An ultrafast polarisation spectroscopy study of internal conversion and orientational relaxation of the chromophore of the green fluorescent protein

Conical Intersection Accessibility Dictates Brightness in Red Fluorescent Proteins

Red fluorescent protein (RFP) variants are highly sought after for in vivo imaging since longer wavelengths improve depth and contrast in fluorescence imaging. However, the lower energy emission wavelength usually correlates with a lower fluorescent quantum yield compared to their green emitting counterparts. To guide the rational design of bright variants, we have theoretically assessed two variants (mScarlet and mRouge) which are reported to have very different brightness. Using an α-CASSCF QM/MM framework (chromophore and all protein residues within 6 Å of it in the QM region, for a total of more than 450 QM atoms), we identify key points on the ground and first excited state potential energy surfaces. The brighter variant mScarlet has a rigid scaffold, and the chromophore stays largely planar on the ground state. The dimmer variant mRouge shows more flexibility and can accommodate a pretwisted chromophore conformation which provides easier access to conical intersections. The main difference between the variants lies in the intersection seam regions, which appear largely inaccessible in mScarlet but partially accessible in mRouge. This observation is mainly related with changes in the cavity charge distribution, the hydrogen-bonding network involving the chromophore and a key ARG/THR mutation (which changes both charge and steric hindrance).

Developing Bright Green Fluorescent Protein (GFP)-like Fluorogens for Live-Cell Imaging with Nonpolar Protein-Chromophore Interactions

Fluorescence-activating proteins (FAPs) that bind a chromophore and activate its fluorescence have gained popularity in bioimaging. The fluorescence-activating and absorption-shifting tag (FAST) is a light-weight FAP that enables fast reversible fluorogen binding, thus advancing multiplex and super-resolution imaging. However, the rational design of FAST-specific fluorogens with large fluorescence enhancement (FE) remains challenging. Herein, a new fluorogen directly engineered from green fluorescent protein (GFP) chromophore by a unique double-donor-one-acceptor strategy, which exhibits an over 550-fold FE upon FAST binding and a high extinction coefficient of approximately 100,000 M^-1  cm^-1 , is reported. Correlation analysis of the excited state nonradiative decay rates and environmental factors reveal that the large FE is caused by nonpolar protein-fluorogen interactions. Our deep insights into structure-function relationships could guide the rational design of bright fluorogens for live-cell imaging with extended spectral properties such as redder emissions.

Excited State Torsional Processes in Chalcogenopyrylium Monomethine Dyes

Chalcogenopyrylium monomethine (CGPM) dyes represent a class of environmentally activated singlet oxygen generators with applications in photodynamic therapy (PDT) and photoassisted chemotherapy (PACT). Upon binding to genomic material, the dyes are presumed to rigidify, allowing for intersystem crossing to outcompete excited state deactivation by internal conversion. This results in large triplet yields and hence large singlet oxygen yields. To understand the nature of the internal conversion process that controls the activity of the dyes, femtosecond transient absorption experiments were performed on a series of S-, Se-, and Te-substituted CGPM dyes. For S- and Se-substituted species in methanol, rapid internal conversion from the singlet excited state, S₁, occurs in ∼5 ps, deactivating the optically active excited state. The internal conversion produces a distorted ground-state species that returns to its equilibrium structure in ∼20 ps. For Te-substituted species, the internal conversion competes with rapid intersystem crossing to the lowest triplet state, T₁, which occurs with a ∼ 100 ps time constant in methanol. In more viscous methanol/glycerol mixtures, the internal conversion to the ground state slows by 2 orders of magnitude, occurring in 500-600 ps. For Se- and Te-substituted species in viscous environments, the slower internal conversion rate allows a larger triplet yield. Using femtosecond stimulated Raman spectroscopy (FSRS) and time-dependent density functional theory (TD-DFT), the internal conversion is determined to occur by twisting of the pyrylium rings about the monomethine bridge. Evolution from the distorted ground state occurs by twisting back to the S₀ equilibrium structure. The environmentally dependent photoactivity of CGPM dyes is discussed in the context of PDT and PACT applications.

