Origin, nature, and fate of the fluorescent state of the green fluorescent protein chromophore at the CASPT2//CASSCF resolution

Isomerization in fluorescent protein chromophores involves addition/elimination

The green fluorescent protein (GFP) chromophore undergoes both photochemical and thermal isomerizations. Typically, the Z form is more stable and undergoes photochemical conversion to the E form followed by thermal reversion over a period of seconds or minutes. Although the mechanism of the thermal reversion has been the subject of some investigations, the surprisingly low activation energy for this process has not sparked any controversy. We now show that the chromophore is surprisingly stable in both E and Z forms and that the facile thermal reversion is the result of a novel nucleophilic addition/elimination mechanism. This observation may have implications for the intervention of such processes, as well as blinking and kindling, in fluorescent proteins.

Ultrafast Electronic and Vibrational Dynamics of Stabilized A State Mutants of the Green Fluorescent Protein (GFP): Snipping the Proton Wire

Two blue absorbing and emitting mutants (S65G/T203V/E222Q and S65T at pH 5.5) of the green fluorescent protein (GFP) have been investigated through ultrafast time resolved infra-red (TRIR) and fluorescence spectroscopy. In these mutants, in which the excited state proton transfer reaction observed in wild type GFP has been blocked, the photophysics are dominated by the neutral A state. It was found that the A* excited state lifetime is short, indicating that it is relatively less stabilised in the protein matrix than the anionic form. However, the lifetime of the A* state can be increased through modifications to the protein structure. The TRIR spectra show that a large shifts in protein vibrational modes on excitation of the A* state occurs in both these GFP mutants. This is ascribed to a change in H-bonding interactions between the protein matrix and the excited state.

Operation of the proton wire in green fluorescent protein. A quantum dynamics simulation

A nuclear quantum dynamical simulation of the proton shuttle operating in the green fluorescent protein has been carried out on a high-quality, high-dimensionality potential energy surface describing the photoactive pipi* excited state, and including motion of both the three protons and of the donor and acceptor atoms of the hydrogen bonds in a closed proton wire. The results of the simulations show that proton transfer along the wire is essentially concerted, synchronous, and very fast, with a substantial amount of the green fluorescent species forming within several tens of femtoseconds. In this regard, analysis of the population of the fluorescent species indicates that at least two dynamical regimes are present for its formation. Within the first hundreds of femtoseconds, dynamics is very fast and impulsive. Later on, a slower pace of formation appears. It is discussed that the two largest decay times for the protonated chromophore reported experimentally (Chattoraj, M.; King, B. A.; Bublitz, G. U.; Boxer, S. G. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8362-8367) might correspond to some irreversible process occurring after formation of the fluorescent species, rather than to cleavage of the chromophore's phenolic O-H bond.

Chromophore protonation state controls photoswitching of the fluoroprotein asFP595

Fluorescent proteins have been widely used as genetically encodable fusion tags for biological imaging. Recently, a new class of fluorescent proteins was discovered that can be reversibly light-switched between a fluorescent and a non-fluorescent state. Such proteins can not only provide nanoscale resolution in far-field fluorescence optical microscopy much below the diffraction limit, but also hold promise for other nanotechnological applications, such as optical data storage. To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements to their properties requires a detailed understanding of the molecular switching mechanism, which is currently unknown. Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 at the atomic level by multiconfigurational ab initio (CASSCF) calculations and QM/MM excited state molecular dynamics simulations with explicit surface hopping. Our simulations explain measured quantum yields and excited state lifetimes, and also predict the structures of the hitherto unknown intermediates and of the irreversibly fluorescent state. Further, we find that the proton distribution in the active site of the asFP595 controls the photochemical conversion pathways of the chromophore in the protein matrix. Accordingly, changes in the protonation state of the chromophore and some proximal amino acids lead to different photochemical states, which all turn out to be essential for the photoswitching mechanism. These photochemical states are (i) a neutral chromophore, which can trans-cis photoisomerize, (ii) an anionic chromophore, which rapidly undergoes radiationless decay after excitation, and (iii) a putative fluorescent zwitterionic chromophore. The overall stability of the different protonation states is controlled by the isomeric state of the chromophore. We finally propose that radiation-induced decarboxylation of the glutamic acid Glu215 blocks the proton transfer pathways that enable the deactivation of the zwitterionic chromophore and thus leads to irreversible fluorescence. We have identified the tight coupling of trans-cis isomerization and proton transfers in photoswitchable proteins to be essential for their function and propose a detailed underlying mechanism, which provides a comprehensive picture that explains the available experimental data. The structural similarity between asFP595 and other fluoroproteins of interest for imaging suggests that this coupling is a quite general mechanism for photoswitchable proteins. These insights can guide the rational design and optimization of photoswitchable proteins.

