An alternate proton acceptor for excited-state proton transfer in green fluorescent protein: rewiring GFP

The neutral form of the chromophore in wild-type green fluorescent protein (wtGFP) undergoes excited-state proton transfer (ESPT) upon excitation, resulting in characteristic green (508 nm) fluorescence. This ESPT reaction involves a proton relay from the phenol hydroxyl of the chromophore to the ionized side chain of E222, and results in formation of the anionic chromophore in a protein environment optimized for the neutral species (the I* state). Reorientation or replacement of E222, as occurs in the S65T and E222Q GFP mutants, disables the ESPT reaction and results in loss of green emission following excitation of the neutral chromophore. Previously, it has been shown that the introduction of a second mutation (H148D) into S65T GFP allows the recovery of green emission, implying that ESPT is again possible. A similar recovery of green fluorescence is also observed for the E222Q/H148D mutant, suggesting that D148 is the proton acceptor for the ESPT reaction in both double mutants. The mechanism of fluorescence emission following excitation of the neutral chromophore in S65T/H148D and E222Q/H148D has been explored through the use of steady state and ultrafast time-resolved fluorescence and vibrational spectroscopy. The data are contrasted with those of the single mutant S65T GFP. Time-resolved fluorescence studies indicate very rapid (< 1 ps) formation of I* in the double mutants, followed by vibrational cooling on the picosecond time scale. The time-resolved IR difference spectra are markedly different to those of wtGFP or its anionic mutants. In particular, no spectral signatures are apparent in the picosecond IR difference spectra that would correspond to alteration in the ionization state of D148, leading to the proposal that a low-barrier hydrogen bond (LBHB) is present between the phenol hydroxyl of the chromophore and the side chain of D148, with different potential energy surfaces for the ground and excited states. This model is consistent with recent high-resolution structural data in which the distance between the donor and acceptor oxygen atoms is < or = 2.4 A. Importantly, these studies indicate that the hydrogen-bond network in wtGFP can be replaced by a single residue, an observation which, when fully explored, will add to our understanding of the various requirements for proton-transfer reactions within proteins.     

Common pathway for the red chromophore formation in fluorescent proteins and chromoproteins

The mechanism of the chromophore maturation in members of the green fluorescent protein (GFP) family such as DsRed and other red fluorescent and chromoproteins was analyzed. The analysis indicates that the red chromophore results from a chemical transformation of the protonated form of the GFP-like chromophore, not from the anionic form, which appears to be a dead-end product. The data suggest a rational strategy to achieve the complete red chromophore maturation utilizing substitutions to favor the formation of the neutral phenol in GFP-like chromophore. Our approach to detect the neutral chromophore form expands the application of fluorescent timer proteins to faster promoter activities and more spectrally distinguishable fluorescent colors. Light sensitivity found in the DsRed neutral form, resulting in its instant transformation to the mature red chromophore, could be exploited to accelerate the fluorescence acquisition.     

Ultrafast excited-state intermolecular proton transfer of cyanine fluorochrome dyes

Steady-state and time-resolved emission spectroscopy techniques were employed to study the excited-state proton transfer (ESPT) to water and D(2)O from QCy7, a recently synthesized near-infrared (NIR)-emissive dye with a fluorescence band maximum at 700 nm. We found that the ESPT rate constant, k(PT), of QCy7 excited from its protonated form, ROH, is ~1.5 × 10(12) s(-1). This is the highest ever reported value in the literature thus far, and it is comparable to the reciprocal of the longest solvation dynamics time component in water, τ(S) = 0.8 ps. We found a kinetic isotope effect (KIE) on the ESPT rate of ~1.7. This value is lower than that of weaker photoacids, which usually have KIE value of ~3, but comparable to the KIE on proton diffusion in water of ~1.45, for which the average time of proton transfer between adjacent water molecules is similar to that of QCy7.     

Carbazole as an excited state proton transfer fluorescent probe for lipid bilayers in alkaline medium

In our effort to look for novel excited state proton transfer (ESPT) fluorescent probes in alkaline pH range, we have examined carbazole as a possible candidate because of its high extinction coefficient, high quantum yield and a larger difference in ionization constant between the ground and excited state (pKa - pKa*). The photodissociation of carbazole was studied in liposome membrane by steady state fluorescence measurements at alkaline pH ranges. The neutral form and the anionic form of carbazole emit at 362 and 417 nm, respectively. This large shift in emission makes it convenient to monitor the physical properties of liposomes. The neutral form fluorescence intensity of carbazole is sensitive to phase changes in the membrane and also shows a maximum at phase transition temperature. This variation of intensity can be explained in terms of redistribution of probe between the surface and interior of the liposomes. Cholesterol induced phase changes of liposomes were also sensed by the ESPT of carbazole.     

