Chromophore Analogues Research Articles

Synthesis of fluorescent dipeptidomimetics and their ribosomal incorporation into green fluorescent protein

The synthesis and incorporation into position 66 of green fluorescent protein (GFP) by in vitro protein translation of novel oxazole and thiazole based dipeptidomimetics are described. The compounds may be regarded as GFP chromophore analogues, and are strongly fluorescent. An α-amido-β-ketoester intermediate was obtained via bisacylation of a protected glycine. The intermediate underwent dehydrative cyclization to afford the 1,3-oxazole and was treated with Lawesson's reagent to furnish the 1,3-thiazole. When these fluorophores were introduced into position 66 of GFP in place of Tyr66, the resulting GFP analogues exhibited fluorescence emission several-fold greater than wild-type GFP; the emission was also shifted to shorter wavelength. It may be noted that compared to the typical fluorophores formed in the natural and modified fluorescent proteins, the oxazole and thiazole fluorophores are completely stable and do not require activation by posttranslational modification to exhibit fluorescence.

Synthesis and fluorescence properties of 4-diarylmethylene analogues of the green fluorescent protein chromophore

New green fluorescent protein (GFP) chromophore analogues, namely 4-(diarylmethylene)imidazolinones (DAINs), were readily synthesized under weakly acidic conditions using a novel condensation reaction between methyl imidate (or thioimidate) and ethyl N-(diarylmethylene)glycinate. DAINs showed notable fluorescence properties. Although they were nearly non-fluorescent in the solution, visible emissions were detected in most of their frozen solution states and crystalline powder states. Therefore, control of the molecular motions significantly affected emissions by DAINs. Comparison of the fluorescence properties of DAIN 5a with those of the corresponding GFP-chromophore analogues 8 revealed that 5a possessed superior solid-state fluorescence properties.

Introduction of an electron push-pull system yields a planar Red Kaede fluorescence protein chromophore analogue stabilized by a C = O…π interaction

Crystal structures of four red kaede fluorescence protein chromophore analogues are reported here. Molecules I-III adopt a non-planar geometry stabilized by π…π stacking and hydrogen bonding. Introduction of an electron push-pull system induces molecule IV to be planar and a C = O…π supramolecular interaction is observed as well. Strong electron withdrawing and donating groups also ensure formation of a higher order two and three dimensional supramolecular architecture through hydrogen bonds in molecules I and IV. All the analogues exhibit good photoluminescence properties and emit in the red region with excellent quantum yields. Crystal structures of four Red Fluorescence Protein (rfp) chromophore analogues are reported. Molecules I-III are non planar despite having a linear π-conjugated system. All these three structures are mainly stabilized by π…π interactions, C-H…π and hydrogen bonding. In molecule IV, incorporation of an electron push-pull system introduced a weak C=O…π interaction that made the molecule planar.

An experimental and theoretical study of the photoisomerization and thermal reversion on 5-arylmethylene-2-thioxoimidazolidin-4-one.

Unraveling the photochemical behaviour of the green fluorescent protein chromophore has lately attracted widespread attention among scientists. In this paper we present the study of the photochemical isomerization Z → E and the back reaction of the chromophore analog, 5-arylmethylene-2- thioxoimidazolidin-4-one. Experimental results are supported with ab initio calculations at the DFT, (B3LYP/6-31+g(d,p)), TD-DFT (B3LYP/6-311++g(3df,3pd)) and CASSCF levels. A first excitation to the S2 state, where the isomerization occurs, is proposed followed by two conical intersections to S1 and S0 respectively. Three different mechanisms were analyzed for thermal reversion, concluding that the preferred channel involves an intersystem crossing between the S0 and T1 states with the formation of a biradical.

Strong electron donation induced differential nonradiative decay pathways for para and meta GFP chromophore analogues.

Z-E Isomerisation because of rotation around the exocyclic double bond (known as the τ-twist) and not any other internal conversion has been reported to be the major nonradiative decay channel for non-hydroxylic unconstrained para and meta GFP chromophore analogues. The equation Φf + 2ΦZE = 1 has been shown to hold well for both para and meta GFP chromophore analogues. If the above equation holds true, then upon reducing the extent of Z-E isomerisation (ΦZE), the fluorescence quantum yield (Φf) should increase. To probe the above proposition two sets of non-hydroxylic unconstrained para and meta GFP chromophore analogues were synthesized. Quite interestingly by introducing the strongly electron donating -NEt2 group to the benzenic moiety these para and meta GFP chromophore analogues were shown to exhibit differential optical behaviour w.r.t. the extent of the solvatochromic shift, Φf, ΦZE, and τf. For the first time it has been shown that the well accepted equation Φf + 2ΦZE = 1 does not hold at all for these non-hydroxylic unconstrained meta analogues. Although ΦZE has been shown to be <10%, Φf is much lower than the expected near unity value for these meta analogues. After detailed investigation into the nonradiative excited state decay channel, contrary to literature reports, energy gap law governed internal conversion and not Z-E isomerisation was shown to be the major nonradiative decay channel for these meta analogues. Two models are put forward to understand the differential optical behaviour of these para and meta GFP chromophore analogues. Support from X-ray crystal structures, NMR experiments, and computational calculations has also been provided.

