Conformationally locked chromophores as models of excited-state proton transfer in fluorescent proteins

Members of the green fluorescent protein (GFP) family form chromophores by modifications of three internal amino acid residues. Previously, many key characteristics of chromophores were studied using model compounds. However, no studies of intermolecular excited-state proton transfer (ESPT) with GFP-like synthetic chromophores have been performed because they either are nonfluorescent or lack an ionizable OH group. In this paper we report the synthesis and photochemical study of two highly fluorescent GFP chromophore analogues: p-HOBDI-BF2 and p-HOPyDI:Zn. Among known fluorescent compounds, p-HOBDI-BF(2) is the closest analogue of the native GFP chromophore. These irrreversibly (p-HOBDI-BF(2)) and reversibly (p-HOPyDI:Zn) locked compounds are the first examples of fully planar GFP chromophores, in which photoisomerization-induced deactivation is suppressed and protolytic photodissociation is observed. The photophysical behavior of p-HOBDI-BF2 and p-HOPyDI:Zn (excited state pK(a)'s, solvatochromism, kinetics, and thermodynamics of proton transfer) reveals their high photoacidity, which makes them good models of intermolecular ESPT in fluorescent proteins. Moreover, p-HOPyDI:Zn is a first example of "super" photoacidity in metal-organic complexes.     

Computational prediction of absorbance maxima for a structurally diverse series of engineered green fluorescent protein chromophores

By virtue of its self-sufficiency to form a visible wavelength chromophore within the confines of its tertiary structure, the Aequorea victoria green fluorescent protein (GFP) is single-handedly responsible for the ever-growing popularity of fluorescence imaging of recombinant fusion proteins in biological research. Engineered variants of GFP with altered excitation or emission wavelength maxima have helped to expand the range of applications of GFP. The engineering of the GFP variants is usually done empirically by genetic modifications of the chromophore structure and/or its environment in order to find variants with new photophysical properties. The process of identifying improved variants could be greatly facilitated if augmented or guided by computational studies of the chromophore ground and excited-state properties and dynamics. In pursuit of this goal, we now report a thorough investigation of computational methods for prediction of the absorbance maxima for an experimentally validated series of engineered GFP chromophore analogues. The experimental dataset is composed of absorption maxima for 10 chemically distinct GFP chromophore analogues, including a previously unreported Y66D variant, measured under identical denaturing conditions. For each chromophore analogue, excitation energies and oscillator strengths were calculated using configuration interaction with single excitations (CIS), CIS with perturbative correction for double substitutions [CIS(D)], and time-dependent density functional theory (TD DFT) using several density functionals with solvent effects included using a polarizable continuum model. Comparison of the experimental and computational results show generally poor quantitative agreement with all methods attempted. However, good linear correlations between the calculated and experimental excitation energies (R2>0.9) could be obtained. Oscillator strengths obtained with TD DFT using pure density functionals also correlate well with the experimental values. Interestingly, most of the computational methods used in this work fail in the case of nonaromatic Y66S and Y66L protein chromophores, which may be related to a significant contribution of double excitations to their excited-state wavefunctions. These results provide an important benchmark of the reliability of the computational methods as applied to GFP chromophore analogues and lays a foundation for the computational design of GFP variants with improved properties for use in biological imaging.     

Fluorescent Turn-on Probe Based on Napthalimide Fused Triphenylamine Unit for Quickly Detecting Thiophenol in Aqueous Solution

A novel molecular probe system(NapTpa-dnbs) was prepared based on the chromophore napthalimide fused triphenylamine unit. NapTpa-dnbs was tuned to absorb a large fraction of UV and near-infrared radiation. The turn-on fluorescent response of NapTpa-dnbs to thiophenol caused an increased fluorescent emission by a factor of 11.5 at 597 nm in a PBS buffer solution. The photoinduced electron transform(PET) process of the probe became less feasible with the addition of thiophenol than that of the free probe. NapTpa-dnbs demonstrated high selective and sensitive detection toward thiophenol with respect to other competitive amine acids. The detection limit was determined to be 2.03×10^-7 mol/L thiophenol. The sensing process is rapid(3 min). NapTpa-dnbs can accurately detect the thiophenol with a qualified recovery in real water samples. NapTpa-dnbs on test strips can detect the thiophenol vapour in the atmosphere.     

