Role of green fluorescent proteins and their variants in development of FRET-based sensors

Exploring the landscape of FRET-based molecular sensors: Design strategies and recent advances in emerging applications

Probing biological processes in living organisms that could provide one-of-a-kind insights into real-time alterations of significant physiological parameters is a formidable task that calls for specialized analytic devices. Classical biochemical methods have significantly aided our understanding of the mechanisms that regulate essential biological processes. These methods, however, are typically insufficient for investigating transient molecular events since they focus primarily on the end outcome. Fluorescence resonance energy transfer (FRET) microscopy is a potent tool used for exploring non-invasively real-time dynamic interactions between proteins and a variety of biochemical signaling events using sensors that have been meticulously constructed. Due to their versatility, FRET-based sensors have enabled the rapid and standardized assessment of a large array of biological variables, facilitating both high-throughput research and precise subcellular measurements with exceptional temporal and spatial resolution. This review commences with a brief introduction to FRET theory and a discussion of the fluorescent molecules that can serve as tags in different sensing modalities for studies in chemical biology, followed by an outlining of the imaging techniques currently utilized to quantify FRET highlighting their strengths and shortcomings. The article also discusses the various donor-acceptor combinations that can be utilized to construct FRET scaffolds. Specifically, the review provides insights into the latest real-time bioimaging applications of FRET-based sensors and discusses the common architectures of such devices. There has also been discussion of FRET systems with multiplexing capabilities and multi-step FRET protocols for use in dual/multi-analyte detections. Future research directions in this exciting field are also mentioned, along with the obstacles and opportunities that lie ahead.

Fluorescence-Based HTS Assays for Ion Channel Modulation in Drug Discovery Pipelines

Ion channels represent a druggable family of transmembrane pore-forming proteins with important (patho)physiological functions. While electrophysiological measurement (manual patch clamp) remains the only direct method for detection of ion currents, it is a labor-intensive technique. Although automated patch clamp instruments have become available to date, their high costs limit their use to large pharma companies or commercial screening facilities. Therefore, fluorescence-based assays are particularly important for initial screening of compound libraries. Despite their numerous disadvantages, they are highly amenable to high-throughput screening and in many cases, no sophisticated instrumentation or materials are required. These features predispose them for implementation in early phases of drug discovery pipelines (hit identification), even in an academic environment. This review summarizes the advantages and pitfalls of individual methodological approaches for identification of ion channel modulators employing fluorescent probes (i. e., membrane potential and ion flux assays) with emphasis on practical aspects of their adaptation to high-throughput format.

Molecular Dynamics Simulation Combined with Neural Relationship Inference and Markov Model to Reveal the Relationship between Conformational Regulation and Bioluminescence Properties of Gaussia Luciferase

Gaussia luciferase (Gluc) is currently known as the smallest naturally secreted luciferase. Due to its small molecular size, high sensitivity, short half-life, and high secretion efficiency, it has become an ideal reporter gene and is widely used in monitoring promoter activity, studying protein-protein interactions, protein localization, high-throughput drug screening, and real-time monitoring of tumor occurrence and development. Although studies have shown that different Gluc mutations exhibit different bioluminescent properties, their mechanisms have not been further investigated. The purpose of this study is to reveal the relationship between the conformational changes of Gluc mutants and their bioluminescent properties through molecular dynamics simulation combined with neural relationship inference (NRI) and Markov models. Our results indicate that, after binding to the luciferin coelenterazine (CTZ), the α-helices of the 109-119 residues of the Gluc Mutant2 (GlucM2, the flash-type mutant) are partially unraveled, while the α-helices of the same part of the Gluc Mutant1 (GlucM1, the glow-type mutant) are clearly formed. The results of Markov flux analysis indicate that the conformational differences between glow-type and flash-type mutants when combined with luciferin substrate CTZ mainly involve the helicity change of α7. The most representative conformation and active pocket distance analysis indicate that compared to the flash-type mutant GlucM2, the glow-type mutant GlucM1 has a higher degree of active site closure and tighter binding. In summary, we provide a theoretical basis for exploring the relationship between the conformational changes of Gluc mutants and their bioluminescent properties, which can serve as a reference for the modification and evolution of luciferases.

