Dimension conversion and scaling of disordered protein chains.

Femtosecond upconversion, single-molecule fluorescence resonance energy transfer (sm-FRET) and fluorescence correlation spectroscopy (FCS) are applied to study the competition between excited-state proton transfer (ESPT) and FRET [to rhodamine 6G (R6G)] of 8-hydroxypyranine-1,3,6-trisulfonate (HPTS) in cetyltrimethylammonium chloride (CTAC) micelles. Pyranine exhibits dual emission at λ(em)=430 nm for ROH and 520 nm for RO(-). The absorption spectrum of R6G (acceptor) has very good overlap with the RO(-) emission and poor overlap with ROH emission. It is observed that FRET occurs readily from the RO(-)* state of HPTS (donor) to R6G (acceptor). Multiple timescales of FRET were detected from the rise time of acceptor emission. The different timescales correspond to different donor-acceptor distances. The ultrafast components (8.5 and 13 ps) are assigned to FRET at a close contact of donor and acceptor (≈20 Å). The longer components (500 and 800 ps) arise from long-distance FRET from the donor to the acceptor (≈40 Å) located in different regions of the CTAC micelle. The larger donor-acceptor distances agree with those obtained from an sm-FRET study. On addition of 4 M NaCl to CTAC, the rate of proton transfer (k(PT)) slowed by about eight and two times, respectively, for the fast and slow sites of the CTAC micelle. As a result, the intensity of the ROH emission increases and that of RO(-) decreases. The decrease in the intensity of the RO(-) emission causes a decrease in the efficiency of FRET.

An Integrative Approach to Single-Molecule FRET Spectroscopy and Molecular Dynamics Simulations for the Study of Intrinsically Disordered Proteins

Single-Molecule and FRET Fluorescence Correlation Spectroscopy Analyses of Phage DNA Packaging: Colocalization of Packaged Phage T4 DNA Ends within the Capsid

Many biological molecules respond to external stimuli that can cause their conformational states to shift from one steady state to another. Single-molecule FRET (Fluorescence Resonance Energy Transfer) is of particular interest to not only define the steady-state conformational ensemble usually averaged out in the ensemble of molecules but also characterize the dynamics of biomolecules. To study steady-state transitions, i.e., non-equilibrium transitions, a data analysis methodology is necessary to analyze single-molecule FRET photon trajectories, which contain mixtures of contributions from two steady-state statuses and include non-equilibrium transitions. In this study, we introduce a novel methodology called WAVE (Wasserstein distance Analysis in steady-state Variations in smFRET) to detect and locate non-equilibrium transition positions in FRET trajectories. Our method first utilizes a combined STaSI-HMM (Stepwise Transitions with State Inference Hidden Markov Model) algorithm to convert the original FRET trajectories into discretized trajectories. We then apply Maximum Wasserstein Distance analysis to differentiate the FRET state compositions of the fitting trajectories before and after the non-equilibrium transition. Forward and backward algorithms, based on the Minimum Description Length (MDL) principle, are used to find the refined positions of the non-equilibrium transitions. This methodology allows us to observe changes in experimental conditions in chromophore-tagged biomolecules or vice versa.

Fluorescence Resonance Energy Transfer (FRET) spectroscopy is an ideal tool to assess protein-protein interactions in cells. FRET occurs if suitable fluorophores are less than 10nm apart and thus may be used to probe molecular scale interactions. To obviate the need for fixation and staining, the proteins of interest can be linked to Green Fluorescent Protein (GFP) variants, which can then be expressed in intact living cells. However, FRET is inherently difficult to validate and interpret in such environments, making suitable positive controls vital. In this study cyan and yellow variants of GFP (CFP and YFP) were linked by amino acid chains of known lengths (6, 14, 16, 18, and 22 amino acids). Ratiometric FRET measurements were obtained via the acceptor photobleaching technique. The data was analyzed by new FRET analysis software developed by this group, which will be made available to the public. The evaluation method is novel in that it assesses an entire field of view for FRET efficiencies, thus making high throughput data analysis possible. A perfect candidate for FRET studies is the cyclin-CDK switch, responsible for the regulation of mitosis. Preliminary results with CyclinB1-CFP and cdk1-YFP are presented.

