Anionic Chromophore Research Articles

External Charges Influence Fluorescent Protein Proton Wires

Genetically encoded voltage indicators (GEVIs) based on the fluorescent protein Superecliptic pHluorin have been shown to alter fluorescent output in a voltage-dependent manner. The dimer affinity of the fluorescent proteins (FP) and specific charged residues in the dimer interface are involved in the mechanism of how the fluorescent output changes have been implicated in the optical signal. Here we show that the critical negative charge on the exterior of the β-can structure of the FP (A227D) can affect proton wires that ultimately affect the chromophore of the FP. When the negative charge is moved along the exterior of the β-barrel, the polarity of the voltage-dependent optical signal inverts. One hypothesis to explain this behavior is that the transient movement of the negative charge shifts the equilibrium of the protonation state of the chromophore. To test this hypothesis, alternating the excitation wavelength from 390 nm to 470 nm was performed revealing that the kinetics of the optical signal, voltage range of the optical signal, and the optimal linker length were wavelength dependent. These results suggest that the proton wires capable of responding to the external negative charge of a neighboring probe are different for the protonated chromophore and the anionic chromophore. To further investigate the effect on proton wires, several E222 mutations were tested which has been implicated as the proton release point for excited state proton transfer of GFP. The results imply that ArcLight-derived GEVIs can be used to alter and thereby study proton wires of fluorescent proteins. Combined with structural data, these GEVIs may enable the mapping of proton wires, which would enable the development of voltage sensors with large dynamic range.

Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins

Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.

Quantum mechanical/molecular mechanical trajectory surface hopping molecular dynamics simulation by spin-flip time-dependent density functional theory.

This paper presents the nonadiabatic molecular dynamics simulation in the solution phase using the spin-flip time-dependent density functional theory (SF-TDDFT). Despite the single-reference level of theory, the SF-TDDFT method can generate the correct topology of S0/S1 crossing points, thus providing a natural S1 → S0 nonadiabatic transition. We extend the gas-phase trajectory surface hopping simulation with the SF-TDDFT [N. Minezawa and T. Nakajima, J. Chem. Phys. 150, 204120 (2019)] to the hybrid quantum mechanical/molecular mechanics (QM/MM) scheme. To this end, we modify the code to evaluate the electrostatic interaction between the QM and MM atoms and to extract the classical MM energy and forces from the MM program package. We apply the proposed method to the photoisomerization reaction of aqueous E-azomethane and anionic green fluorescent protein chromophore in water and compare the results with those of the previous simulation studies based on the multireference methods.

Ultrafast valence to non-valence excited state dynamics in a common anionic chromophore

Non-valence states in neutral molecules (Rydberg states) have well-established roles and importance in photochemistry, however, considerably less is known about the role of non-valence states in photo-induced processes in anions. Here, femtosecond time-resolved photoelectron imaging is used to show that photoexcitation of the S1(ππ*) state of the methyl ester of deprotonated para-coumaric acid – a model chromophore for photoactive yellow protein (PYP) – leads to a bifurcation of the excited state wavepacket. One part remains on the S1(ππ*) state forming a twisted intermediate, whilst a second part leads to the formation of a non-valence (dipole-bound) state. Both populations eventually decay independently by vibrational autodetachment. Valence-to-non-valence internal conversion has hitherto not been observed in the intramolecular photophysics of an isolated anion, raising questions into how common such processes might be, given that many anionic chromophores have bright valence states near the detachment threshold.

Organic nanoparticles of anion-based fluorophore 8-anilino-1-naphthalenesulfonate (ANS): Effects of ion-association and post-dilution

On the basis of a modified ion-association method, fluorescent organic nanoparticles of 8-anilino-1-naphthalenesulfonate (ANS) are synthesized in pure aqueous solution. The ANS dye is an anionic chromophore having a strongly hydrophilic sulfonate group, so the use of bulky, bis-quaternary phosphonium co-cation, that is, o-xylylenebis(triphenylphosphonium) cation (XTPP), is very effective for producing ion-based nanoparticles with a diameter of 150–250 nm. Binding of ANS with XTPP significantly modulates the intensity and peak position of the dye fluorescence, but interestingly, the emission properties are strongly influenced by post-dilution of the native dispersions. Electron microscopy and dynamic light scattering experiments reveal that, upon post-dilution, native ANS nanoparticles are etched, and the size-reduced particles are interconnected with each other to form a particle network of about ∼200 nm, resulting in a remarkable change in the dye fluorescence.