A conserved interaction with the chromophore of fluorescent proteins

The chromophore of fluorescent proteins, including the green fluorescent protein (GFP), contains a highly conjugated imidazolidinone ring. In many fluorescent proteins, the carbonyl group of the imidazolidinone ring engages in a hydrogen bond with the side chain of an arginine residue. Prior studies have indicated that such an electrophilic carbonyl group in a protein often accepts electron density from a main-chain oxygen. A survey of high-resolution structures of fluorescent proteins indicates that electron lone pairs of a main-chain oxygen-Thr62 in GFP-donate electron density into an antibonding orbital of the imidazolidinone carbonyl group. This n→π* electron delocalization prevents structural distortion during chromophore excitation that could otherwise lead to fluorescence quenching. In addition, this interaction is present in on-pathway intermediates leading to the chromophore, and thus could direct its biogenesis. Accordingly, this n→π* interaction merits inclusion in computational and photophysical analyses of the chromophore, and in speculations about the molecular evolution of fluorescent proteins.

Excited state relaxation dynamics of model green fluorescent protein chromophore analogs: evidence for cis-trans isomerism

Two green fluorescent protein (GFP) chromophore analogs (4Z)-4-(N,N-dimethylaminobenzylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-5-one (DMPI) and (4Z)-4-(N,N-diphenylaminobenzylidene)-1-methyl-2-phenyl-1,4-dihydro-5H-imidazolin-5-one (DPMPI) were investigated using femtosecond fluorescence up-conversion spectroscopy and quantum chemical calculations with the results being substantiated by HPLC and NMR measurements. The femtosecond fluorescence transients are found to be biexponential in nature and the time constants exhibit a significant dependence on solvent viscosity and polarity. A multicoordinate relaxation mechanism is proposed for the excited state relaxation behavior of the model GFP analogs. The first time component (τ(1)) was assigned to the formation of twisted intramolecular charge transfer (TICT) state along the rotational coordinate of N-substituted amine group. Time resolved intensity normalized and area normalized emission spectra (TRES and TRANES) were constructed to authenticate the occurrence of TICT state in subpicosecond time scale. Another picosecond time component (τ(2)) was attributed to internal conversion via large amplitude motion along the exomethylenic double bond which has been enunciated by quantum chemical calculations. Quantum chemical calculation also forbids the involvement of hula-twist because of high activation barrier of twisting. HPLC profiles and proton-NMR measurements of the irradiated analogs confirm the presence of Z and E isomers, whose possibility of formation can be accomplished only by the rotation along the exomethylenic double bond. The present observations can be extended to p-HBDI in order to understand the role of protein scaffold in reducing the nonradiative pathways, leading to highly luminescent nature of GFP.

ELECTRONIC EXCITATIONS OF GREEN FLUORESCENT PROTEINS: MODELING SOLVATOCHROMATIC SHIFTS OF CHROMOPHORE MODEL COMPOUNDS IN SOLUTIONS

Green fluorescent protein (GFP) is a spontaneously fluorescent protein due to its p-hydroxylbenzylideneimidazolidinone chromophore. In this work, we have investigated the electronic structures, liquid structures, and solvent shifts of the GFP chromophore model compounds 4′-hydroxylbenzylidene-2,3-dimethylimidazolin-5-one (HBDI) and 4′-hydroxylbenzylidene-2-methyl-imidazoin-5-one-3-acetate (HBMIA) in NaOH /aqueous solutions, in which both compounds are protonated at anionic state. The electronic structure calculations predict that both model compounds could adopt both cis and trans conformations in solutions. Moreover, liquid simulations elucidate an extensive well-defined hydrogen-bonding network between the solvent and the solute in the ground state. Furthermore, solvent shifts calculations indicate that contributions from the specific solute-solvent hydrogen-bonding interactions are negligible for the solvatochromatic shifts observed in the absorption spectrum of the model compounds in solutions; rather, the solvent shifts are dominated by the dipolar solvation in which both permanent charge–charge interactions and many-body polarizations contribute significantly. Self-Consistent Reaction-Field (SCRF) approach could be the efficient method for studying the unusual optical properties of the GFP chromophore in solutions and proteins.

Structural and Relaxation Effects in Proton Wire Energetics: Model Studies of the Green Fluorescent Protein Photocycle

We present the results of a systematic series of constrained minimum energy pathway calculations on ground state potential energy surfaces, for a cluster model of the proton chain transfer that mediates the photocycle of the green fluorescent protein, as well as for a model including the solvated protein environment. The calculations vary in terms of the types of modes that are assumed to be capable of relaxing in concert with the movement of the protons and the results demonstrate that the nature and extent of dynamical relaxation has a substantive impact on the activation energy for the proton transfer. We discuss the implications of this in terms of currently available dynamical models and chemical rate theories that might be brought to bear on the kinetics of this important example of proton chain transfer in a biological system.