Proteins whose fluorescence can be reversibly switched on and off hold great promise for applications in high-resolution optical microscopy and nanotechnology. To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements of their properties requires a detailed understanding of the molecular switching mechanism. Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 by atomistic molecular dynamics simulations. Our simulations explain measured quantum yields and excited state lifetimes, and also predict the structures of the hitherto unknown intermediates and of the irreversibly fluorescent state. Further, we find that the proton distribution in the active site of the asFP595 controls the photochemical conversion pathways of the chromophore in the protein matrix. Our results show that a tight coupling between trans-cis isomerization of the chromophore and proton transfer is essential for the function of asFP595. The structural similarity between asFP595 and other fluoroproteins suggests that this coupling is a quite general mechanism for photoswitchable proteins. These insights can guide the rational design and optimization of photoswitchable proteins.

Meta and para effects in the ultrafast excited-state dynamics of the green fluorescent protein chromophores

Femtosecond transient absorption and fluorescence upconversion experiments have been performed to investigate the photoinduced dynamics of the meta isomer of the green fluorescent protein chromophore, m-HBDI, and its O-methylated derivative, m-MeOBDI, in various solvent mixtures at neutral, acidic, and basic pH. The para isomer, p-HBDI, and its O- and N-methylated derivatives, p-MeOBDI and p-HBDIMe(+), were also studied for comparison. In all cases, fast quenching of the excited S1 state by internal conversion (IC) to the ground state was observed. In the para compounds, IC, presumably promoted by the internal twisting, arises in <1 ps. A similar process takes place in the meta compounds in nonaqueous solvents but with notably slower kinetics. In aqueous solutions, the meta compounds undergo ultrafast intermolecular excited-state proton transfer that competes with isomerization.

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.

Photoisomerization of the green fluorescence protein chromophore and the meta- and para-amino analogues

The Z --> E photoisomerization and fluorescence quantum yields for the wild-type green fluorescence protein (GFP) chromophore (p-HBDI) and its meta- and para-amino analogues (m-ABDI and p-ABDI) in aprotic solvents (hexane, THF, and acetonitrile) and protic solvents (methanol and 10-20% H(2)O in THF) are reported. The dramatic decrease in the quantum yields on going from aprotic to protic solvents indicates the important role of solvent-solute hydrogen bonding in the nonradiative decay pathways. The enhanced fluorescence of m-ABDI is also discussed.

Electronic excitations of green fluorescent proteins: modeling solvatochromatic shifts of red fluorescent protein chromophore model compound in aqueous solutions

While green fluorescent proteins (GFPs) have been widely used as tools in biochemistry, cell biology, and molecular genetics, novel red fluorescent proteins (RFPs) with red fluorescence emission have also been identified, as complements to the existing GFP technology. The unusual spectrophotometric and fluorescence properties of GFPs and RFPs are controlled by the protonation states and possibly cis/trans isomerization within their chromophores. In this work, we have investigated the electronic structures, liquid structures, and solvent shifts of the possible neutral and anionic protonated states and the cis/trans isomerization of a RFP chromophore model compound HBMPI in aqueous solutions. The calculations reproduced the experimental absorption solvatochromatic shifts of dilute HBMPI in water under neutral and anionic conditions. Unlike the GFP chromophore, the RFP chromophore model compound HBMPI in basic solution can only adopt a conformation where the C=C bond between the bridge group and the imidazolinone ring and the C-C bond between the imidazolinone and ethylene groups exist in cis and trans conformations, respectively. Moreover, the solvent-solute hydrogen-bonding interactions are found to contribute significantly to the total solvent shifts of pi-pi* excitations of aqueous HBMPI solutions, signifying the importance of protein environment in the determination of the conformation of the chromophores in red fluorescent proteins.