Structural photodynamics of camptothecin, an anticancer drug in aqueous solutions

Steady-state and time-resolved picosecond emission studies were carried out to study the role of the proton concentration in the acid-base properties of the anticancer drug camptothecin (CPT) in its ground and electronically first excited states. The results show that, under acidic conditions, the excited-state proton-transfer (ESPT) reaction is irreversible, in contrast to previous literature data. We found that the prototropic species are equilibrated at the excited state (pK(a)* = 1.85) only in a restricted range of pH (1.5 < pH < 3), whereas only one species, either the neutral form (τ(N) = 3.76 ns) or the protonated form (τ(C) = 2.83 ns), can be detected at pH > 3 and pH < 1.5, respectively. The proton motion from the acidic solution to the neutral form in the pH 1-2 domain is diffusion-controlled. Within the range of pH 1-2, the reaction rate constant for the formation (k(d)) of the encounter complex between the proton and the neutral form ranges from 1.17 × 10(10) to 7.33 × 10(10) M(-1) s(-1), respectively. Under more acidic conditions (pH 0.9-0.95), the protonation of CPT does not depend on the diffusive step, because of the large amount of protons. The direct proton-transfer rate constant (k(DPT)*) increases with the proton concentration (time constants change from 24 ps to ～1 ns at pH 0.9 and 2, respectively). The number of protons involved in the proton transfer changes from approximately one, for the diffusive regime, to approximately four, for the static regime. We found good agreement between the Birks model for equilibrated flourophores and the Debye-Smoluchowski equation (DSE) to accurately explain the ESPT reaction of CPT with acidic water in the reversible range. The proton motion at pH 2 (equilibrium range) exhibits diffusion-controlled behavior and can be explained using the Smoluchowski model. Our results show that the interaction of CPT with acidic water depends on the concentration of the acid, which changes the nature of both the structure and dynamics.     

Comparative study of the photoprotolytic reactions of D-luciferin and oxyluciferin

Optical steady-state and time-resolved spectroscopic methods were used to study the photoprotolytic reaction of oxyluciferin, the active bioluminescence chromophore of the firefly's luciferase-catalyzed reaction. We found that like D-luciferin, the substrate of the firefly bioluminescence reaction, oxyluciferin is a photoacid with pK(a)* value of ～0.5, whereas the excited-state proton transfer (ESPT) rate coefficient is 2.2 × 10(10) s(-1), which is somewhat slower than that of D-luciferin. The kinetic isotope effect (KIE) on the fluorescence decay of oxyluciferin is 2.5 ± 0.1, the same value as that of D-luciferin. Both chromophores undergo fluorescence quenching in solutions with a pH value below 3.     

Ultrafast relaxation dynamics of a biologically relevant probe dansyl at the micellar surface

We report picosecond-resolved measurement of the fluorescence of a well-known biologically relevant probe, dansyl chromophore at the surface of a cationic micelle (cetyltrimethylammonium bromide, CTAB). The dansyl chromophore has environmentally sensitive fluorescence quantum yields and emission maxima, along with large Stokes shift. In order to study the solvation dynamics of the micellar environment, we measured the fluorescence of dansyl chromophore attached to the micellar surface. The fluorescence transients were observed to decay (with time constant approximately 350 ps) in the blue end and rise with similar timescale in the red end, indicative of solvation dynamics of the environment. The solvation correlation function is measured to decay with time constant 338 ps, which is much slower than that of ordinary bulk water. Time-resolved anisotropy of the dansyl chromophore shows a bi-exponential decay with time constants 413 ps (23%) and 1.3 ns (77%), which is considerably slower than that in free solvents revealing the rigidity of the dansyl-micelle complex. Time-resolved area-normalized emission spectroscopic (TRANES) analysis of the time dependent emission spectra of the dansyl chromophore in the micellar environment shows an isoemissive point at 21066 cm-1. This indicates the fluorescence of the chromophore contains emission from two kinds of excited states namely locally excited state (prior to charge transfer) and charge transfer state. The nature of the solvation dynamics in the micellar environments is therefore explored from the time-resolved anisotropy measurement coupled with the TRANES analysis of the fluorescence transients. The time scale of the solvation is important for the mechanism of molecular recognition.     

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.     

