Acceptor Photobleaching Research Articles

From principles to practice: a comprehensive guide to FRET-FLIM in plants

Abstract Förster Resonance Energy Transfer combined with Fluorescence Lifetime Imaging Microscopy (FRET-FLIM) is revolutionizing plant biology, by enabling the study of protein–protein interactions (PPIs) within live cells. This manuscript describes the principles of FRET and the practical application of FRET acceptor photobleaching (FRET-APB) in exploring PPIs in vivo. It mainly focuses on the superior characteristics of FRET-FLIM and details the materials and methods for implementing this technique in plants. It provides a profound overview about the required instruments, protocols for sample preparation, methods for calibration and acquisition, and pipelines for data analyses including novel analyses for binding and FRET efficiencies. Furthermore, it discusses the potential pitfalls and challenges related to the sample autofluorescence, protein expression heterogeneity, and acquisition photodamage or bleaching. This works aims to highlight the great prospects of FRET-FLIM in advancing our understanding of PPIs in living plant cells.

De Novo Designed Cell-Penetrating Peptide Self-Assembly Featuring Distinctive Tertiary Structure.

Recent attention has focused on the de novo design of proteins, paralleling advancements in biopharmaceuticals. Achieving protein designs with both structure and function poses a significant challenge, particularly considering the importance of quaternary structures, such as oligomers, in protein function. The cell penetration properties of peptides are of particular interest as they involve the penetration of large molecules into cells. We previously suggested a link between the oligomerization propensity of amphipathic peptides and their cell penetration abilities, yet concrete evidence at cellular-relevant concentrations was lacking due to oligomers' instability. In this study, we sought to characterize oligomerization states using various techniques, including X-ray crystallography, acceptor photobleaching Förster resonance energy transfer (FRET), native mass spectrometry (MS), and differential scanning calorimetry (DSC), while exploring the function related to oligomer status. X-ray crystallography revealed the atomic structures of oligomers formed by LK-3, a bis-disulfide bridged dimer with amino acid sequence LKKLCLKLKKLCKLAG, and its derivatives, highlighting the formation of hexamers, specifically the trimer of dimers, which exhibited a stable hydrophobic core. FRET experiments showed that LK-3 oligomer formation was associated with cell penetration. Native MS confirmed higher-order oligomers of LK-3, while an intriguing finding was the enhanced cell-penetrating capability of a 1:1 mixture of l/d-peptide dimers compared to pure enantiomers. DSC analysis supported the notion that this enantiomeric mixture promotes the formation of functional oligomers, crucial for cell penetration. In conclusion, our study provides direct evidence that amphipathic peptide LK-3 forms oligomers at low nanomolar concentrations, underscoring their significance in cell penetration behavior.

Assessment of the FRET-based Teen sensor to monitor ERK activation changes preceding morphological defects in a RASopathy zebrafish model and phenotypic rescue by MEK inhibitor

BackgroundRASopathies are genetic syndromes affecting development and having variable cancer predisposition. These disorders are clinically related and are caused by germline mutations affecting key players and regulators of the RAS-MAPK signaling pathway generally leading to an upregulated ERK activity. Gain-of-function (GOF) mutations in PTPN11, encoding SHP2, a cytosolic protein tyrosine phosphatase positively controlling RAS function, underlie approximately 50% of Noonan syndromes (NS), the most common RASopathy. A different class of these activating mutations occurs as somatic events in childhood leukemias.MethodHere, we evaluated the application of a FRET-based zebrafish ERK reporter, Teen, and used quantitative FRET protocols to monitor non-physiological RASopathy-associated changes in ERK activation. In a multi-level experimental workflow, we tested the suitability of the Teen reporter to detect pan-embryo ERK activity correlates of morphometric alterations driven by the NS-causing Shp2D61G allele.ResultsSpectral unmixing- and acceptor photobleaching (AB)-FRET analyses captured pathological ERK activity preceding the manifestation of quantifiable body axes defects, a morphological pillar used to test the strength of SHP2 GoF mutations. Last, the work shows that by multi-modal FRET analysis, we can quantitatively trace back the modulation of ERK phosphorylation obtained by low-dose MEK inhibitor treatment to early development, before the onset of morphological defects.ConclusionThis work proves the usefulness of FRET imaging protocols on both live and fixed Teen ERK reporter fish to readily monitor and quantify pharmacologically- and genetically-induced ERK activity modulations in early embryos, representing a useful tool in pre-clinical applications targeting RAS-MAPK signaling.

