Collapse and recovery of green fluorescent protein chromophore emission through topological effects

Unidirectional Photoisomerization of the Green Fluorescent Protein Chromophore in a Reversibly Photoswitchable Fluorescent Protein rsKiiro: Insights from Quantum Mechanics/Molecular Mechanics Simulations

In this study, a quantum mechanics/molecular mechanics (QM/MM) framework combined with the CASPT2//CASSCF approach was used to investigate the excited-state decay and isomerization of the rsKiiro green fluorescent protein (GFP) from its neutral "OFF" trans state. Upon irradiation at 400 nm, the trans conformation is initially excited to the bright S1 state. A rapid decay of the excited state then occurs and ultimately leads the molecule to the ground state. Notably, the clockwise and counterclockwise rotations of the C8C9C11N12 [or C5C8C9C11] dihedral angle are asymmetric or unidirectional, with only one direction of rotation effectively driving the excited-state relaxation. This process is shaped by hydrogen-bonding networks and steric constraints within the protein. In addition, trans-cis isomerization may not occur directly in the S1 state because the energy of the S1 cis minimum is relatively higher than that of the S1 trans minimum. Instead, the S1 cis minimum may be generated through the reabsorption of light near 400 nm, as the vertical excitation energy of the S0 cis minimum is close to that of the S0 trans minimum. This work provides important insights into the early photodynamics of rsKiiro GFP and aids in the design of novel GFP-like fluorescent proteins.

Photofunctional cyclophane host-guest systems

Modulation of optical properties through smart protein matrices is exemplified by a few examples in nature such as rhodopsin (absorption wavelength tuning) and the green fluorescence protein (emission), but in general, the scope found in nature for the matrix-controlled photofunctions remains rather limited. In this review, we present cyclophane-based supramolecular host-guest complexes for which electronic interactions between the cyclophane host and mostly planar aromatic guest molecules can actively modulate excited-state properties in a more advanced way involving both singlet and triplet excited states. We begin by highlighting photofunctional host-guest systems for on-off fluorescence switching and chiroptical functions using bay-functionalized perylene bisimide cyclophanes. Next, we examine the impact of π-extension in perylene bisimide cyclophanes for multiple guest binding, showcasing photofunctional properties including circularly polarized luminescence (CPL). We then focus on triplet-generating cyclophanes, i.e. coronene bisimide cyclophane, with high intersystem crossing (ISC) rates, where we demonstrate modulation of excited state pathways upon guest encapsulation and triplet sensitization through phosphorescence and thermally activated delayed fluorescence (TADF). Furthermore, using supramolecular strategies, we advance non-covalent designs, involving either heavy-atom-based Pt(acac)2 guests or heavy-atom free charge transfer complexes, for triplet harvesting under ambient conditions and demonstrate the role of supramolecular nanoenvironments in stabilizing triplet excitons in aerated solutions. Additionally, we showcase examples for triplet-triplet annihilation (TTA) upconversion in defined cyclophane complexes in aqueous solutions and the application of host-guest chemistry in organic light-emitting diodes (OLEDs).

Guest-Mediated Modulation of Photophysical Pathways in a Coronene Bisimide Cyclophane

The properties and functions of chromophores utilized by nature are strongly affected by the environment formed by the protein structure in the cells surrounding them. This concept is transferred here to host-guest complexes with the encapsulated guests acting as an environmental stimulus. A new cyclophane host based on coronene bisimide is presented that can encapsulate a wide variety of planar guest molecules with binding constants up to (4.29 ± 0.32) × 1010 M-1 in chloroform. Depending on the properties of the chosen guest, the excited state deactivation of the coronene bisimide chromophore can be tuned by the formation of host-guest complexes toward fluorescence, exciplex formation, charge separation, room-temperature phosphorescence (RTP), or thermally activated delayed fluorescence (TADF). The photophysical processes were investigated by UV/vis absorption, emission, and femto- and nanosecond transient absorption spectroscopy. To enhance the TADF, two different strategies were used by employing suitable guests: the reduction of the singlet-triplet gap by exciplex formation and the external heavy atom effect. Altogether, by using supramolecular host-guest complexation, a versatile multimodal chromophore system is achieved with the coronene bisimide cyclophane.

Self-assembly solid-state enhanced fluorescence emission of GFP chromophore analogues: Formation of microsheets and microtubes oriented by molecular skeleton

The p-, m- and o-N,N-dimethylamino analogs of the green fluorescent protein (GFP) chromophore (denoted as p-DBHI, m-DBHI and o-DBHI) were synthesized by 2,3-cycloaddition. These three compounds were structurally characterized by NMR, HRMS and single crystal X-ray diffraction and were shown to be in the Z-form in both the solid phase and solution. Their fluorescence properties and self-assembly behaviors were investigated by UV-Vis, photoluminescence spectroscopy, fluorescence microscopy and scanning electron microscopy. They exhibited low fluorescence quantum yields in both protic and aprotic solvents, which was consistent with the reported results, and strong emissions in the solid state, thus exhibiting aggregation-induced emission (AIE) behaviors. By a solvent exchange method, the p-DBHI and o-DBHI were assembled into microsheets, while the m-DBHI was assembled into microtubule-like structures. The photoluminescence properties of the assemblies were compared with those of the pristine microcrystalline powders obtained by evaporation from organic solvents. The fluorescence quantum yields of the microcrystals obtained by self-assembly were recorded to 9.86 %, 3.37 % and 31.65 %, respectively, which were much higher than those of the corresponding pristine powders (4.71 %, 2.51 % and 17.03 %). This indicated that the fluorescence properties in the solid state depended on the morphologies of the particles.

