Long- and Short-Range Electrostatic Fields in GFP Mutants: Implications for Spectral Tuning

Enhancing Two-Photon Absorption of Green Fluorescent Protein by Quantum Entanglement

Exploring the electronic states of molecules through excitation with entangled and classical photon pairs offers new insights into the nature of light-matter interactions and stimulates the development of quantum spectroscopy. Here, we address the importance of temporal entanglement of light in two-photon absorption (TPA) upon the S0 → S1 transition by the green fluorescent protein (GFP)─a key molecular unit in the bioimaging of living cells. By invoking a two-level model applicable when permanent dipole pathways dominate the two-photon transition, we derive a convenient closed-form analytical expression for the entangled TPA strength. For the first time, we disclose specific molecular properties that cause classical and entangled two-photon absorptions to be qualitatively different when exciting the same state. We reveal a new nonclassical contribution to the TPA strength, which is defined by the magnitude and directional alignment of permanent dipole moments in the initial and final states. Using high-level electronic structure theory, we show that the nonclassical contribution is intrinsically larger than the classical counterpart in GFP, leading to an enhancement of the TPA strength due to quantum entanglement by several orders of magnitude. We also present evidence that the classical and quantum TPA strengths can be modulated differently by the protein environment and demonstrate how to control the outcome by alterations in the local electric field of the protein caused by a single amino acid replacement. Our findings establish physical grounds for enhancing TPA in photoactive proteins by quantum entanglement, facilitating the rational design of high-efficiency biomarkers for future applications that utilize quantum light.

pH Sensitivity of YFPs is Reduced Upon AlphaRep Binding: Proof of Concept in Vitro and in Living Cells

Yellow fluorescent proteins (YFPs) are commonly used in biology to track cellular processes, particularly as acceptors in experiments using the Förster Resonant Energy Transfer (FRET) phenomenon. However, their fluorescence intensity is strongly pH-dependent, limiting their utility in acidic environments. Here, we explore the pH sensitivity of YFPs upon binding with an artificial repeat protein (αRep) both in vitro and in living cells. We show that αRep binds to Citrine, with high affinity in the nanomolar range at physiological and acidic pHs, leading to increased thermal stability of the complex. Moreover, αRep binding reduces Citrine's pKa by 0.75 pH units, leading to a decreased sensitivity to pH fluctuations. This effect can be generalized to other YFPs as Venus and EYFP in vitro. An efficient binding of αRep to Citrine has also been observed in living cells both at pH 7.4 and pH 6. This interaction leads to reduced variations of Citrine fluorescence intensity in response to pH variations in cells. Overall, the study highlights the potential of αReps as a tool to modulate the pH sensitivity of YFPs, paving the way for future exploration of biological events in acidic environments by FRET in combination with a pH-insensitive cyan donor.

Statistics of protein electrostatics

Molecular dynamics simulations of a small redox-active protein plastocyanin address two questions. (i) Do protein electrostatics equilibrate to the Gibbsian ensemble? (ii) Do the electrostatic potential and electric field inside proteins follow the Gaussian distribution? The statistics of electrostatic potential and electric field are probed by applying small charge and dipole perturbations to different sites within the protein. Nonergodic (non-Gibbsian) sampling is detectable through violations of exact statistical rules constraining the first and second statistical moments (fluctuation-dissipation relations) and the linear relation between free-energy surfaces of the collective coordinate representing the Hamiltonian electrostatic perturbation. We find weakly nonergodic statistics of the electrostatic potential (simulation time of 0.4-1.0 μs) and non-Gibbsian and non-Gaussian statistics of the electric field. A small dipolar perturbation of the protein results in structural instabilities of the protein-water interface and multi-modal distributions of the Hamiltonian energy gap. The variance of the electrostatic potential passes through a crossover at the glass transition temperature Ttr ≃ 170 K. The dipolar susceptibility, reflecting the variance of the electric field inside the protein, strongly increases, with lowering temperature, followed by a sharp drop at Ttr. The linear relation between free-energy surfaces can be directly tested by combining absorption and emission spectra of optical dyes. It was found that the statistics of the electrostatic potential perturbation are nearly Gibbsian/Gaussian, with little deviations from the prescribed statistical rules. On the contrary, the (nonergodic) statistics of dipolar perturbations are strongly non-Gibbsian/non-Gaussian due to structural instabilities of the protein hydration shell.

