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The neuropeptide Y (NPY) Y 4 receptor (Y 4 R), a member of the family of NPY receptors, is physiologically activated by the linear 36-amino acid peptide pancreatic polypeptide (PP). The Y 4 R is involved in the regulation of various biological processes, most importantly pancreatic secretion, gastrointestinal motility, and regulation of food intake. So far, Y 4 R binding affinities have been mostly studied in radiochemical binding assays. Except for a few fluorescently labeled PP derivatives, fluorescence-tagged Y 4 R ligands with high affinity have not been reported. Here, we introduce differently fluorescence-labeled (Sulfo-Cy5, Cy3B, Py-1, Py-5) Y 4 R ligands derived from recently reported cyclic hexapeptides showing picomolar Y 4 R binding affinity. With p K i values of 9.22-9.71 (radioligand competition binding assay), all fluorescent ligands ( 16 - 19 ) showed excellent Y 4 R affinity. Y 4 R saturation binding, binding kinetics, and competition binding with reference ligands were studied using different fluorescence-based methods: flow cytometry (Sulfo-Cy5, Cy3B, and Py-1 label), fluorescence anisotropy (Cy3B label), and NanoBRET (Cy3B label) binding assays. These experiments confirmed the high binding affinity to Y 4 R (equilibrium p K d : 9.02-9.9) and proved the applicability of the probes for fluorescence-based Y 4 R competition binding studies and imaging techniques such as single-receptor molecule tracking., Competing Interests: The authors declare no competing financial interest., (© 2024 The Authors. Published by American Chemical Society.)

Derivatives of the rhodamine-based dye 5-TAMRA (5-carboxy-tetramethylrhodamine) and the indocarbocyanine-type Cy3B (cyclized derivative of the cyanine dye Cy3), both representing important fluorophores frequently used for the labeling of biomolecules (proteins, nucleic acids) and bioactive compounds, such as receptor ligands, were photophysically investigated in aqueous solution, i.e., in neat phosphate-buffered saline (PBS) and in PBS supplemented with 1 wt % bovine serum albumin (BSA). The dyes exhibit comparable absorption (λ abs,max : 550-569 nm) and emission wavelengths (λ em,max : 580-582 nm), and similar S 1 lifetimes (2.27-2.75 ns), and their excited state deactivation proceeds mainly via the lowest excited singlet state (triplet quantum yield ca. 1%). However, the probes show marked differences with respect to their fluorescence quantum yield and photostability. While 5-TAMRA shows a lower quantum yield (37-39%) than the Cy3B derivative (ca. 57%), its photostability is considerably higher compared to Cy3B. Generally, the impact of the protein on the photophysics is low. However, on prolonged illumination, both fluorescent dyes undergo a photocatalytic reaction with tryptophan residues of BSA mediated by sensitized singlet oxygen resulting in a tryptophan photoproduct with an absorption maximum around 330 nm. The overall results of this work will assist in choosing the right dye for the labeling of bioactive compounds, and the study demonstrates that experiments performed with 5-TAMRA or Cy3B-labeled compounds in a biological environment may be influenced by photochemical modification of experimentally relevant proteins at aromatic amino acid residues.

The family of human neuropeptide Y receptors (YRs) comprises four subtypes (Y 1 R, Y 2 R, Y 4 R, and Y 5 R) that are involved in the regulation of numerous physiological processes. Until now, Y 4 R binding studies have been predominantly performed in hypotonic sodium-free buffers using 125 I-labeled derivatives of the endogenous YR agonists pancreatic polypeptide or peptide YY. A few tritium-labeled Y 4 R ligands have been reported; however, when used in buffers containing sodium at a physiological concentration, their Y 4 R affinities are insufficient. Based on the cyclic hexapeptide UR-AK86C, we developed a new tritium-labeled Y 4 R radioligand ([ 3 H]UR-JG102, [ 3 H] 20 ). In sodium-free buffer, [ 3 H] 20 exhibits a very low Y 4 R dissociation constant ( K d 0.012 nM). In sodium-containing buffer (137 mM Na + ), the Y 4 R affinity is lower ( K d 0.11 nM) but still considerably higher compared to previously reported tritiated Y 4 R ligands. Therefore, [ 3 H] 20 represents a useful tool compound for the determination of Y 4 R binding affinities under physiological-like conditions.