Predictions of novel two-photon absorption bands in fluorescent proteins

By means of time-dependent density functional theory, we calculate the two-photon cross-sections for the lowest relevant excitations in some model chromophores of intrinsically fluorescent proteins. The two-photon strength of the first, one-photon active transition varies among the various chromophores, in line with experimental findings. Interestingly, additional transitions with large two-photon cross-sections are found in the 500-700 nm region arising from near-resonant enhancement, as revealed by few-state model analysis. Multiphoton excitation of fluorescent proteins in this spectral region can lead to relevant application for bioimaging.

Variation of spectral, structural, and vibrational properties within the intrinsically fluorescent proteins family: a density functional study

We report an extensive (time-dependent) density functional study of the whole series of the chromophores within the Intrinsically Fluorescent Protein family, in the relevant conformations and protonation states. Over 30 structures are considered, including three newly discovered chromophores (zFP, Kaede, and the Orange variant of DsRed). Ab initio calculations on selected structures are also performed in order to assess the performances of TDDFT along the family. The use of a uniform scheme for all structures allows to establish relationships between the absorption energy and electrostatic, structural or vibrational properties of the chromophores.

Photoabsorption of green and red fluorescent protein chromophore anions in vacuo

Photoabsorption properties of green and red fluorescent protein chromophore anions in vacuo were investigated theoretically, based on the experimental results in gas phase [Phys. Rev. Lett. 2001, 87, 228102; Phys. Rev. Lett. 2003, 90, 118103]. Their calculated transition energies in absorption with TD-DFT and ZINDO methods are directly compared to the experimental reports in gas phase, and the calculations with ZINDO method can correctly reproduce the absorption spectra. The orientation and strength of their transition dipole moments were revealed with transition density. We also showed the orientation and result of their intramolecular charge transfer with transition difference density. The calculated results show that with the increase of the extended conjugated system, the orientation of transition dipole moments and the orientation of charge transfer can be reversed. They are the linear responds with the external electric fields. These theoretical results reveal the insight understanding of the photoinduced dynamics of green and red fluorescent protein chromophore anions and cations in vacuo.

Deactivation mechanism of the green fluorescent chromophore

We report time-resolved fluorescence data for the anion of p-hydroxybenzylidene dimethylimidazolinone (p-HBDI), a model chromophore of the green fluorescence protein, in viscous glycerol-water mixtures over a range of temperatures, T. The markedly nonexponential decay of the excited electronic state is interpreted with the aid of an inhomogeneous model possessing a Gaussian coordinate-dependent sink term. A nonlinear least-squares fitting routine enables us to achieve quantitative fits by adjusting a single activation parameter, which is found to depend linearly on 1/T. We derive an analytic expression for the absolute quantum yield, which is compared with the integrated steady-state fluorescence spectra. The microscopic origins of the model are discussed in terms of two-dimensional dynamics, coupling the phenyl-ring rotation to a swinging mode that brings this flexible molecule to the proximity of a conical intersection on its multidimensional potential energy surface.

Electronic spectroscopy and solvatochromism in the chromophore of GFP and the Y66F mutant

The electronic spectra of the chromophore of the wild type green fluorescent protein, GFP, and of a mutant form Y66F GFP in which the chromophore lacks the hydroxyl group have been studied. The acid-base properties, solvatochromism, vibronic structure and edge excitation red shift have all been measured. The results are compared with the spectra of the chromophore in the protein environment. These data suggest that the transition energy for the GFP chromophore is influenced by a number of factors in its environment, and in particular by hydrogen bonding.