Excited-state dynamics and fluorescence lifetime of cryogenically cooled green fluorescent protein chromophore anions

Time-resolved action spectroscopy together with a fs-pump probe scheme is used in an electrostatic ion-storage ring to address lifetimes of specific vibrational levels in electronically excited states. Here we specifically consider the excited-state lifetime of cryogenically cooled green fluorescent protein (GFP) chromophore anions which is systematically measured across the S0-S1 spectral region (450-482 nm). A long lifetime of 5.2 ± 0.3 ns is measured at the S0-S1 band origin. When exciting higher vibrational levels in S1, the lifetime changes dramatically. It decreases by more than two orders of magnitude in a narrow energy region ∼250 cm-1 (31 meV) above the 0-0 transition. This is attributed to the opening of internal conversion over an excited-state energy barrier. The applied experimental technique provides a new way to uncover even small energy barriers, which are crucial for excited-state dynamics.

Fluorescence Amplification of Unsaturated Oxazolones Using Palladium: Photophysical and Computational Studies

Weakly fluorescent (Z)-4-arylidene-5-(4H)-oxazolones (1), Φ_PL < 0.1%, containing a variety of conjugated aromatic fragments and/or charged arylidene moieties, have been orthopalladated by reaction with Pd(OAc)₂. The resulting dinuclear complexes (2) have the oxazolone ligands bonded as a C^N-chelate, restricting intramolecular motions involving the oxazolone. From 2, a variety of mononuclear derivatives, such as [Pd(C^N-oxazolone)(O₂CCF₃)(py)] (3), [Pd(C^N-oxazolone)(py)₂](ClO₄) (4), [Pd(C^N-oxazolone)(Cl)(py)] (5), and [Pd(C^N-oxazolone)(X)(NHC)] (6, 7), have been prepared and fully characterized. Most of complexes 3-6 are strongly fluorescent in solution in the range of wavelengths from green to yellow, with values of Φ_PL up to 28% (4h), which are among the highest values of quantum yield ever reported for organometallic Pd complexes with bidentate ligands. This means that the introduction of the Pd in the oxazolone scaffold produces in some cases an amplification of the fluorescence of several orders of magnitude from the free ligand 1 to complexes 3-6. Systematic variations of the substituents of the oxazolones and the ancillary ligands show that the wavelength of emission is tuned by the nature of the oxazolone, while the quantum yield is deeply influenced by the change of ligands. TD-DFT studies of complexes 3-6 show a direct correlation between the participation of the Pd orbitals in the HOMO and the loss of emission through non-radiative pathways. This model allows the understanding of the amplification of the fluorescence and the future rational design of new organopalladium systems with improved properties.

Multiple Photoisomerization Pathways of the Green Fluorescent Protein Chromophore in a Reversibly Photoswitchable Fluorescent Protein: Insights from Quantum Mechanics/Molecular Mechanics Simulations

Herein, we have employed a combined CASPT2//CASSCF approach within the quantum mechanics/molecular mechanics (QM/MM) framework to explore the early time photoisomerization of rsEGFP2 starting from its two OFF trans states, i.e., Trans1 and Trans2. The results show similar vertical excitation energies to the S₁ state in their Franck-Condon regions. Considering the clockwise and counterclockwise rotations of the C11-C9 bond, four pairs of the S₁ excited-state minima and low-lying S₁/S₀ conical intersections were optimized, based on which we determined four S₁ photoisomerization paths that are essentially barrierless to the relevant S₁/S₀ conical intersections leading to efficient excited-state deactivation to the S₀ state. Most importantly, our work first identified multiple photoisomerization and excited-state decay paths, which must be seriously considered in the future. This work not only sheds significant light on the primary trans-cis photoisomerization of rsEGFP2 but also aids in the understanding of the microscopic mechanism of GFP-like RSFPs and the design of novel GFP-like fluorescent proteins.

A Biomimetic Emitter Inspired from Green Fluorescent Protein

The unique tripeptide structure of green fluorescent protein (GFP), a Ser-Tyr-Gly motif, generates the mature chromophore in situ to define the emission profiles of GFP. Here, we describe the rational design and discovery of a biomimetic fluorescent emitter, MBP, by mimicking the key structure of the Ser-Tyr-Gly motif. Through systematically tailoring the tripeptide, a family of four chromophores were engineered, while only MBP exhibited bright fluorescence in different fluid solvents with highly enhanced quantum yields. Distinct to previous hydrogen-bonding-induced fluorescence quenching of GFP chromophore analogues, the emission of MBP was only slightly decreased in protic solvents. Heteronuclear multiple bond correlation techniques demonstrated the fundamental mechanism for enhanced fluorescence emission owing to the synergy of the formation of the intramolecular hydrogen-bonding-ring structure and the self-restricted effect, which was further illustrated via theoretical calculations. This work puts forward an extraordinary approach toward highly emissive biomimicking fluorophores, which gives new insights into the emission mechanisms and photophysics of GFP-like chromophores.

Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme

The past decades have witnessed an explosion of de novo protein designs with a remarkable range of scaffolds. It remains challenging, however, to design catalytic functions that are competitive with naturally occurring counterparts as well as biomimetic or nonbiological catalysts. Although directed evolution often offers efficient solutions, the fitness landscape remains opaque. Green fluorescent protein (GFP), which has revolutionized biological imaging and assays, is one of the most redesigned proteins. While not an enzyme in the conventional sense, GFPs feature competing excited-state decay pathways with the same steric and electrostatic origins as conventional ground-state catalysts, and they exert exquisite control over multiple reaction outcomes through the same principles. Thus, GFP is an "excited-state enzyme". Herein we show that rationally designed mutants and hybrids that contain environmental mutations and substituted chromophores provide the basis for a quantitative model and prediction that describes the influence of sterics and electrostatics on excited-state catalysis of GFPs. As both perturbations can selectively bias photoisomerization pathways, GFPs with fluorescence quantum yields (FQYs) and photoswitching characteristics tailored for specific applications could be predicted and then demonstrated. The underlying energetic landscape, readily accessible via spectroscopy for GFPs, offers an important missing link in the design of protein function that is generalizable to catalyst design.