Engineering a Red Fluorescent Protein Chromophore for Visualization of RNA G-Quadruplexes

Synthetic red fluorescent protein (RFP) chromophores have emerged as valuable tools for biological imaging and therapeutic applications, but their application in the visualization of endogenous RNA G-quadruplexes (G4s) in living cells has been rarely reported so far. Here, by integrating the group of the excellent G4 dye ThT, we modulate RFP chromophores to create a novel fluorescent probe DEBIT with red emission. DEBIT selectively recognizes the G4 structure with the advantage of strong binding affinity, high selectivity, and excellent photostability. Using DEBIT as a fluorescent indicator, the real-time monitoring of RNA G4 in biological systems can be achieved. In summary, our work expands the application of synthetic RFP chromophores and provides an essential dye category to the classical G4 probes.

Differential regulation of Shigella Spa47 ATPase activity by a native C-terminal product of Spa33

Shigella is a Gram-negative bacterial pathogen that relies on a single type three secretion system (T3SS) as its primary virulence factor. The T3SS includes a highly conserved needle-like apparatus that directly injects bacterial effector proteins into host cells, subverting host cell function, initiating infection, and circumventing resulting host immune responses. Recent findings have located the T3SS ATPase Spa47 to the base of the Shigella T3SS apparatus and have correlated its catalytic function to apparatus formation, protein effector secretion, and overall pathogen virulence. This critical correlation makes Spa47 ATPase activity regulation a likely point of native control over Shigella virulence and a high interest target for non-antibiotic- based therapeutics. Here, we provide a detailed characterization of the natural 11.6 kDa C-terminal translation product of the Shigella T3SS protein Spa33 (Spa33C), showing that it is required for proper virulence and that it pulls down with several known T3SS proteins, consistent with a structural role within the sorting platform of the T3SS apparatus. In vitro binding assays and detailed kinetic analyses suggest an additional role, however, as Spa33C differentially regulates Spa47 ATPase activity based on Spa47s oligomeric state, downregulating Spa47 monomer activity and upregulating activity of both homo-oligomeric Spa47 and the hetero-oligomeric MxiN2Spa47 complex. These findings identify Spa33C as only the second known differential T3SS ATPase regulator to date, with the Shigella protein MxiN representing the other. Describing this differential regulatory protein pair begins to close an important gap in understanding of how Shigella may modulate virulence through Spa47 activity and T3SS function.

Real-Time Temperature Sensing Using a Ratiometric Dual Fluorescent Protein Biosensor

Accurate temperature control within biological and chemical reaction samples and instrument calibration are essential to the diagnostic, pharmaceutical and chemical industries. This is particularly challenging for microlitre-scale reactions typically used in real-time PCR applications and differential scanning fluorometry. Here, we describe the development of a simple, inexpensive ratiometric dual fluorescent protein temperature biosensor (DFPTB). A combination of cycle three green fluorescent protein and a monomeric red fluorescent protein enabled the quantification of relative temperature changes and the identification of temperature discrepancies across a wide temperature range of 4-70 °C. The maximal sensitivity of 6.7% °C^-1 and precision of 0.1 °C were achieved in a biologically relevant temperature range of 25-42 °C in standard phosphate-buffered saline conditions at a pH of 7.2. Good temperature sensitivity was achieved in a variety of biological buffers and pH ranging from 4.8 to 9.1. The DFPTB can be used in either purified or mixed bacteria-encapsulated formats, paving the way for in vitro and in vivo applications for topologically precise temperature measurements.

Cleavable Linker Incorporation into a Synthetic Dye-Nanobody-Fluorescent Protein Assembly: FRET, FLIM and STED Microscopy

A bright and photostable fluorescent dye with a disulfide (S-S) linker and maleimide group (Rho594-S2-mal), as cleavable and reactive sites, was synthesized and conjugated with anti-GFP nanobodies (NB). The binding of EGFP (FRET donor) with anti-GFP NB labeled with one or two Rho594-S2-mal residues was studied in vitro and in cellulo. The linker was cleaved with dithiothreitol recovering the donor (FP) signal. The bioconjugates (FP-NB-dye) were applied in FRET-FLIM assays, confocal imaging, and superresolution STED microscopy.