Theoretical Insight into the Fluorescence Spectral Tuning Mechanism: A Case Study of Flavin-Dependent Bacterial Luciferase

Bioluminescence of bacteria is widely applied in biological imaging, environmental toxicant detection, and many other situations. Understanding the spectral tuning mechanism not only helps explain the diversity of colors observed in nature but also provides principles for bioengineering new color variants for practical applications. In this study, time-dependent density functional theory (TD-DFT) and quantum mechanics and molecular mechanics (QM/MM) calculations have been employed to understand the fluorescence spectral tuning mechanism of bacterial luciferase with a focus on the electrostatic effect. The spectrum can be tuned by both a homogeneous dielectric environment and oriented external electric fields (OEEFs). Increasing the solvent polarity leads to a redshift of the fluorescence emission maximum, λF, accompanied by a substantial increase in density. In contrast, applying an OEEF along the long axis of the isoalloxazine ring (X-axis) leads to a significant red- or blue-shift in λF, depending on the direction of the OEEF, yet with much smaller changes in intensity. The effect of polar solvents is directionless, and the red-shifts can be attributed to the larger dipole moment of the S1 state compared with that of the S0 state. However, the effect of OEEFs directly correlates with the difference dipole moment between the S1 and S0 states, which is directional and is determined by the charge redistribution upon deexcitation. Moreover, the electrostatic effect of bacterial luciferase is in line with the presence of an internal electric field (IEF) pointing in the negative X direction. Finally, the key residues that contribute to this IEF and strategies for modulating the spectrum through site-directed point mutations are discussed.

Remarkable Insensitivity of Protein Diffusion to Protein Charge

Friction to translational diffusion of ionic particles in polar liquids should scale linearly with the squared ion charge, according to standard theories. Substantial slowing of translational diffusion is expected for proteins in water. In contrast, our simulations of charge mutants of green fluorescent proteins in water show remarkable insensitivity of the translational diffusion constant to protein's charge in the range of charges between -29 and +35. The friction coefficient is given as a product of the force variance and the memory function relaxation time. We find remarkably accurate equality between the variance of the electrostatic force and the negative cross-correlation of the electrostatic and van der Waals forces. The charge invariance of the diffusion constant is a combined effect of the force variance and relaxation time invariances with the protein charge. The temperature dependence of the protein diffusion constant is highly non-Arrhenius, with a fragile-to-strong crossover at the glass transition.

Conformational Effects on the Absorption Spectra of Phytochromes

Bacteriophytochrome is a photoreceptor protein that contains the biliverdin (BV) chromophore as its active component. The spectra of BV upon mutation remain remarkably unchanged, as far as spectral positions are concerned. This points toward the minimal effect of electrostatic effects on the electronic structure of the chromophore. However, the relative intensities of the Q and Soret bands of the chromophore change dramatically upon mutation. In this work, we delve into the molecular origin of this unusual intensity modulation. Using extensive classical MD and QM/MM calculations, we show that due to mutation, the conformational population of the chromophore changes significantly. The noncovalent interactions, especially the stacking interactions, lead to extra stabilization of the cyclic form in the D207H mutated species as opposed to the open form in the wild-type BV. Thus, unlike the commonly observed direct electrostatic effect on the spectral shift, in the case of BV the difference observed is in varying intensities, and this in turn is driven by a conformational shift due to enhanced stacking interaction.

Comment on "Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin" by O. Kontkanen, D. Biriukov and Z. Futera, Phys. Chem. Chem. Phys., 2023, , 12479

Polarizability is a fundamental property of all molecular systems describing the deformation of the molecular electronic density in response to an applied electric field. The question of whether polarizability of the active site needs to be included in theories of enzymatic activity remains open. Hybrid quantum mechanical/molecular mechanical calculations are hampered by difficulties faced by many quantum-chemistry algorithms to provide sufficiently accurate estimates of the anisotropic second-rank tensor of molecular polarizability. In this Comment, we provide general theoretical arguments for the values of polarizability of the quantum region or a molecule which have to be reproduced by electronic structure calculations.

Impact of the Protein Environment on Two-Photon Absorption Cross-Sections of the GFP Chromophore Anion Resolved at the XMCQDPT2 Level of Theory

The search for fluorescent proteins with large two-photon absorption (TPA) cross-sections and improved brightness is required for their efficient use in bioimaging. Here, we explored the impact of a single-point mutation close to the anionic form of the GFP chromophore on its TPA activity. We considered the lowest-energy transition of EGFP and its modification EGFP T203I. We focused on a methodology for obtaining reliable TPA cross-sections for mutated proteins, based on conformational sampling using molecular dynamics simulations and a high-level XMCQDPT2-based QM/MM approach. We also studied the numerical convergence of the sum-over-states formalism and provide direct evidence for the applicability of the two-level model for calculating TPA cross-sections in EGFP. The calculated values were found to be very sensitive to changes in the permanent dipole moments between the ground and excited states and highly tunable by internal electric field of the protein environment. In the case of the GFP chromophore anion, even a single hydrogen bond was shown to be capable of drastically increasing the TPA cross-section. Such high tunability of the nonlinear photophysical properties of the chromophore anions can be used for the rational design of brighter fluorescent proteins for bioimaging using two-photon laser scanning microscopy.

