Toward understanding the redox properties of model chromophores from the green fluorescent protein family: an interplay between conjugation, resonance stabilization, and solvent effects

First and Second Reductions in an Aprotic Solvent: Comparing Computational and Experimental One-Electron Reduction Potentials for 345 Quinones

Using reference reduction potentials of quinones recently measured relative to the saturated calomel electrode (SCE) in N,N-dimethylformamide (DMF), we benchmark absolute one-electron reduction potentials computed for 345 Q/Q•- and 265 Q•-/Q2- half-reactions using adiabatic electron affinities computed with density functional theory and solvation energies computed with four continuum solvation models: IEF-PCM, C-PCM, COSMO, and SM12. Regression analyses indicate a strong linear correlation between experimental and absolute computed Q/Q•- reduction potentials with Pearson's correlation coefficient (r) between 0.95 and 0.96 and the mean absolute error (MAE) relative to the linear fit between 83.29 and 89.51 mV for different solvation methods when the slope of the regression is constrained to 1. The same analysis for Q•-/Q2- gave a linear regression with r between 0.74 and 0.90 and MAE between 95.87 and 144.53 mV, respectively. The y-intercept values obtained from the linear regressions are in good agreement with the range of absolute reduction potentials reported in the literature for the SCE but reveal several sources of systematic error. The y-intercepts from Q•-/Q2- calculations are lower than those from Q/Q•- by around 320-410 mV for IEF-PCM, C-PCM, and SM12 compared to 210 mV for COSMO. Systematic errors also arise between molecules having different ring sizes (benzoquinones, naphthoquinones, and anthraquinones) and different substituents (titratable vs nontitratable). SCF convergence issues were found to be a source of random error that was slightly reduced by directly optimizing the solute structure in the continuum solvent reaction field. While SM12 MAEs were lower than those of the other solvation models for Q/Q•-, SM12 had larger MAEs for Q•-/Q2- pointing to a larger error when describing multiply charged anions in DMF. Altogether, the results highlight the advantages of, and further need for, testing computational methods using a large experimental data set that is not skewed (e.g., having more titratable than nontitratable substituents on different parent groups or vice versa) to help further distinguish between sources of random and systematic errors in the calculations.

Excited-state dynamics and fluorescence lifetime of cryogenically cooled green fluorescent protein chromophore anions

Time-resolved action spectroscopy together with a fs-pump probe scheme is used in an electrostatic ion-storage ring to address lifetimes of specific vibrational levels in electronically excited states. Here we specifically consider the excited-state lifetime of cryogenically cooled green fluorescent protein (GFP) chromophore anions which is systematically measured across the S0-S1 spectral region (450-482 nm). A long lifetime of 5.2 ± 0.3 ns is measured at the S0-S1 band origin. When exciting higher vibrational levels in S1, the lifetime changes dramatically. It decreases by more than two orders of magnitude in a narrow energy region ∼250 cm-1 (31 meV) above the 0-0 transition. This is attributed to the opening of internal conversion over an excited-state energy barrier. The applied experimental technique provides a new way to uncover even small energy barriers, which are crucial for excited-state dynamics.

Multiphoton Bleaching of Red Fluorescent Proteins and the Ways to Reduce It

Red fluorescent proteins and biosensors built upon them are potentially beneficial for two-photon laser microscopy (TPLM) because they can image deeper layers of tissue, compared to green fluorescent proteins. However, some publications report on their very fast photobleaching, especially upon excitation at 750-800 nm. Here we study the multiphoton bleaching properties of mCherry, mPlum, tdTomato, and jREX-GECO1, measuring power dependences of photobleaching rates K at different excitation wavelengths across the whole two-photon absorption spectrum. Although all these proteins contain the chromophore with the same chemical structure, the mechanisms of their multiphoton bleaching are different. The number of photons required to initiate a photochemical reaction varies, depending on wavelength and power, from 2 (all four proteins) to 3 (jREX-GECO1) to 4 (mCherry, mPlum, tdTomato), and even up to 8 (tdTomato). We found that at sufficiently low excitation power P, the rate K often follows a quadratic power dependence, that turns into higher order dependence (K~Pα with α > 2) when the power surpasses a particular threshold P*. An optimum intensity for TPLM is close to the P*, because it provides the highest signal-to-background ratio and any further reduction of laser intensity would not improve the fluorescence/bleaching rate ratio. Additionally, one should avoid using wavelengths shorter than a particular threshold to avoid fast bleaching due to multiphoton ionization.