Folding-induced Fluorescence Enhancement in a Series of Merocyanine Hetero-Folda-Trimers

Many dyes suffer from fast non-radiative decay pathways, thereby showing only short-lived excited states and weak photoluminescence. Here we show a pronounced fluorescence enhancement for a weakly fluorescent merocyanine (MC) dye by being co-facially stacked to other dyes in hetero-folda-trimer architectures. By means of fluorescence spectroscopy (lifetime, quantum yield) the fluorescence enhancement was explained by the rigidification of the emitting chromophore in the defined foldamer architecture and the presence of a non-forbidden lowest exciton state in H-coupled hetero-aggregates. This folding-induced fluorescence enhancement (FIFE) for specific sequences of π-stacked dyes points at a viable strategy toward improved fluorophores that relates to the approach used by nature in the green fluorescent protein (GFP).

Computational redesign of a fluorogen activating protein with Rosetta

The use of unnatural fluorogenic molecules widely expands the pallet of available genetically encoded fluorescent imaging tools through the design of fluorogen activating proteins (FAPs). While there is already a handful of such probes available, each of them went through laborious cycles of in vitro screening and selection. Computational modeling approaches are evolving incredibly fast right now and are demonstrating great results in many applications, including de novo protein design. It suggests that the easier task of fine-tuning the fluorogen-binding properties of an already functional protein in silico should be readily achievable. To test this hypothesis, we used Rosetta for computational ligand docking followed by protein binding pocket redesign to further improve the previously described FAP DiB1 that is capable of binding to a BODIPY-like dye M739. Despite an inaccurate initial docking of the chromophore, the incorporated mutations nevertheless improved multiple photophysical parameters as well as the overall performance of the tag. The designed protein, DiB-RM, shows higher brightness, localization precision, and apparent photostability in protein-PAINT super-resolution imaging compared to its parental variant DiB1. Moreover, DiB-RM can be cleaved to obtain an efficient split system with enhanced performance compared to a parental DiB-split system. The possible reasons for the inaccurate ligand binding pose prediction and its consequence on the outcome of the design experiment are further discussed.

Computational approaches have recently made significant progress in the protein engineering field evolving from a tool for helping experimentalists to prioritize or short-list mutations for testing to being capable of making fully reliable predictions. However, not all the fields of protein modeling are evolving at a similar pace. That is why evaluating the capabilities of computational tools on different tasks is important to provide other scientists with up-to-date information on the state of the field. Here we tested the performance of Rosetta (one of the leading macromolecule modeling tools) in improving small molecule-binding proteins. We successfully redesigned a fluorogen binding protein DiB1 –a protein that binds a non-fluorescent molecule and enforces its fluorescence in the obtained complex–for improved brightness and better performance in super-resolution imaging. Our results suggest that such tasks can be already achieved without laborious library screenings. However, the flexibility of the proteins might still be underestimated during standard modeling protocols and should be closely evaluated.

Photo-Switching of Protein Dynamical Collectivity

We examine changes in the picosecond structural dynamics with irreversible photobleaching of red fluorescent proteins (RFP) mCherry, mOrange2 and TagRFP-T. Measurements of the protein dynamical transition using terahertz time-domain spectroscopy show in all cases an increase in the turn-on temperature in the bleached state. The result is surprising given that there is little change in the protein surface, and thus, the solvent dynamics held responsible for the transition should not change. A spectral analysis of the measurements guided by quasiharmonic calculations of the protein absorbance reveals that indeed the solvent dynamical turn-on temperature is independent of the thermal stability/photostate however the protein dynamical turn-on temperature shifts to higher temperatures. This is the first demonstration of switching the protein dynamical turn-on temperature with protein functional state. The observed shift in protein dynamical turn-on temperature relative to the solvent indicates an increase in the required mobile waters necessary for the protein picosecond motions, that is, these motions are more collective. Melting-point measurements reveal that the photobleached state is more thermally stable, and structural analysis of related RFP’s shows that there is an increase in internal water channels as well as a more uniform atomic root mean squared displacement. These observations are consistent with previous suggestions that water channels form with extended light excitation providing O2 access to the chromophore and subsequent fluorescence loss. We report that these same channels increase internal coupling enhancing thermal stability and collectivity of the picosecond protein motions. The terahertz spectroscopic characterization of the protein and solvent dynamical onsets can be applied generally to measure changes in collectivity of protein motions.

Confinement-guided photophysics in MOFs, COFs, and cages

In this review, the dependence of the photophysical response of chromophores in the confined environments associated with crystalline scaffolds, such as metal-organic frameworks (MOFs), covalent-organic frameworks (COFs), and molecular cages, has been carefully evaluated. Tunability of the framework aperture, cavity microenvironment, and scaffold topology significantly affects emission profiles, quantum yields, or fluorescence lifetimes of confined chromophores. In addition to the role of the host and its effect on the guest, the methods for integration of a chromophore (e.g., as a framework backbone, capping linker, ligand side group, or guest) are discussed. The overall potential of chromophore-integrated frameworks for a wide-range of applications, including artificial biomimetic systems, white-light emitting diodes, photoresponsive devices, and fluorescent sensors with unparalleled spatial resolution are highlighted throughout the review.