4-Cyanotryptophan as a Sensitive Fluorescence Probe of Local Electric Field of Proteins

Electrostatic interactions are key determinants of protein structure, dynamics, and function. Since protein electrostatics are nonuniform, assessment of the internal electric fields (EFs) of proteins requires spatial resolution at the amino acid residue level. In this regard, vibrational Stark spectroscopy, in conjunction with various unnatural amino acid-based vibrational probes, has become a common method for site-specific interrogation of protein EFs. However, application of this method is often limited to proteins with relatively high solubility, due to the intrinsically low oscillator strength of vibrational transitions. Therefore, it would be useful to develop an alternative method that can overcome this limitation. To this end, we show that, using solvatochromic study and molecular dynamics simulations, the frequency of maximum emission intensity of the fluorophore of 4-cyanotryptophan (4CN-Trp), 3-methyl-1H-indole-4-carbonitrile, exhibits a linear dependence on the local EF. Since the absorption and emission spectra of 4CN-Trp are easily distinguishable from those of naturally occurring aromatic amino acids, we believe that this linear relationship provides an easier and more sensitive means to determine the local EF of proteins.

Quantum chemistry study of the multiphoton absorption in enhanced green fluorescent protein at the single amino acid residue level

The chromophore (CRO) of fluorescent proteins (FPs) is embedded in a complex environment that is a source of specific interactions with the CRO. Understanding how these interactions influence FPs spectral properties is important for a directed design of novel markers with desired characteristics. In this work, we apply computational chemistry methods to gain insight into one-, two- and three-photon absorption (1PA, 2PA, 3PA) tuning in enhanced green fluorescent protein (EGFP). To achieve this goal, we built EGFP models differing in: i) number and position of hydrogen-bonds (h-bonds) donors to the CRO and ii) the electric field, as approximated by polarizable force  field, acting on the CRO. We  find that h-bonding to the CRO's phenolate oxygen results in stronger one- and multiphoton absorption. The brighter absorption can be also achieved by creating more positive electric field near the CRO's phenolate moiety. Interestingly, while individual CRO-environment h-bonds usually enhance 1PA and 2PA, it takes a few h-bond donors to enhance 3PA. Clearly, response of the absorption intensity to many-body effects depends on the excitation mechanism.  We further employ symmetry-adapted perturbation theory (SAPT) to reveal excellent (2PA) and good (3PA) correlation of multiphoton intensity with electrostatic and induction interaction energies. This points to importance of accounting for mutual CRO-environment polarization in quantitative calculations of absorption spectra in FPs.

Complexation of Green and Red Kaede Fluorescent Protein Chromophores by a Zwitterion to Probe Electrostatic and Induction Field Effects

The photophysics of green fluorescent protein (GFP) and red Kaede fluorescent protein (rKFP) are defined by the intrinsic properties of the light-absorbing chromophore and its interaction with the protein binding pocket. This work deploys photodissociation action spectroscopy to probe the absorption profiles for a series of synthetic GFP and rKFP chromophores as the bare anions and as complexes with the betaine zwitterion, which is assumed as a model for dipole microsolvation. Electronic structure calculations and energy decomposition analysis using Symmetry-Adapted Perturbation Theory are used to characterize gas-phase structures and complex cohesion forces. The calculations reveal a preponderance for coordination of betaine to the phenoxide deprotonation site predominantly through electrostatic forces. Calculations using the STEOM-DLPNO-CCSD method are able to reproduce absolute and relative vertical excitation energies for the bare anions and anion-betaine complexes. On the other hand, treatment of the betaine molecule with a point-charge model, in which the charges are computed from some common electron density population analysis schemes, show that just electrostatic and point-charge induction interactions are unable to account for the betaine-induced spectral shift. The present methodology could be applied to investigate cluster forces and optical properties in other gas-phase ion-zwitterion complexes.