Single-molecule fluorescence resonance energy transfer (smFRET) measurement provides a unique and powerful approach to understand complex biological processes including conformational and structural dynamics of individual biomolecules. For effective smFRET analysis of protein, site-specific dual-labeling with two fluorophores as an energy donor and an acceptor is crucial. Here we demonstrate that site-specific dual-labeling of protein via incorporation of unnatural amino acid provides a clearer picture for the folded and unfolded states of the protein in smFRET analysis than conventional labeling using double cysteines. As a model study, maltose-binding protein (MBP) was dually labeled via incorporation of ρ-azido-l-phenylalanine and cysteine at specific positions, immobilized on a surface, and subjected to smFRET analysis under native and denaturing conditions. The resulting histograms show that site-specific dual-labeling results in a more homogeneous distribution in protein populations, enabling a precise smFRET analysis of protein.

Kinetics of Complexin Binding to the SNARE Complex: Correcting Single Molecule FRET Measurements for Hidden Events

A subfamily of regulators of G protein signaling (RGS) proteins consisting of RGS6, -7, -9, and -11 is characterized by the presence of a unique Ggamma-like domain through which they form obligatory dimers with the G protein subunit Gbeta5 in vivo. In Caenorhabditis elegans, orthologs of Gbeta5.RGS dimers are implicated in regulating both Galphai and Galphaq signaling, and in cell-based assays these dimers regulate Galphai/o- and Galphaq/11-mediated pathways. However, initial studies with purified Gbeta5.RGS6 or Gbeta5.RGS7 showed that they only serve as GTPase activating proteins for Galphao. Pull-down assays and co-immunoprecipitation with these dimers failed to detect their binding to either Galphao or Galphaq, indicating that the interaction might require additional factors present in vivo. Here, we asked if the RGS7.Gbeta5 complex binds to Galphaq using fluorescence resonance energy transfer (FRET) in transiently transfected mammalian cells. RGS7, Gbeta5, and Galpha subunits were tagged with yellow variants of green fluorescent protein. First we confirmed the functional activity of the fusion proteins by co-immunoprecipitation and also their effect on signaling. Second, we again demonstrate the interaction between RGS7 and Gbeta5 using FRET. Finally, using both FRET spectroscopy on cell suspensions and microscopy of individual cells, we showed FRET between the yellow fluorescence protein-tagged RGS7.Gbeta5 complex and cyan fluorescence protein-tagged Galphaq, indicating a direct interaction between these molecules.

Once nanoparticles enter into the biological milieu, nanoparticle-biomacromolecule complexes, especially the protein corona, swiftly form, which cause obvious effects on the physicochemical properties of both nanoparticles and proteins. Here, the thermodynamic parameters of the interactions between water-soluble GSH-CdSe/ZnS core/shell quantum dots (GSH-QDs) and human serum albumin (HSA) were investigated with the aid of labeling fluorescence of HSA. It was proved that the labeling fluorescence originating from a fluorophore (BDP-CN for instance) could be used to investigate the interactions between QDs and HSA. Gel electrophoresis displayed that the binding ratio between HSA and QDs was ∼2:1 by direct visualization. Fluorescence resonance energy transfer (FRET) results indicated that the distance between the QDs and the fluorophore BDP-CN in HSA was 7.2 nm, which indicated that the distance from the fluorophore to the surface of the QDs was ∼4.8 nm. Fluorescence correlation spectroscopy (FCS) results showed that HSA formed a monolayer of a protein corona with a thickness of 5.5 nm. According to the spatial structure of HSA, we could speculate that the binding site of QDs was located at the side edge (not the triangular plane) of HSA with an equilateral triangular prism. The elaboration of the thermodynamic parameters, binding ratio, and interaction orientation will highly improve the fundamental understanding of the formation of protein corona. This work has guiding significance for the exploration of the interactions between proteins and nanomaterials.