Fluorescent Orthopalladated Complexes of 4-Aryliden-5(4H)-oxazolones from the Kaede Protein: Synthesis and Characterization

The goal of the work reported here was to amplify the fluorescent properties of 4-aryliden-5(4H)-oxazolones by suppression of the hula-twist non-radiative deactivation pathway. This aim was achieved by simultaneous bonding of a Pd center to the N atom of the heterocycle and the ortho carbon of the arylidene ring. Two different 4-((Z)-arylidene)-2-((E)-styryl)-5(4H)-oxazolones, the structures of which are closely related to the chromophore of the Kaede protein and substituted at the 2- and 4-positions of the arylidene ring (1a OMe; 1b F), were used as starting materials. Oxazolones 1a and 1b were reacted with Pd(OAc)₂ to give the corresponding dinuclear orthometalated palladium derivates 2a and 2b by regioselective C–H activation of the ortho-position of the arylidene ring. Reaction of 2a (2b) with LiCl promoted the metathesis of the bridging carboxylate by chloride ligands to afford dinuclear 3a (3b). Mononuclear complexes containing the orthopalladated oxazolone and a variety of ancillary ligands (acetylacetonate (4a, 4b), hydroxyquinolinate (5a), aminoquinoline (6a), bipyridine (7a), phenanthroline (8a)) were prepared from 3a or 3b through metathesis of anionic ligands or substitution of neutral weakly bonded ligands. All species were fully characterized and the X-ray determination of the molecular structure of 7a was carried out. This structure has strongly distorted ligands due to intramolecular interactions. Fluorescence measurements showed an increase in the quantum yield (QY) by up to one order of magnitude on comparing the free oxazolone (QY < 1%) with the palladated oxazolone (QY = 12% for 6a). This fact shows that the coordination of the oxazolone to the palladium efficiently suppresses the hula-twist deactivation pathway.

Local Electric Field Controls Fluorescence Quantum Yield of Red and Far-Red Fluorescent Proteins

Genetically encoded probes with red-shifted absorption and fluorescence are highly desirable for imaging applications because they can report from deeper tissue layers with lower background and because they provide additional colors for multicolor imaging. Unfortunately, red and especially far-red fluorescent proteins have very low quantum yields, which undermines their other advantages. Elucidating the mechanism of nonradiative relaxation in red fluorescent proteins (RFPs) could help developing ones with higher quantum yields. Here we consider two possible mechanisms of fast nonradiative relaxation of electronic excitation in RFPs. The first, known as the energy gap law, predicts a steep exponential drop of fluorescence quantum yield with a systematic red shift of fluorescence frequency. In this case the relaxation of excitation occurs in the chromophore without any significant changes of its geometry. The second mechanism is related to a twisted intramolecular charge transfer in the excited state, followed by an ultrafast internal conversion. The chromophore twisting can strongly depend on the local electric field because the field can affect the activation energy. We present a spectroscopic method of evaluating local electric fields experienced by the chromophore in the protein environment. The method is based on linear and two-photon absorption spectroscopy, as well as on quantum-mechanically calculated parameters of the isolated chromophore. Using this method, which is substantiated by our molecular dynamics simulations, we obtain the components of electric field in the chromophore plane for seven different RFPs with the same chromophore structure. We find that in five of these RFPs, the nonradiative relaxation rate increases with the strength of the field along the chromophore axis directed from the center of imidazolinone ring to the center of phenolate ring. Furthermore, this rate depends on the corresponding electrostatic energy change (calculated from the known fields and charge displacements), in quantitative agreement with the Marcus theory of charge transfer. This result supports the dominant role of the twisted intramolecular charge transfer mechanism over the energy gap law for most of the studied RFPs. It provides important guidelines of how to shift the absorption wavelength of an RFP to the red, while keeping its brightness reasonably high.

Access to highly functionalized imidazolones bearing α-amino acid esters via KOH-promoted annulation of amidines, nitrosoarenes and malonic esters

An efficient approach to obtain highly functionalized imidazolones bearing α-amino acid esters through KOH-mediated one-pot three-component annulation of amidines, nitrosoarenes and malonic esters is reported. This reaction features broad substrate scope, a cheap and readily available promoter, good to high yields for most substrates and mild reaction conditions. The mechanism study shows that the KOH-mediated formation of the imine intermediate via the reaction of nitrosoarenes with malonic esters is a key step.

Fluorescence in "Nonfluorescent" Polymers

Recently, a great deal of research has been started on generating fairly strong photoluminescence from organic molecules without having any conjugated π-system or fluorophore. Discrete chromophores or auxochromophores termed as "subfluorophores" may undergo "space conjugation" via co-operative intramolecular conformation followed by intermolecular aggregation to generate fluorescence or sometimes phosphorescence emission. Polymeric materials are important in this regard as nonconjugated polymers self-assemble/aggregate in a moderately concentrated solution and also in the solid state, producing membranes, films, and so forth with good physical and mechanical properties. Therefore, promoting fluorescence in these commodity polymers is very much useful for sensing, organic light emitting diodes (OLED), and biological applications. In this perspective, we have discussed the aggregation-induced emission from four different types of architectures, for example, (i) dendrimers or hyperbranched polymers, (ii) entrapped polymeric micellar self-assembly, (iii) cluster formation, and (iv) stretching-induced aggregation, begining with the genesis of fluorescence from aggregation of propeller-shaped small organic molecules. The mechanism of induced fluorescence of polymers with subfluorophoric groups is also discussed from the theoretical calculations of the energy bands in the aggregated state. Also, an attempt has been made to highlight some useful applications in the sensing of surfactants, bacteria, cell imaging, drug delivery, gene delivery, OLED, and so forth.