The role of hydrogen bonds and electrostatic interactions in enhancing two-photon absorption in green and yellow fluorescent proteins

The spectral properties of fluorescent proteins (FPs) depend on the protein environment of the chromophore (CRO). A deeper understanding of the CRO - environment interactions in terms of FPs spectral characteristics will allow for a rational design of novel markers with desired properties. Here, we are taking a step towards achieving this important goal. With the time-dependent density functional theory (TDDFT), we calculate one- and two-photon absorption (OPA and TPA) spectra for 5 green FPs (GFPs) and 3 yellow FPs (YFPs) differing in amino acid sequence. The goal is to reveal a role of: (i) electrostatic interactions, (ii) hydrogen-bonds (h-bonds), and (iii) h-bonds together with distant electrostatic field in absorption spectra tuning. Our results point to design hypothesis towards FPs optimised for TPA-based applications. Both h-bonds and electrostatic interactions co-operate in enhancing TPA cross-section (σ TPA ) for the S 0 ->S 1   transition in GFPs. Furthermore, it seems that details of h-bonds network in the CRO's vicinity influences σ TPA   response to CRO - environment electrostatic interactions in YFPs. We postulate that engineering FPs with more hydrophilic CRO's environment can lead to greater σ TPA . We also find that removing h-bonds formed with the CRO's phenolate leads to TPA enhancement for transition to higher excited states than S 1 . Particularly Y145 and T203 residues are important in this regard.

Modeling Spectral Tuning in Red Fluorescent Proteins Using the Dipole Moment Variation upon Excitation

We describe a model for spectral tuning in red fluorescent proteins (RFPs) based on the relation between an electronic structure descriptor, the dipole moment variation upon excitation (DMV), and the excitation energy of a protein. This approach aims to overcome the problem of accurate prediction of excitation energies in RFPs, which span a very narrow window of band maxima. The latter roughly corresponds to the energy range of 0.1 eV, which is comparable with typical errors in calculations of the excitation energy by conventional quantum chemistry methods. In this work, we demonstrate a strong quantitative correlation between DMV values, obtained computationally with modest efforts, and excitation energies ΔE_ex at the experimental excitation band maxima for a series of RFPs with bands between 570 and 605 nm. Protein models are constructed by motifs of the relevant crystal structures, and atomic coordinates are optimized in quantum mechanics/molecular mechanics (QM/MM) calculations with QM-subsystems composed of large chromophore-containing regions. DMV values are evaluated with the electron density computed at the time-dependent density functional theory (TDDFT) level using several functionals and basis sets. We show that the results obtained with the CAM-B3LYP, BHHLYP, and M06-2X functionals demonstrate favorable correlations between DMV and ΔE_ex with the mean absolute error less than 0.01 eV. Taking into account the solid theoretical grounds of the relation between the DMV and the excitation energy in fluorescent proteins, the described modeling strategy presents a rational tool for spectral tuning in these efficient markers for in vivo imaging.

Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation

We present the implementation of a fully coupled polarizable QM/MM/continuum model based on the AMOEBA polarizable force field and the domain decomposition implementation of the conductor-like screening model. Energies, response properties, and analytical gradients with respect to both QM and MM nuclear positions are available, and a generic, atomistic cavity can be employed. The model is linear scaling in memory requirements and computational cost with respect to the number of classical atoms and is therefore suited to model large, complex systems. Using three variants of the green-fluorescent protein, we investigate the overall computational cost of such calculations and the effect of the continuum model on the convergence of the computed properties with respect to the size of the embedding. We also demonstrate the fundamental role of polarization effects by comparing polarizable and nonpolarizable embeddings to fully QM ones.

Structure-Function Dataset Reveals Environment Effects within a Fluorescent Protein Model System*

Anisotropic environments can drastically alter the spectroscopy and photochemistry of molecules, leading to complex structure-function relationships. We examined this using fluorescent proteins as easy-to-modify model systems. Starting from a single scaffold, we have developed a range of 27 photochromic fluorescent proteins that cover a broad range of spectroscopic properties, including the determination of 43 crystal structures. Correlation and principal component analysis confirmed the complex relationship between structure and spectroscopy, but also allowed us to identify consistent trends and to relate these to the spatial organization. We find that changes in spectroscopic properties can come about through multiple underlying mechanisms, of which polarity, hydrogen bonding and presence of water molecules are key modulators. We anticipate that our findings and rich structure/spectroscopy dataset can open opportunities for the development and evaluation of new and existing protein engineering methods.