The recent crystallization of the neuropeptide Y Y 1 receptor (Y 1 R) in complex with the argininamide-type Y 1 R selective antagonist UR-MK299 ( 2 ) opened up a new approach toward structure-based design of nonpeptidic Y 1 R ligands. We designed novel fluorescent probes showing excellent Y 1 R selectivity and, in contrast to previously described fluorescent Y 1 R ligands, considerably higher (∼100-fold) binding affinity. This was achieved through the attachment of different fluorescent dyes to the diphenylacetyl moiety in 2 via an amine-functionalized linker. The fluorescent ligands exhibited picomolar Y 1 R binding affinities (p K i values of 9.36-9.95) and proved to be Y 1 R antagonists, as validated in a Fura-2 calcium assay. The versatile applicability of the probes as tool compounds was demonstrated by flow cytometry- and fluorescence anisotropy-based Y 1 R binding studies (saturation and competition binding and association and dissociation kinetics) as well as by widefield and total internal reflection fluorescence (TIRF) microscopy of live tumor cells, revealing that fluorescence was mainly localized at the plasma membrane.

The family of neuropeptide Y (NPY) receptors comprises four subtypes (Y 1 R, Y 2 R, Y 4 R, Y 5 R), which are addressed by at least three endogenous peptides, i.e., NPY, peptide YY, and pancreatic polypeptide (PP), the latter showing a preference for Y 4 R. A series of cyclic oligopeptidic Y 4 R ligands were prepared by applying a novel approach, i.e., N-terminus to arginine side-chain cyclization. Most peptides acted as Y 4 R partial agonists, showing up to 60-fold higher Y 4 R affinity compared to the linear precursor peptides. Two cyclic hexapeptides ( 18 , 24 ) showed higher Y 4 R potency (Ca 2+ aequorin assay) and, with p K i values >10, also higher Y 4 R affinity compared to human pancreatic polypeptide (hPP). Compounds such as 18 and 24 , exhibiting considerably lower molecular weight and considerably more pronounced Y 4 R selectivity than PP and previously described dimeric peptidic ligands with high Y 4 R affinity, represent promising leads for the preparation of labeled tool compounds and might support the development of drug-like Y 4 R ligands.

Background: Many functional analysis tools have been developed to extract functional and mechanistic insight from bulk transcriptome data. With the advent of single-cell RNA sequencing (scRNA-seq), it is in principle possible to do such an analysis for single cells. However, scRNA-seq data has characteristics such as drop-out events and low library sizes. It is thus not clear if functional TF and pathway analysis tools established for bulk sequencing can be applied to scRNA-seq in a meaningful way., Results: To address this question, we perform benchmark studies on simulated and real scRNA-seq data. We include the bulk-RNA tools PROGENy, GO enrichment, and DoRothEA that estimate pathway and transcription factor (TF) activities, respectively, and compare them against the tools SCENIC/AUCell and metaVIPER, designed for scRNA-seq. For the in silico study, we simulate single cells from TF/pathway perturbation bulk RNA-seq experiments. We complement the simulated data with real scRNA-seq data upon CRISPR-mediated knock-out. Our benchmarks on simulated and real data reveal comparable performance to the original bulk data. Additionally, we show that the TF and pathway activities preserve cell type-specific variability by analyzing a mixture sample sequenced with 13 scRNA-seq protocols. We also provide the benchmark data for further use by the community., Conclusions: Our analyses suggest that bulk-based functional analysis tools that use manually curated footprint gene sets can be applied to scRNA-seq data, partially outperforming dedicated single-cell tools. Furthermore, we find that the performance of functional analysis tools is more sensitive to the gene sets than to the statistic used.