Photophysics and dihedral freedom of the chromophore in yellow, blue, and green fluorescent protein

Green fluorescent protein (GFP) and GFP-like fluorescent proteins owe their photophysical properties to an autocatalytically formed intrinsic chromophore. According to quantum mechanical calculations, the excited state of chromophore model systems has significant dihedral freedom, which may lead to fluorescence quenching intersystem crossing. Molecular dynamics simulations with freely rotating chromophoric dihedrals were performed on green, yellow, and blue fluorescent proteins in order to model the dihedral freedom available to the chromophore in the excited state. Most current theories suggest that a restriction in the rotational freedom of the fluorescent protein chromophore will lead to an increase in fluorescence brightness and/or quantum yield. According to our calculations, the dihedral freedom of the systems studied (BFP > A5 > YFP > GFP) increases in the inverse order to the quantum yield. In all simulations, the chromophore undergoes a negatively correlated hula twist (also known as a bottom hula twist mechanism).

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.

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.

Exploring Chromophore−Protein Interactions in Fluorescent Protein cmFP512 from Cerianthus membranaceus: X-ray Structure Analysis and Optical Spectroscopy

Autofluorescent proteins of the GFP family all share the same three-dimensional beta-can fold; yet they exhibit widely different optical properties, arising either from chemical modification of the chromophore itself or from specific interactions of the chromophore with the surrounding protein moiety. Here we present a structural and spectroscopic characterization of the green fluorescent protein cmFP512 from Cerianthus membranaceus, a nonbioluminescent, azooxanthellate cnidarian, which has only approximately 22% sequence identity with Aequorea victoria GFP. The X-ray structure, obtained by molecular replacement at a resolution of 1. 35 A, shows the chromophore, formed from the tripeptide Gln-Tyr-Gly, in a hydrogen-bonded cage in the center of an 11-stranded beta-barrel, tightly restrained by adjacent residues and structural water molecules. It exists in a neutral (A) and an anionic (B) species, with absorption/emission maxima at 392/460 (pH 5) and 503/512 nm (pH 7). Their fractional populations and peak positions depend sensitively on pH, reflecting protonation of groups adjacent to the chromophore. The pH dependence of the spectra is explained by a protonation mechanism involving a hydrogen-bonded cluster of charged/polar groups. Cryospectroscopy at 12 K was also performed to analyze the vibronic coupling of the electronic transitions.

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.

Electronic excitations of green fluorescent proteins: protonation states of chromophore model compound in solutions

Green fluorescent proteins (GFPs) are widely used as tools in biochemistry, cell biology, and molecular genetics due to their unusual optical spectroscopic characteristics. The spectrophotometric and fluorescence properties of GFPs are controlled by the protonation states and possibly cis-trans isomerization of the chromophore (p-hydroxybenzylideneimidazolinone). In this work, we have investigated electronic structures, liquid structures, and solvent shifts of the three possible protonated states (neutral, anionic, and zwitterionic) and their cis-trans isomerization of a model compound 4'-hydroxybenzylidene-2-methyl-imidazolin-5-one-3-acetate (HBMIA) in aqueous solutions. Our calculated results suggest that HBMIA could adopt both cis and trans conformations in a solution, and it exists in three different protonation states depending on the pH conditions. The absorption spectrum observed in neutral solution is thus assigned to the electronic excitations within the neutral form and the cis isomer of the zwitterionic form, while the absorption band at 425 nm in the basic solution is due to the excitations within the anionic form and the trans isomer of the zwitterionic form. Some technical problems related to the computation of electronic excitations within the HBMIA at the anionic state are also discussed.

Solvent effects on the vibrational activity and photodynamics of the green fluorescent protein chromophore: a quantum-chemical study

Vibrational activities in the Raman and resonance Raman spectra of the cationic, neutral, and anionic forms of 4'-hydroxybenzylidene-2,3-dimethyl-imidazolinone, a model compound for the green fluorescent protein chromophore, have been obtained from quantum-chemical calculations in vacuo and with the inclusion of solvent effects through the polarizable continuum model. It is found that inclusion of solvent effects improves slightly the agreement with experimental data for the cationic and neutral forms, whose spectra are qualitatively well-described already by calculations in vacuo. In contrast, inclusion of solvent effects is crucial to reproduce correctly the activities of the anionic form. The structural effects of solvation are remarkable both in the ground and in the lowest excited state of the anionic chromophore and influence not only the vibrational activity but also the photodynamics of the lowest excited state. CASPT2//CASSCF photoreaction paths, computed by including solvent effects at the CASSCF level, indicate a facile torsional deformation around both exocyclic CC bonds. Rotation around the exocyclic CC double bond is shown to lead to a favored radiationless decay channel, more efficient than that in gas phase, and which explains the ultrafast fluorescence decay and ground-state recovery observed in solution. Conversely, rotation around the exocyclic CC single bond accounts for the bottleneck observed in the ground-state recovery cycle. It is also speculated that the ultrafast radiationless decay channel would be hampered in protein for unfavorable electrostatic interactions and steric reasons.