Local Electric Field Controls Fluorescence Quantum Yield of Red and Far-Red Fluorescent Proteins

Genetically encoded probes with red-shifted absorption and fluorescence are highly desirable for imaging applications because they can report from deeper tissue layers with lower background and because they provide additional colors for multicolor imaging. Unfortunately, red and especially far-red fluorescent proteins have very low quantum yields, which undermines their other advantages. Elucidating the mechanism of nonradiative relaxation in red fluorescent proteins (RFPs) could help developing ones with higher quantum yields. Here we consider two possible mechanisms of fast nonradiative relaxation of electronic excitation in RFPs. The first, known as the energy gap law, predicts a steep exponential drop of fluorescence quantum yield with a systematic red shift of fluorescence frequency. In this case the relaxation of excitation occurs in the chromophore without any significant changes of its geometry. The second mechanism is related to a twisted intramolecular charge transfer in the excited state, followed by an ultrafast internal conversion. The chromophore twisting can strongly depend on the local electric field because the field can affect the activation energy. We present a spectroscopic method of evaluating local electric fields experienced by the chromophore in the protein environment. The method is based on linear and two-photon absorption spectroscopy, as well as on quantum-mechanically calculated parameters of the isolated chromophore. Using this method, which is substantiated by our molecular dynamics simulations, we obtain the components of electric field in the chromophore plane for seven different RFPs with the same chromophore structure. We find that in five of these RFPs, the nonradiative relaxation rate increases with the strength of the field along the chromophore axis directed from the center of imidazolinone ring to the center of phenolate ring. Furthermore, this rate depends on the corresponding electrostatic energy change (calculated from the known fields and charge displacements), in quantitative agreement with the Marcus theory of charge transfer. This result supports the dominant role of the twisted intramolecular charge transfer mechanism over the energy gap law for most of the studied RFPs. It provides important guidelines of how to shift the absorption wavelength of an RFP to the red, while keeping its brightness reasonably high.

Dipole Moment Variation Clears Up Electronic Excitations in the π-Stacked Complexes of Fluorescent Protein Chromophores

We propose a quantitative structure-property relationship (QSPR) model for prediction of spectral tuning in cyan, green, orange, and red fluorescent proteins, which are engineered by motifs of the green fluorescent protein. Protein variants, in which their chromophores are involved in the π-stacking interaction with amino acid residues tyrosine, phenylalanine, and histidine, are prospective markers useful in bioimaging and super-resolution microscopy. In this work, we constructed training sets of the π-stacked complexes of four fluorescent protein chromophores (of the green, orange, red, and cyan series) with various substituted benzenes and imidazoles and tested the use of dipole moment variation upon excitation (DMV) as a descriptor to evaluate the vertical excitation energies in these systems. To validate this approach, we computed and analyzed electron density distributions of the π-stacked complexes and correlated the QSPR predictions with the reference values of the transition energies obtained using the high-level ab initio quantum chemistry methods. According to our results, the use of the DMV descriptor allows one to predict excitation energies in the π-stacked complexes with errors not exceeding 0.1 eV, which makes this model a practically useful tool in the development of efficient fluorescent markers for in vivo imaging.

Mechanism of Color and Photoacidity Tuning for the Protonated Green Fluorescent Protein Chromophore

The neutral or A state of the green fluorescent protein (GFP) chromophore is a remarkable example of a photoacid naturally embedded in the protein environment and accounts for the large Stokes shift of GFP in response to near UV excitation. Its color tuning mechanism has been largely overlooked, as it is less preferred for imaging applications than the redder anionic or B state. Past studies, based on site-directed mutagenesis or solvatochromism of the isolated chromophore, have concluded that its color tuning range is much narrower than its anionic counterpart. However, as we performed extensive investigation on more GFP mutants, we found that the color of the neutral chromophore can be more sensitive to protein electrostatics than can the anionic counterpart. Electronic Stark spectroscopy reveals a fundamentally different electrostatic color tuning mechanism for the neutral state of the chromophore that demands a three-form model as compared to that of the anionic state, which requires only two forms ( J. Am. Chem. Soc. 2019, 141, 15250-15265). Specifically, an underlying zwitterionic charge-transfer state is required to explain its sensitivity to electrostatics. As the Stokes shift is tightly linked to excited-state proton transfer (ESPT) of the protonated chromophore, we infer design principles of the GFP chromophore as a photoacid through the color tuning mechanisms of both protonation states. The three-form model could also be applied to similar biological and nonbiological dyes and complements the failure of the two-form model for donor-acceptor systems with localized ground-state electronic distributions.