A squaraine based fluorescent probe for mercury ion via coordination induced deaggregation signaling

Due to the high affinity between dithiocarbamate(DTC) and Hg2+,a fluorescent probe based on squaraine chromophore with DTC side arm for Hg2+via coordination induced deaggregation signaling has been designed and synthesized.Squaraine has a high tendency to aggregate in aqueous solution,and such self-aggregation usually results in a dramatic absorption spectral broadening with fluorescence emission quenching.The combination of the DTC side arm of the probe with Hg2+induces steric hindrance,leading to the deaggregation of the dye complex,companying with a fluorescence emission restoration.In EtOH–H2O(20:80,v/v) solution,this ‘‘turn on' fluorescent probe has high selectivity and sensitivity toward Hg2+over other metal ions,and the limit of detection for Hg2+was estimated as2.19 ? 10à8mol/L by 3s/k.     

Analogues of uracil nucleosides with intrinsic fluorescence (NIF-analogues): synthesis and photophysical properties

Uridine cannot be utilized as fluorescent probe due to its extremely low quantum yield. For improving the uracil fluorescence characteristics we extended the natural chromophore at the C5 position by coupling substituted aromatic rings directly or via an alkenyl or alkynyl linker to create fluorophores. Extension of the uracil base was achieved by treating 5-I-uridine with the appropriate boronic acid under the Suzuki coupling conditions. Analogues containing an alkynyl linker were obtained from 5-I-uridine and the suitable boronic acid in a Sonogashira coupling reaction. The uracil fluorescent analogues proposed here were designed to satisfy the following requirements: a minimal chemical modification at a position not involved in base-pairing, resulting in relatively long absorption and emission wavelengths and high quantum yield. 5-((4-Methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6b, was found to be a promising fluorescent probe. Probe 6b exhibits a quantum yield that is 3000-fold larger than that of the natural chromophore (Φ 0.12), maximum emission (478 nm) which is 170 nm red shifted as compared to uridine, and a Stokes shift of 143 nm. In addition, since probe 6b adopts the anti conformation and S sugar puckering favored by B-DNA, it makes a promising nucleoside analogue to be incorporated in an oligonucleotide probe for detection of genetic material.     

Water Diffusion In And Out Of The β-Barrel Of GFP and The Fast Maturing Fluorescent Protein, TurboGFP

The chromophore of fluorescent proteins is formed by an internal cyclization of the tripeptide 65SYG67 fragment and a subsequent oxidation. The oxidation is slow - the kinetics of this step is presumably improved in fast maturing GFPs. Water molecules can aid in the chromophore formation. We have used 50 ns molecular dynamics simulations of the mature and immature forms of avGFP and TurboGFP to examine the diffusion of water molecules in-and-out of the protein β-barrel. Most crystal structures of GFPs have well-structured waters within hydrogen-bonding distance of Glu222 and Arg96. It has been proposed that they have an important role in chromophore formation. Stable waters are found in similar positions in all simulations conducted. The simulations confirm the existence of a pore that leads to the chromophore in the rapidly maturing TurboGFP; decreased water diffusion upon chromophore formation; and increased water diffusion due to the pore formation.     