Abstract 1672 Validating the use of acceptor photobleach FRET in quantifying protein-protein interactions between K+ channel alpha-subunits hERG and KvLQT1

Abstract 1672 Validating the use of acceptor photobleach FRET in quantifying protein-protein interactions between K+ channel alpha-subunits hERG and KvLQT1

2 in 1 Vectors Improve in Planta BiFC and FRET Analysis.

Protein-protein interactions (PPIs) play vital roles in all subcellular processes, and a number of tools have been developed for their detection and analysis. Each method has its unique set of benefits and drawbacks that need to be considered prior application. In fact, researchers are spoilt for choice when it comes to deciding which method to use for the initial detection of a PPI and which to corroborate the findings. With constant improvements in microscope development, the possibilities of techniques to study PPIs in vivo, and in real time, are continuously enhanced and expanded. Here, we describe three common approaches, their recent improvements incorporating a 2-in-1 cloning approach, and their application in plant cell biology: ratiometric bimolecular fluorescence complementation (rBiFC), FRET acceptor photobleaching (FRET-AB), and fluorescent lifetime imaging (FRET-FLIM), using Nicotiana benthamiana leaves and Arabidopsis thaliana cell culture protoplasts as transient expression systems.

Controlling Three-Color Förster Resonance Energy Transfer in an Optical Fabry–Pérot Microcavity at Low Mode Order

We study three-color Förster resonance energy transfer (triple FRET) between three spectrally distinct fluorescent dyes, a donor and two acceptors, which are embedded in a single polystyrene nanosphere. The presence of triple FRET energy transfer is confirmed by selective acceptor photobleaching. We show that the fluorescence lifetimes of the three dyes are selectively controlled using the Purcell effect by modulating the radiative rates and relative fluorescence intensities when the nanospheres are embedded in an optical Fabry–Pérot microcavity. The strongest fluorescence intensity enhancement for the second acceptor can be observed as a signature of the FRET process by tuning the microcavity mode to suppress the intermediate dye emission and transfer more energy from donor to the second acceptor. Additionally, we show that the triple FRET process can be modeled by coupled rate equations, which allow to estimate the energy transfer rates between donor and acceptors. This fundamental study has the potential to extend the classical FRET approach for investigating complex systems, e.g., optical energy switching, photovoltaic devices, light-harvesting systems, or in general interactions between more than two constituents.