Green fluorescent protein inspired fluorophores

Green fluorescence proteins (GFP) are appealing to a variety of biomedical and biotechnology applications, such as protein fusion, subcellular localizations, cell visualization, protein-protein interaction, and genetically encoded sensors. To mimic the fluorescence of GFP, various compounds, such as GFP chromophores analogs, hydrogen bond-rich proteins, and aromatic peptidyl nanostructures that preclude free rotation of the aryl-alkene bond, have been developed to adapt them for a fantastic range of applications. Herein, we firstly summarize the structure and luminescent mechanism of GFP. Based on this, the design strategy, fluorescent properties, and the advanced applications of GFP-inspired fluorophores are then carefully discussed. The diverse advantages of bioinspired fluorophores, such as biocompatibility, structural simplicity, and capacity to form a variety of functional nanostructures, endow them potential candidates as the next-generation bio-organic optical materials.

Live-Cell FRET Reveals that Malaria Nutrient Channel Proteins CLAG3 and RhopH2 Remain Associated throughout Their Tortuous Trafficking

Malaria parasites increase their host erythrocyte's permeability to various nutrients, fueling intracellular pathogen development and replication. The plasmodial surface anion channel (PSAC) mediates this uptake and is linked to the parasite-encoded RhopH complex, consisting of CLAG3, RhopH2, and RhopH3. While interactions between these subunits are well established, it is not clear whether they remain associated from their synthesis in developing merozoites through erythrocyte invasion and trafficking to the host membrane. Here, we explored protein-protein interactions between RhopH subunits using live-cell imaging and Förster resonance energy transfer (FRET) experiments. Using the green fluorescent protein (GFP) derivatives mCerulean and mVenus, we generated single- and double-tagged parasite lines for fluorescence measurements. While CLAG3-mCerulean served as an efficient FRET donor for RhopH2-mVenus within rhoptry organelles, mCerulean targeted to this organelle via a short signal sequence produced negligible FRET. Upon merozoite egress and reinvasion, these tagged RhopH subunits were deposited into the new host cell's parasitophorous vacuole; these proteins were then exported and trafficked to the erythrocyte membrane, where CLAG3 and RhopH2 remained fully associated. Fluorescence intensity measurements identified stoichiometric increases in exported RhopH protein when erythrocytes are infected with two parasites; whole-cell patch-clamp revealed a concomitant increase in PSAC functional copy number and a dose effect for RhopH contribution to ion and nutrient permeability. These studies establish live-cell FRET imaging in human malaria parasites, reveal that RhopH subunits traffic to their host membrane destination without dissociation, and suggest quantitative contribution to PSAC formation.IMPORTANCE Malaria parasites grow within circulating red blood cells and uptake nutrients through a pore on their host membrane. Here, we used gene editing to tag CLAG3 and RhopH2, two proteins linked to the nutrient pore, with fluorescent markers and tracked these proteins in living infected cells. After their synthesis in mature parasites, imaging showed that both proteins are packaged into membrane-bound rhoptries. When parasites ruptured their host cells and invaded new red blood cells, these proteins were detected within a vacuole around the parasite before they migrated and inserted in the surface membrane of the host cell. Using simultaneous labeling of CLAG3 and RhopH2, we determined that these proteins interact tightly during migration and after surface membrane insertion. Red blood cells infected with two parasites had twice the protein at their surface and a parallel increase in the number of nutrient pores. Our work suggests that these proteins directly facilitate parasite nutrient uptake from human plasma.

The isoelectric point of proteins influences their translocation to the extrahaustorial matrix of the barley powdery mildew fungus

Many biotrophic fungal plant pathogens develop feeding structures, haustoria, inside living plant cells, which are essential for their success. Extrahaustorial membranes (EHMs) surround haustoria and delimit the extrahaustorial matrices (EHMxs). Little is known about transport mechanisms across EHMs and what properties proteins and nutrients need in order to cross these membranes. To investigate this further, we expressed fluorescent proteins in the cytosol of infected barley leaf epidermal cells after particle bombardment and investigated properties that influenced their localisation in the powdery mildew EHMx. We showed that this translocation is favoured by a neutral isoelectric point (pI) between 6.0 and 8.4. However, for proteins larger than 50 kDa, pI alone does not explain their localisation, hinting towards a more complex interplay between pI, size, and sequence properties. We discuss the possibility that an EHM translocon is involved in protein uptake into the EHMx.