Light-activated reassembly of split green fluorescent protein

Truncated green fluorescent protein (GFP) with the 11th β-strand removed is potentially interesting for bioconjugation, imaging, and the preparation of semisynthetic proteins with novel spectroscopic or functional properties. Surprisingly, the truncated GFP generated by removing the 11th strand, once refolded, does not reassemble with a synthetic peptide corresponding to strand 11 but does reassemble following light activation. The mechanism of this process has been studied in detail by absorption, fluorescence, and Raman spectroscopy. The chromophore in this refolded truncated GFP is found to be in the trans configuration. Upon exposure to light a photostationary state is formed between the trans and cis conformations of the chromophore, and only truncated GFP with the cis configuration of the chromophore binds the peptide. A kinetic model describing the light-activated reassembly of this split GFP is discussed. This unique light-driven reassembly is potentially useful for controlling protein-protein interactions.     

利用聚合物自组装实现绿色荧光蛋白生色团的荧光增强

根据绿色荧光蛋白的发光原理,采用聚乙二醇与聚甲基丙烯酸甲酯的两亲性两嵌段聚合物通过自组装包覆生色团的方式,模拟了绿色荧光蛋白发光,考察了组装行为对光学性能的影响,并将其用于细胞成像.通过核磁共振、高分辨质谱、傅里叶变换红外光谱、凝胶渗透色谱、紫外-可见吸收光谱及荧光光谱等表征了生色团分子和聚合物的结构及性能.生色团紫外最大吸收在371 nm,荧光最大发射峰在428 nm.聚合物和生色团进行组装后,其紫外吸收消失,而最大荧光发射峰强度大大增强,且发生了约70 nm的红移,这是因为组装使得生色团的自由旋转受到了限制,且生色团共平面性增加.动态光散射(DLS)和透射电镜(TEM)证明了纳米粒子的结构和尺寸.由于尺寸适合且具有较好的荧光性能,纳米粒子成功应用于细胞成像.这种绿色荧光蛋白生色团的简单自组装方式在生物成像领域具有良好应用前景.     

模仿绿色荧光蛋白的荧光聚合物的合成和光学性质研究

受绿色荧光蛋白(GFP)荧光增强原理启发,采用开环聚合制备了两亲性聚乙二醇-生色团-聚己内酯(PEG-c-PCL)嵌段聚合物.通过核磁共振氢谱和碳谱(1H-,13C-NMR)、傅立叶变换红外光谱(FTIR)、凝胶渗透色谱(GPC)和紫外可见吸收光谱(UV-Vis)等证明其结构和性质.生色团和聚合物有相似的紫外吸收光谱,且最大吸收峰都在371 nm.荧光发射光谱表明,生色团的发射峰在427 nm,但聚合物的荧光发射峰出现了6 nm的红移,这是高分子化引起的结果.透射电镜(TEM)和动态光散射(DLS)证明了该两亲性嵌段聚合物能够组装成为纳米粒子.当聚合物组装成纳米粒子后,荧光强度增大了55倍,并且荧光发射峰出现了14 nm的红移,这些现象可归结于荧光生色团自由旋转的限制和组装导致的相互作用增强.     

A microenvironment-sensitive fluorescent pyrimidine ribonucleoside analogue: synthesis, enzymatic incorporation, and fluorescence detection of a DNA abasic site

Base-modified fluorescent ribonucleoside-analogue probes are valuable tools in monitoring RNA structure and function because they closely resemble the structure of natural nucleobases. Especially, 2-aminopurine, a highly environment-sensitive adenosine analogue, is the most extensively utilized fluorescent nucleoside analogue. However, only a few isosteric pyrimidine ribonucleoside analogues that are suitable for probing the structure and recognition properties of RNA molecules are available. Herein, we describe the synthesis and photophysical characterization of a small series of base-modified pyrimidine ribonucleoside analogues derived from tagging indole, N-methylindole, and benzofuran onto the 5-position of uracil. One of the analogues, based on a 5-(benzofuran-2-yl)pyrimidine core, shows emission in the visible region with a reasonable quantum yield and, importantly, displays excellent solvatochromism. The corresponding triphosphate substrate is effectively incorporated into oligoribonucleotides by T7 RNA polymerase to produce fluorescent oligoribonucleotide constructs. Steady-state and time-resolved spectroscopic studies with fluorescent oligoribonucleotide constructs demonstrate that the fluorescent ribonucleoside photophysically responds to subtle changes in its environment brought about by the interaction of the chromophore with neighboring bases. In particular, the emissive ribonucleoside, if incorporated into an oligoribonucleotide, positively reports the presence of a DNA abasic site with an appreciable enhancement in fluorescence intensity. The straightforward synthesis, amicability to enzymatic incorporation, and sensitivity to changes in the microenvironment highlight the potential of the benzofuran-conjugated pyrimidine ribonucleoside as an efficient fluorescent probe to investigate nucleic acid structure, dynamics, and recognition events.     