Abstract 1436: T-oligo's mechanism of action in melanoma cells

Abstract Telomeres have become an attractive target for anticancer therapeutics and in 2022, an estimated 99,780 new cases and 7,650 people are expected to die of melanoma. T-oligo, a hexanucleotide tandem repeat oligonucleotide that is homologous to the 3′ overhang of telomeres has been shown to have potent anticancer effects in-vitro by inhibiting the growth of cancer cells. There are three mechanisms of action proposed for T-oligo, which are shelterin dissociation model, exposed telomere mimicry model, and G-quadruplex formation. Previous studies utilizing NMR spectroscopy and immunofluorescence assays have shown that T-oligo forms G-quadruplexes in the nucleus of the melanoma cells. We hypothesize that formation of G-quadruplexes can be detected with the help of FRET analysis and T-oligo could be delivered using lipid nanoparticles. Immunofluorescence assays and an acceptor photobleaching method were used to detect FRET and confirm the formation of G-quadruplexes in the nucleus of melanoma cells. Melanoma cells were plated and grown until 70% confluent in 8-well glass chamber slides and were treated with single-labeled FITC-T-oligo (11-mer), and Cy3-T-oligo (11-mer), and double labeled T-oligo 11-mer (T-11) and 22-mer (T-22) labeled with FITC on the 5′ end and Cy3 on the 3′ end. Slides were mounted and cells were observed under a fluorescent microscope. For FRET detection, we used the acceptor photobleaching method in which the acceptor (Cy3) was completely photobleached and any corresponding increase in donor’s intensity was detected and quantified. Any significant increase in donor intensity was considered to be due to FRET. We also performed some preliminary experiments with lipid nanoparticles to study whether these lipid nanoparticles are a viable delivery system for T-oligo. We encapsulated T-oligo in lipid nanoparticles using a microfluidic mixer and studied the encapsulation efficiency, uptake, and efficacy of encapsulated T-11 and T-22 on MM-AN melanoma cells. We found a significant increase of 40% - 150% in donor intensity after acceptor photobleaching in multiple melanoma cell lines. This may be due to G-quadruplex formation causing FRET thus indicating that T-oligo may be utilizing this mechanism of action for its anticancer effects. Preliminary results indicate that lipid nanoparticles encapsulated T-oligo with an efficiency of 72%. Uptake experiments showed that encapsulated T-11 and T-22 were taken up by the cells after an incubation time of 6hrs and the encapsulated T-22 also inhibited cell proliferation by 92%. In conclusion, three melanoma cell lines showed a significant increase in donor intensity after acceptor photobleaching upon treatment with T-22 and T-11 and lipid nanoparticles might be an effective delivery system for T-oligo. Citation Format: Archit Agnihotri, Taylor Rager, Kelly Fan, Hyatt Alaraj, Lawrence Miller, Neelu Puri. T-oligo's mechanism of action in melanoma cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1436.

Detecting RNA–Protein Interactions With EGFP‐Cy3 FRET by Acceptor Photobleaching

Förster Resonance Energy Transfer (FRET) is a great tool for cell biologists to investigate molecular interactions in live specimens. FRET is a distance-dependent phenomenon which can detect molecular interactions at distances between 1-10 nm. Several FRET approaches are reported in the literature for live and fixed cells to study protein-protein interactions; this protocol provides details of acceptor photobleaching as a FRET method to study RNA-Protein interactions. Cy3-labeled RNA foci (FRET acceptors) are photobleached at the intra-cellular site of interest (the nuclei) and the intensity of the EGFP-tagged proteins (FRET donors) at that same site are measured pre- and post- photobleaching. In principle, FRET is detected if the intensity of EGFP increases after photobleaching of Cy3. This protocol describes necessary steps and appropriate controls to conduct FRET measurements by the acceptor photobleaching method. Successful applications of this protocol will provide data to support the conclusion that EGFP-labeled proteins directly interact with Cy3-labeled RNA at the site of photobleaching. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: FRET in fixed cells Alternate Protocol: FRET in live cells.

Fast Screening of Protein-Protein Interactions Using Förster Resonance Energy Transfer (FRET-) Based Fluorescence Plate Reader Assay in Live Cells.

Protein-protein interactions (PPIs) have great importance for intracellular signal transduction and sustaining the homeostasis of an organism. Thus, the identification of PPIs is necessary to better understand the downstream signaling functions of the proteins in healthy and pathological conditions. Förster resonance energy transfer (FRET) between fluorescent proteins (FPs) is a powerful tool for detecting PPIs in living cells. In literature, FRET analysis methods such as donor photobleaching (FLIM), acceptor photobleaching, spectral imaging, and the three-filter cube method (sensitized emission) are abundantly applied to investigate PPIs; however, they require various expensive instrumentations, and their calculation methods are very time consuming. Since confocal microscopy applications and live cell-based techniques of FRET are very costly, scientists sometimes prefer plate readers for FRET experiments. However, plate reader applications also have many disadvantages and considerations compared to confocal fluorescence microscopy, and complex calculation procedures should be performed. To overcome these problems, we propose a FRET-based high-throughput assay method with a standard monochromator-based microplate reader, which is generally available in most biochemistry laboratories, and an alternative calculation procedure. This rapid, low cost, and effective analysis method enables the scientists to prescreen PPIs in living cells as a preliminary study and quick glance at the experiment before preparing the whole experimental setup with the expensive instrumentations. Additionally, the alternative calculation procedure provides the FRET area comparison without complex bleed-through calculations in a non-conventional manner by shortening the analysis processes with this quick and uncomplicated spectral representation.

