Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins

Single-molecule Förster-resonance energy transfer (smFRET) experiments allow the study of biomolecular structure and dynamics in vitro and in vivo. We performed an international blind study involving 19 laboratories to assess the uncertainty of FRET experiments for proteins with respect to the measured FRET efficiency histograms, determination of distances, and the detection and quantification of structural dynamics. Using two protein systems with distinct conformational changes and dynamics, we obtained an uncertainty of the FRET efficiency ≤0.06, corresponding to an interdye distance precision of ≤2 Å and accuracy of ≤5 Å. We further discuss the limits for detecting fluctuations in this distance range and how to identify dye perturbations. Our work demonstrates the ability of smFRET experiments to simultaneously measure distances and avoid the averaging of conformational dynamics for realistic protein systems, highlighting its importance in the expanding toolbox of integrative structural biology.

Enabling Spectrally Resolved Single-Molecule Localization Microscopy at High Emitter Densities

Single-molecule localization microscopy (SMLM) is a powerful super-resolution technique for elucidating structure and dynamics in the life- and material sciences. Simultaneously acquiring spectral information (spectrally resolved SMLM, sSMLM) has been hampered by several challenges: an increased complexity of the optical detection pathway, lower accessible emitter densities, and compromised spatio-spectral resolution. Here we present a single-component, low-cost implementation of sSMLM that addresses these challenges. Using a low-dispersion transmission grating positioned close to the image plane, the +1^stdiffraction order is minimally elongated and is analyzed using existing single-molecule localization algorithms. The distance between the 0^th and 1^st order provides accurate information on the spectral properties of individual emitters. This method enables a 5-fold higher emitter density while discriminating between fluorophores whose peak emissions are less than 15 nm apart. Our approach can find widespread use in single-molecule applications that rely on distinguishing spectrally different fluorophores under low photon conditions.

Targetable Conformationally Restricted Cyanines Enable Photon-Count-Limited Applications*

Cyanine dyes are exceptionally useful probes for a range of fluorescence-based applications, but their photon output can be limited by trans-to-cis photoisomerization. We recently demonstrated that appending a ring system to the pentamethine cyanine ring system improves the quantum yield and extends the fluorescence lifetime. Here, we report an optimized synthesis of persulfonated variants that enable efficient labeling of nucleic acids and proteins. We demonstrate that a bifunctional sulfonated tertiary amide significantly improves the optical properties of the resulting bioconjugates. These new conformationally restricted cyanines are compared to the parent cyanine derivatives in a range of contexts. These include their use in the plasmonic hotspot of a DNA-nanoantenna, in single-molecule Förster-resonance energy transfer (FRET) applications, far-red fluorescence-lifetime imaging microscopy (FLIM), and single-molecule localization microscopy (SMLM). These efforts define contexts in which eliminating cyanine isomerization provides meaningful benefits to imaging performance.

Structural and biophysical characterization of the tandem substrate-binding domains of the ABC importer GlnPQ

The ATP-binding cassette transporter GlnPQ is an essential uptake system that transports glutamine, glutamic acid and asparagine in Gram-positive bacteria. It features two extra-cytoplasmic substrate-binding domains (SBDs) that are linked in tandem to the transmembrane domain of the transporter. The two SBDs differ in their ligand specificities, binding affinities and their distance to the transmembrane domain. Here, we elucidate the effects of the tandem arrangement of the domains on the biochemical, biophysical and structural properties of the protein. For this, we determined the crystal structure of the ligand-free tandem SBD1-2 protein from Lactococcus lactis in the absence of the transporter and compared the tandem to the isolated SBDs. We also used isothermal titration calorimetry to determine the ligand-binding affinity of the SBDs and single-molecule Förster resonance energy transfer (smFRET) to relate ligand binding to conformational changes in each of the domains of the tandem. We show that substrate binding and conformational changes are not notably affected by the presence of the adjoining domain in the wild-type protein, and changes only occur when the linker between the domains is shortened. In a proof-of-concept experiment, we combine smFRET with protein-induced fluorescence enhancement (PIFE–FRET) and show that a decrease in SBD linker length is observed as a linear increase in donor-brightness for SBD2 while we can still monitor the conformational states (open/closed) of SBD1. These results demonstrate the feasibility of PIFE–FRET to monitor protein–protein interactions and conformational states simultaneously.

Transition Path Dynamics of a Dielectric Particle in a Bistable Optical Trap

Many processes in chemistry, physics, and biology involve rare events in which the system escapes from a metastable state by surmounting an activation barrier. Examples range from chemical reactions, protein folding, and nucleation events to the catastrophic failure of bridges. A challenge in understanding the underlying mechanisms is that the most interesting information is contained within the rare transition paths, the exceedingly short periods when the barrier is crossed. To establish a model process that enables access to all relevant timescales, although highly disparate, we probe the dynamics of single dielectric particles in a bistable optical trap in solution. Precise localization by high-speed tracking enables us to resolve the transition paths and relate them to the detailed properties of the 3D potential within which the particle diffuses. By varying the barrier height and shape, the experiments provide a stringent benchmark of current theories of transition path dynamics.