Native Biomolecules in the Gas Phase? The Case of Green Fluorescent Protein

Green fluorescent protein (GFP) was ionized by native electrospray ionization and trapped for many seconds in high vacuum, allowing fluorescence emission to be measured as a probe of its biological function, to answer the question whether GFP exists in the native form in the gas phase or not. Although a narrow charge‐state distribution, a collision cross‐section very close to that expected for correctly folded GFP, and a large stability against dissociation all support a near‐native gas‐phase structure, no fluorescence emission was observed. The loss of the native form is attributed to the absence of residual water in the gas phase, which normally stabilizes the para‐hydroxybenzylidene imidazolone chromophore of GFP.     

Radiationless decay of red fluorescent protein chromophore models via twisted intramolecular charge-transfer states

We use CASSCF and MRPT2 calculations to characterize the bridge photoisomerization pathways of a model red fluorescent protein (RFP) chromophore model. RFPs are homologues of the green fluorescent protein (GFP). The RFP chromophore differs from the GFP chromophore via the addition of an N-acylimine substitution to a common hydroxybenzylidene-imidazolinone (HBI) motif. We examine the substituent effects on the manifold of twisted intramolecular charge-transfer (TICT) states which mediates radiationless decay via bridge isomerization in fluorescent protein chromophore anions. We find that the substitution destabilizes states associated with isomerization about the imidazolinone-bridge bond and stabilizes states associated with phenoxy-bridge bond isomerization. We discuss the results in the context of chromophore conformation and quantum yield trends in the RFP subfamily, as well as recent studies on synthetic models where the acylimine has been replaced with an olefin.     

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.     

Syntheses of highly fluorescent GFP-chromophore analogues

Eight B-containing compounds, i.e., 1a-h, were prepared as mimics of the green fluorescent protein (GFP) fluorophore. The underlying concept was that synthetic GFP chromophore analogues are not fluorescent primarily because of free rotation about an aryl-alkene bond (Figure 1b). This rotation is not possible in the beta-barrel of GFP; hence, the molecule is strongly fluorescent. In compounds 1a-h, radiationless decay via this mechanism is prevented by complexation of the BF2 entity. The target materials were prepared via two methods; most were obtained according to the novel route shown in Scheme 1b, but compound 1f was made via the procedure described in Scheme 2. Both syntheses involved formation of undesired compounds E-4a-h that formed simultaneously with the desired isomeric intermediates Z-4a-h. Both compounds form BF2 adducts, i.e., 1a-h and 5a-h, respectively. Methods used for spectroscopic characterization and differentiation of compounds in the series 1 and 5 are discussed, and these are supported by single-crystal X-ray diffraction analyses for compounds 1c, 5c, 1f, and 5f. Electronic spectra of compounds 1a-h and 5a-h were studied in detail. Those in the 5 series were shown to be only weakly fluorescent, but the 1 series were strongly fluorescent compounds (comparable to the boraindacene, BODIPY, dyes). Compounds 1g and 1h are water soluble, and 1h has particularly significant potential as a probe, since it also has a carboxylic acid group for attachment to biomolecules.     