The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part II: solution phase.

The vibronic spectra of the green fluorescent protein chromophore analogues p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI) and 3,5-tert-butyl-HBDI (35Bu) are similar in the vacuum, but very different in water or ethanol. To understand this difference, we have computed the vibrationally resolved solution spectra of these chromophores, using the polarizable continuum model (PCM) to account for solvent effects on the (harmonic) potential energy surfaces (PES). In agreement with experiment, we found that the vibrational progression increases with the polarity of the solvent, but we could neither reproduce the broadening, nor the large difference between the absorption spectra of HBDI and 35Bu. To account for the inhomogeneous broadening of the solution spectra, we used two approaches. In the first, we estimated the polar broadening from the solvent reorganization energy upon photo-excitation, using the state-specific PCM implementation. In the second, we estimated the broadening from the variance of the vertical excitation energies in molecular dynamics trajectories. Although we found good agreement for the lineshape of 35Bu in ethanol, and to a lesser extent in water, we highly underestimated the broadening for HBDI. To resolve this discrepancy, we explored the PES of HBDI in water and found that in contrast to the PCM result, the ground-state geometry is not planar in explicit solvent. We furthermore found that nonplanar geometries enhance the intramolecular charge transfer upon excitation. Therefore, the solvent reorganization and broadening are much larger and we speculate that the much broader spectrum of HBDI in water is due to the population of nonplanar geometries.

Tuning of intermolecular interactions results in packing diversity in imidazolin-5-ones

Crystal structures of four green fluorescent protein (GFP) chromophore analogues with different packing interactions could be tuned by appropriate substitutions around the imidazolin-5-one ring are reported here. Compound 1 was crystallized from tetrahydrofuran at room temperature while compounds 2-4 have been crystallized from a mixture of methanol and dichloromethane in 3:1 ratio. Molecule 1, 2 and 3 crystallized in monoclinic lattice while molecule 4 preferred to crystallize in a triclinic crystal system. The crystal packing of these molecules was stabilized by C-H…π stacking and C-H… O type of supramolecular interactions. The results reveal that packing diversity can be easily accomplished in these molecules by tuning the substituents around the imidazolin-5-one ring. Photophysical studies also reveal that all have good quantum yield and fluoresce typically in red region due to presence of electron donating groups around the imidazolin-5-one ring. Crystal structures of four green fluorescence protein (GFP) chromophore analogues are reported. Stabilization through packing and packing diversity in crystals are achieved by modulating supramolecular interaction by varying the substituents.

The lineshape of the electronic spectrum of the green fluorescent protein chromophore, part I: gas phase.

In this work we present the vibrationally resolved optical absorption spectrum of p-hydroxybenzylidene-2,3-dimethylimidazolinone (HBDI), the green fluorescent protein (GFP) chromophore, computed at several levels of theory, including time-dependent DFT with various functionals and basis sets, CASSCF, CASPT2 and XMCQDPT2. We also investigated what happens to the spectrum if the ground- and excited-state geometries are optimized at different levels of theory (mixed approach), as has been used previously. The vibrationally resolved absorption spectra obtained by DFT, CASPT2 and XMCQDPT2 are very similar and consist of a main absorption peak and a shoulder that is ∼1500 cm(-1) higher in energy. The vibrational progression increases moderately with temperature. These spectra are in qualitative agreement with experimental action spectra, but much narrower and lack the long tail in the blue, even at high temperatures. Because our calculated emission spectra, which are equally narrow, are in good agreement with the emission of green fluorescent protein at 253 K, we argue that the action spectrum are too broad to be considered as the absorption spectrum. The CASSCF method and the mixed approaches overestimate the vibrational progressions with respect to CAM-B3LYP, CASPT2 and XMCQDPT2, due to inaccuracies in the geometric S0 →S1 displacements. Finally, we computed the vibronic spectra of four chromophore analogues with different substitutions on the rings and found that these substitutions hardly affect the lineshape in vacuum.

