Ratiometric Flapping Force Probe That Works in Polymer Gels

A ratiometric flapping force probe that can evaluate the nanoscale stress concentration in the polymer chain network of common organogels has been developed. Stress-dependent dual-fluorescence properties of the chemically doped flapping force probe has been demonstrated even when the probe is solvated in the wet materials (Figure 1). The fluorescence ratiometric analysis is robust against the local concentration change induced by the macroscopic polymer deformation. While the force-responsive FRET dyads, widely used in mechanobiology, are sensitive to the distance and orientation of the two chromophores, the flapping fluorophore works as a single-component flexible force probe regardless of the FRET efficiency. Realtime and reversible spectral response to the mechanical stress is observed with a low threshold on the order of sub-MPa compression due to its conformational flexibility. The previously reported flapping probe only shows a negligible response in the solvated environments because the undesired spontaneous planarization occurs in the S1 excited state, even without mechanical force. The excited-state engineering by changing the flapping wings from the anthraceneimide units to the pyreneimide units endows this molecule with the force probe function in the wet conditions. The structurally modified force probe also has an advantage in terms of a wide dynamic range of the fluorescence response in solvent-free elastomers, which enabled the ratiometric fluorescence imaging of the molecular-level stress concentration during the crack growth in a stretched polyurethane film. The percentage of the stressed force probes has been experimentally estimated to be approximately 30–40% before the fracture of the elastomers. The flapping force probe is useful for elucidating the toughening mechanism of recently focused unique topological gels and elastomers at molecular level.

Probing the Structural Dynamics of the Activation Gate of KcsA Using Homo-FRET Measurements

The allosteric coupling between activation and inactivation processes is a common feature observed in K+ channels. Particularly, in the prokaryotic KcsA channel the K+ conduction process is controlled by the inner gate, which is activated by acidic pH, and by the selectivity filter (SF) or outer gate, which can adopt non-conductive or conductive states. In a previous study, a single tryptophan mutant channel (W67 KcsA) enabled us to investigate the SF dynamics using time-resolved homo-Förster Resonance Energy Transfer (homo-FRET) measurements. Here, the conformational changes of both gates were simultaneously monitored after labelling the G116C position with tetramethylrhodamine (TMR) within a W67 KcsA background. At a high degree of protein labeling, fluorescence anisotropy measurements showed that the pH-induced KcsA gating elicited a variation in the homo-FRET efficiency among the conjugated TMR dyes (TMR homo-FRET), while the conformation of the SF was simultaneously tracked (W67 homo-FRET). The dependence of the activation pKa of the inner gate with the ion occupancy of the SF unequivocally confirmed the allosteric communication between the two gates of KcsA. This simple TMR homo-FRET based ratiometric assay can be easily extended to study the conformational dynamics associated with the gating of other ion channels and their modulation.

Abstract P368: Caveolin-3 Prevents Swelling-induced Cell Lysis Via Regulation Of I Cl,swell Expression And Activity