Unraveling the Effect on Luminescent Properties by Postsynthetic Covalent and Noncovalent Grafting of gfp Chromophore Analogues in Nanoscale MOF-808

Here, we demonstrate mimicking of photophysical properties of native green fluorescent protein (gfp) by immobilizing the gfp chromophore analogues in nanoscale MOF-808 and further exploring the bioimaging applications. The two virtually nonfluorescent gfp chromophore analogues carrying different functionalities, BDI-AE (COOH/COOMe) and BDI-EE (COOMe/COOMe) were immobilized in nanosized MOF-808 via postsynthetic modification. An ¹H NMR and IR study confirms that BDI-AE was coordinated in NMOF-808, whereas BDI-EE was just noncovalently encapsulated. Interestingly, the extremely weakly fluorescent monomers BDI-AE and BDI-EE (QY = 0.01-0.03%, lifetime = 0.01-0.03 ns) showed a 10²-fold increase in quantum efficiency with a significantly longer excited-state lifetime (QY = 1.8-5.6%, lifetime 0.89-1.49 ns) after immobilization in the NMOF-808 scaffold. Moreover, BDI-AE@MOF-808 has 4 times higher quantum efficiency as well as longer excited-state lifetime in comparison to BDI-EE@NMOF-808 due to the rigidity imposed in the chromophore upon coordination with Zr⁴⁺ in the former case. Further, a cell viability test performed for BDI-AE@NMOF-808 in HeLa cells confirmed the nontoxic nature of the material and, more importantly, bioimaging applications have also been explored successfully.

Devising Efficient Red-Shifting Strategies for Bioimaging: A Generalizable Donor-Acceptor Fluorophore Prototype

Long emission wavelengths, high fluorescence quantum yields (FQYs), and large Stokes shifts are highly desirable features for fluorescent probes in biological imaging. However, the current development of many fluorescent probes remains largely trial-and-error and lacks efficiency. Moreover, to achieve far-red/near-infrared emission, a significant extension in the π -conjugation is usually adopted but accompanied by other drawbacks such as fluorescence loss. In this review, we discuss an effective red-shifting strategy built upon the green fluorescent protein chromophore, which enables a synergistic tuning of both the electronic ground and excited states. This approach could shorten the path toward redder emission in comparison to the conventional intramolecular charge transfer (ICT) strategy. We envision that this spectroscopy and computation-aided strategy may advance the noncanonical fluorescent protein design and be generalized to various fluorophore scaffolds for redder emission while preserving other superior properties such as high FQYs.

Dual-Self-Restricted GFP Chromophore Analogues with Significantly Enhanced Emission

The tremendous gap of fluorescence emission of synthetic green fluorescent protein (GFP) chromophore to the protein itself makes it impossible to use for applications in molecular and cellular imaging. Here, we developed an efficient methodology to enhance the photoluminescence response of synthetic GFP chromophore analogues by constructing dual-self-restricted chromophores. Single self-restricted chromophores were first generated with 2,5-dimethoxy substitution on the aromatic ring, which were further modified with phenyl or 2,5-dimethoxy phenyl to form dual-self-restricted chromophores. These two chromophores showed an obvious solvatofluorochromic color palette across blue to yellow with a maximum emission Stokes shift of 95 nm and dramatically enhanced fluorescence emission in various aprotic solvents, especially in hexane, where the QY reached around 0.6. Importantly, in acetonitrile and dimethyl sulfoxide, the fluorescence QYs of both chromophores were over 0.22, which were the highest reported so far in high polar organic solvents. Meanwhile, the fluorescence lifetimes also improved obviously with the maximum of around 4.5 ns. Theoretical calculations revealed a more favorable Mülliken atomic charge translocation over the double-bond bridge and illustrated much higher energy barriers for the Z/E photoisomerization together with larger bond orders compared with the GFP core chromophore, p-HBDI. Our work significantly improved the fluorescence emission of synthetic GFP chromophore analogues in polar solvents while reserved the multicolor emitting function, providing a solid molecular motif for engineering high-performance fluorescent probes.

Crystal structure and spectral studies of green fluorescent protein (GFP) chromophore analogue ethyl 2-[(4Z)-(6-hydroxy naphthalen-2-yl) methylene)-2-methyl-5-oxo-4,5-di hydro-1H-imidazol-1-yl] acetate

Synthetically modified green fluorescent protein chromophore derivative was prepared, its crystal structure and spectral properties were studied. Crystal data for C19H18N2O4: triclinic, space group P-1 (no. 2), a = 8.2506(17) Å, b = 11.934(2) Å, c = 17.461(4) Å, α = 102.89(3)°,   β = 94.62(3)°, γ = 96.68(3)°, V = 1654.5(6) Å3, Z = 4, T = 173(2) K, μ(MoKα) = 0.096 mm-1, Dcalc = 1.358 g/cm3, 7227 reflections measured (4.722° ≤ 2Θ ≤ 53.996°), 7227 unique (Rint = 0.0453, Rsigma = 0.0662) which were used in all calculations. The final R1 was 0.0561 (I > 2σ(I)) and wR2 was 0.1658 (all data). The single crystal structure showed, the benzylidine moiety adopts Z-conformation in solid state and the molecules were associated by various O−H···O and C−H···O non-covalent interactions. The UV absorption-emission spectral analysis indicated that a significant red shift of emission observed at alkaline pH indicating its utility for live cell imaging applications.