Add and Go: FRET Acceptor for Live-Cell Measurements Modulated by Externally Provided Ligand.

A substantial number of genetically encoded fluorescent sensors rely on the changes in FRET efficiency between fluorescent cores, measured in ratiometric mode, with acceptor photobleaching or by changes in fluorescence lifetime. We report on a modulated FRET acceptor allowing for simplified one-channel FRET measurement based on a previously reported fluorogen-activating protein, DiB1. Upon the addition of the cell-permeable chromophore, the fluorescence of the donor-fluorescent protein mNeonGreen decreases, allowing for a simplified one-channel FRET measurement. The reported chemically modulated FRET acceptor is compatible with live-cell experiments and allows for prolonged time-lapse experiments with dynamic energy transfer evaluation.

A Combined Acceptor Photobleaching and Donor Fluorescence Lifetime Imaging Microscopy Approach to Analyze Multi-Protein Interactions in Living Cells.

Protein–protein interaction studies often provide new insights, i.e., into the formation of protein complexes relevant for structural oligomerization, regulation of enzymatic activity or information transfer within signal transduction pathways. Mostly, biochemical approaches have been used to study such interactions, but their results are limited to observations from lysed cells. A powerful tool for the non-invasive investigation of protein–protein interactions in the context of living cells is the microscopic analysis of Förster Resonance Energy Transfer (FRET) among fluorescent proteins. Normally, FRET is used to monitor the interaction state of two proteins, but in addition, FRET studies have been used to investigate three or more interacting proteins at the same time. Here we describe a fluorescence microscopy-based method which applies a novel 2-step acceptor photobleaching protocol to discriminate between non-interacting, dimeric interacting and trimeric interacting states within a three-fluorophore setup. For this purpose, intensity- and fluorescence lifetime-related FRET effects were analyzed on representative fluorescent dimeric and trimeric FRET-constructs expressed in the cytosol of HEK293 cells. In particular, by combining FLIM- and intensity-based FRET data acquisition and interpretation, our method allows to distinguish trimeric from different types of dimeric (single-, double- or triple-dimeric) protein–protein interactions of three potential interaction partners in the physiological setting of living cells.

Insight into Sodium Pump Regulation by FXYD Proteins

The sodium pump (Na+/K+-ATPase, NKA) is a membrane transport ATPase responsible for establishing the vital gradients of sodium and potassium across the plasma membrane of all mammalian cells. NKA activity is regulated by FXYD proteins, a family of transmembrane proteins that serve as auxiliary subunits of the sodium pump. in the heart, NKA activity is modulated by phospholemman (FXYD1), but the structural determinants of this regulatory mechanism are incompletely understood. We used time-resolved and steady-state FRET techniques to study the stoichiometry and affinity of fluorescently labeled NKA and FXYD1. Progressive acceptor photobleaching revealed multiple acceptor-labeled FXYD1 bound to donor-labeled NKA. Complementary global analysis of time-correlated single photon counting experiments revealed presence of medium- and high-FRET species within the population of NKA-FXYD1 complexes. To explore the quaternary structure of the regulatory complex, we obtained fluorescence lifetime data from hundreds of cells spanning a wide range of protein expression level. Over this range, the high FRET species increased with increasing protein concentration at the expense of the medium-FRET population. We attribute these subpopulations to NKA-NKA dimers decorated with either one FXYD1 (at low concentration) or two (at high concentration). Moreover, acceptor photobleaching experiments revealed FRET between donor- and acceptor-labeled NKA α subunits consistent with NKA oligomerization. in addition, we quantified FRET between NKA α and β essential subunits to monitor changes in the dynamic equilibrium between open (E2) and closed (E1) states of NKA. Treatment of NKA with the specific inhibitor ouabain induced a shift in the dynamic equilibrium of NKA toward a higher FRET state, suggesting that the α and β n-termini moved closer together. The experiments reveal new insight into the regulation of NKA by FXYD proteins and by NKA oligomerization.