Isomerization Through Conical Intersections

The standard model for photoinduced cis-trans isomerization about carbon double bonds is framed in terms of two electronic states and a one-dimensional reaction coordinate. We review recent work that suggests that a minimal picture of the reaction mechanism requires the consideration of at least two molecular coordinates and three electronic states. In this chapter, we emphasize the role of conical intersections and charge transfer in the photoisomerization mechanism.

Origin of the anomalous two-photon absorption in fluorescent protein DsRed

The red fluorescent protein DsRed displays a two-photon excitation band around 760 nm which is not accompanied by any feature in the corresponding one-photon spectral region (380 nm). By means of time-dependent density functional theory, we are able to explain such an effect, as arising from an electronic excitation of the DsRed chromophore with ability to couple with a charge-transfer state, through an effective two-photon absorption channel.

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.

Proton relay reaction in green fluorescent protein (GFP): Polarization-resolved ultrafast vibrational spectroscopy of isotopically edited GFP

The complex transient vibrational spectra of wild type (wt) GFP have been assigned through polarization anisotropy measurements on isotopically edited proteins. Protein chromophore interactions modify considerably the vibrational structure, compared to the model chromophore in solution. An excited-state vibrational mode yields information on excited-state electronic structure. The proton relay pathway is characterized in more detail, and the protonation of the remote E222 residue is shown to occur in a concerted step. Modifications to protein vibrational modes are shown to occur following electronic excitation, and the potential for these to act as a trigger to the proton relay reaction is discussed.

Mechanistic aspects of proton chain transfer in the green fluorescent protein : Part II. A comparison of minimal quantum chemical models

In this paper we report the results of extensive quantum chemical reaction pathway calculations for the electronic ground state of several different cluster models that mimic the proton chain transfer path within the green fluorescent protein (GFP). Our principal objective is to establish the robustness with respect to variations in the model of our recent mechanistic inferences for the ground state proton chain transfer [S. Wang and S. C. Smith, J. Phys. Chem. B, 2006, 110, 5084]. Additionally, comparison of our ground state results with the excited state proton transfer (ESPT) study by Vendrell et al. [O. Vendrell, R. Gelabert, M. Moreno and J. M. Lluch, J. Am. Chem. Soc., 2006, 128, 3564] leads to the conclusion that the mechanism of proton chain transfer may be expected to be analogous in ground and excited states, principally because in both cases the loss of the chromophore's phenolic proton contributes strongly to the reaction coordinate only late in the reaction path.

Prediction of GFP spectral properties using artificial neural network

The prediction of the excitation and the emission maxima of green fluorescent protein (GFP) chromophores were investigated by a quantitative structure-property relationship study. A data set of 19 GFP color variants and an additional data set consisting of 29 synthetic GFP chromophores were collected from the literature. Artificial neural network implementing the back-propagation algorithm was employed. The proposed computational approach reliably predicted the excitation and the emission maxima of GFP chromophores with correlation coefficient exceeding 0.9. The usefulness of quantum chemical descriptors was revealed by a comparative study with other molecular descriptors. Assignment of appropriate protonation state of the chromophore for the GFP color variants data set was shown to be necessary for good predictive performance. Results suggest that the confinement of the GFP chromophore has no significant influence on the predictive performance of the data set used. A comparative investigation with the traditional modeling methods, particularly multiple linear regression and partial least squares, reveals that artificial neural network is the most suitable modeling approach for the GFP spectral properties. It is anticipated that this methodology has great potential in accelerating the design and engineering of novel GFP color variants of scientific or industrial interest.