Background: Caveolae membrane structures harbor mechanosensitive chloride channels (MCCs) which form a swelling-activated chloride current ( I Cl,swell ) and play an important role in cell volume regulation and mechano-electrical signal transduction. However, the role of muscle-specific caveolar scaffolding protein caveolin-3 (Cav3) in regulation of MCCs expression, activity, and contribution to cell viability in response to mechanical stress remains unclear. We hypothesized that Cav3-based mechano-protection is enabled by complimentary expression of MCCs. Methods and Results: Experiments were performed on native (Cav3-) and Cav3-transfected (Cav3+) HEK-293 cells. Cell stretch was mimicked by light (220 mOsM) or extreme hypoosmotic swelling (<20mOsM). Cav3+ HEK-293 cells were significantly resistant to extreme hypotonic solutions (15 minute incubation) compared to Cav3- HEK-293 cells, and this mechano-protection was significantly reduced when exposed to I Cl,swell selective inhibitor DCPIB (1 μM). We found that three MCCs (ClC-2, ClC-3, and SWELL1, also known as LRRC8A) contain caveolin-binding motifs in their structure, indicating their possible localization in caveolae structures. Co-IP analysis confirmed association of SWELL1 with Cav3. Interestingly, Cav3+ HEK-293 cells showed a significant (by 2-fold) increase of SWELL1 protein level, while ClC-2/3 protein levels remained unchanged. This was accompanied by a 2-fold increase of I Cl,swell , but no change in mRNA expression levels. FRET analysis showed a <10 nm membrane and intracellular association between Cav3 and tested MCCs. Furthermore, Cav3/SWELL1 membrane FRET efficiency was halved in light hypoosmotic solution, as well as after disruption of caveolae structures via cholesterol depletion by 1-hour treatment with 10 μM methyl-β-cyclodextrin. Cav3/ClC-2/3 average membrane FRET efficiency remained unchanged in hypotonic solution. Conclusions: We concluded that of MCCs tested, SWELL1 abundance and activity is regulated by Cav3 and that their association relies on membrane tension and caveolae integrity. The present study highlights the mechano-protective properties of Cav3 which are partially facilitated by complimentary SWELL1 expression and activity.

Unfavorable Effects of Fixatives on the Fluorescence Intensity and Biological Functions of Fluorescent Proteins in HEK293T Cells and Transgenic Mice

Fluorescent proteins (FPs) are commonly used probes for coding genes that enable specific protein or whole-cell labeling. Their fluorescence intensity is used for molecular quantitation and intermolecular interaction analysis. Since FPs are usually small soluble proteins, they easily cross the membranes if cell integrity is disrupted, resulting in FP signal attenuation/loss. Specimen prefixation to preserve FP localization within cells/tissues is therefore useful. However, specific fixatives can weaken or eliminate FP signals. We studied the effects of five common fixatives on FP fluorescence intensity and biological functions to determine their suitability for FP signal and FRET efficiency preservation in cells and tissues. FP (GFP, YFP, CFP and RFP)-expressing HEK293T cells with methanol, 95% ethanol, 4% PFA, acetone and glutaraldehyde, and brain tissue sections of EGFP- and tdTomato-labeled transgenic fluorescent mice was fixed with 4% PFA. The FP signals in HEK293T cells and brain tissue from transgenic fluorescent mice were weakened or even eliminated after fixation with these fixatives. The fixatives affected FP biological function, and the FP FRET efficiency significantly differed between prefixation and postfixation (all p<0.01). Thus, fixatives impair FP fluorescence to some extent, leading to attenuation/loss of signals or even biological functions. Fixatives should be applied carefully in FP-related experiments to avoid bias.

Effect of A-tract-mediated linker histone orientation on trinucleosome compaction

Linker histones (LH) have been shown to preferentially bind to AT-rich DNA, and specifically to A-tracts, contiguous stretches of adenines. Recently, using spFRET (single pair Foerster/Fluorescence Resonance Energy Transfer), we showed that the globular domain (gH) of Xenopus laevis H1.0b LH orients towards A-tracts present on the linker-DNA (L-DNA) in LH:mononucleosome complexes. We investigated the impact of this A-tract mediated orientation of the gH on the compaction of higher-order structures by studying trinucleosomes as minimal models for chromatin. Two 600 bp DNA sequences were constructed containing three Widom 601 core sequences separated by about 40 bp linkers and A-tracts inserted on either the outer or the inner L-DNAs flanking the 1st and the 3rd Widom 601 sequences. The two inner L-DNAs were fluorescently labelled at their midpoints. Trinucleosomes were reconstituted using the doubly-labelled 600 bp DNA, core histone octamers and the full-length H1.0b LH. SpFRET was performed for a range of NaCl concentrations. While the LH compacted the trinucleosomes, surprisingly, the extent of compaction was similar for trinucleosomes with A-tracts either on the two outer or on the two inner L-DNAs. Modeling constrained by the FRET efficiency suggests that the trinucleosomes adopt a zig-zagged conformation with the 1st and 3rd nucleosomes stacked on top of each other. Even though we expect that the gH of neighbouring (1st and 3rd) LHs are oriented towards the A-tracts, our models suggest that they are not sufficiently close to dimerize and affect compaction. Thus, despite differences in A-tract placements, the LH compacts trinucleosomes similarly.