Driving integrative structural modeling with serial capture affinity purification

Streamlined characterization of protein complexes remains a challenge for the study of protein interaction networks. Here we describe serial capture affinity purification (SCAP), in which two separate proteins are tagged with either the HaloTag or the SNAP-tag, permitting a multistep affinity enrichment of specific protein complexes. The multifunctional capabilities of this protein-tagging system also permit in vivo validation of interactions using acceptor photobleaching Förster resonance energy transfer and fluorescence cross-correlation spectroscopy quantitative imaging. By coupling SCAP to cross-linking mass spectrometry, an integrative structural model of the complex of interest can be generated. We demonstrate this approach using the Spindlin1 and SPINDOC protein complex, culminating in a structural model with two SPINDOC molecules docked on one SPIN1 molecule. In this model, SPINDOC interacts with the SPIN1 interface previously shown to bind a lysine and arginine methylated sequence of histone H3. Our approach combines serial affinity purification, live cell imaging, and cross-linking mass spectrometry to build integrative structural models of protein complexes.

Imaging-based assays for investigating functions of the RNA polymerase II elongation factor Elongin and the Elongin ubiquitin ligase.

Elongin A binds to Elongins B and C to form the RNA polymerase II transcription elongation factor Elongin. It also functions as the substrate recognition subunit of a ubiquitin ligase that is formed by binding of Elongin to Cullin protein CUL5 and RING finger protein RBX2 and that targets RNA polymerase II for ubiquitination. In this article, we describe use of acceptor photobleaching fluorescence resonance energy transfer (AP-FRET) and laser microirradiation-based assays to study regulated assembly of the Elongin ubiquitin ligase and its recruitment to regions of localized DNA damage.

Mapping Membrane Protein Complex Assembly Pathways in Live Cells with Progressive Acceptor Photobleaching

Mapping Membrane Protein Complex Assembly Pathways in Live Cells with Progressive Acceptor Photobleaching

Imaging Protein-Protein Interactions by Förster Resonance Energy Transfer (FRET) Microscopy in Live Cells.

This updated unit compares three methods to acquire Förster Resonance Energy Transfer (FRET) data in living cells using a confocal microscope: Acceptor photobleaching, Acceptor-sensitized emission FRET, and Donor fluorescence lifetime imaging. Detailed protocols for live cell husbandry, image acquisition, and data analysis are provided. In addition to providing instructions for manufacturer's analysis tool sets, we provide an easy-to-use, MATLAB-based code to calculate FRET efficiency from data obtained using the Acceptor photobleaching or Acceptor-sensitized emission method, which can be freely downloaded. © 2018 by John Wiley & Sons, Inc.

The Toolbox to Study Protein–Protein Interactions in Plants

The ability to detect the interaction partners of a protein and how those interactions occur are central to the study of biology. Indeed, such knowledge can provide important clues to unravel the functional context of proteins in specific pathways. This review provides an overview of the different techniques available to plant researchers to study protein–protein interactions (PPIs), and briefly summarizes key benefits and disadvantages of each technique. We discuss the most commonly used in vitro-based techniques (i.e., co-immunoprecipitation and microscale thermophoresis), yeast-based screening methods (i.e., yeast two-hybrid and the split-ubiquitin system), as well as imaging and FRET-based approaches (i.e., bimolecular fluorescence complementation, modification of intracellular localisation, protein mobility measurements, acceptor photobleaching, fluorescence lifetime imaging microscopy, and fluorescence polarization/anisotropy) that are used in the field of plant biology. Finally, we offer suggestions that may provide future directions for how to best use and combine these techniques.