Unified Model for Photophysical and Electro-Optical Properties of Green Fluorescent Proteins.

Green fluorescent proteins (GFPs) have become indispensable imaging and optogenetic tools. Their absorption and emission properties can be optimized for specific applications. Currently, no unified framework exists to comprehensively describe these photophysical properties, namely the absorption maxima, emission maxima, Stokes shifts, vibronic progressions, extinction coefficients, Stark tuning rates, and spontaneous emission rates, especially one that includes the effects of the protein environment. In this work, we study the correlations among these properties from systematically tuned GFP environmental mutants and chromophore variants. Correlation plots reveal monotonic trends, suggesting that all these properties are governed by one underlying factor dependent on the chromophore's environment. By treating the anionic GFP chromophore as a mixed-valence compound existing as a superposition of two resonance forms, we argue that this underlying factor is defined as the difference in energy between the two forms, or the driving force, which is tuned by the environment. We then introduce a Marcus-Hush model with the bond length alternation vibrational mode, treating the GFP absorption band as an intervalence charge transfer band. This model explains all of the observed strong correlations among photophysical properties; related subtopics are extensively discussed in the Supporting Information. Finally, we demonstrate the model's predictive power by utilizing the additivity of the driving force. The model described here elucidates the role of the protein environment in modulating the photophysical properties of the chromophore, providing insights and limitations for designing new GFPs with desired phenotypes. We argue that this model should also be generally applicable to both biological and nonbiological polymethine dyes.

Effect of Ions on the Optical Absorption Spectra of Aqueously Solvated Chromophores.

In the condensed phase, ions often create heterogeneous local environments around a solute, which may impart chemical reactivity or perturbations to physicochemical properties. Although the former has been the subject of some study, the latter-particularly as is pertains to optical absorption spectroscopy-is much less understood. In this work, the computed UV-vis absorption spectrum is examined for the aqueously solvated chromophore anion of green fluorescent protein for different local ion configurations. The strong ability of water to screen the ions from the chromophore results in little change in excitation energy compared to a purely aqueous environment. However, upon forming a contact ion pair with a sodium ion at either of the two electronegative oxygen sites of the chromophore, there is a spectral shift to either higher or lower energies. Surprisingly, our analysis suggests that the cause of the spectral shift is dominated not by the electrostatic presence of the ion but instead by ion disruption of the hydrogen bond network at the oxygen contact ion pair site.

Modeling Charge Flux by Interpolating Atomic Partial Charges.

Although the charge flux effect or the geometric dependence of the atomic partial charges have been known for a long time, how it can be effectively handled is not yet established. Here, we present a charge interpolation scheme as a new general tool for representing the charge flux in an analytically well-defined manner. By applying it to the anionic GFP chromophore with the diabatically represented atomic charges, we show that the charge interpolation provides a substantial improvement on the accuracy of the geometry-dependent changes in the molecular dipole moments in the gas phase. We also test the scheme toward describing the electrostatic term in the solvation energy in the aqueous environment and observe that it is also improved but that the extent of the improvement is somewhat limited. We show that the remaining errors can be largely corrected by introducing atomic polarizabilities. Overall, our results show that charge interpolation is an amenable approach for describing the charge flux effect and that its description in the condensed phase should be accompanied by proper treatments of polarization effects.

A photoelectron imaging and quantum chemistry study of the deprotonated cyan fluorescent protein chromophore anion

Cyan fluorescent protein (CFP), a blue-shifted analogue of green fluorescent protein, is used widely as a fluorescence resonance energy transfer donor in live cell fluorescence imaging. Here, we use a combination of anion photoelectron spectroscopy experiments and quantum chemistry calculations to probe the electronic structure of the CFP chromophore in its deprotonated anionic form. The vertical detachment energy measured as the maximum in the photoelectron spectrum is eV, which is an improvement on our earlier measurement. We see evidence for competing internal conversion following resonant excitation of electronically excited states of the anion lying in the detachment continuum. We find that the first electronically excited valence state of the anion lies very close to the detachment threshold, supporting the conclusions of gas-phase photodestruction action spectroscopy measurements, and that the second electronically excited valence state lies around 1.25 eV above the detachment threshold. These electronic states have shape resonance character and mixed excited shape and Feshbach resonance character, respectively.

