Fluorescent Chromophore Research Articles

Absorption Spectrum of the Green Fluorescent Protein Chromophore: A Difficult Case for ab Initio Methods?

We perform a thorough comparative investigation of the excitation energies of the anionic and neutral forms of the green fluorescent protein (GFP) chromophore in the gas phase using a variety of first-principle theoretical approaches commonly used to access excited state properties of photoactive molecules. These include time-dependent density functional theory (TDDFT), complete-active-space second-order perturbation theory (CASPT2), equation-of-motion coupled cluster (EOM-CC), and quantum Monte Carlo (QMC) methods. We find that all approaches give roughly the same vertical excitation for the anionic form, while TDDFT predicts an excitation for the neutral chromophore significantly lower than the highly correlated methods. Our findings support the picture emerging from the extrapolation of the Kamlet-Taft fit of absorption experimental data in solution and indicate that the protein gives rise to a considerable bathochromic shift with respect to vacuum. These results also open some questions on the interpretation of photodestruction spectroscopy experiments in the gas phase as well as on the accuracy of previous theoretical calculations in the more complex protein environment.

Synthesis and Spectral and Chemical Properties of the Yellow Fluorescent Protein zFP538 Chromophore

Members of the green fluorescent protein (GFP) family become chromophoric through a unique pathway based on autocatalytic modifications of their amino acid residues. The yellow fluorescent protein zFP538 from the button polyp Zoanthus possesses unique spectral characteristics that are intermediate between those of the green and orange-red fluorescent proteins. In this study, we used chemical synthesis to resolve conflicting data from crystallographic and biochemical analyses of the zFP538 chromophore structure. We synthesized 2-(5-amino-1-oxopentyl)-5-(4-hydroxybenzylidene)-3-methyl-3,5-dihydro-4H-imidazol-4-one (5), which can spontaneously react intramolecularly to form cyclic imine (7). Compound 7 represents the native chromophore structure reported in the crystallographic study. We have also discovered an unusual isomerization of a 2-acylimidazolone to a 2,6-diketopiperazine derivative. The zFP538 chromophore is a complex system with intriguing chemical and spectral behavior, properties that have led to discrepancies in the interpretation of its structure. Our study supports the findings of previous crystallographic work, which postulated a cyclic imine chromophore structure within the native zFP538 protein, and also provides an explanation for experimental results obtained in the biochemical characterization of zFP538-derived chromopeptides.

Triplet States of the Nonlinear Optical Chromophore DCM in Single Crystals of Potassium Hydrogen Phthalate and Their Relationship to Single-Molecule Dark States

Single-molecule dark states are often attributed to photoexcited triplets with scant evidence of the participation of paramagnetic molecules. The photodynamics of blinking single molecules of 4-dicyanomethylene-2-methyl-6-p-dimethylaminostyryl-4H-pyran (DCM) in crystals of potassium hydrogen phthalate (KAP) were compared with the lifetimes of DCM triplet states, likewise in KAP, whose zero-field splitting (ZFS) tensors were fully characterized by time-resolved electron paramagnetic resonance (TR-EPR) spectroscopy. Luminescent mixed crystals of KAP were grown from solutions containing 10(-4) -10(-9) M DCM, a model optically nonlinear chromophore. The luminescent dye was localized in the {111} crystalline growth sectors. The photoexcited triplets states of DCM in the heavily dyed (10(-4) M) crystals were analyzed by TR-EPR spectroscopy. The photoexcited singlet states of DCM in lightly dyed crystals (10(-9) M) were analyzed by single-molecule microscopy. Large blue shifts in the absorption and emission spectra of DCM in KAP were interpreted as a consequence of protonation at the dimethylamino nitrogen atom, an assignment supported by calculations of the zero-field splitting (ZFS) tensors of molecules in their triplet states. Experimental ZFS tensors with eigenvalues comparable to those of the computed tensors were determined from the angular dependence of the EPR spectra of DCMH(+) triplets within KAP single crystals with respect to the applied magnetic field. Data from individual growth sectors failed to show magnetically equivalent site occupancies, evidence of the kinetic ordering during growth. The intermittent fluorescence of individual chromophores was analyzed. The distributions of on(off) times were characterized by distributed rates fit to power laws. The lifetime of the triplet states was analyzed from the time decay of the EPR signals between 100 and 165 K. The data were well fit with a single time constant for the signal decay, a result wholly inconsistent with the blinking of single molecules with off times commonly of tens of seconds. Triplet decay was extrapolated to approximately 25 micros at room temperature. Therefore, the assumption that single-molecule dark states originate with triplet excited states is not sustainable for single DCM molecules in KAP.