Delayed vibrational modulation of the solvated GFP chromophore into a conical intersection

Green fluorescent protein (GFP) has revolutionized bioimaging and life sciences. Its successes have inspired modification of the chromophore structure and environment to tune emission properties, but outside the protein cage, the chromophore is essentially non-fluorescent. In this study, we employ the tunable femtosecond stimulated Raman spectroscopy (FSRS) and transient absorption (TA) to map the energy dissipation pathways of GFP model chromophore (HBDI) in basic aqueous solution. Strategic tuning of the Raman pump to 550 nm exploits the stimulated emission band to enhance excited state vibrational motions as HBDI navigates the non-equilibrium potential energy landscape to pass through a conical intersection. The time-resolved FSRS uncovers prominent anharmonic couplings between a global out-of-plane bending mode of ∼227 cm-1 and two modes at ∼866 and 1572 cm-1 before HBDI reaches the twisted intramolecular charge transfer (TICT) state on the ∼3 ps time scale. Remarkably, the wavelet transform analysis reveals a ∼500 fs delayed onset of the coupling peaks, in correlation with the emergence of an intermediate charge-separated state en route to the TICT state. This mechanism is corroborated by the altered coupling matrix for the HBDI Raman modes in the 50% (v/v) water-glycerol mixture, and a notable lengthening of the picosecond time constant. The real-time molecular "movie" of the general rotor-like HBDI isomerization reaction following photoexcitation represents a significant advance in comprehending the photochemical reaction pathways of the solvated GFP chromophore, therefore providing a crucial foundation to enable rational design of diverse nanomachines from efficient molecular rotors to bright fluorescent probes.

Volume-conserving photoisomerization of a nonplanar GFP chromophore derivative: Nonadiabatic dynamics simulation

Nonadiabatic dynamics of a nonplanar green fluorescent protein (GFP) chromophore derivative was examined theoretically by trajectory surface hopping approach at the CASSCF level based on Zhu-Nakamura theory. The geometry optimizations show that there are four ground-state minima and four conical intersections between the ground (S₀) and first excited (S₁) states. Four S₁-state minima were found at a perpendicularly twisted conformation around the imidazolinone-bridged bond. Upon excitation to S₁ state, the main decay pathways of four isomers involve different S₀/S₁ potential energy surface conical intersections. The dominant excited-state relaxation mechanism of this GFP chromophore derivative is the twists of two bridging bonds and the methyl group in the bridge combined with the pyramidalization character of the central carbon atom. Further twists of two bridging bonds and the methyl group occur sequentially in the S₀ state. It is worth to mention that the special volume-conserving motion of this molecule is attributed to twists of two bridging bonds in the same direction during the whole photoisomerization processes. The theoretical investigation presented herein provides important insights into the volume-conserving photoisomerization mechanisms of a nonplanar GFP chromophore derivative. We believe that the present work can benefit the design of the photochromic molecule devices in confined media.

Characterization of the Photophysical Behavior of DFHBI Derivatives: Fluorogenic Molecules that Illuminate the Spinach RNA Aptamer

( Z)-5-(3,5-Difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4 H-imidazol-4-one (DFHBI) and its analogues are fluorogenic molecules that bind the Spinach aptamer (a small RNA molecule), which was selected for imaging RNA. They are extremely weakly fluorescent in liquid solvents. It had been hypothesized that photoisomerization is a very efficient nonradiative process of deactivation. We show, consistent with the results of other studies, that if the isomerization is impeded, the fluorescence signal is enhanced significantly. In addition, we provide a thorough characterization of the photophysical behavior of DFHBI and its derivatives, notably that of ( Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-((perfluorophenyl)methyl)-3,5-dihydro-4 H-imidazol-4-one (PFP-DFHBI) in various solvent environments. Solvent-dependent studies were performed with various mixtures of solvents. The results suggest that hydrogen bonding or strong interactions of the solvents with the phenolic-OH group change the absorption band near 420-460 nm and the nature of emission near 430 and 500 nm through various degrees of stabilization and the transformation between the neutral and the anionic species at both ground and excited states. These observations are confirmed by using a methoxy-substituted molecule (( Z)-5-(4-methoxybenzylidene)-2,3-dimethyl-3,5-dihydro-4 H-imidazol-4-one), where the 420-460 nm band is absent in the presence of methanol and the spectra are similar to those of PFP-DFHBI in noninteracting solvents, such as acetonitrile and dichloromethane. Thus, in addition to the major role of photoisomerization as a nonradiative process of deactivation of the excited state, the fluorescence of DFHBI-type molecules is very sensitively dependent upon the pH of the medium as well as upon solvent-specific interactions, such as hydrogen-bonding ability and polarity.

Gfp chromophore integrated conjugated microporous polymers: topological and ESPT effects on emission properties

A metal free topological approach is demonstrated to mimic the photophysical properties of natural gfp by synthesizing two gfp chromophore integrated conjugated microporous polymers (o-HBDI-TEB-CMP and o-MBDI-TEB-CMP). Interestingly, owing to the structural rigidity, the emission (λem = 515 nm) and excited state lifetime (4.1 ns) of hydroxy substituted o-HBDI-TEB-CMP are found to be similar to the natural gfp. The crucial role of the -OH group for the green emission is further supported by -OMe substituted o-MBDI-TEB-CMP (λem = 440 nm) and also validated theoretically.

Morphology-Dependent Luminescence in Complex Liquid Colloids

Complex liquid colloids hold great promise as transducers in sensing applications as a result of their tunable morphology and intrinsic optical properties. Herein, we introduce meta-amino substituted green fluorescence protein chromophore (GFPc) surfactants that localize at the organic-water interface of complex multiphase liquid colloids. The meta-amino GFPc exhibits hydrogen-bonding (HB) mediated fluorescence quenching, and are nearly nonemissive in the presence of protic solvents. We demonstrate morphology-dependent fluorescence of complex liquid colloids and investigate the interplay between GFPc surfactants and other simple surfactants. This environmentally responsive surfactant allows us to observe morphological changes of complex emulsions in randomized orientations. We demonstrate utility with an enzyme activity based fluorescence "turn-ON" scheme. The latter employs an oligopeptide-linked GFPc that functions as both a surfactant and trypsin target. The cleavage of hydrophilic peptide results in a morphology change and ultimately a fluorescence turn-on. Fluorescent complex colloids represent a new approach for biosensing in liquid environments.