A knowledge-based method for configurational entropy prediction of proteins is presented; this methodology is extremely fast, compared to previous approaches, because it does not involve any type of configurational sampling. Instead, the configurational entropy of a query fold is estimated by evaluating an artificial neural network, which was trained on molecular-dynamics simulations of ∼1000 proteins. The predicted entropy can be incorporated into a large class of protein software based on cost-function minimization/evaluation, in which configurational entropy is currently neglected for performance reasons. Software of this type is used for all major protein tasks such as structure predictions, proteins design, NMR and X-ray refinement, docking, and mutation effect predictions. Integrating the predicted entropy can yield a significant accuracy increase as we show exemplarily for native-state identification with the prominent protein software FoldX. The method has been termed Popcoen for Prediction of Protein Configurational Entropy. An implementation is freely available at http://fmc.ub.edu/popcoen/ .

Luminopsins are fusion proteins of luciferase and opsin that allow interrogation of neuronal circuits at different temporal and spatial resolutions by choosing either extrinsic physical or intrinsic biological light for its activation. Building on previous development of fusions of wild-type Gaussia luciferase with channelrhodopsin, here we expanded the utility of luminopsins by fusing bright Gaussia luciferase variants with either channelrhodopsin to excite neurons (luminescent opsin, LMO) or a proton pump to inhibit neurons (inhibitory LMO, iLMO). These improved LMOs could reliably activate or silence neurons in vitro and in vivo. Expression of the improved LMO in hippocampal circuits not only enabled mapping of synaptic activation of CA1 neurons with fine spatiotemporal resolution but also could drive rhythmic circuit excitation over a large spatiotemporal scale. Furthermore, virus-mediated expression of either LMO or iLMO in the substantia nigra in vivo produced not only the expected bidirectional control of single unit activity but also opposing effects on circling behavior in response to systemic injection of a luciferase substrate. Thus, although preserving the ability to be activated by external light sources, LMOs expand the use of optogenetics by making the same opsins accessible to noninvasive, chemogenetic control, thereby allowing the same probe to manipulate neuronal activity over a range of spatial and temporal scales.

Design of complex alpha-beta protein topologies poses a challenge because of the large number of alternative packing arrangements. A similar challenge presumably limited the emergence of large and complex protein topologies in evolution. Here, we demonstrate that protein topologies with six and seven-stranded beta sheets can be designed by insertion of one de novo designed beta sheet containing protein into another such that the two beta sheets are merged to form a single extended sheet, followed by amino acid sequence optimization at the newly formed strand-strand, strand-helix, and helix-helix interfaces. Crystal structures of two such designs closely match the computational design models. Searches for similar structures in the SCOP protein domain database yield only weak matches with different beta sheet connectivities. A similar beta sheet fusion mechanism may have contributed to the emergence of complex beta sheets during natural protein evolution.

Plasmonic resonances in metallic nano-triangles have been investigated by irradiating these structures with short laser pulses and imaging the resulting ablation and melting patterns. The triangular gold structures were prepared on Si substrates and had a thickness of 40 nm and a side length of ca. 500 nm. Irradiation was carried out with single femtosecond and picosecond laser pulses at a wavelength of 800 nm, which excited higher order plasmon modes in these triangles. The ablation distribution as well as the local melting of small parts of the nanostructures reflect the regions of large near-field enhancement. The observed patterns are reproduced in great detail by FDTD simulations with a 3-dimensional model, provided that the calculations are not based on idealized, but on realistic structures. In this realistic model, details like the exact shape of the triangle edges and the dielectric environment of the structures are taken into account. The experimental numbers found for the field enhancement are typically somewhat smaller than the calculated ones. The results demonstrate the caveats for FDTD simulations and the potential and the limitations of "near field photography" by local ablation and melting for the mapping of complex plasmon fields and their applications.