Molecular details of dimerization kinetics reveal negligible populations of transient \xb5-opioid receptor homodimers at physiological concentrations

Various experimental and computational techniques have been employed over the past decade to provide structural and thermodynamic insights into G Protein-Coupled Receptor (GPCR) dimerization. Here, we use multiple microsecond-long, coarse-grained, biased and unbiased molecular dynamics simulations (a total of ~4 milliseconds) combined with multi-ensemble Markov state models to elucidate the kinetics of homodimerization of a prototypic GPCR, the µ-opioid receptor (MOR), embedded in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC)/cholesterol lipid bilayer. Analysis of these computations identifies kinetically distinct macrostates comprising several different short-lived dimeric configurations of either inactive or activated MOR. Calculated kinetic rates and fractions of dimers at different MOR concentrations suggest a negligible population of MOR homodimers at physiological concentrations, which is supported by acceptor photobleaching fluorescence resonance energy transfer (FRET) experiments. This study provides a rigorous, quantitative explanation for some conflicting experimental data on GPCR oligomerization.

2in1 Vectors Improve In Planta BiFC and FRET Analyses.

Protein-protein interactions (PPIs) play vital roles in all subcellular processes and a number of tools have been developed for their detection and analysis. Each method has its unique set of benefits and drawbacks that need to be considered prior to theirapplication. In fact, researchers are spoilt for choice when it comes to deciding which method to use for the initial detection of a PPI, and which to corroborate the findings. With constant improvements in microscope development, the possibilities of techniques to study PPIs in vivo, and in real time, are continuously enhanced, and expanded. Here, we describe three common approaches, their recent improvements incorporating a 2in1-cloning approach, and their application in plant cell biology: ratiometric Bimolecular Fluorescence Complementation (rBiFC), FRET Acceptor Photobleaching (FRET-AB), and Fluorescent Lifetime Imaging (FRET-FLIM), using Nicotiana benthamiana leaves and Arabidopsis thaliana cell culture protoplasts as transient expression systems.

Focal Adhesion Kinase Regulatory Interactions Quantified by TIRF-FRET

Focal adhesion kinase related non-kinase (FRNK) is an inhibitor of focal adhesion kinase (FAK)-dependent cell growth, survival, and migration pathways. In vascular smooth muscle cells, both FAK and FRNK are upregulated after vascular injury, suggesting balanced stimulation and inhibition of growth during recovery. Here we propose a novel mechanism by which FRNK can inhibit FAK: direct binding of FRNK to FAK forming an inhibitory complex within focal adhesions. This hypothesis is supported by co-immunoprecipitation of FAK and FRNK. In addition, total internal reflection fluorescence (TIRF)-mode fluorescence resonance energy transfer (FRET) measurements suggest that FRNK binds directly to FAK within focal adhesions of live vascular smooth muscle cells. We hypothesized that this interaction might be regulated by serine phosphorylation of FRNK S217, a site we found to be basally highly phosphorylated at S217 by extracellular signal-regulated kinase 1/2 (ERK). To determine the significance of S217 phosphorylation, we generated a non-phosphorylatable mutant FRNK by mutating S217 to alanine. S217A-FRNK exhibited significantly higher amounts of FRET compared to wild type FRNK, suggesting increased interaction with FAK. Progressive acceptor photobleaching analysis revealed that the FRNK-FAK complex consisted of FRNK and multiple FAK proteins in a high order hetero-oligomer. To determine the functional role of the proposed regulatory site we performed an apoptosis assay using flow cytometry. S217A FRNK was a much more potent inducer of apoptosis in vascular smooth muscle cells compared to wild type FRNK. Additionally, we determined that S217A FRNK was a more potent inhibitor of FAK signaling by examining FAK Y397 phosphorylation. We conclude that dephosphorylation of FRNK at S217 during response to injury results in increased FRNK-FAK complex formation, thereby inhibiting FAK signaling.