Substrate Recognition of Anthrax Lethal Factor Examined by Combinatorial and Pre-steady-state Kinetic Approaches

Lethal factor (LF), a zinc-dependent protease of high specificity produced by Bacillus anthracis, is the effector component of the binary toxin that causes death in anthrax. New therapeutics targeting the toxin are required to reduce systemic anthrax-related fatalities. In particular, new insights into the LF catalytic mechanism will be useful for the development of LF inhibitors. We evaluated the minimal length required for formation of bona fide LF substrates using substrate phage display. Phage-based selection yielded a substrate that is cleaved seven times more efficiently by LF than the peptide targeted in the protein kinase MKK6. Site-directed mutagenesis within the metal-binding site in the LF active center and within phage-selected substrates revealed a complex pattern of LF-substrate interactions. The elementary steps of LF-mediated proteolysis were resolved by the stopped-flow technique. Pre-steady-state kinetics of LF proteolysis followed a four-step mechanism as follows: initial substrate binding, rearrangement of the enzyme-substrate complex, a rate-limiting cleavage step, and product release. Examination of LF interactions with metal ions revealed an unexpected activation of the protease by Ca(2+) and Mn(2+). Based on the available structural and kinetic data, we propose a model for LF-substrate interaction. Resolution of the kinetic and structural parameters governing LF activity may be exploited to design new LF inhibitors.

Fluorescence spectroscopy in the detection of oral dysplasia

Modalities All tissues fluoresce due to the presence of fluorescent chromophores (fluorophores) within them. The commonly fluorophores are NADH, collagen, elastin and cofactors such as flavins (FAD, FMN). FS can detect these substances and provide characteristic spectra that reflect biochemical changes within the tissues. There are three main ways to obtain fluorescence, autofluorescence (induced by UV light) Laser-induced and enhanced/dye which can be by either topical or systemic application of 5-aminolaevulinic acid (5-ALA). Dysplastic and malignant tissues, as well as having different spectral characteristics, tend to have increased red fluorescence and decreased green fluorescence. Therefore, significant increase in the red/green fluorescence ratio is an accurate predictor of dysplasia and malignancy.

Quantum Chemical Benchmark Studies of the Electronic Properties of the Green Fluorescent Protein Chromophore. 1. Electronically Excited and Ionized States of the Anionic Chromophore in the Gas Phase.

We present the results of quantum chemical calculations of the electronic properties of the anionic form of the green fluorescent protein chromophore in the gas phase. The vertical detachment energy of the chromophore is found to be 2.4-2.5 eV, which is below the strongly absorbing ππ* state at 2.6 eV. The vertical excitation of the lowest triplet state is around 1.9 eV, which is below the photodetachment continuum. Thus, the lowest bright singlet state is a resonance state embedded in the photodetachment continuum, whereas the lowest triplet state is a regular bound state. Based on our estimation of the vertical detachment energy, we attribute a minor feature in the action spectrum as due to the photodetachment transition. The benchmark results for the bright ππ* state demonstrated that the scaled opposite-spin method yields vertical excitation within 0.1 eV (20 nm) from the experimental maximum at 2.59 eV (479 nm). We also report estimations of the vertical excitation energy obtained with the equation-of-motion coupled cluster with the singles and doubles method, a multireference perturbation theory corrected approach MRMP2 as well as the time-dependent density functional theory with range-separated functionals. Expanding the basis set with diffuse functions lowers the ππ* vertical excitation energy by 0.1 eV at the same time revealing a continuum of "ionized" states, which embeds the bright ππ* transition.