Excited state structural dynamics of 4-cyano-4′-hydroxystilbene: deciphering the signatures of proton-coupled electron transfer using ultrafast Raman loss spectroscopy

The photo-initiated proton-coupled electron transfer process in the 4-cyano-4′-hydroxystilbene–tert-butylamine adduct strongly affects the excited-state structural dynamics of CHSB.

Uncovering the Hidden Excited State toward Fluorescence of an Intracellular pH Indicator

Intracellular pH (pH_i) imaging is of paramount importance for life sciences. In this work, we implement the ultrafast electronic and stimulated Raman spectroscopies to unravel the fluorescence mechanism of an excitation-ratiometric pH_i indicator in basic aqueous solution. After photoexcitation of the pH_i indicator HPTS, a hidden charge-transfer (CT) state following the locally excited (LE) state is uncovered as an essential step prior to fluorescence and this LE → CT transition is gated by ultrafast solvation dynamics. A 835 cm^-1 intermolecular vibrational mode is identified to potentially facilitate the CT-state formation on the 700 fs time scale. Dynamic correlation with the other excited-state Raman marker bands suggests that the transition between transient electronic states is aided by solvation events mostly in the molecular plane of HPTS. These vivid structural dynamics insights can enable the rational design of more efficient and bright pH_i indicators in an H-bonding environment with controllable properties.

Femtosecond Time-Resolved Raman Spectroscopy Reveals Structural Evidence for meta Effect in Stilbenols

The meta effect in substituted aromatics plays a crucial role in their excited-state photophysical properties. Meta-substituted hydroxyarenes such as naphthols, stilbenols, and chromophoric constituents of green fluorescent proteins show unusual photoacidity and enhanced fluorescence lifetime and quantum yield when compared to their para-derivatives. Variation in the excited state features of the meta-derivatives when compared to the para-derivatives in stilbenols has been attributed to the enhanced torsional barrier for interconversion between the planar and the twisted perpendicular forms. Herein, we employed femtosecond time-resolved Raman spectroscopy to provide the direct structural evidence for the enhanced torsional barrier in meta-stilbenol. The Raman band profiles of the olefinic C═C stretch related to the torsional motion are found to decay with time constants of ∼750 and ∼13 ps in meta-stilbenol and para-stilbenol respectively, unraveling the structural evidence for the observed enhanced photoacidity originating from enhanced rates of excited-state proton transfer. Further, time-resolved fluorescence measurements are performed to elucidate the relaxation pathways of the excited states of the stilbenols.

Synthesis and Properties of the p-Sulfonamide Analogue of the Green Fluorescent Protein (GFP) Chromophore: The Mimic of GFP Chromophore with Very Strong N-H Photoacid Strength

The para-sulfonamide analogue ( p-TsABDI) of a green fluorescent protein (GFP) chromophore was synthesized to mimic the GFP chromophore. Its S₁ excited-state p K_a^* value in dimethylsulfoxide (DMSO) is -1.5, which is strong enough to partially protonate dipolar aprotic solvents and causes excited-state proton transfer (ESPT), so it can partially mimic the GFP chromophore to further study the ESPT-related photophysics and the blinking phenomenon of GFP. In comparison with 8-hydroxypyrene-1,3,6-trisulfonate (HPTS) (p K_a = 7.4, p K_a^* = 1.3 in water), p-TsABDI (p K_a = 6.7, p K_a^* = -1.5 in DMSO) is a better photoacid for pH-jump studies.

A new twist in the photophysics of the GFP chromophore: a volume-conserving molecular torsion couple

Dynamics of a nonplanar GFP chromophore are studied experimentally and theoretically. Coupled torsional motion is responsible for the ultrafast decay.

The simple structure of the chromophore of the green fluorescent protein (GFP), a phenol and an imidazolone ring linked by a methyne bridge, supports an exceptionally diverse range of excited state phenomena. Here we describe experimentally and theoretically the photochemistry of a novel sterically crowded nonplanar derivative of the GFP chromophore. It undergoes an excited state isomerization reaction accompanied by an exceptionally fast (sub 100 fs) excited state decay. The decay dynamics are essentially independent of solvent polarity and viscosity. Excited state structural dynamics are probed by high level quantum chemical calculations revealing that the fast decay is due to a conical intersection characterized by a twist of the rings and pyramidalization of the methyne bridge carbon. The intersection can be accessed without a barrier from the pre-twisted Franck–Condon structure, and the lack of viscosity dependence is due to the fact that the rings twist in the same direction, giving rise to a volume-conserving decay coordinate. Moreover, the rotation of the phenyl, methyl and imidazolone groups is coupled in the sterically crowded structure, with the methyl group translating the rotation of one ring to the next. As a consequence, the excited state dynamics can be viewed as a torsional couple, where the absorbed photon energy leads to conversion of the out-of-plane orientation from one ring to the other in a volume conserving fashion. A similar modification of the range of methyne dyes may provide a new family of devices for molecular machines, specifically torsional couples.

A new GFP fluorophore-based probe for lysosome labelling and tracing lysosomal viscosity in live cells

A new GFP (green fluorescent protein) fluorophore-based probe (Lys-V) was designed and synthesized for mapping lysosomal viscosity in live cells.

Origin of the Intrinsic Fluorescence of the Green Fluorescent Protein

Green fluorescent protein, GFP, has revolutionized biology, due to its use in bioimaging. It is widely accepted that the protein environment makes its chromophore fluoresce, whereas the fluorescence is completely lost when the native chromophore is taken out of GFP. By the use of a new femtosecond pump-probe scheme, based on time-resolved action spectroscopy, we demonstrate that the isolated deprotonated GFP chromophore can be trapped in the first excited state when cooled to 100 K. The trapping is shown to last for 1.2 ns, which is long enough to establish conditions for fluorescence and consistent with calculated trapping barriers in the electronically excited state. Thus, GFP fluorescence is traced back to an intrinsic chromophore property, and by improving excited-state trapping, protein interactions enhance the molecular fluorescence.