To acquire accurate structural and dynamical information on complex biomolecular machines using single-molecule fluorescence resonance energy transfer (sm-FRET), a large flux of donor and acceptor photons is needed. To achieve such fluxes, one may use higher laser excitation intensity; however, this induces increased rates of photobleaching. Anti-oxidant additives have been extensively used for reducing acceptor's photobleaching. Here we focus on deciphering the initial step along the photobleaching pathway. Utilizing an array of recently developed single-molecule and ensemble spectroscopies and doubly labeled Acyl-CoA binding protein and double-stranded DNA as model systems, we study these photobleaching pathways, which place fundamental limitations on sm-FRET experiments. We find that: (i) acceptor photobleaching scales with FRET efficiency, (ii) acceptor photobleaching is enhanced under picosecond-pulsed (vs continuous-wave) excitation, and (iii) acceptor photobleaching scales with the intensity of only the short wavelength (donor) excitation laser. We infer from these findings that the main pathway for acceptor's photobleaching is through absorption of a short wavelength photon from the acceptor's first excited singlet state and that donor's photobleaching is usually not a concern. We conclude by suggesting the use of short pulses for donor excitation, among other possible remedies, for reducing acceptor's photobleaching in sm-FRET measurements.

We developed a new single nucleotide polymorphism (SNP) genotyping method based on single-molecule multi-color fluorescence resonance energy transfer (FRET). We demonstrated that this new method uses less than 1 fmol of sample and is also highly quantitative with a detection level of 1% or lower in the minor allele fraction.

We demonstrate a new 512x16 single photon avalanche diode (SPAD) based line sensor with per-pixel TCSPC histogramming for time-resolved, time-zoomable, FRET spectroscopy. The line sensor can operate in single photon counting (SPC) mode as well as time-correlated single photon counting (TCSPC) and per-pixel histogramming modes. TCSPC has been the preferred method for fluorescence lifetime measurements due to its collection of full decays as a histogram of arrival times. However, TCSPC is slow due to only capturing one photon per exposure and large timestamp data transfer requirements for offline histogramming. On-chip histogramming improves the data rate by allowing multiple SPAD pulses (up to one pulse per laser period) to be processed in each exposure cycle, along with secondly reducing the I/O bottleneck as only the final histogram is transferred. This can enable 50x higher acquisition rates (up to 10 billion counts per second), along with time-zoomable histogramming operation from 1.6ns to 205ns with 50ps resolution. A broad spectral range can be interrogated with the sensor (450-900nm). Overall, these sensors provide a unique combination of light sensing capabilities for use in high speed, sensitive, optical instrumentation in the time/wavelength domain. We test the sensor performance by observation of fluorescence resonance energy transfer (FRET) between FAM and TAMRA and between EGFP and RFP FRET standards.

Conformational Dynamics of Titin PEVK Explored with FRET Spectroscopy

Fluorescence resonance energy transfer (FRET) is a non-invasive characterization method for studying molecular structures and dynamics, providing high spatial resolution at nanometer scale. Over the past decades, FRET-based measurements are developed and widely implemented in synthetic polymer systems for understanding and detecting a variety of nanoscale phenomena, enabling significant advances in polymer science. In this review, the basic principles of fluorescence and FRET are briefly discussed. Several representative research areas are highlighted, where FRET spectroscopy and imaging can be employed to reveal polymer morphology and kinetics. These examples include understanding polymer micelle formation and stability, detecting guest molecule release from polymer host, characterizing supramolecular assembly, imaging composite interfaces, and determining polymer chain conformations and their diffusion kinetics. Finally, a perspective on the opportunities of FRET-based measurements is provided for further allowing their greater contributions in this exciting area.

Dynamic polymorphism of Ras observed by single molecule FRET is the basis for molecular recognition