Sodium induces simultaneous changes in cytosolic calcium and pH in salt-tolerant quince protoplasts

Previous experiments with salt-resistant quince BA29 (Cydonia oblonga cv. Mill.) have shown that this cultivar takes up sodium transiently into the cytosol of shoot protoplasts only in the absence of calcium chloride, or at <1mM calcium chloride. Addition of NaCl > or =100mM to single protoplasts from in vitro-cultivated quince in the presence of 1.0mM calcium induced instant changes in the cytosolic concentrations of calcium and protons. These changes were investigated by use of tetra [acetoxymethyl] esters of the fluorescent stilbene chromophores Fura 2 and bis-carboxyethyl-carboxyfluorescein (BCECF), respectively. The cytosolic Ca(2+) dynamics in the protoplasts were dependent on the concentration of NaCl added. The changes in calcium differed in amplitude and final concentration and were correlated in time mainly with changes in pH. Addition of 100-400mM NaCl to the protoplasts caused an oscillating increase in the cytosolic level of calcium, and then a decrease. Addition of mannitol, of equiosmolar concentration to NaCl, did not increase the cytosolic calcium concentration. Moreover, there was no increase in cytosolic calcium when NaCl was added in the presence of calcium binding ethylene glycol-bis(beta-aminoethylether)-N,N,N',N'-tetra acetic acid (EGTA), or lantan or verapamil, two inhibitors of plasma membrane calcium channels. Therefore, we conclude that, in salt-resistant quince, sodium induces an influx of calcium into the cytosol by plasma membrane calcium channels, and a simultaneous increase in cytosolic pH. Because these changes were obtained in the presence of 1mM calcium in the medium, they were not due to sodium uptake into the cytosol.

A diabatic three-state representation of photoisomerization in the green fluorescent protein chromophore

We give a quantum chemical description of the photoisomerization reaction of green fluorescent protein (GFP) chromophores using a representation over three diabatic states. Photoisomerization leads to nonradiative decay, and competes with fluorescence in these systems. In the protein, this pathway is suppressed, leading to fluorescence. Understanding the electronic states relevant to photoisomerization is a prerequisite to understanding how the protein suppresses it, and preserves the emitting state of the chromophore. We present a solution to the state-averaged complete active space problem, which is spanned at convergence by three fragment-localized orbitals. We generate the diabatic-state representation by block diagonalization transformation of the Hamiltonian calculated for the anionic chromophore model HBDI with multireference, multistate perturbation theory. The diabatic states are charge localized and admit a natural valence-bond interpretation. At planar geometries, the diabatic picture of the optical excitation reduces to the canonical two-state charge-transfer resonance of the anion. Extension to a three-state model is necessary to describe decay via two possible pathways associated with photoisomerization of the (methine) bridge. Parametric Hamiltonians based on the three-state ansatz can be fit directly to data generated using the underlying active space. We provide an illustrative example of such a parametric Hamiltonian.

Fluorescent Silica Nanoparticles by Silylation

Shining nanosil: Fluorescent trimethoxysilanes were prepared by the hydrosilylation of N-allyl perylene tetracarboxylic diimides and used for the covalent grafting of silica and silica nanoparticles (see picture). The fluorescent chromophores operate independently at the surface of these particles.

Microglia Mediate the Clearance of Soluble Aβ through Fluid Phase Macropinocytosis

Alzheimer's disease is characterized by the progressive deposition of beta-amyloid (Abeta) within the brain parenchyma and its subsequent accumulation into senile plaques. Pathogenesis of the disease is associated with perturbations in Abeta homeostasis and the inefficient clearance of these soluble and insoluble peptides from the brain. Microglia have been reported to mediate the clearance of fibrillar Abeta (fAbeta) through receptor-mediated phagocytosis; however, their participation in clearance of soluble Abeta peptides (sAbeta) is largely unknown. We report that microglia internalize sAbeta from the extracellular milieu through a nonsaturable, fluid phase macropinocytic mechanism that is distinct from phagocytosis and receptor-mediated endocytosis both in vitro and in vivo. The uptake of sAbeta is dependent on both actin and tubulin dynamics and does not involve clathrin assembly, coated vesicles or membrane cholesterol. Upon internalization, fluorescently labeled sAbeta colocalizes to pinocytic vesicles. Microglia rapidly traffic these soluble peptides into late endolysosomal compartments where they are subject to degradation. Additionally, we demonstrate that the uptake of sAbeta and fAbeta occurs largely through distinct mechanisms and upon internalization are segregated into separate subcellular vesicular compartments. Significantly, we found that upon proteolytic degradation of fluorescently labeled sAbeta, the fluorescent chromophore is retained by the microglial cell. These studies identify an important mechanism through which microglial cells participate in the maintenance of Abeta homeostasis, through their capacity to constitutively clear sAbeta peptides from the brain.