Subatomic resolution X-ray structures of green fluorescent protein.

Green fluorescent protein (GFP) is a light-emitting protein that does not require a prosthetic group for its fluorescent activity. As such, GFP has become indispensable as a molecular tool in molecular biology. Nonetheless, there has been no subatomic elucidation of the GFP structure owing to the structural polymorphism around the chromophore. Here, subatomic resolution X-ray structures of GFP without the structural polymorphism are reported. The positions of H atoms, hydrogen-bonding network patterns and accurate geometric parameters were determined for the two protonated forms. Compared with previously determined crystal structures and theoretically optimized structures, the anionic chromophores of the structures represent the authentic resonance state of GFP. In addition, charge-density analysis based on atoms-in-molecules theory and noncovalent interaction analysis highlight weak but substantial interactions between the chromophore and the protein environment. Considered with the derived chemical indicators, the lone pair-π interactions between the chromophore and Thr62 should play a sufficient role in maintaining the electronic state of the chromophore. These results not only reveal the fine structural features that are critical to understanding the properties of GFP, but also highlight the limitations of current quantum-chemical calculations.

Direct Observation of the Photoreduction Products of Mn(NDI-bpy)(CO)3X CO2 Reduction Catalysts Using Femtosecond Transient IR Spectroscopy

The electrochemical reduction of the Mn(bpy)(CO)3X CO2 reduction catalyst is thought to proceed by the initial reduction of MnI to Mn0. We have covalently attached a naphthalenediimide radical anion (NDI•–) chromophore to the 4-, 5-, or 6-position of the bpy via a phenyl bridge to produce Mn(NDI•–-bpy)(CO)3X, where X = Br, CH3CN, or DMF, and have used femtosecond and nanosecond transient IR spectroscopy to directly observe the intermediates produced by two electron-transfer reactions following selective photoexcitation of NDI•– to its lowest excited doublet state, 2*NDI•–. In complexes where NDI•– is attached at the 4- or 5-position of bipyridine, only the reaction Mn(2*NDI•–-bpy)(CO)3X → Mn(NDI-bpy•–)(CO)3X is observed, whereas in the complex where NDI•– is attached to the 6-position of bipyridine, the reaction sequence Mn(2*NDI•–-bpy)(CO)3X → Mn(NDI-bpy•–)(CO)3X → Mn0(NDI-bpy)(CO)3 is observed. Moreover, in the complexes with an NDI•– bound to the 6-position of bipyridine, Mn0(NDI-bpy)(CO)3 exhibits a l...

Assessment of Functionals for TDDFT Calculations of One- and Two-Photon Absorption Properties of Neutral and Anionic Fluorescent Proteins Chromophores

Performance of DFT functionals with different percentages of exact Hartree-Fock exchange energy (EX) is assessed for recovery of the CC2 reference one- (OPA) and two-photon absorption (TPA) spectra of fluorescent proteins chromophores in vacuo. The investigated DFT functionals, together with their EX contributions are BLYP (0%), B3LYP (20%), B1LYP (25%), BHandHLYP (50%), and CAM-B3LYP (19% at short range and 65% at long range). Our test set consists of anionic and neutral chromophores as naturally occurring in the fluorescent proteins. For the first time, we compare TDDFT and CC2 methods for higher excited states than the S1 state, exhibiting relatively large TPA intensity. Our TDDFT results for neutral chromophores reveal an increase in excitation energies as well as TPA and OPA intensities errors, compared to CC2-derived results, as the DFT functional contains less exact exchange. The long-range-corrected CAM-B3LYP functional performs the best, closely followed by BHandHLYP, while BLYP usually significantly underestimates all investigated spectral properties, hence being the worst in reproducing the reference CC2 results. The hybrid B3LYP and B1LYP functionals can be roughly placed in between. We propose that TDDFT may underestimate the TPA intensities for neutral chromophores of fluorescent proteins due to underestimated oscillator strengths between some excited states. In the case of anionic chromophores, we find that B3LYP and B1LYP functionals overcome others in terms of reproducing CC2 excitation energies. On the other hand, however, TPA intensity is usually significantly underestimated, and in this respect, CAM-B3LYP functional seems to be again superior. In contrast to the case of neutral chromophores, it seems that a large magnitude of excited-state dipole moments or changes in dipole moments upon excitation may be the driving force behind high TPA transition moments.

