Engineering of a Red Fluorogenic Protein/Merocyanine Complex for Live-Cell Imaging

A semi-automated quantum-mechanical workflow for the generation of molecular monolayers and aggregates

Organic electronics (OE) such as organic light-emitting diodes or organic solar cells represent an important and innovative research area to achieve global goals like environmentally friendly energy production. To accelerate OE material discovery, various computational methods are employed. For the initial generation of structures, a molecular cluster approach is employed. Here, we present a semi-automated workflow for the generation of monolayers and aggregates using the GFNn-xTB methods and composite density functional theory (DFT-3c). Furthermore, we present the novel D11A8MERO dye interaction energy benchmark with high-level coupled cluster reference interaction energies for the assessment of efficient quantum chemical and force-field methods. GFN2-xTB performs similar to low-cost DFT, reaching DFT/mGGA accuracy at two orders of magnitude lower computational cost. As an example application, we investigate the influence of the dye aggregate size on the optical and electrical properties and show that at least four molecules in a cluster model are needed for a qualitatively reasonable description.

Regulation of Absorption and Emission in a Protein/Fluorophore Complex

Human cellular retinol binding protein II (hCRBPII) was used as a protein engineering platform to rationally regulate absorptive and emissive properties of a covalently bound fluorogenic dye. We demonstrate the binding of a thio-dapoxyl analog via formation of a protonated imine between an active site lysine residue and the chromophore's aldehyde. Rational manipulation of the electrostatics of the binding pocket results in a 204 nm shift in absorption and a 131 nm shift in emission. The protein is readily expressed in mammalian systems and binds with exogenously delivered fluorophore as demonstrated by live-cell imaging experiments.

Design and Photonics of Merocyanine Dyes

Merocyanines, thanks to their easily adjustable electronic structure, appear to be the most versatile and promising functional dyes. Their D-π-A framework offers ample opportunities for custom design through variations in both donor/acceptor end-groups and the π-conjugated polymethine chain, and leads to a broad range of practical properties, including noticeable solvatochromism, high polarizability/hyperpolarizabilities, and the ability to sensitize various physicochemical processes. Accordingly, merocyanines are applied and extensively studied in various fields, such as light-converting materials for optoelectronics, nonlinear optics, optical storage, solar cells, fluorescent probes, and antitumor agents in photodynamic therapy. This review encompasses both classical and novel more important publications on the structure-property relationships in merocyanines, with particular emphasis on the results by A.  I. Kiprianov and his followers in Institute of Organic Chemistry in Kyiv, Ukraine.

Efficient calculation of electronic coupling integrals with the dimer projection method via a density matrix tight-binding potential

Designing organic semiconductors for practical applications in organic solar cells, organic field-effect transistors, and organic light-emitting diodes requires understanding charge transfer mechanisms across different length and time scales. The underlying electron transfer mechanisms can be efficiently explored using semiempirical quantum mechanical (SQM) methods. The dimer projection (DIPRO) method combined with the recently introduced non-self-consistent density matrix tight-binding potential (PTB) [Grimme et al., J. Chem. Phys. 158, 124111 (2023)] is used in this study to evaluate charge transfer integrals important for understanding charge transport mechanisms. PTB, parameterized for the entire Periodic Table up to Z = 86, incorporates approximate non-local exchange, allowing for efficient and accurate calculations for large hetero-organic compounds. Benchmarking against established databases, such as Blumberger's HAB sets, or our newly introduced JAB69 set and comparing with high-level reference data from ωB97X-D4 calculations confirm that DIPRO@PTB consistently performs well among the tested SQM approaches for calculating coupling integrals. DIPRO@PTB yields reasonably accurate results at low computational cost, making it suitable for screening purposes and applications to large systems, such as metal-organic frameworks and cyanine-based molecular aggregates further discussed in this work.

Light controlled reversible Michael addition of cysteine: a new tool for dynamic site-specific labeling of proteins

Cysteine-based Michael addition is a widely employed strategy for covalent conjugation of proteins, peptides, and drugs. The covalent reaction is irreversible in most cases, leading to a lack of control over the process. Utilizing spectroscopic analyses along with X-ray crystallographic studies, we demonstrate Michael addition of an engineered cysteine residue in human Cellular Retinol Binding Protein II (hCRBPII) with a coumarin analog that creates a non-fluorescent complex. UV-illumination reverses the conjugation, yielding a fluorescent species, presumably through a retro-Michael process. This series of events can be repeated between a bound and non-bound form of the cysteine reversibly, resulting in the ON-OFF control of fluorescence. The details of the mechanism of photoswitching was illuminated by recapitulation of the process in light irradiated single crystals, confirming the mechanism at atomic resolution.

Design of Large Stokes Shift Fluorescent Proteins Based on Excited State Proton Transfer of an Engineered Photobase

The incredible potential for fluorescent proteins to revolutionize biology has inspired the development of a variety of design strategies to address an equally broad range of photophysical characteristics, depending on potential applications. Of these, fluorescent proteins that simultaneously exhibit high quantum yield, red-shifted emission, and wide separation between excitation and emission wavelengths (Large Stokes Shift, LSS) are rare. The pursuit of LSS systems has led to the formation of a complex, obtained from the marriage of a rationally engineered protein (human cellular retinol binding protein II, hCRBPII) and different fluorogenic molecules, capable of supporting photobase activity. The large increase in basicity upon photoexcitation leads to protonation of the fluorophore in the excited state, dramatically red-shifting its emission, leading to an LSS protein/fluorophore complex. Essential for selective photobase activity is the intimate involvement of the target protein structure and sequence that enables Excited State Proton Transfer (ESPT). The potential power and usefulness of the strategy was demonstrated in live cell imaging of human cell lines.

Genetically Encoded Activators of Small Molecules for Imaging and Drug Delivery

Chemical biologists have developed many tools based on genetically encoded macromolecules and small, synthetic compounds. The two different approaches are extremely useful, but they have inherent limitations. In this Minireview, we highlight examples of strategies that combine both concepts to tackle challenging problems in chemical biology. We discuss applications in imaging, with a focus on super-resolved techniques, and in probe and drug delivery. We propose future directions in this field, hoping to inspire chemical biologists to develop new combinations of synthetic and genetically encoded probes.

Next-Generation Fluorogen-Based Reporters and Biosensors for Advanced Bioimaging

Our ability to observe biochemical events with high spatial and temporal resolution is essential for understanding the functioning of living systems. Intrinsically fluorescent proteins such as the green fluorescent protein (GFP) have revolutionized the way biologists study cells and organisms. The fluorescence toolbox has been recently extended with new fluorescent reporters composed of a genetically encoded tag that binds endogenously present or exogenously applied fluorogenic chromophores (so-called fluorogens) and activates their fluorescence. This review presents the toolbox of fluorogen-based reporters and biosensors available to biologists. Various applications are detailed to illustrate the possible uses and opportunities offered by this new generation of fluorescent probes and sensors for advanced bioimaging.