Crystal Structures of the GCaMP Calcium Sensor Reveal the Mechanism of Fluorescence Signal Change and Aid Rational Design

The genetically encoded calcium indicator GCaMP2 shows promise for neural network activity imaging, but is currently limited by low signal-to-noise ratio. We describe x-ray crystal structures as well as solution biophysical and spectroscopic characterization of GCaMP2 in the calcium-free dark state, and in two calcium-bound bright states: a monomeric form that dominates at intracellular concentrations observed during imaging experiments and an unexpected domain-swapped dimer with decreased fluorescence. This series of structures provides insight into the mechanism of Ca2+-induced fluorescence change. Upon calcium binding, the calmodulin (CaM) domain wraps around the M13 peptide, creating a new domain interface between CaM and the circularly permuted enhanced green fluorescent protein domain. Residues from CaM alter the chemical environment of the circularly permuted enhanced green fluorescent protein chromophore and, together with flexible inter-domain linkers, block solvent access to the chromophore. Guided by the crystal structures, we engineered a series of GCaMP2 point mutants to probe the mechanism of GCaMP2 function and characterized one mutant with significantly improved signal-to-noise. The mutation is located at a domain interface and its effect on sensor function could not have been predicted in the absence of structural data.

Diaminoterephthalates: Scaffolds for Combinatorial Chemistry

Fluorescent building blocks: Tetracarboxyamides with a central fluorescent diaminoterephthalate unit were prepared from succinyl succinates following a combinatorial-like strategy. The 2,5-diaminoterephthalates (see scheme; PG=protecting group) possess four points of diversification and are introduced as new scaffolds for combinatorial chemistry.2,5-Diaminoterephthalates that possess four points of diversification are introduced as new scaffolds for combinatorial chemistry. A straightforward synthesis of an orthogonally protected platform compound was developed. This platform was transformed by stepwise deprotection and amidation of the two amino and two carboxylic acid moieties into tetra-amides with a central aromatic ring as a fluorescence chromophore.

Selective Zinc(II)‐Ion Fluorescence Sensing by a Functionalized Mesoporous Material Covalently Grafted with a Fluorescent Chromophore and Consequent Biological Applications

AbstractA highly ordered 2D‐hexagonal mesoporous silica material is functionalized with 3‐aminopropyltriethoxysilane. This organically modified mesoporous material is grafted with a dialdehyde fluorescent chromophore, 4‐methyl‐2,6‐diformyl phenol. Powder X‐ray diffraction, transmission electron microscopy, N2 sorption, Fourier transform infrared spectroscopy, and UV‐visible absorption and emission have been employed to characterize the material. This material shows excellent selective Zn2+ sensing, which is due to the fluorophore moiety present at its surface. Fluorescence measurements reveal that the emission intensity of the Zn2+‐bound mesoporous material increases significantly upon addition of various concentrations of Zn2+, while the introduction of other biologically relevant (Ca2+, Mg2+, Na+, and K+) and environmentally hazardous transition‐metal ions results in either unchanged or weakened intensity. The enhancement of fluorescence is attributed to the strong covalent binding of Zn2+, evident from the large binding constant value (0.87 × 104 M−1). Thus, this functionalized mesoporous material grafted with the fluorescent chromophore could monitor or recognize Zn2+ from a mixture of ions that contains Zn2+ even in trace amounts and can be considered as a selective fluorescent probe. We have examined the application of this mesoporous zinc(II) sensor to cultured living cells (A375 human melanoma and human cervical cancer cell, HeLa) by fluorescence microscopy.

Synthesis and Application of Thiadiazoloquinoxaline-Containing Chromophores as Dopants for Efficient Near-Infrared Organic Light-Emitting Diodes

A series of a donor−acceptor−donor type of near-infrared (NIR) fluorescent chromophores based on [1,2,5]thiadiazolo[3,4-g]quinoxaline (TQ) as an electron acceptor and triphenylamine as an electron donor are synthesized and characterized. By introducing pendent phenyl groups or changing the π-conjugation length in the TQ core, we tuned the energy levels of these chromophores, resulting in the NIR emission in a range from 784 to 868 nm. High thermal stability and glass transition temperatures allow these chromophores to be used as dopant emitters, which can be processed by vapor deposition for the fabrication of organic light-emitting diodes (OLEDs) having the multilayered structure of ITO/MoO3/NPB/Alq3:dopant emitter/BCP/Alq3/LiF/Al. The electroluminescence spectra of the devices based on these new chromophores cover a range from 748 to 870 nm. With 2 wt % of dopant 1, the LED device shows an exclusive NIR emission at 752 nm with the external quantum efficiency (EQE) as high as 1.12% over a wide range of current density (e.g., around 200 mA cm−2). The radiance reaches the largest value of 2880 mW Sr−1 m−2 at an operating voltage of 15 V.