The effect of polarizable environment on two-photon absorption cross sections characterized by the equation-of-motion coupled-cluster singles and doubles method combined with the effective fragment potential approach.

We report an extension of a hybrid polarizable embedding method incorporating solvent effects in the calculations of two-photon absorption (2PA) cross sections. We employ the equation-of-motion coupled-cluster singles and doubles method for excitation energies (EOM-EE-CCSD) for the quantum region and the effective fragment potential (EFP) method for the classical region. We also introduce a rigorous metric based on 2PA transition densities for assessing the domain of applicability of QM/MM (quantum mechanics/molecular mechanics) schemes for calculating 2PA cross sections. We investigate the impact of the environment on the 2PA cross sections of low-lying transitions in microhydrated clusters of para-nitroaniline, thymine, and the deprotonated anionic chromophore of photoactive yellow protein (PYPb). We assess the performance of EOM-EE-CCSD/EFP by comparing the 2PA cross sections against full QM calculations as well as against the non-polarizable QM/MM electrostatic embedding approach. We demonstrate that the performance of QM/EFP improves when few explicit solvent molecules are included in the QM subsystem. We correlate the errors in the 2PA cross sections with the errors in the key electronic properties-identified by the analysis of 2PA natural transition orbitals and 2PA transition densities-such as excitation energies, transition moments, and dipole-moment differences between the initial and final states. Finally, using aqueous PYPb, we investigate the convergence of 2PA cross sections to bulk values.

Observation of Near-Threshold Resonances in the Flavin Chromophore Anions Alloxazine and Lumichrome.

Lumichrome (LC) is the chromophore of the flavin family of photoactive biomolecules, where key biochemical activity involves interplay between redox and photophysical events. Questions remain about the relationship between the redox status of the ground and excited states and demand an improved understanding of the intrinsic photochemistry. Using anion photodissociation spectroscopy, we have measured the intrinsic electronic spectroscopy (564-220 nm) and accompanying photodegradation pathways of the deprotonated anionic form of LC. Experiments were also performed on alloxazine (AL), which is equivalent to LC minus two methyl groups. We observe a resonance state close to 3.8 eV for both anions for the first time, which we tentatively assign to dipole-bound excited states. For AL this state is sufficiently long-lived to facilitate dissociative electron attachment. Our results suggest that the presence of methyl group rotors at key positions along the molecular dipole may reduce the lifetime of the resonance state and hence provide a structural barrier to valence electron capture, and ensuing molecular dissociation.

Raman spectra of the GFP-like fluorescent proteins

The objective of the study was to elucidate optical characteristics of the chromophore structures of fluorescent proteins. Raman spectra of commonly used GFP-like fluorescent proteins (FPs) with diverse emission wavelengths (green, yellow, cyan and red), including the enhanced homogenous FPs EGFP, EYFP, and ECFP (from jellyfish) as well as mNeptune (from sea anemone) were measured. High-quality Raman spectra were obtained and many marker bands for the chromophore of the FPs were identified via assignment of Raman spectra bands. We report the presence of a positive linear correlation between the Raman band shift of C5=C6 and the excitation energy of FPs, demonstrated by plotting absorption maxima (cm−1) against the position of the Raman band C5=C6 in EGFP, ECFP, EYFP, the anionic chromophore and the neutral chromophore. This study revealed new Raman features in the chromophores of the observed FPs, and may contribute to a deeper understanding of the optical properties of FPs.

Genetically Encoding Quinoline Reverses Chromophore Charge and Enables Fluorescent Protein Brightening in Acidic Vesicles.