Conservation of estrogen receptor function in invertebrate reproduction

Background

Rotifers are microscopic aquatic invertebrates that reproduce both sexually and asexually. Though rotifers are phylogenetically distant from humans, and have specialized reproductive physiology, this work identifies a surprising conservation in the control of reproduction between humans and rotifers through the estrogen receptor. Until recently, steroid signaling has been observed in only a few invertebrate taxa and its role in regulating invertebrate reproduction has not been clearly demonstrated. Insights into the evolution of sex signaling pathways can be gained by clarifying how receptors function in invertebrate reproduction.

Results

In this paper, we show that a ligand-activated estrogen-like receptor in rotifers binds human estradiol and regulates reproductive output in females. In other invertebrates characterized thus far, ER ligand binding domains have occluded ligand-binding sites and the ERs are not ligand activated. We have used a suite of computational, biochemical and biological techniques to determine that the rotifer ER binding site is not occluded and can bind human estradiol.

Conclusions

Our results demonstrate that this mammalian hormone receptor plays a key role in reproduction of the ancient microinvertebrate Brachinous manjavacas. The presence and activity of the ER within the phylum Rotifera indicates that the ER structure and function is highly conserved throughout animal evolution.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-017-0909-z) contains supplementary material, which is available to authorized users.

Emission enhancement of GFP chromophore in aggregated state via combination of self-restricted effect and supramolecular host–guest complexation

The emission response of GFP chromophore in aggregated state is greatly enhanced more than 100-fold due to the inhibition of conformational motion and the reduction of strong π–π interaction.

Conjugates of Benzoxazole and GFP Chromophore with Aggregation-Induced Enhanced Emission: Influence of the Chain Length on the Formation of Particles and on the Dye Uptake by Living Cells

Six conjugates of benzoxazole and green fluorescent protein chromophore that differ by the length of their alkyl chain (from C1 to C16) are investigated. They exhibit rigidofluorochromism and clear aggregation-induced emission enhancement (AIEE) behavior with emission in the orange-red that is specific to the solid state. A preparation method based on solvent exchange is used to prepare particles. The self-association properties of these molecules depend on the length of the alkyl chain. Microfibers, platelets, and rounded microparticles are successively obtained by increasing the chain length. The same method is used to prepare nanoparticles (NPs) that are fully characterized. In particular, homogeneous populations of stable NPs measuring around 70 nm are obtained with the analogs whose chains contain four to eight carbon atoms. The behavior with respect to living cells is also influenced by the nature of the compounds. Only the dyes with intermediate hydrophobicity are efficiently uptaken by both normal and tumor cells, and fluorescence only originates from dispersed dye molecules. There is no evidence for incorporation of NPs into cells. This work shows that small variations of the chemical structure must be taken into account for making the best use of AIEE compounds in view of precise applications.

Self-Restricted Green Fluorescent Protein Chromophore Analogues: Dramatic Emission Enhancement and Remarkable Solvatofluorochromism

The confinement effect of the β-barrel defines the emission profiles of the chromophores of the green fluorescent protein (GFP) family. Here, we describe the design strategy and mimicking of confinement effects via the chromophore itself, termed the self-restricted effect. By systematically tailoring the GFP core, a family of 2,5-dialkoxy-substituted GFP chromophore analogues is found to be highly emissive and show remarkable solvatofluorochromism in fluid solvents. Fluorescence quantum yield (QY) and lifetime measurements, in combination with theoretical calculations, illustrate the mechanism relying on inhibition of torsional rotation around the exocyclic CC bond. Meanwhile, theoretical calculations further reveal that the electrostatic interaction between the solvent and the imidazolinone oxygen can contribute to suppress the radiationless decay channel around the exocyclic C═C double bond. Our findings put forward a universal approach toward unlocked highly emissive GFPc analogues, potentially promoting the understanding of the photophysics and biochemical application of GFP chromophore analogues.

Synthesis and Evaluation of a Library of Fluorescent Dipeptidomimetic Analogues as Substrates for Modified Bacterial Ribosomes

Described herein are the synthesis and photophysical characterization of a library of aryl-substituted oxazole- and thiazole-based dipeptidomimetic analogues, and their incorporation into position 66 of green fluorescent protein (GFP) in lieu of the natural fluorophore. These fluorescent analogues resemble the fluorophore formed naturally by GFP. As anticipated, the photophysical properties of the analogues varied as a function of the substituents at the para position of the phenyl ring. The fluorescence emission wavelength maxima of compounds in the library varied from ∼365 nm (near-UV region) to ∼490 nm (visible region). The compounds also exhibited a large range of quantum yields (0.01-0.92). The analogues were used to activate a suppressor tRNACUA and were incorporated into position 66 of GFP using an in vitro protein biosynthesizing system that employed engineered ribosomes selected for their ability to incorporate dipeptides. Four analogues with interesting photophysical properties and reasonable suppression yields were chosen, and the fluorescent proteins (FPs) containing these fluorophores were prepared on a larger scale for more detailed study. When the FPs were compared with the respective aminoacyl-tRNAs and the actual dipeptide analogues, the FPs exhibited significantly enhanced fluorescence intensities at the same concentrations. Part of this was shown to be due to the presence of the fluorophores as an intrinsic element of the protein backbone. There were also characteristic shifts in the emission maxima, indicating the environmental sensitivity of these probes. Acridon-2-ylalanine and oxazole 1a were incorporated into positions 39 and 66 of GFP, respectively, and were shown to form an efficient Förster resonance energy transfer (FRET) pair, demonstrating that the analogues can be used as FRET probes.