Theoretical insights into the antiradical activity and copper-catalysed oxidative damage of mexidol in the physiological environment

Mexidol (MD, 2-ethyl-6-methyl-3-hydroxypyridine) is a registered therapeutic agent for the treatment of anxiety disorders. The chemical structure suggests that MD may also act as an antioxidant. In this study, the hydroperoxyl radical scavenging activity of MD was studied to establish baseline antioxidant activity, followed by an investigation of the effect of MD on the copper-catalysed oxidative damage in biological systems, using computational methods. It was found that MD exhibits moderate radical scavenging activity against HOO• in water and pentyl ethanoate solvents following the single electron transfer and formal hydrogen transfer mechanisms, respectively. MD can chelate Cu(II), forming complexes that are much harder to reduce than free Cu(II): MD chelation completely quenches the Cu(II) reduction by ascorbic acid and suppresses the rate of reduction reaction byO 2 ⋅ - that are the main reductants of Cu(II) in biological environments. Therefore, MD exerts its anti-HO• activity primarily as an OIL-1 inhibitor.

The hydroperoxyl radical scavenging activity of sulfuretin: insights from theory

Sulfuretin (SFR), which is isolated from Rhus verniciflua, Toxicodendron vernicifluum, Dahlia, Bidens tripartite and Dipterx lacunifera, is one of the most important natural flavonoids. This compound is known to have numerous biological activities; among these, the antioxidant activity has not been thoroughly studied yet. In this study, the hydroperoxyl scavenging activity of SFR was examined by using density functional theory calculations. SFR is predicted to be an excellent HOO• scavenger in water at pH = 7.40 with k overall = 4.75 × 107 M-1 s-1, principally due to an increase in the activity of the anionic form following the single-electron transfer mechanism. Consistently, the activity of the neutral form is more prominent in the non-polar environment with k overall = 1.79 × 104 M-1 s-1 following the formal hydrogen transfer mechanism. Thus, it is predicted that SFR exhibits better HOO• antiradical activity than typical antioxidants such as resveratrol, ascorbic acid or Trolox in the lipid medium. The hydroperoxyl radical scavenging of SFR in the aqueous solution is approximately 530 times faster than that of Trolox and similar to ascorbic acid or resveratrol. This suggests that SFR is a promising radical scavenger in physiological environments.

Excited state structural dynamics of 4-cyano-4′-hydroxystilbene: deciphering the signatures of proton-coupled electron transfer using ultrafast Raman loss spectroscopy

The photo-initiated proton-coupled electron transfer process in the 4-cyano-4′-hydroxystilbene–tert-butylamine adduct strongly affects the excited-state structural dynamics of CHSB.

ortho and para chromophores of green fluorescent protein: controlling electron emission and internal conversion

Green fluorescent protein (GFP) continues to play an important role in the biological and biochemical sciences as an efficient fluorescent probe and is also known to undergo light-induced redox transformations. Here, we employ photoelectron spectroscopy and quantum chemistry calculations to investigate how the phenoxide moiety controls the competition between electron emission and internal conversion in the isolated GFP chromophore anion, following photoexcitation with ultraviolet light in the range 400-230 nm. We find that moving the phenoxide group from the para position to the ortho position enhances internal conversion back to the ground electronic state but that adding an additional OH group to the para chromophore, at the ortho position, impedes internal conversion. Guided by quantum chemistry calculations, we interpret these observations in terms of torsions around the C-C-C bridge being enhanced by electrostatic repulsions or impeded by the formation of a hydrogen-bonded seven-membered ring. We also find that moving the phenoxide group from the para position to the ortho position reduces the energy required for detachment processes, whereas adding an additional OH group to the para chromophore at the ortho position increases the energy required for detachment processes. These results have potential applications in tuning light-induced redox processes of this biologically and technologically important fluorescent protein.

Photoinduced Chemistry in Fluorescent Proteins: Curse or Blessing?

Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10^-4-10^-6 for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant. Depending on the task at hand, fluorescent protein photochemistry is regarded either as an asset facilitating new applications or as a nuisance leading to the loss of optical output. The phenomena arising due to phototransformations include (i) large Stokes shifts, (ii) photoconversions, photoactivation, and photoswitching, (iii) phototoxicity, (iv) blinking, (v) permanent bleaching, and (vi) formation of long-lived intermediates. The focus of this review is on the most recent experimental and theoretical work on photoinduced transformations in fluorescent proteins. We also provide an overview of the photophysics of fluorescent proteins, highlighting the interplay between photochemistry and other channels (fluorescence, radiationless relaxation, and intersystem crossing). The similarities and differences with photochemical processes in other biological systems and in dyes are also discussed.