Conversion of red fluorescent protein into a bright blue probe

We used a red chromophore formation pathway, in which the anionic red chromophore is formed from the neutral blue intermediate, to suggest a rational design strategy to develop blue fluorescent proteins with a tyrosine-based chromophore. The strategy was applied to red fluorescent proteins of the different genetic backgrounds, such as TagRFP, mCherry, HcRed1, M355NA, and mKeima, which all were converted into blue probes. Further improvement of the blue variant of TagRFP by random mutagenesis resulted in an enhanced monomeric protein, mTagBFP, characterized by the substantially higher brightness, the faster chromophore maturation, and the higher pH stability than blue fluorescent proteins with a histidine in the chromophore. The detailed biochemical and photochemical analysis indicates that mTagBFP is the true monomeric protein tag for multicolor and lifetime imaging, as well as the outstanding donor for green fluorescent proteins in F?rster resonance energy transfer applications.     

Ultrafast dynamics of flavins in five redox states

We report here our systematic studies of excited-state dynamics of two common flavin molecules, FMN and FAD, in five redox states--oxidized form, neutral and anionic semiquinones, and neutral and anionic fully reduced hydroquinones--in solution and in inert protein environments with femtosecond resolution. Using protein environments, we were able to stabilize two semiquinone radicals and thus observed their weak emission spectra. Significantly, we observed a strong correlation between their excited-state dynamics and the planarity of their flavin isoalloxazine ring. For a bent ring structure, we observed ultrafast dynamics from a few to hundreds of picoseconds and strong excitation-wavelength dependence of emission spectra, indicating deactivation during relaxation. A butterfly bending motion is invoked to get access to conical intersection(s) to facilitate deactivation. These states include the anionic semiquinone radical and fully reduced neutral and anionic hydroquinones in solution. In a planar configuration, flavins have a long lifetime of nanoseconds, except for the stacked conformation of FAD, where intramolecular electron transfer between the ring and the adenine moiety in 5-9 ps as well as subsequent charge recombination in 30-40 ps were observed. These observed distinct dynamics, controlled by the flavin ring flexibility, are fundamental to flavoenzyme's functions, as observed in photolyase with a planar structure to lengthen the lifetime to maximize DNA repair efficiency and in insect type 1 cryptochrome with a flexible structure to vary the excited-state deactivation to modulate the functional channel.     

Regulation of the extent and dynamics of excited-state proton transfer in 2-(2'-pyridyl)benzimidazole in nafion membranes by cation exchange

The effect of the microenvironment of a Nafion membrane on the excited-state proton transfer (ESPT) of 2-(2'-pyridyl)benzimidazole (2PBI) has been investigated by steady-state and time-resolved fluorescence spectroscopy. The mechanism of the ESPT is found to depend remarkably on the water content of the membrane. In the protonated form of the membrane, ESPT is found to involve the dicationic (D) form of the fluorophore, whereas in cation-exchanged membranes, it is found to involve the monocation (C). The change in the mechanism and extent of ESPT in cation-exchanged membranes can be explained by considering dehydration of the membrane as well as the less acidic environment around the 2PBI molecules. The slow dynamics is found to result from two factors, namely, slow and incomplete solvation of the transition state, leading to a slowing down of the proton-transfer process, and a slow solvation of the polar tautomeric excited state.     

Excitation ratiometric chloride sensing in a standalone yellow fluorescent protein is powered by the interplay between proton transfer and conformational reorganization

Natural and laboratory-guided evolution has created a rich diversity of fluorescent protein (FP)-based sensors for chloride (Cl⁻). To date, such sensors have been limited to the Aequorea victoria green fluorescent protein (avGFP) family, and fusions with other FPs have unlocked ratiometric imaging applications. Recently, we identified the yellow fluorescent protein from jellyfish Phialidium sp. (phiYFP) as a fluorescent turn-on, self-ratiometric Cl⁻ sensor. To elucidate its working mechanism as a rare example of a single FP with this capability, we tracked the excited-state dynamics of phiYFP using femtosecond transient absorption (fs-TA) spectroscopy and target analysis. The photoexcited neutral chromophore undergoes bifurcated pathways with the twisting-motion-induced nonradiative decay and barrierless excited-state proton transfer. The latter pathway yields a weakly fluorescent anionic intermediate , followed by the formation of a red-shifted fluorescent state that enables the ratiometric response on the tens of picoseconds timescale. The redshift results from the optimized π–π stacking between chromophore Y66 and nearby Y203, an ultrafast molecular event. The anion binding leads to an increase of the chromophore pK_a and ESPT population, and the hindrance of conversion. The interplay between these two effects determines the turn-on fluorescence response to halides such as Cl⁻ but turn-off response to other anions such as nitrate as governed by different binding affinities. These deep mechanistic insights lay the foundation for guiding the targeted engineering of phiYFP and its derivatives for ratiometric imaging of cellular chloride with high selectivity.