Excited states of GFP chromophore and active site studied by the SAC-CI method: Effect of protein-environment and mutations

Excited states of fluorescent proteins were studied using symmetry-adapted cluster-configuration interaction (SAC-CI) method. Protein-environmental effect on the excitation and fluorescence energies was investigated. In green fluorescent protein (GFP), the overall protein-environmental effect on the first excitation energy is not significant. However, glutamine (Glu) 94 and arginine (Arg96) have the red-shift contribution as reported in a previous study (Laino et al., Chem Phys 2004, 298, 17). The excited states of GFP active site (GFP-W22-Ser205-Glu222-Ser65) were also calculated. Such large-scale SAC-CI calculations were performed with an improved code containing a new algorithm for the perturbation selection. The SAC-CI results indicate that a charge-transfer state locates at 4.19 eV, which could be related to the channel of the photochemistry as indicated in a previous experimental study. We also studied the excitation and fluorescence energies of blue fluorescent protein, cyan fluorescent protein, and Y66F. The SAC-CI results are very close to the experimental ones. The protonation state of blue fluorescent protein was determined. Conformation of cyan fluorescent protein indicated by the present calculation agrees to the experimentally observed structure.

Computational study of the absorption spectra of green fluorescent protein mutants

In this work, we present a theoretical study of the relationship between molecular structure and the red-shift in absorption spectra of S65G and S65T green fluorescent protein (GFP) mutants. To identify the effects of the protein environment, we combined results from molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics calculations to obtain structural properties, and applied time-dependent density functional theory to calculate the excitation energies. By using results from the MD simulations, we were able to provide a systematic analysis of the structural details that may effect the red-shift in the absorption spectra when taking into account temperature effects. Furthermore, a detailed study of hydrogen bonding during the MD simulations demonstrated differences between S65G and S65T, for example, regarding hydrogen bonding with Glu222. An analysis of the absorption spectra for different forms of the chromophore emphasized the dominance of the anionic forms in solution for the S65G and S65T GFP mutants.

Quantum Chemical Methods for the Investigation of Photoinitiated Processes in Biological Systems: Theory and Applications

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.

The gas-phase absorption spectrum of a neutral GFP model chromophore

We have studied the gas-phase absorption properties of the green fluorescent protein (GFP) chromophore in its neutral (protonated) charge state in a heavy-ion storage ring. To accomplish this we synthesized a new molecular chromophore with a charged NH(3) group attached to a neutral model chromophore of GFP. The gas-phase absorption cross section of this chromophore molecule as a function of the wavelength is compared to the well-known absorption profile of GFP. The chromophore has a maximum absorption at 415 +/- 5 nm. When corrected for the presence of the charged group attached to the GFP model chromophore, the unperturbed neutral chromophore is predicted to have an absorption maximum at 399 nm in vacuum. This is very close to the corresponding absorption peak of the protein at 397 nm. Together with previous data obtained with an anionic GFP model chromophore, the present data show that the absorption of GFP is primarily determined by intrinsic chromophore properties. In other words, there is strong experimental evidence that, in terms of absorption, the conditions in the hydrophobic interior of this protein are very close to those in vacuum.

Ground-State Structures and Vertical Excitations for the Kindling Fluorescent Protein asFP595

Geometry configurations of a large fraction of the kindling fluorescent protein asFP595 around the chromophore region were optimized by using the effective fragment potential quantum mechanical-molecular mechanical (QM/MM) method. The initial coordinates of heavy atoms were taken from the structure from the Protein Data Bank archive corresponding to the dark-adapted state of the Ala143 --> Gly mutant of asFP595. Optimization of geometry parameters was performed for all internal coordinates in the QM part composed of the chromophore unit and the side chains of His197, Glu215, and Arg92 as well as for positions of effective fragments constituting the MMpart. The structures corresponding to the anion trans, anion cis, and zwitterion trans moieties were considered among various alternatives for the chromophore unit inside the protein matrix. The QM/MM simulations show that the protein environment provides stabilization for the trans-zwitterion isomer compared to the gas-phase conditions. By using the multiconfigurational CASSCF and the time-dependent density functional theory calculations, we estimated positions of spectral bands corresponding to vertical S(0)-S(1) transitions. The results of simulations support the assumption that the dark state of asFP595 corresponds to the anionic or zwitterionic trans-conformation, while the kindled state corresponds to the anionic cis-conformation.