Acidic vesicles and organelles play fundamental roles in a broad range of cellular events such as endocytosis, lysosomal degradation, synaptic transmission, pathogen fate, and drug delivery. Fluorescent reporters will be invaluable for studying these complex and multifunctional systems with spatiotemporal resolution, yet common fluorescent proteins are generally nonfluorescent at acidic conditions due to the decrease of anionic chromophores upon protonation, but are fluorescent at physiological pH, creating interfering fluorescence from nonvesicle regions. Here we developed a novel acid-brightening fluorescent protein (abFP) that fluoresces strongly at acidic pH but is nonfluorescent at or above neutral pH, boasting a pH profile opposite to that of common fluorescent proteins. Through expansion of the genetic code, we incorporated a quinoline-containing amino acid Qui into the chromophore of EGFP to reverse the chromophore charge. Protonation of Qui rendered a cationic chromophore, which resulted in unique fluorescence increase only at acidic pH in vitro, in E. coli cells, and on the mammalian cell surface. We further demonstrated that abFP-tagged δ opioid receptors were fluorescently imaged in lysosome showing distinct features and without background fluorescence from other cellular regions, whereas EGFP-tagged receptors were invisible in lysosome. This Qui-rendered cationic chromophore strategy may be generally applied to other fluorescent proteins to generate a palette of colors for acidic imaging with minimal background, and these abFPs should facilitate the study of molecules in association with various acidic vesicles and organelles in different cells and model organisms.

Unraveling electronic absorption spectra using nuclear quantum effects: Photoactive yellow protein and green fluorescent protein chromophores in water.

Many physical phenomena must be accounted for to accurately model solution-phase optical spectral line shapes, from the sampling of chromophore-solvent configurations to the electronic-vibrational transitions leading to vibronic fine structure. Here we thoroughly explore the role of nuclear quantum effects, direct and indirect solvent effects, and vibronic effects in the computation of the optical spectrum of the aqueously solvated anionic chromophores of green fluorescent protein and photoactive yellow protein. By analyzing the chromophore and solvent configurations, the distributions of vertical excitation energies, the absorption spectra computed within the ensemble approach, and the absorption spectra computed within the ensemble plus zero-temperature Franck-Condon approach, we show how solvent, nuclear quantum effects, and vibronic transitions alter the optical absorption spectra. We find that including nuclear quantum effects in the sampling of chromophore-solvent configurations using ab initio path integral molecular dynamics simulations leads to improved spectral shapes through three mechanisms. The three mechanisms that lead to line shape broadening and a better description of the high-energy tail are softening of heavy atom bonds in the chromophore that couple to the optically bright state, widening the distribution of vertical excitation energies from more diverse solvation environments, and redistributing spectral weight from the 0-0 vibronic transition to higher energy vibronic transitions when computing the Franck-Condon spectrum in a frozen solvent pocket. The absorption spectra computed using the combined ensemble plus zero-temperature Franck-Condon approach yield significant improvements in spectral shape and width compared to the spectra computed with the ensemble approach. Using the combined approach with configurations sampled from path integral molecular dynamics trajectories presents a significant step forward in accurately modeling the absorption spectra of aqueously solvated chromophores.

The Effect of an Electric Field on the Spectroscopic Properties of the Isolated Green Fluorescent Protein Chromophore Anion

AbstractThe front cover artwork is provided by the groups of Profs. Lars H. Andersen and Steen Brøndsted Nielsen, both at Aarhus University. The image shows the Green Fluorescent Protein as a jigsaw puzzle. The chromophore is colored blue and experiences a high electric field at one end. Read the full text of the Communication at 10.1002/cphc.201800225.

Front Cover: The Effect of an Electric Field on the Spectroscopic Properties of the Isolated Green Fluorescent Protein Chromophore Anion (ChemPhysChem 14/2018)

Front Cover: The Effect of an Electric Field on the Spectroscopic Properties of the Isolated Green Fluorescent Protein Chromophore Anion (ChemPhysChem 14/2018)

The Effect of an Electric Field on the Spectroscopic Properties of the Isolated Green Fluorescent Protein Chromophore Anion.

Here we uncover the direct effect of a high electric field on the absorption by the Green Fluorescent Protein chromophore anion isolated in vacuo based on gas-phase action spectroscopy. Betaine is a strong molecular dipole that creates an electric field of ∼70 MV/cm when attached to the ion at the phenolate oxygen, more than half the actual field from the protein matrix and pointing in the same direction. Nevertheless, the shift in absorption is limited (0.08 eV), supporting earlier conclusions, but subject to much debate, that the protein is rather innocent in perturbing the transition energy. The betaine complexes are readily made by electrospray ionization and in contrast to the bare ions, they dissociate after one-photon absorption. Also, electron detachment is not an open channel complicating the bare ion case. As steric constraints are absent in vacuo, the possibility of turning on fluorescence by an electric field can be tested from experiments on complexes with betaine.