Structure-fluorescence activation relationships of a large Stokes shift fluorogenic RNA aptamer

The Chili RNA aptamer is a 52 nt long fluorogen-activating RNA aptamer (FLAP) that confers fluorescence to structurally diverse derivatives of fluorescent protein chromophores. A key feature of Chili is the formation of highly stable complexes with different ligands, which exhibit bright, highly Stokes-shifted fluorescence emission. In this work, we have analyzed the interactions between the Chili RNA and a family of conditionally fluorescent ligands using a variety of spectroscopic, calorimetric and biochemical techniques to reveal key structure–fluorescence activation relationships (SFARs). The ligands under investigation form two categories with emission maxima of ∼540 or ∼590 nm, respectively, and bind with affinities in the nanomolar to low-micromolar range. Isothermal titration calorimetry was used to elucidate the enthalpic and entropic contributions to binding affinity for a cationic ligand that is unique to the Chili aptamer. In addition to fluorescence activation, ligand binding was also observed by NMR spectroscopy, revealing characteristic signals for the formation of a G-quadruplex only upon ligand binding. These data shed light on the molecular features required and responsible for the large Stokes shift and the strong fluorescence enhancement of red and green emitting RNA–chromophore complexes.

Development of a green fluorescence protein (GFP)-based bioassay for detection of antibiotics and its application in milk

Antibiotics are one of the most widely used types of drugs in pharmaceutics. However, efficiency of these drugs has decreased recently owing to the threat of antibiotic resistance. One of the important factors causing antibiotic resistance is the excessive use of antibacterials in animals. Therefore, detection of antibiotics in foods of animal origin is crucial. The aim of this study was to develop a novel whole-cell based bioassay to be used for detection of some antibiotics. Green fluorescent protein (GFP)-expressing Escherichia coli cells were used as a recognition agent, and antibiotic detection was carried out by pursuing the inhibition rate of fluorescence intensity as a result of the inhibition of viable cells by the time of progress. The performance of bioassay was tested for different antibiotics, and the obtained results showed that the developed method can be used successfully for detection of ampicillin, benzylpenicillin, gentamicin, neomycin, and tetracycline with the limit of detection (LOD) values of 3.33, 0.29, 28.00, 618.36, and 33.17 µg/L, respectively. The assay was also tested with antibiotic spiked milk samples (skimmed UHT, full-fat UHT, and whole raw milk). According to obtained recovery values, developed method was successful for all samples. The precision and bias values of the method were found between the range of 1.30% to 7.54% and -8.00% to 0.64%, respectively. The developed method, which is inexpensive and simple with detection limits in line with the regulatory limits, is promising for use in milk quality monitoring. Method has potential to be used as a screening method after comprehensive validation. PRACTICAL APPLICATION: This method could be used in animal husbandry to check whether the antibiotic prescribed for the treatment of sick animals is still present in their milk as residual. For dairy industry, detection of residual antibiotics in milk is crucial because of their inhibition effects on the fermentation processes. Therefore, the proposed method can be used for routine analysis of raw milk reception in dairy industries. In addition, it is considered to have a wide range of applications for all foods.

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

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

The key to the yellow-to-cyan tuning in the green fluorescent protein family is polarisation

Computational approaches have to date failed to fully capture the large (about 0.4 eV) excitation energy tuning displayed by the nearly identical anionic chromophore in different green fluorescent protein (GFP) variants. Here, we present a thorough comparative study of a set of proteins in this sub-family, including the most red- (phiYFP) and blue-shifted (mTFP0.7) ones. We employ a classical polarisable embedding through induced dipoles and combine it with time-dependent density functional theory and multireference perturbation theory in order to capture both state-specific induction contributions and the coupling of the polarisation of the protein to the chromophore transition density. The obtained results show that only upon inclusion of both these two effects generated by the mutual polarisation between the chromophore and the protein can the full spectral tuning be replicated. We finally discuss how this mutual polarisation affects the correlation between excitation energies, dipole moment variation, and molecular electrostatic field.

Subatomic resolution X-ray structures of green fluorescent protein

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

Understanding the Fluorescence Change in Red Genetically Encoded Calcium Ion Indicators