Cyan fluorescent protein: molecular dynamics, simulations, and electronic absorption spectrum

The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A' and B' of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A' and B' are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the beta barrel near the His148 residue, which allows the access of one solvent molecule inside the protein in conformation A'. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A' and B' exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.

Charge transfer in green fluorescent protein

Charge transfer reactions that contribute to the photoreactions of the wild type green fluorescent protein (GFP) do not occur in the isolated p-hydroxybenzylidene-imidazolidinone chromophore, demonstrating the role of the protein environment. The high quantum efficiency of the fluorescence photocycle that includes excited state proton transfer and the suppression of non-radiative pathways by the protein environment have been correlated with structural dynamics in the chromophore environment. A low quantum efficiency competing phototransformation reaction of GFP is accompanied by both proton and electron transfer, and closely mimics the charge redistribution that is occurring in the fluorescence photocycle. The protein response to this destabilising event has been demonstrated by cryo-trapping of early products in the reaction pathway and is found to be strong even at 100 K, including displacements of chromophore, protein, solvent and a photogenerated CO2 molecule derived from the decarboxylated Glu 222 side chain. We discuss the ramifications of the observation of strong conformational perturbations below the protein dynamical transition at approximately 200 K, in view of low temperature work on other light sensitive proteins such as myoglobin and bacteriorhodopsin. The proton and electron transfer in the phototransformation pathway mimics the proton and charge transfer which occurs during the fluorescence cycle, which leads to common structural responses in both photoreactions as shown by ultrafast spectroscopy. We review and discuss literature on light-induced and thermal charge transfer events, focusing on recent findings addressing conformational dynamics and implications for thermodynamic properties.

Potential Energy Landscape of the Photoinduced Multiple Proton-Transfer Process in the Green Fluorescent Protein: Classical Molecular Dynamics and Multiconfigurational Electronic Structure Calculations

The green fluorescent protein proton wire operating upon photoexcitation of the internally caged chromophore is investigated by means of classical molecular dynamics and multiconfigurational electronic structure calculations. The structure of the proton wire is studied for the solvated protein, showing that the wire is likely to be found in a configuration ready to operate as soon as the chromophore is photoexcited, and leading to a total of three proton translocations in the vicinity of the chromophore. Multiconfigurational CASSCF and CASPT2 calculations provide a detailed overview of the energy landscape of the proton wire for the ground electronic state S0, the photoactive 1pi pi* state, and the charge-transfer 1pi sigma* state. The results allow discussion of the operation of the wire in terms of the sequence of proton-transfer events and the participation of each electronic state.

Mechanistic Aspects of Proton Chain Transfer: A Computational Study for the Green Fluorescent Protein Chromophore

We explore several models for the ground-state proton chain transfer pathway between the green fluorescent protein chromophore and its surrounding protein matrix, with a view to elucidating mechanistic aspects of this process. We have computed quantum chemically the minimum energy pathways (MEPs) in the ground electronic state for one-, two-, and three-proton models of the chain transfer. There are no stable intermediates for our models, indicating that the proton chain transfer is likely to be a single, concerted kinetic step. However, despite the concerted nature of the overall energy profile, a more detailed analysis of the MEPs reveals clear evidence of sequential movement of protons in the chain. The ground-state proton chain transfer does not appear to be driven by the movement of the phenolic proton off the chromophore onto the neutral water bridge. Rather, this proton is the last of the three protons in the chain to move. We find that the first proton movement is from the bridging Ser205 moiety to the accepting Glu222 group. This is followed by the second proton moving from the bridging water to the Ser205--for our model this is where the barrier occurs. The phenolic proton on the chromophore is hence the last in the chain to move, transferring to a bridging "water" that already has substantial negative charge.

