET pair with a larger Ro value (54 A) than any previously obtained with biarsenical dyes.
beta-O-N-Acetyl-d-glucosamine (O-GlcNAc) is a dynamic carbohydrate modification that is involved in cell signaling and has been implicated in a variety of disease states, including Alzheimer's and type-II diabetes. Despite the importance of this modification, little is known about the spatial and temporal localization of O-GlcNAc during signaling. This is due to the lack of methods for the study of O-GlcNAc in living cell systems. Herein we report the first genetically encoded FRET-based sensor for the detection of O-GlcNAc dynamics in live mammalian cells.
Generation of functionally active biomolecular monolayers is important in both analytical science and biophysical analyses. Our ability to monitor the redox-active state of immobilized proteins or enzymes at a molecular level, from which stochastic and surface-induced variations would be apparent, is impeded by comparatively slow electron-transfer kinetics and associated signal:noise difficulties. We demonstrate herein that by covalently tethering an appropriate dye to the copper protein azurin a highly oxidation-state-sensitive FRET process can be established which enables redox switching to be optically monitored at protein levels down to the zeptomolar limit. The surface-potential-induced cycling of emission enables the redox potential of clusters of a few hundred molecules to be determined.
We report gold nanoparticle based FRET assay to monitor the cleavage of DNA by nucleases. Fluorescence signal enhancement is observed by a factor of 120 after the cleavage reaction in the presence of S1 nuclease. The mechanism of distant dependent fluorescence quenching has been discussed. Our experimental results on distance dependent fluorescence quenching match quite well with theoretical findings obtained from the fluorescence quenching model by Gersten and Nitzan (Surf. Sci. 1985, 158, 165). Our experimental observation paradigm for the design of optical based molecular ruler strategies at distances more than double the distances achievable using traditional dipole-dipole Columbic energy transfer based methods.
A combination of shape memory characteristics, pseudoelasticity, and good damping properties make near-equiatomic nickel-titanium (Ni-Ti) alloy a desirable candidate material for certain biomedical device applications. The alloy has moderately good wear resistance, however, further improvements in this regard would be beneficial from the perspective of reducing wear debris generation, improving biocompatibility, and preventing failure during service. Fretting wear tests of Ni-Ti in both austenitic and martensitic microstructural conditions were performed with the goal of simulating wear which medical devices such as stents may experience during surgical implantation or service. The tests were performed using a stainless steel stylus counter-wearing surface under dry conditions and also with artificial plasma containing 80 g/L albumen protein as lubricant. Additionally, the research explores the feasibility of surface modification by sequential ion implantation with argon and oxygen to enhance the wear characteristics of the Ni-Ti alloy. Each of these implantations was performed to a dose of 3 x 10(17) atom/cm(2) and an energy of 50 kV, using the plasma source ion implantation process. Improvements in wear resistance were observed for the austenitic samples implanted with argon and oxygen. Ion implantation with argon also reduced the surface Ni content with respect to Ti due to differential sputtering rates of the two elements, an effect that points toward improved biocompatibility.