High satiety expectations of a first course promote selection of less energy in a main course picture task

One of the factors determining meal size is the expectation one has about satiating properties of foods. Foods eliciting low satiety expectations are often chosen in larger portions. We investigated whether satiety expectations of one food lead to a different portion size selection of other foods, using an online picture task. One hundred and twenty-six subjects (64 unrestrained, 62 restrained) participated in three conditions (within-subject). In two conditions subjects were asked to imagine they consumed soup as a first course. They were shown pictures of soups differing in terms of visual attributes, e.g. colour intensity, ingredients variety, etc. that conveyed a high or low expected satiety. In the control condition, no picture was shown. After viewing either a soup picture or no picture, subjects chose an ideal menu and portion size out of several other foods (meat, side dishes and vegetables) via an online choice task, specifically developed for this experiment. The energy (kcal) and weight (grams) selected for the main course was measured. More energy was chosen in the low satiety compared with the high satiety soup picture condition, but this effect was only significant for restrained eaters. This study shows that satiety expectations of a first course 'carry over' to the rest of the menu in people who carefully watch their diet, i.e. restrained eaters make satiety estimations for an entire menu. Our online choice task was able to capture these estimations in an implicit manner.

Elucidating the aggregation number of dopamine-induced α-synuclein oligomeric assemblies

Conventional methods to determine the aggregation number, that is, the number of monomers per oligomer, struggle to yield reliable results for large protein aggregates, such as amyloid oligomers. We have previously demonstrated the use of a combination of single-molecule photobleaching and substoichiometric fluorescent labeling to determine the aggregation number of oligomers of human α-synuclein, implicated in Parkinson's disease. We show here that this approach is capable of accurately resolving mixtures of multiple distinct molecular species present in the same sample of dopamine-induced α-synuclein oligomers, and that we can determine the respective aggregation numbers of each species from a single histogram of bleaching steps. We found two distinct species with aggregation numbers of 15-19 monomers and 34-38 monomers. These results show that this single-molecule approach allows for the systematic study of the aggregation numbers of complex supramolecular assemblies formed under different aggregation conditions.

Nanophotonic control of the Förster resonance energy transfer efficiency

We have studied the influence of the local density of optical states (LDOS) on the rate and efficiency of Förster resonance energy transfer (FRET) from a donor to an acceptor. The donors and acceptors are dye molecules that are separated by a short strand of double-stranded DNA. The LDOS is controlled by carefully positioning the FRET pairs near a mirror. We find that the energy transfer efficiency changes with LDOS, and that, in agreement with theory, the energy transfer rate is independent of the LDOS, which allows one to quantitatively control FRET systems in a new way. Our results imply a change in the characteristic Förster distance, in contrast to common lore that this distance is fixed for a given FRET pair.

The effects of food viscosity on bite size, bite effort and food intake

Two studies investigated the effect of a food's viscosity on bite size, bite effort and food intake using a standardized protocol in which subjects sipped through a straw every 20 s for a period of 15 min from one of two products, a chocolate-flavored dairy drink and a chocolate-flavored dairy semi-solid, matched for energy density. In the first study, subjects consumed 47% more from the liquid than from the semi-solid to reach the same degree of satiation, with larger bite sizes for the liquid throughout the 15 minute period (8.7+/-0.45 g) compared to the semi-solid (5.8+/-0.3 g, p<0.01). In the second study bite effort was eliminated by using a peristaltic pump to present the products every 20 s. Oral processing time before swallowing was set at 5 s (both products) or 8 s (semi-solid). With the elimination of bite effort and a standardized oral processing time, subjects consumed as much from the semi-solid as from the liquid to reach the same degree of satiation. Bite size for liquids started relatively small and grew gradually over successive bites, whereas the bite size for the semi-solid food started relatively large and became gradually smaller. The latter effect was even more pronounced when the oral processing time was increased from 5 to 8 s. In conclusion, semi-solids resulted in smaller bite sizes and lower intake than liquids, but these differences disappeared when differences in bite effort were eliminated.

Delineation and physical separation of novel translocation breakpoints on chromosome 1p in two genetically closely associated childhood tumors

Sporadic childhood tumors associated with Beckwith-Wiedemann syndrome (BWS) all show abnormalities of the same region on chromosome 11. In addition to chromosome 11, other chromosome regions are affected in some of these tumor types. In this study we analyzed the region on chromosome 1p involved in the etiology of BWS-associated tumors, Wilms tumor, rhabdomyosarcoma, and hepatoblastoma. For this purpose we determined the location of two novel translocation breakpoints in this chromosome region in cells from a Wilms tumor and cells from a rhabdomyosarcoma. We constructed a map of the region and found that both breakpoints are separated by at least 875 kb. We identified a PAC clone which crosses the rhabdomyosarcoma breakpoint and found several exons within this clone. We established that this breakpoint is located proximal to the PAX7 gene and, therefore, identified a new region involved in the etiology of rhabdomyosarcomas.