For over 20 years, genetically encoded Ca²⁺ indicators have illuminated dynamic Ca²⁺ signaling activity in living cells and, more recently, whole organisms. We are just now beginning to understand how they work. Various fluorescence colors of these indicators have been developed, including red. Red ones are promising because longer wavelengths of light scatter less in tissue, making it possible to image deeper. They are engineered from a red fluorescent protein that is circularly permuted and fused to a Ca²⁺-sensing domain. When Ca²⁺ binds, a conformational change in the sensing domain causes a change in fluorescence. Three factors can contribute to this fluorescence change: 1) a shift in the protonation equilibrium of the chromophore, 2) a change in fluorescence quantum yield, and 3) a change in the extinction coefficient or the two-photon cross section, depending on if it is excited with one or two photons. Here, we conduct a systematic study of the photophysical properties of a range of red Ca²⁺ indicators to determine which factors are the most important. In total, we analyzed nine indicators, including jRGECO1a, K-GECO1, jRCaMP1a, R-GECO1, R-GECO1.2, CAR-GECO1, O-GECO1, REX-GECO1, and a new variant termed jREX-GECO1. We find that these could be separated into three classes that each rely on a particular set of factors. Furthermore, in some cases, the magnitude of the change in fluorescence was larger with two-photon excitation compared to one-photon because of a change in the two-photon cross section, by up to a factor of two.

Long-Range Modulations of Electric Fields in Proteins

Electrostatic interactions are essential for controlling the protein structure and function. Whereas so far experimental and theoretical efforts focused on the effect of local electrostatics, this work aims at elucidating the long-range modulation of electric fields in proteins upon binding to charged surfaces. The study is based on cytochrome c (Cytc) variants carrying nitrile reporters for the vibrational Stark effect that are incorporated into the protein via genetic engineering and chemical modification. The Cytc variants were thoroughly characterized with respect to possible structural perturbations due to labeling. For the proteins in solution, the relative hydrogen bond occupancy and the calculated electric fields, both obtained from molecular dynamics (MD) simulations, and the experimental nitrile stretching frequencies were used to develop a relationship for separating hydrogen-bonding and non-hydrogen-bonding electric field effects. This relationship provides an excellent description for the stable Cytc variants in solution. For the proteins bound to Au electrodes coated with charged self-assembled monolayers (SAMs), the underlying MD simulations can only account for the electric field changes Δ E_ads due to the formation of the electrostatic SAM-Cytc complexes but not for the additional contribution, Δ E_int, representing the consequences of the potential drops over the electrode/SAM/protein interfaces. Both Δ E_ads and Δ E_int, determined at distances between 20 and 30 Å with respect to the SAM surface, are comparable in magnitude to the non-hydrogen-bonding electric field in the unbound protein. This long-range modulation of the internal electric field may be of functional relevance for proteins in complexes with partner proteins (Δ E_ads) and attached to membranes (Δ E_ads + Δ E_int).

Systematic Excited State Studies of Reversibly Switchable Fluorescent Proteins

The reversibly switchable fluorescent proteins Dronpa, rsFastLime, rsKame, Padron, and bsDronpa feature the same chromophore but display a 40 nm variation in absorption maxima and an only 18 nm variation in emission maxima. In the present contribution, we employ QM/MM models to investigate the mechanism of such remarkably different spectral variations, which are caused by just a few amino acid replacements. We show that the models, which are based on CASPT2//CASSCF level of QM theory, reproduce the observed trends in absorption maxima, with only a 3.5 kcal/mol blue-shift, and in emission maxima, with an even smaller 1.5 kcal/mol blue-shift with respect to the observed quantities. In order to explain the variations across the series, we look at the chromophore's electronic structure change during absorption and emission. Such analysis indicates that a change in charge-transfer character, which is more pronounced during absorption, triggers a cascade of hydrogen-bond-network rearrangements, suggesting preparation to an isomerization event. We also show how the contribution of Arg 89 and Arg 64 residues to the chromophore conformational changes correlate with the spectral variations in absorption and emission. Furthermore, we describe how the conical intersection stability is related to the protein's photophysical properties. While for the Dronpa, rsFastLime, and rsKame triad, the stability correlates with the photoswitching speed, this does not happen for bsDronpa and Padron, suggesting a less obvious photoisomerization mechanism.

Blue-Shifted Green Fluorescent Protein Homologues Are Brighter than Enhanced Green Fluorescent Protein under Two-Photon Excitation

Fluorescent proteins (FPs) are indispensable markers for two-photon imaging of live tissue, especially in the brains of small model organisms. The quantity of physiologically relevant data collected, however, is limited by heat-induced damage of the tissue due to the high intensities of the excitation laser. We seek to minimize this damage by developing FPs with improved brightness. Among FPs with the same chromophore structure, the spectral properties can vary widely due to differences in the local protein environment. Using a physical model that describes the spectra of FPs containing the anionic green FP (GFP) chromophore, we predict that those that are blue-shifted in one-photon absorption will have stronger peak two-photon absorption cross sections. Following this prediction, we present 12 blue-shifted GFP homologues and demonstrate that they are up to 2.5 times brighter than the commonly used enhanced GFP (EGFP).