We discovered an interplay between proton transfer and conformational reorganization that powers a standalone fluorescent-protein-based excitation-ratiometric biosensor for chloride imaging.     

Excited-state double proton transfer dynamics of model DNA base pairs: 7-hydroxyquinoline dimers

The excited-state double proton transfer of model DNA base pairs, 7-hydroxyquinoline dimers, in benzene has been investigated using picosecond time-resolved fluorescence spectroscopy. Upon excitation, whereas singly hydrogen-bonded noncyclic dimers do not go through tautomerization within the relaxation time of 1400 ps, doubly hydrogen-bonded cyclic dimers undergo excited-state double proton transfer on the time scale of 25 ps to form tautomeric dimers, which subsequently undergo a conformational change in 180 ps to produce singly hydrogen-bonded tautomers. The rate constant of the double proton transfer reaction is temperature-independent, showing a large kinetic isotope effect of 5.2, suggesting that the rate is governed mostly by tunneling.     

Excited-state dynamics of donor-acceptor bridged systems containing a boron-dipyrromethene chromophore: interplay between charge separation and reorientational motion

The excited-state dynamics of a series of electron donor-acceptor bridged systems (DABS) consisting of a boron-dipyrromethene chromophore covalently linked to a dinitro-substituted triptycene has been investigated using femtosecond time-resolved spectroscopy. The chromophores differ by the number of bromine atom substituents. The fluorescence lifetime of the DABS without any bromine atom is strongly reduced when going from toluene to polar solvents, this shortening being already present in chloroform. This effect is about 10 times weaker with a single bromine atom and negligible with two bromine atoms on the chromophore. The excited-state lifetime shortening is ascribed to a charge transfer from the excited chromophore to a nitrobenzene moiety, the driving force of this process depending on the number of bromine substituents. The occurrence of this process is further confirmed by the investigation of the excited-state dynamics of the chromophore alone in pure nitrobenzene. Surprisingly, no correlation between the charge separation time constant and the dielectric properties of the solvents could be observed. However, a good correlation between the charge separation time constant and the diffusional reorientation time of the chromophore alone, measured by fluorescence anisotropy, was found. Quantum chemistry calculations suggest that quasi-free rotation about the single bond linking the chromophore to the triptycene moiety permits a sufficient coupling of the donor and the acceptor to ensure efficient charge separation. The charge separation dynamics in these molecules is thus controlled by the reorientational motion of the donor relative to the acceptor.     

Absorption and emission spectroscopic characterization of lumichrome in aqueous solutions

The spectroscopic behavior of lumichrome (7,8-dimethyl-alloxazine, LC) in aqueous solutions in a pH range from -1.08 to 14.6 is studied. Absorption spectra, fluorescence quantum distributions, quantum yields, and lifetimes are determined. The ionization stage of ground-state LC changes with rising pH from the cationic form (LCH(2)(+)) to the neutral form (LCH) with a mid-point pH of pK(c) ≈ -0.53, and to the anionic form (LC(-)) with a mid-point pH of pK(a) ≈ 12.5. Above pH 7 a partial ground-state tautomerization of LCH to 7,8-dimethyl-isoalloxazine (IAH) occurs by N1-N10 intra-molecular proton transfer. For pH > pK(a) ≈ 12.5 LCH and IAH change to the anionic forms LC(-) and IA(-), and above pH 14 LC(-) tautomerizes completely to IA(-). In the excited state some neutral lumichrome (LCH*) converts to cationic lumichrome (LCH(2)(+)) at low pH by proton transfer from H(3)O(+) to LCH*. No photoinduced excited-state tautomerization of lumichrome was observed. LCH for pH > 3 and IAH are reasonably fluorescent. The fluorescence efficiencies of LC(-) and IA(-) are lower than those of LCH and IAH. The fluorescence of LCH(2)(+) is strongly quenched likely by intra-molecular diabatic charge transfer and excited-state relaxation by potential surface touching with the ground state.     