Steering the excited state dynamics of a photoactive yellow protein chromophore analogue with external electric fields

The first excited state of the Photoactive Yellow Protein chromophore exhibits a strong charge transfer character and the dipole moments of the excited and ground states differ significantly. Furthermore, the excited state charge distribution changes during the isomerization of this chromophore. These observations suggest that external electric fields can be used to control photo-isomerization, providing a new concept for developing photochromic devices, such as e-paper or optical memory. To test this idea, we performed excited state dynamics simulations and static calculations of a PYP chromophore analogue (pCK−) in an external electric field. By adjusting direction and strength of the field, we were able to control both selectivity (i.e., which bond isomerizes) and efficiency (excited state lifetime) of the isomerization process. Simulations like these could potentially be useful in validating whether a given chromophore could be suitable for electrochromic applications.

Synthesis and Biological Evaluation of Quinaldopeptin

The second-generation total synthesis of quinaldopeptin (1) was established via a Staudinger/aza-Wittig/diastereoselective Ugi three-component reaction sequence and a racemization-free [5 + 5] coupling and macrolactamization. A single-crystal X-ray structure of the chromophore analogue 26 confirmed the structural and stereochemical assignments of the macrocycle. Synthetic 1 successfully unwound supercoiled DNA to form a relaxed DNA in a dose-dependent manner, the binding affinity of 1 to four dsODNs was within a similar range (K(b) = 1.45-2.53 × 10(7) M(-1)), and the sequence selectivity was subtle. It was suggested that 1 possesses biological behaviors similar to those of sandramycin (2) in terms of cytotoxic activity against human cancer cell lines (IC50 = 3.2-12 nM) and HIF-1 inhibitory activity.

Synthesized Blue Fluorescent Protein Analogue with Tunable Colors from Excited-State Intramolecular Proton Transfer through an N-H···N Hydrogen Bond.

A synthesized blue fluorescent protein (BFP) chromophore analogue 2-BFP ((4Z)-4-[(1H-imidazol-2-yl)methylene]-1-methyl-2-phenyl-1H-imidazol-5(4H)-one) displays dual fluorescent emission that arises from the same Z-isomer. The larger Stokes shift emission is a result of excited-state intramolecular proton transfer (ESIPT) mediated by an N-H···N type of hydrogen bond. Compared to other green fluorescent protein (GFP) analogues with ESIPT such as o-HBDI, 2-BFP possesses greatly enhanced quantum yields and much slower proton-transfer rates. In addition, fluorescence up-conversion experiments revealed two rising components of lifetime for the tautomer formation of 2-BFP. The results imply that the relaxation of the N* state in 2-BFP triggers the proton transfer of the molecule. The weaker photoacidity of N-H is proposed to be crucial for these photophysical and photochemical properties. Finally, the ESIPT process in 2-BFP is inhibited in protic solvents (MeOH) or by the formation of metal-chelate complexes, providing insights for further developments and applications of ESIPT molecules.

Total Synthesis of Quinaldopeptin and Its Analogues

The first total synthesis of quinaldopeptin (1) was accomplished. Our approach to the synthesis of 1 includes the solid-phase peptide synthesis of the linear decapeptide 4 followed by macrocyclization and introduction of the quinoline chromophores 2 at a late stage of the synthesis. As for the preparation of 4, a fragment coupling approach was applied considering the C2 symmetrical structure of 1. Chromophore analogues 22 and 23 and desmethyl analogue 27 were also prepared in a manner similar to the synthesis of 1. Synthetic 1 exhibits a strong cytotoxicity with the IC50 value of 3.2 nM. On the other hand, the activity of 23 and 27 was largely reduced.

Geometries and Vertical Excitation Energies in Retinal Analogues Resolved at the CASPT2 Level of Theory: Critical Assessment of the Performance of CASSCF, CC2, and DFT Methods.

A systematic investigation of structural properties and vertical excitation energies of a series of structurally modified 11-cis-retinal chromophores in vacuo was performed by means of multiconfigurational second-order perturbation theory (CASPT2). CASPT2-based geometries agree reasonably well with Møller-Plesset second-order perturbation theory (MP2), local second-order approximate coupled cluster singles and doubles (LCC2), and density functional theory (DFT) geometries, while the complete active space self-consistent field (CASSCF) method exaggerates dramatically the bond length pattern in the polyene chain. The quality of the resulting vertical excitation energies obtained by employing CASSCF, second-order approximate coupled cluster singles and doubles (CC2), LCC2, and time-dependent density functional theory (TD-DFT) approaches is assessed with respect to the CASPT2 data. We show that the commonly used CASSCF/CASPT2 approach works reasonably well in the case of vertical excitation energies of planar structures, but lack of dynamic correlation leads to large errors in energetics for strongly strained structures. For example, the highly twisted conformers of 9,10-dimethyl and 9,10,13-trimethyl species are found as global minima at the CASSCF level, whereas they turn almost planar at the CASPT2, MP2, LCC2, and DFT levels of theory. The CC2 method has shown a remarkable performance, manifested by a maximum deviation of 0.05 eV from the reference CASPT2 results, whereas the local version of CC2 seems to fail to describe the charge-transfer character of the S0 → S1 transitions correctly. We believe that our CASPT2 benchmark set will provide a reference that can be utilized for validation and development studies on 11-cis-retinal protonated Schiff base chromophore analogues.

