A never ending race for new and improved fluorescent proteins

Red Fluorescent Protein Variant with a Dual-Peak Emission of Fluorescence

The marine environment is a rich reservoir of diverse biological entities, many of which possess unique properties that are of immense value to biotechnological applications. One such example is the red fluorescent protein derived from the coral Discosoma sp. This protein, encoded by the DsRed gene, has been the subject of extensive research due to its potential applications in various fields. In the study, a variant of the red fluorescent protein was generated through random mutagenesis using the DsRed2 gene as a template. The process employed error-prone PCR (epPCR) to introduce random mutations, leading to the isolation of twelve gene variants. Among these, one variant stood out due to its unique spectral properties, exhibiting dual fluorescence emission at both 480 nm (green) and 550 nm (red). This novel variant was expressed in both Escherichia coli and zebrafish (Danio rerio) muscle, confirming the dual fluorescence emission in both model systems. One of the immediate applications of this novel protein variant is in ornamental aquaculture. The dual fluorescence can serve as a unique marker or trait, enhancing the aesthetic appeal of aquatic species in ornamental settings.

Analysis insights for three FRET pairs of chemically unlinked two-molecule FRET cytometry

Förster resonance energy transfer (FRET) is the direct energy exchange between two-component fluorescent molecules. FRET methods utilize chemically linked molecules or unlinked fluorescence protein-protein interactions. FRET is therefore a powerful indicator of molecular proximity, but standardized determination of FRET efficiency is challenged when investigating natural (chemically unlinked) interactions. In this paper, we have examined the interactions of tumor necrosis factor receptor-1 (TNFR1) molecules expressed as recombinant fusion proteins of cyan, yellow, or red fluorescent protein (-CFP, -YFP, or -RFP) to evaluate two-molecule chemically unlinked FRET by flow cytometry. We demonstrate three independent FRET pairs CFP→YFP (FRET-1), YFP→RFP (FRET-2) and CFP→RFP (FRET-3), comparing TNFR1+TNFR1 with non-interacting TNFR1+CD27 proteins, on both LSR-II and Fortessa X-20 cytometers. We describe genuine FRET activities reflecting TNFR1 homotypic interactions. FRET events can be visualized during sample acquisition via the use of "spiked" FRET donor cells, together with TNFR1+TNFR1 co-transfected cells, as FRET channel MFI overlays. FRET events are subsequentially indicated by comparing concatenated files of cells expressing either FRET positive events (TNFR1+TNFR1) or FRET negative events (TNFR1+CD27) to generate single-cell scatter plots showing loss of FRET donor brightness. Robust determination of FRET efficiency is then confirmed at the single-cell level by applying matrix calculations based on the measurements of FRET donor, acceptor and FRET fluorescent intensities (I), detector channel emission coefficient (S), fluorescent protein extinction coefficients (ε) and α factor. In this TNFR based system, the mean CFP→YFP FRET-1 efficiency is 0.43 (LSR-II) and 0.41 (Fortessa), the mean YFP→RFP FRET-2 efficiency is 0.30 (LSR-II) and 0.29 (Fortessa), and the mean CFP→RFP FRET-3 efficiency is 0.56 (LSR-II) and 0.54 (Fortessa). This study also embraces multidimensional clustering using t-SNE, Fit-SNE, UMAP, Tri-Map and PaCMAP to further demonstrate FRET. These approaches establish a robust system for standardized detection of chemically unlinked TNFR1 homotypic interactions with three individual FRET pairs.

Concepts in bio-molecular spectroscopy: vibrational case studies on metalloenzymes

Challenges and chances in bio-molecular spectroscopy are exemplified by vibrational case studies on metalloenzymes.

Fluorescence fluctuation spectroscopy approaches to the study of receptors in live cells

Communication between cells and their environment, including other cells, is often mediated by cell surface receptors. Fluorescence methodologies are among the most important techniques used to study receptors and their interactions, and in the past decade, fluorescence fluctuation spectroscopy (FFS) approaches have been increasingly utilized. In this overview, we illustrate how diverse FFS approaches have been used to elucidate important aspects of receptor systems, including interactions of receptors with their ligands and receptor oligomerization and clustering. We also describe the most popular methods used to introduce fluorescent moieties into the biological systems. Finally, specific attention will be given to cell maintenance and transfection strategies especially as related to microscopy studies.