Photophysical properties of Cerulean and Venus fluorescent proteins

Cerulean and Venus are recently developed fluorescent proteins, often used as a donor-acceptor pair by researchers in Forster resonance energy transfer-based colocalization studies. We characterized the fluorescent properties of these two proteins in a broad spectral range (form ultraviolet to visible region). Excitation spectra, lifetimes, and polarization spectra show significant energy transfer from aromatic amino acids to the fluorescent protein chromophore. High steady-state anisotropy values and the lack of a fast component in anisotropy decays show that the fluorescent protein chromophore is rigidly fixed within the protein structure. Furthermore, we show that the chromophores are not accessible to external quenchers, such as acrylamide or potassium iodide (KI), allowing the removal of "unwanted" background in the environment with external quencher, while leaving the Cerulean/Venus fluorescence unchanged.

Photoabsorption studies of neutral green fluorescent protein model chromophores in vacuo

We report on gas-phase experimental and theoretical studies on the neutral form of the green-fluorescent protein (GFP) chromophore using six different models, each carrying a spectator positive charge. Theoretical studies were carried out to quantify the effect of the spectator charge on the absorption maximum of the true neutral. The study also includes models having the possibility of forming intra-molecular hydrogen bonds, and their effect on the absorption profile is analyzed. The charge redistribution caused by a strong intra-molecular hydrogen bond was found to give rise to a red shift in going from non-hydrogen bonded to hydrogen bonded models. For the non-hydrogen bonded models, the length of the side chain as well as the group carrying the spectator charge, was varied to explore the possibility of shifts in absorption maximum due to these variations. No shifts were observed. The implications of these results in tuning the absorption maximum of the neutral form of the GFP chromophores are discussed.

Fluorescent protein red Kaede chromophore; one-step, high-yield synthesis and potential application for solar cells

The one-step condensation between the Green Fluorescence Protein (GFP) chromophore and 1H-imidazole-5-carbaldehyde catalyzed by ZnCl(2) proved to be a facile method to synthesize the red Kaede chromophore and its derivatives (1a-d, 2, and 3 > 70%), among which 1a then demonstrated its potential as a dye in solar cell, with a moderate conversion efficiency (eta) of 3.04%.

Synthesis and characterization of photoluminescent vinylbiphenyl decorated polyhedral oligomeric silsesquioxanes

Grubbs cross-metathesis has been used to functionalize octavinylsilsesquioxane with fluorescent vinylbiphenyl-modified chromophores to design new hybrid organic-inorganic nanomaterials. Those macromolecules have been characterized by NMR, microanalyses, MALDI-TOF mass spectrometry and photoluminescence. This last method was shown to be an interesting tool in the analysis of the purity of the cube derivatives.

Manipulation of fluorescent and colorimetric changes of fluorescein derivatives and applications for sensing silver ions

Three structurally similar compounds, , bearing a fluorescence chromophore to which are appended morpholine, thiomorpholine and methylpiperazine substituents, display opposite fluorescence responses to pH changes, in contrast to that observed for fluorescein; and have extremely high binding selectivity towards Ag(+) ions and show completely different fluorescent and colorimetric changes upon addition of Ag(+), and the differences are proposed to be associated with different binding modes of and to this metal ion.

Activation and Tuning of Green Fluorescent Protein Chromophore Emission by Alkyl Substituent-Mediated Crystal Packing

O-Alkyl synthetic analogues of the green fluorescent protein chromophore are nonfluorescent in solution but demonstrate a bright emission in the crystalline state. Three-dimensional steady-state and time-resolved emission spectroscopies in the solid state, as well as single-crystal X-ray diffraction, reveal the nature of complex emission in the crystals. A hypsochromic emission shift with an increase of the alkyl size is determined by the monomer-aggregate emission ratio.