Probing the Decay Coordinate of the Green Fluorescent Protein: Arrest of Cis−Trans Isomerization by the Protein Significantly Narrows the Fluorescence Spectra

The fluorescence spectra of the wild-type green fluorescence protein (wt-GFP) and the anionic form of p-hydroxybenzylidenedimethylimidazolone (p-HBDI), which models the protein chromophore, were obtained in the 80-300 K temperature range in glycerol/water solvent. The protein spectra have pronounced and well-resolved vibronic structure, at least at lower temperatures. In contrast, the chromophore spectra are very broad and structureless even at the lowest temperatures. Analysis of the spectra shows that the experimentally observed red-shift of the protein spectrum upon heating is apparently caused by quadratic vibronic coupling of the torsional deformation (TD) of the phenyl single bond of the chromophore to the electronic transition. The broad spectra of the chromophore manifest the contribution of different conformations in the glycerol/water solvent. In particular, the lowest-temperature spectrum reflects the distribution over the same TD coordinate in the excited electronic state, which essentially contributes to the asymmetry of the spectrum. Upon heating, motion along this coordinate leads to a configuration from which the radiationless transition takes place. This narrows the distribution along the TD coordinate, causing a more symmetric fluorescence spectrum. We were able to reconstruct the broad, structureless fluorescence spectra of p-HBDI in glycerol/water solutions at various temperatures by convoluting the original wt-GFP spectra with the function describing the distribution of the transition energies of the p-HBDI chromophore. Thus, both the fluorescence broadening and increase in radiationless transition upon removal of the protein chromophore to bulk solvent are consistent with decay by a barrierless TD of the phenyl single bond.

The Role of the Protein Matrix in Green Fluorescent Protein Fluorescence

In the ground state of the highly conjugated green fluorescent protein (GFP), the chromophore should be planar. However, numerous crystal structures of GFP and GFP-like proteins have been reported with slightly twisted chromophores. We have previously shown that the protein cavity surrounding the chromophore in wild-type GFP is not complementary with a planar chromophore. This study shows that the crystal structure of wild-type GFP is not an anomaly: most of the GFP and GFP-like proteins in the protein databank have a protein matrix that is not complementary with a planar chromophore. When the pi-conjugation across the ethylenic bridge of the chromophore is removed the protein matrix will significantly twist the freely rotating chromophore from the relatively planar structures found in the crystal structures. The possible consequences of this nonplanar deformation on the photophysics of GFP are discussed. A volume analysis of the cis-trans-isomerization of HBDI, a GFP chromophore model compound, reveals that its hula-twist motion is volume conserving. This means that, if the GFP chromophore or GFP chromophore model compounds undergo a cis-trans-isomerization in a volume-constricting medium, such as a protein matrix or viscous liquid, it will probably isomerize by means of a HT-type motion.

Improving autofluorescent proteins: Comparative studies of the effective brightness of Green Fluorescent Protein (GFP) mutants

We study the photophysical behavior of 8 mutants of Green Fluorescent Protein (GFP) using fluorescence correlation spectroscopy (FCS) on the single molecule level and double resonance excitation of bulk samples. Experimental data reported here and the previously published data on the RH/R(-) equilibrium and fluorescence quantum yields Phi(Fl) (Jung et al., 2005; Biophys J 88:1932-1947) are analyzed with respect to single molecule as well as conventional fluorescence microscopy. The fraction of GFP molecules in a dark state, [D], reduces the effective absorption cross section under photostationary conditions. The determination of the excitable fraction [B] and its fluorescence quantum yield Phi(Fl) gives the effective brightness Phi(eff). Our results show that in its wavelength range, eGFP is, among the GFPs, the best fluorophore for most microscopic applications. However, in the red shifted YFP-proteins, there is still potential for improvement, since a pronounced dark state population is detectable in all mutants investigated so far. We propose to use the mutant T203Y/E222Q in imaging studies, whenever the expression yield is not a limiting factor. In FCS experiments, where the useful concentration range of the expressed molecules is restricted to concentrations below micromolarity, our data suggest the use of wt-GFP or mutant T203Y, as these represent photochemical buffers. Both mutants might surpass the limitations given by out-of-focus bleaching in live cell microscopy.