Mechanism and bottlenecks in strand photodissociation of split green fluorescent proteins (GFPs)

Split GFPs have been widely applied for monitoring protein-protein interactions by expressing GFPs as two or more constituent parts linked to separate proteins that only fluoresce on complementing with one another. Although this complementation is typically irreversible, it has been shown previously that light accelerates dissociation of a noncovalently attached β-strand from a circularly permuted split GFP, allowing the interaction to be reversible. Reversible complementation is desirable, but photodissociation has too low of an efficiency (quantum yield <1%) to be useful as an optogenetic tool. Understanding the physical origins of this low efficiency can provide strategies to improve it. We elucidated the mechanism of strand photodissociation by measuring the dependence of its rate on light intensity and point mutations. The results show that strand photodissociation is a two-step process involving light-activated cis-trans isomerization of the chromophore followed by light-independent strand dissociation. The dependence of the rate on temperature was then used to establish a potential energy surface (PES) diagram along the photodissociation reaction coordinate. The resulting energetics-function model reveals the rate-limiting process to be the transition from the electronic excited-state to the ground-state PES accompanying cis-trans isomerization. Comparisons between split GFPs and other photosensory proteins, like photoactive yellow protein and rhodopsin, provide potential strategies for improving the photodissociation quantum yield.

Deciphering the molecular mechanism responsible for GCaMP6m's Ca2+-dependent change in fluorescence

The goal of this work is to determine how GCaMP6m's fluorescence is altered in response to Ca2+-binding. Our detailed spectroscopic study reveals the simplest explanation for how GCaMP6m changes fluorescence in response to Ca2+ is with a four-state model, in which a Ca2+-dependent change of the chromophore protonation state, due to a shift in pKa, is the predominant factor. The pKa shift is quantitatively explained by a change in electrostatic potential around the chromophore due to the conformational changes that occur in the protein when calmodulin binds Ca2+ and interacts with the M13 peptide. The absolute pKa values for the Ca2+-free and Ca2+-saturated states of GCaMP6m are critical to its high signal-to-noise ratio. This mechanism has important implications for further improvements to GCaMP6m and potentially for other similarly designed biosensors.

Electric Field Keeps Chromophore Planar and Produces High Yield Fluorescence in Green Fluorescent Protein

The green fluorescent protein and its designed variants fluoresce efficiently. Because the isolated chromophore is not fluorescent in a practical sense, it is apparent that the protein environment plays a crucial role in its efficiency. Because of various obstacles in studying excited state dynamics of complex systems, however, the detailed mechanism of this efficiency enhancement is not yet clearly elucidated. Here, by adopting excited state nonadiabatic molecular dynamics simulations together with an interpolated quantum chemical potential model of the chromophore, we find that the strong electric field from the protein matrix contributes dominantly to the motional restriction of the chromophore. The delay in twisting motion subsequently obstructs the nonradiative decay that competes with fluorescence, leading naturally to an enhancement in light-emitting efficiency. Surprisingly, steric constraints make only a minor contribution to these aspects. Through residue specific analyses, we identify a group of key residues that control the excited state behavior. Testing a series of mutant GFPs with different brightnesses also supports the view regarding the importance of protein electrostatics. Our findings may provide a useful guide toward designing new fluorescent chemical systems in the future.

Temperature and pressure effects on GFP mutants: explaining spectral changes by molecular dynamics simulations and TD-DFT calculations

By combining spectroscopic measurements under high pressure with molecular dynamics simulations and quantum mechanics calculations we investigate how sub-angstrom structural perturbations are able to tune protein function. We monitored the variations in fluorescence output of two green fluorescent protein mutants (termed Mut2 and Mut2Y, the latter containing the key T203Y mutation) subjected to pressures up to 600 MPa, at various temperatures in the 280-320 K range. By performing 150 ns molecular dynamics simulations of the protein structures at various pressures, we evidenced subtle changes in conformation and dynamics around the light-absorbing chromophore. Such changes explain the measured spectral tuning in the case of the sizable 120 cm(-1) red-shift observed for pressurized Mut2Y, but absent in Mut2. Previous work [Barstow et al., Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 13362] on pressure effects on GFP also involved a T203Y mutant. On the basis of cryocooling X-ray crystallography, the pressure-induced fluorescence blue shift at low temperature (77 K) was attributed to key changes in relative conformation of the chromophore and Tyr203 phenol ring. At room temperature, however, a red shift was observed at high pressure, analogous to the one we observe in Mut2Y. Our investigation of structural variations in compressed Mut2Y also explains their result, bridging the gap between low-temperature and room-temperature high-pressure effects.