ChemInform Abstract: A Synthetic Approach to GFP Chromophore Analogues from 3‐Azidocinnamates. Role of Methyl Rotors in Chromophore Photophysics.

AbstractA combinatorial approach to otherwise inaccessible green fluorescent protein chromophore analogs is presented.

Active Site Structure of Photoactive Yellow Protein with a Locked Chromophore Analogue Revealed by Near-Infrared Raman Optical Activity

Many biological cofactors, such as light-absorbing chromophores in photoreceptors, are intrinsically planar molecules. A protein environment, however, causes structural distortions of the cofactor, and such structural changes can lead to a modulation of chemical properties of the cofactor to maximize its biological activity. Here, we investigate the active site structure of photoactive yellow protein (PYP), a blue light photoreceptor that contains a p-coumaric acid (pCA) chromophore, by a near-infrared excited Raman optical activity (ROA). Specifically, we measured the ROA spectra of PYP, whose chromophore is replaced with a locked pCA analogue. Furthermore, we show that a spectral analysis based on quantum mechanical/molecular mechanical (QM/MM) calculations of the whole protein molecule is useful to obtain structural information from the observed ROA spectra. The use of the near-infrared ROA combined with QM/MM calculations is a novel and generally applicable spectroscopic tool to study the chromophore distortions within a protein environment.

1P239 近赤外ラマン円偏光二色性分光による光受容タンパク質の活性部位構造解析(18A. 光生物:視覚・光受容,ポスター,日本生物物理学会年会第51回(2013年度))

1P239 近赤外ラマン円偏光二色性分光による光受容タンパク質の活性部位構造解析(18A. 光生物:視覚・光受容,ポスター,日本生物物理学会年会第51回(2013年度))

A synthetic approach to GFP chromophore analogs from 3-azidocinnamates. Role of methyl rotors in chromophore photophysics

We have suggested a novel combinatorial approach for synthesis of otherwise inaccessible GFP chromophore analogs, and studied the influence of aliphatic substituents on their pH-dependent spectral properties. We found that the demethylation at C or N positions of the imidazolone ring leads to a decrease in the excited state lifetime.

Imaging of Static Dielectric Permittivity In Vitro and in Living Cells by a Bioconjugable GFP Chromophore Analog

Static dielectric constant e modulates the activity of many biomolecules, thereby affecting their biological roles. Yet, spatial maps of dielectric constant in living cells is still a challenging task. Indeed, dielectric spectroscopy is unable to yield spatial e maps in cells, and AFM measurements are restricted to plasma membranes. Fluorescent probes are suitable for polarity measurements, but their readout is usually related to complex polarity functions.Here, we describe a fluorescent probe structurally similar to the GFP chromophore, able to report on local static dielectric constant (e) with good accuracy both in vitro and in living cells. Notably, we found that Generalized Polarization (GP), a classical parameter for ratiometric imaging in cell microscopy, shows a linear dependence upon the logarithm of e,thus making the probean effective indicator of local e through GP measurements.Our probe is suitable for bioconjugation, and its norbiotinamine or phospholipids derivatives can report on local polarity of micelles, LUVs, and protein surfaces in cuvette.Finally, we set out measurements in cultured CHO cells by confocal microscopy, obtaining spatially resolved dielectric constant maps of e for many subcellular compartments, such as endoplasmic reticulum, nuclear envelope and plasma membrane.Our probe has a broad applicability both in vitro, allowing for accurate measurements of physico-chemical parameters, and in cell or tissue imaging, being a robust tool to monitor local changes in bioenvironments caused by external stimuli and/or alterations of cell homeostasis.1. Signore G. et al.; J. Am. Chem. Soc., 2010, 132(4), 1276–1288.2. Gaus, K. et al.; Mol Membr Biol, 2006, 23, 41.

Imaging the static dielectric constant in vitro and in living cells by a bioconjugable GFP chromophore analog

A fluorescent probe structurally similar to the GFP chromophore is demonstrated to report the local static dielectric constant. This probe can be chemically functionalized for selective targeting at the intracellular level.

Design and Concise Synthesis of a Novel Type of Green Fluorescent Protein Chromophore Analogue

A small molecular model compound for the green fluorescent protein chromophore was readily synthesized by a novel condensation reaction of (thio)imidate with imino-ester via an aziridine intermediate. This compound showed fluorescence in the solid and frozen solution states but not in the solution state. Its fluorescent property was successfully applied in the detection of dsDNA.