Development and Characterization of Green Fluorescent Protein Mutants with Altered Lifetimes

Multiple-probe fluorescence imaging applications demand an ever-increasing number of resolvable probes, and the use of fluorophores with resolvable fluorescence lifetimes can help meet this demand. Green fluorescent protein (GFP) and its variants have been widely used in spectrally resolved multiprobe imaging, but as yet, there has not been a systematic set of mutants generated with resolvable lifetimes. Therefore, to generate such mutants, we have utilized error-prone PCR and fluorescence lifetime imaging to screen for mutants of UV-excited green fluorescent protein (GFPuv) that exhibit altered fluorescence decay lifetimes. This has resulted in the isolation of GFPuv mutants displaying at least three distinctly different lifetimes in the range of 1.9-2.8 ns. Mutation of Y145 to either histidine or cysteine was found to shift the fluorescence lifetime of GFPuv from 3.03 +/- 0.03 to 2.78 +/- 0.05 ns for the Y145H mutant and to 2.74 +/- 0.05 ns for Y145C. Some of the shorter-lifetime mutants exhibited excitation peaks that were red-shifted relative to their maximal absorption, indicating that the mutations allowed the adoption of additional conformations relative to wtGFPuv. The utility of these mutants for applications in simultaneous imaging and quantification is shown by the ability to quantify the composition of binary mixtures in time-resolved images using a single detector channel. The application of the screening method for generating lifetime mutants of other fluorescent proteins is also discussed.

Structure and mechanism of the reversible photoswitch of a fluorescent protein

Proteins that can be reversibly photoswitched between a fluorescent and a nonfluorescent state bear enormous potential in diverse fields, such as data storage, in vivo protein tracking, and subdiffraction resolution light microscopy. However, these proteins could hitherto not live up to their full potential because the molecular switching mechanism is not resolved. Here, we clarify the molecular photoswitching mechanism of asFP595, a green fluorescent protein (GFP)-like protein that can be transferred from a nonfluorescent "off" to a fluorescent "on" state and back again, by green and blue light, respectively. To this end, we establish reversible photoswitching of fluorescence in whole protein crystals and show that the switching kinetics in the crystal is identical with that in solution. Subsequent x-ray analysis demonstrated that upon the absorption of a green photon, the chromophore isomerizes from a trans (off) to a cis (on) state. Molecular dynamics calculations suggest that isomerization occurs through a bottom hula twist mechanism with concomitant rotation of both bonds of the chromophoric methine ring bridge. This insight into the switching mechanism should facilitate the targeted design of photoswitchable proteins. Reversible photoswitching of the protein chromophore system within intact crystals also constitutes a step toward the use of fluorescent proteins in three-dimensional data recording.

Femtosecond S3→S1 Conversion and Structural Reorganisation oftrans-3-Phenylprop-2-enaldehyde and Derivatives in Solution

Photoinduced excited-state relaxation of trans-3-phenylprop-2-enaldehyde (cinnamaldehyde) and three derivatives was studied in hexane and acetonitrile with the pump-supercontinuum-probe technique. Transient spectra were measured with 50 fs resolution in the range 260-660 nm after S3<--S0 excitation at 288 nm. The early spectra reveal an ultrafast, 0.1-0.5 ps, interchange of intensity between two excited-state absorption (ESA) bands followed by a approximately 3 ps decay of ESA. This behaviour is interpreted with the help of semiempirical calculations, which indicate that the sub-picosecond evolution is consistent with S3-->S1 excited-state relaxation while the picosecond decay should be due to a structural intramolecular rearrangement. The latter may consist of a twist of the phenyl ring and rotation around the C==C bond to a perpendicular conformation which corresponds to the global energy minimum in the S1 state and serves as source for trans and cis isomers in the ground state.