Deconstructing green fluorescent protein

Green fluorescent protein (GFP) has been reassembled from two pieces, a large fragment 214 amino acids in length that is produced recombinantly (GFP 1-10) and a short synthetic peptide corresponding to the 11th stave of the beta-barrel that is 16 amino acids long (synthetic GFP 11), following a system developed by Waldo and co-workers (Cabantous, S.; et al. Nat. Biotechnol. 2005, 23, 102-7) as an in vivo probe for protein association and folding. We demonstrate that the reassembled protein has identical absorption and excited-state proton transfer dynamics as a whole protein of the identical sequence. We show that the reassembled protein can be taken apart and the peptide replaced with a different synthetic peptide designed to perturb the chromophore absorption. Thus, this semisynthetic reassembly process offers a general route for studying the assembly of the beta-barrel as well as the introduction of unnatural amino acids.     

Cis-trans photoisomerization of fluorescent-protein chromophores

Photochromic variants of fluorescent proteins are opening the way to a number of opportunities for high-sensitivity regioselective studies in the cellular environment and may even lead to applications in information and communication technology. Yet, the detailed photophysical processes at the basis of photoswitching have not been fully clarified. In this paper, we used synthetic FP chromophores to clarify the photophysical processes associated with the photochromic behavior. In particular, we investigated the spectral modification of synthetic chromophore analogues of wild-type green fluorescent protein (GFP), Y66F GFP (BFPF), and Y66W GFP (CFP) upon irradiation in solutions of different polarities. We found that the cis-trans photoisomerization mechanism can be induced in all the chromophores. The structural assignments were carried out both by NMR measurements and DFT calculations. Remarkably, we determined for the first time the spectra of neutral trans isomers in different solvents. Finally, we calculated the photoconversion quantum yields by absorption measurements under continuous illumination at different times and by a nanosecond laser-flash photolysis method. Our results indicate that cis-trans photoisomerization is a general mechanism of FP chromophores whose efficiency is modulated by the detailed mutant-specific protein environment.     

Synthesis and spectroscopic studies of model red fluorescent protein chromophores

[reaction: see text]. Here we describe the synthesis and spectroscopic characterization of two compounds designed to model the chromophore in DsRed, a red fluorescent protein. Comparison with model green fluorescent protein (GFP) chromophores indicates that the additional conjugation in the DsRed models can account, in part, for the red-shifted absorption and emission properties of DsRed compared to those of GFP. In contrast to the GFP models, the DsRed models are fluorescent with quantum yields of 0.002-0.01 in CHCl3.     

β-Cyclodextrin as a mimetic of the natural GFP-chromophore environment

The green fluorescent protein (GFP) chromophore has been anchored to β-cyclodextrin (βCD) via a copper(I)-catalyzed azide-alkyne cycloaddition. The photophysical properties of this new GFP-CD derivative have been evaluated, showing the formation of a self-inclusion complex and enhancement of fluorescence of the GFP-chromophore covalently bound to the βCD. This enhancement of fluorescence by encapsulation and hence fixation of the chromophore in a binding pocket mimics the effect exerted by the natural protein environment.     

Hydrogen Bonding-Induced H-Aggregation for Fluorescence Turn-On of the GFP Chromophore: Supramolecular Structural Rigidity

To turn on the fluorescence of the native green fluorescence protein (GFP) chromophore, 4-hydroxybenzylidene-dimethylimidazolinone (HBDI), in an artificial supramolecular system has been a challenging task, because it requires high local environmental rigidity. This work shows that the formation of H-aggregates of an HBDI-containing organogelator results in two orders of magnitude fluorescence enhancement (Φ_f=2.9 vs. 0.02 %), in which the inter-HBDI OH⋅⋅⋅OH H-bonds play a crucial role. The aggregation-induced fluorescence enhancement of HBDI has important implications on the origin of the high fluorescence quantum efficiency of HBDI in the GFP β-barrel and on the supramolecular strategy for a full fluorescence recovery of HBDI. These results reveal a new approach to designing rigid chromophore aggregates for high-performance optoelectronic properties.