Biophysical characterization of natural and mutant fluorescent proteins cloned from zooxanthellate corals

Two novel colored fluorescent proteins were cloned and biophysically characterized from zooxanthellate corals (Anthozoa). A cyan fluorescent protein derived from the coral Montastrea cavernosa (mcCFP) is a trimeric complex with strong blue-shifted excitation and emission maxima at 432 and 477 nm, respectively. The native complex has a fluorescence lifetime of 2.66+/-0.01 ns and an inferred absolute quantum yield of 0.385. The spectroscopic properties of a green fluorescent protein cloned from Meandrina meandrites (mmGFP) resemble the commercially available GFP derived originally from the hydrozoan Aequorea victoria (avGFP). mmGFP is a monomeric protein with an excitation maximum at 398 nm and an emission maximum at 505 nm, a fluorescence lifetime of 3.10+/-0.01 ns and an absolute quantum yield of 0.645. Sequence homology with avGFP and the red fluorescent protein (DsRed) indicates that the proteins adopt the classic beta-barrel configuration with 11 beta-strands. The three amino acid residues that comprise the chromophore are QYG for mcCFP and TYG for mmGFP, compared with SYG for avGFP. A single point mutation, Ser-110 to Asn, was introduced into mmGFP by random mutagenesis. Denaturation and refolding experiments showed that the mutant has reduced aggregation, increased solubility and more efficient refolding relative to the wild type. Time-resolved emission lifetimes and anisotropies suggest that the electronic structure of the chromophore is highly dependent on the protonation state of adjoining residues.

Conical intersection dynamics in solution: The chromophore of Green Fluorescent Protein

We use ab initio results to reparameterize a multi-reference semiempirical method to reproduce the ground and excited state potential energy surfaces (PESs) for the chromophore of Green Fluorescent Protein (GFP). The validity of the new parameter set is tested, and the new method is combined with a quantum mechanical/molecular mechanical (QM/MM) treatment so that it can be applied in the solution phase. Solvent effects on the energetics of the relevant conical intersections are explored. We then combine this representation of the ground and excited state PESs with the full multiple spawning (FMS) nonadiabatic wavepacket dynamics method to simulate the photodynamics of the neutral GFP chromophore in both gas and solution phases. In these calculations, the PESs and their nonadiabatic couplings are evaluated simultaneously with the nuclear dynamics, ie. "on-the-fly". The effect of solvation is seen to be quite dramatic, resulting in an order of magnitude decrease in the excited state lifetime. We observe a correlated torsion about a double bond and its adjacent single bond in both gas and solution phases. This is discussed in the context of previous proposals about minimal volume isomerization mechanisms in protein environments.

Electronic excitations of the green fluorescent protein chromophore in its protonation states: SAC/SAC-CI study

Two ground-state protonation forms causing different absorption peaks of the green fluorescent protein chromophore were investigated by the quantum mechanical SAC/SAC-CI method with regard to the excitation energy, fluorescence energy, and ground-state stability. The environmental effect was taken into account by a continuum spherical cavity model. The first excited state, HOMO-LUMO excitation, has the largest transition moment and thus is thought to be the source of the absorption. The neutral and anionic forms were assigned to the protonation states for the experimental A- and B-forms, respectively. The present results support the previous experimental observations.

Ground state isomerization of a model green fluorescent protein chromophore

The relationship between ground state cis-trans isomerization and protonation state is explored for a model green fluorescent protein chromophore, 4-hydroxybenzylidene-1,2-dimethylimidazolinone (HBDI). We find that the protonation state has only a modest effect on the free energy differences between cis and trans isomers and on the activation energies for isomerization. Specifically, the experimental free energy differences are 3.3, 8.8, and 9.6 kJ/mol for cationic, neutral, and anionic forms of HBDI, respectively, and the activation energies are 48.9, 54.8, and 54.8 kJ/mol for cationic, neutral, and anionic forms, respectively. Furthermore, these activation energies are much smaller than might be expected based on comparison with similar systems. These results suggest that there may be a sub-population of the chromophore, which is nearly equally accessible to all three protonation states, through which thermal isomerization may proceed.