Excited-state proton transfer behavior of 7-hydroxy-4-methylcoumarin in AOT reverse micelles

The excited-state proton transfer and phototautomerization of 7-hydroxy-4-methylcoumarin (7H4MC) dye has been studied in the confined water pools of AOT reverse micelles using steady-state and time-resolved fluorescence measurements. In the "dry" reverse micelles ([water]/[AOT], w(0) = 0), only the neutral form of the dye is present both in the ground and the excited states. At higher w(0) values, three prototropic forms, namely, neutral, anionic, and tautomeric, can be identified in the excited state, although only the neutral form of the dye is present in the ground state. From steady-state fluorescence results and time-resolved area-normalized emission spectra (TRANES), it is indicated that the anionic and tautomeric forms of the dye are the excited-state reaction products and that they arise apparently independently from the excited neutral form of the dye. In bulk water, however, there is no evidence of the tautomeric species and only the anionic form is observed in the excited state. The fluorescence quenching results of the three forms of 7H4MC by the different quenchers, potassium iodide, aniline, and N, N-dimethylaniline, suggest that the distribution of 7H4MC molecules in the reverse micelles is not diverse but that the different prototropic forms arise from the same population of the excited dye in the interfacial region.     

(Sub)-picosecond spectral evolution of fluorescence in photoactive proteins studied with a synchroscan streak camera system

The spectral evolution of three photoactive proteins has been investigated by measuring the fluorescence with good temporal and wavelength resolution and a high signal-to-noise ratio. Upon excitation at 400 nm wild-type (wt) PYP both at neutral pH and in the low-pH blueshifted pBdark state exhibited a strong quenching of the fluorescence, the major part of which could be described by lifetimes of about 1.7 and 7.7 ps. The remaining fluorescence decay occurred multiexponentially with lifetimes between 30 and 125 ps. Additionally, in wtPYP at neutral pH, a dynamic Stokes shift was found to occur with a time constant of about 0.25 ps. In a PYP preparation that was reconstituted with the chromophore 7-hydroxy-coumarin-3- carboxylic acid rather than the native coumaric acid, and which is therefore not capable of performing the cis-trans-isomerization that initiates the photocycle in wtPYP, the fluorescence was found to decay multiexponentially with lifetimes of 51 ps, 0.33 and 3.77 ns. Additionally, dynamic Stokes shifts were observed with time constants of about 0.1 and 3.5 ps. Upon comparison of the dynamics of this preparation with that of wtPYP the multiexponential decay with lifetimes of 1.7 and 7.7 ps found in wtPYP was attributed to photochemistry of the p-coumaric-acid chromophore. The emission from bacteriorhodopsin mutant D85S upon excitation at 635 nm decays biexponentially with estimated lifetimes of 5.2 and 19.1 ps. No dynamic Stokes shift was observed here. Four lifetimes were needed to describe the decay of the emission from the A* state in the green fluorescent protein. From a target analysis it was concluded that the longer lifetimes are accompanied by a decreasing probability of forming I*, which approaches zero with the longest A* lifetime of 1.5 ns. These observations may be explained by heterogeneity of A and by relaxation of A*. In all three systems studied, multiexponential decay of emission was present, suggesting that heterogeneity is a common feature of these chromophore protein complexes.     

Excited-state Acidity of Bifunctional Compounds. 7. Long Distance, Solvent-assisted Excited-state Proton Transfer in Olivacine

Abstract— By use of fluorescence spectroscopy and time-correlated single photon counting, solvent-assisted excited-state proton transfer (ESPT) has been observed for olivacine in two organic solvents, 1,4-dioxane and methanol. Because of spectral overlap, factor analysis was used to determine the emission spectrum of the proton-transferred (PT) species. The ESPT is not observed in the nonpolar solvent n -hexane. For the first time in a system of this type, the individual excited-state rate constants have been calculated exactly from time-resolved single photon counting results. Because the PT process involves a path of more than 6 Å, its individual rate constant is extremely low, approximately 10⁷ s⁻¹.     

Kinetics of proton transfer in a green fluorescent protein: A laser-induced pH jump study

The sub-millisecond protonation dynamics of the chromophore in S65T mutant form of the green fluorescent protein (GFP) was tracked after a rapid pH jump following laser-induced proton release from the caged photolabile compoundo-nitrobenzaldehyde. Following a jump in pH from 8 to 5 (which is achieved within 2 μs), the fluorescence of S65T GFP decreased as a single exponential with a time constant of ∼90 μs. This decay is interpreted as the conversion of the deprotonated fluorescent GFP chromophore to a protonated non-fluorescent species. The protonation kinetics showed dependence on the bulk viscosity of the solvent, and therefore implicates bulk solvent-controlled protein dynamics in the protonation process. The protonation is proposed to be a sequential process involving two steps: (a) proton transfer from solvent to the chromophore, and (b) internal structural rearrangements to stabilize a protonated chromophore. The possible implications of these observations to protein dynamics in general is discussed