Evaluation of FRET X for Single-Molecule Protein Fingerprinting

Single-molecule protein identification is a novel, as of yet unrealized concept with potentially ground-breaking applications in biological research. We propose a method called FRET X (Förster Resonance Energy Transfer via DNA eXchange) fingerprinting, in which the FRET efficiency is read out between exchangeable dyes on protein-bound DNA docking strands, and accumulated FRET efficiency values constitute the fingerprint for a protein. To evaluate the feasibility of this approach, we simulated fingerprints for hundreds of proteins using a coarse-grained lattice model and experimentally demonstrated FRET X fingerprinting on a system of model peptides. Measured fingerprints are in agreement with our simulations, corroborating the validity of our modeling approach. In a simulated complex mixture of >300 human proteins of which only cysteines, lysines and arginines were labeled, a support vector machine was able to identify constituents with 95% accuracy. We anticipate that our FRET X fingerprinting approach will form the basis of an analysis tool for targeted proteomics.

Linear Behavior of the Phase Lifetime in Frequency-Domain Fluorescence Lifetime Imaging of FRET Constructs

We utilize a cost-effective frequency-domain fluorescence lifetime imaging microscope to measure the phase lifetime of mTFP1 in mTFP1-mVenus fluorescence resonance energy transfer (FRET) constructs relevant to the VinTS molecular tension probe. Our data were collected at 15 modulation frequencies ω/2π selected between 14 and 70 MHz. The lifetime of mTFP1 was τD = 3.11 ± 0.02 ns in the absence of acceptor. For modulation frequencies, ω, such that (ω · τD) &lt; 1.1, the phase lifetime of mTFP1in the presence of acceptor (mVenus), τϕDA, was directly related to the amplitude-weighted lifetime τaveDA inferred from the known FRET efficiency (EFRETtrue) of the constructs. A linear fit to a plot of (ω·τϕDA) vs. (ω·τaveDA) yielded a slope of 0.79 ± 0.05 and intercept of 0.095 ± 0.029 (R2 = 0.952). Thus, our results suggest that a linear relationship exists between the apparent EFRETapp based on the measured phase lifetime and EFRETtrue for frequencies such that (ω · τD) &lt; 1.1. We had previously reported a similar relationship between EFRETapp and EFRETtrue at 42 MHz. Our current results provide additional evidence in support of this observation, but further investigation is still required to fully characterize these results. A direct relationship between τϕDAand τaveDA has the potential to simplify significantly data acquisition and interpretation in fluorescence lifetime measurements of FRET constructs.

Multi-parameter photon-by-photon hidden Markov modeling

Single molecule FRET (smFRET) is a useful tool for studying biomolecular sub-populations and their dynamics. Advanced smFRET-based techniques often track multiple parameters simultaneously, increasing the information content of the measurement. Photon-by-photon hidden Markov modelling (H2MM) is a smFRET analysis tool that quantifies FRET dynamics of single biomolecules, even if they occur in sub-milliseconds. However, sub-populations can be characterized by additional experimentally-derived parameters other than the FRET efficiency. We introduce multi-parameter H2MM (mpH2MM) that identifies sub-populations and their transition dynamics based on multiple experimentally-derived parameters, simultaneously. We show the use of this tool in deciphering the number of underlying sub-populations, their mean characteristics and the rate constants of their transitions for a DNA hairpin exhibiting milliseconds FRET dynamics, and for the RNA polymerase promoter open complex exhibiting sub-millisecond FRET dynamics of the transcription bubble. Overall, we show that using mpH2MM facilitates the identification and quantification of biomolecular sub-populations in smFRET measurements that are otherwise difficult to identify. Finally we provide the means to use mpH2MM in analyzing FRET dynamics in advanced multi-color smFRET-based measurements.