Extension of the Effective Fragment Potential Method to Macromolecules

The effective fragment potential (EFP) approach, which can be described as a nonempirical polarizable force field, affords an accurate first-principles treatment of noncovalent interactions in extended systems. EFP can also describe the effect of the environment on the electronic properties (e.g., electronic excitation energies and ionization and electron-attachment energies) of a subsystem via the QM/EFP (quantum mechanics/EFP) polarizable embedding scheme. The original formulation of the method assumes that the system can be separated, without breaking covalent bonds, into closed-shell fragments, such as solvent and solute molecules. Here, we present an extension of the EFP method to macromolecules (mEFP). Several schemes for breaking a large molecule into small fragments described by EFP are presented and benchmarked. We focus on the electronic properties of molecules embedded into a protein environment and consider ionization, electron-attachment, and excitation energies (single-point calculations only). The model systems include chromophores of green and red fluorescent proteins surrounded by several nearby amino acid residues and phenolate bound to the T4 lysozyme. All mEFP schemes show robust performance and accurately reproduce the reference full QM calculations. For further applications of mEFP, we recommend either the scheme in which the peptide is cut along the Cα-C bond, giving rise to one fragment per amino acid, or the scheme with two cuts per amino acid, along the Cα-C and Cα-N bonds. While using these fragmentation schemes, the errors in solvatochromic shifts in electronic energy differences (excitation, ionization, electron detachment, or electron-attachment) do not exceed 0.1 eV. The largest error of QM/mEFP against QM/EFP (no fragmentation of the EFP part) is 0.06 eV (in most cases, the errors are 0.01-0.02 eV). The errors in the QM/molecular mechanics calculations with standard point charges can be as large as 0.3 eV.

Emission shaping in fluorescent proteins: role of electrostatics and π-stacking

We obtained the fluorescence spectrum of the GFP with trajectory simulations, and revealed the role of the protein sidechains in emission shifts.

On the Nature of an Extended Stokes Shift in the mPlum Fluorescent Protein

Far-red fluorescent proteins (FPs) enable deep-tissue in vivo imaging. Combining FPs with large and small Stokes shifts enables single-excitation/dual-emission multicolor applications. Using a quantum mechanics/molecular mechanics (QM/MM) scheme, we carried out a series of simulations to identify the origin of an extended Stokes shift (0.2 eV) observed in mPlum, one of the most far-red-shifted FPs. We demonstrated that the red shift of emission is largely due to the excited-state relaxation of the chromophore itself. Rigid protein environment suppresses the relaxation; however, if the hydrogen-bond network around the chromophore is sufficiently flexible, it can rearrange upon electronic excitation, allowing the chromophore to relax. The reorganization of the hydrogen-bond network is driven by changes in bonding and charge distributions of the chromophore in the excited state. The ILE65 and GLU16 residues play the most important role. The MD simulations reveal two ground-state populations with the direct (Chro-ILE65···GLU16) and water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond patterns. In the excited state, both populations relax to a single emitting state with the water-mediated (Chro-ILE65···Wat321···GLU16) hydrogen-bond pattern, which provides a better match for the excited-state charge distribution (the acylimine's oxygen has a larger negative charge in S1 than in S0). The extended Stokes shift arises due to the conversion of the direct hydrogen-bond pattern to the water-mediated one accompanied by large structural relaxation of the electronically excited chromophore. This conclusion is supported by calculations for the GLU16LEU mutant, which has only one hydrogen-bond pattern. Consequently, no interconversion is possible, and the computed Stokes shift is small, in agreement with the experiment. Our theoretical findings provide support to a recent study of the Stokes shifts in mPlum and its mutants.

Multiphoton photochemistry of red fluorescent proteins in solution and live cells

Genetically encoded fluorescent proteins (FPs), and biosensors based on them, provide new insights into how living cells and tissues function. Ultimately, the goal of the bioimaging community is to use these probes deep in tissues and even in entire organisms, and this will require two-photon laser scanning microscopy (TPLSM), with its greater tissue penetration, lower autofluorescence background, and minimum photodamage in the out-of-focus volume. However, the extremely high instantaneous light intensities of femtosecond pulses in the focal volume dramatically increase the probability of further stepwise resonant photon absorption, leading to highly excited, ionizable and reactive states, often resulting in fast bleaching of fluorescent proteins in TPLSM. Here, we show that the femtosecond multiphoton excitation of red FPs (DsRed2 and mFruits), both in solution and live cells, results in a chain of consecutive, partially reversible reactions, with individual rates driven by a high-order (3-5 photon) absorption. The first step of this process corresponds to a three- (DsRed2) or four-photon (mFruits) induced fast isomerization of the chromophore, yielding intermediate fluorescent forms, which then subsequently transform into nonfluorescent products. Our experimental data and model calculations are consistent with a mechanism in which ultrafast electron transfer from the chromophore to a neighboring positively charged amino acid residue triggers the first step of multiphoton chromophore transformations in DsRed2 and mFruits, consisting of decarboxylation of a nearby deprotonated glutamic acid residue.