Excited states of fluorescent proteins, mKO and DsRed: chromophore-protein electrostatic interaction behind the color variations

Protonation Isomer Specific Ion-Molecule Radical Reactions

Through a combination of ion-mobility filtering and laser-equipped quadrupole ion-trap mass spectrometry, the gas-phase reaction kinetics of two protonation isomers of the distonic-radical quinazoline cation are independently measured with ethylene. For these radical addition reactions, protonation site variations drive significant changes in nearby radical reactivity, and this is primarily due to through-space electrostatic effects. Furthermore, quantum chemical methods specifically designed for calculating long-range interactions, such as double-hybrid density functional theory, are required to rationalize the experimentally measured difference in reactivity.

Excited-State Dynamics of a meta-Dimethylamino Locked GFP Chromophore as a Fluorescence Turn-on Water Sensor†

Strategic incorporation of a meta-dimethylamino (-NMe₂ ) group on the conformationally locked green fluorescent protein (GFP) model chromophore (m-NMe₂ -LpHBDI) has drastically altered molecular electronic properties, counterintuitively enhancing fluorescence of only the neutral and cationic chromophores in aqueous solution. A ˜200-fold decrease in fluorescence quantum yield of m-NMe₂ -LpHBDI in alcohols (e.g., MeOH, EtOH and 2-PrOH) supports this GFP-derived compound as a fluorescence turn-on water sensor, with large fluorescence intensity differences between H₂ O and ROH emissions in various H₂ O/ROH binary mixtures. A combination of steady-state electronic spectroscopy, femtosecond transient absorption, ground-state femtosecond stimulated Raman spectroscopy (FSRS) and quantum calculations elucidates an intermolecular hydrogen-bonding chain between a solvent -OH group and the chromophore phenolic ring -NMe₂ and -OH functional groups, wherein fluorescence differences arise from an extended hydrogen-bonding network beyond the first solvation shell, as opposed to fluorescence quenching via a dark twisted intramolecular charge-transfer state. The absence of a meta-NMe₂ group twisting coordinate upon electronic excitation was corroborated by experiments on control samples without the meta-NMe₂ group or with both meta-NMe₂ and para-OH groups locked in a six-membered ring. These deep mechanistic insights stemming from GFP chromophore scaffold will enable rational design of organic, compact and environmentally friendly water sensors.

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.

Biosensors Used for Epifluorescence and Confocal Laser Scanning Microscopies to Study Dickeya and Pectobacterium Virulence and Biocontrol

Promoter-probe vectors carrying fluorescent protein-reporter genes are powerful tools used to study microbial ecology, epidemiology, and etiology. In addition, they provide direct visual evidence of molecular interactions related to cell physiology and metabolism. Knowledge and advances carried out thanks to the construction of soft-rot Pectobacteriaceae biosensors, often inoculated in potato Solanum tuberosum, are discussed in this review. Under epifluorescence and confocal laser scanning microscopies, Dickeya and Pectobacterium-tagged strains managed to monitor in situ bacterial viability, microcolony and biofilm formation, and colonization of infected plant organs, as well as disease symptoms, such as cell-wall lysis and their suppression by biocontrol antagonists. The use of dual-colored reporters encoding the first fluorophore expressed from a constitutive promoter as a cell tag, while a second was used as a regulator-based reporter system, was also used to simultaneously visualize bacterial spread and activity. This revealed the chronology of events leading to tuber maceration and quorum-sensing communication, in addition to the disruption of the latter by biocontrol agents. The promising potential of these fluorescent biosensors should make it possible to apprehend other activities, such as subcellular localization of key proteins involved in bacterial virulence in planta, in the near future.

Far Red Fluorescent Proteins: Where Is the Limit of the Acylimine Chromophore?

The search for new near-infrared probes for fluorescence imaging applications is a rapidly growing field of research. Monomeric fluorescent proteins that autocatalyze their chromophore are the most versatile markers for in vivo applications, but the development of bright far-red fluorescent proteins (RFPs) has proven difficult. In this contribution, we search for the theoretical limit of the red shift and how it can be reached without sacrificing the fluorescence quantum yield. Through extensive excited-state pathway calculations, molecular dynamics sampling, and statistical modeling using QM/MM schemes, we provide a new understanding of the chromophore's photophysics including the role of its acylimine extension, which is the main difference from other families of fluorescent proteins. The excited-state dynamics of the mPlum RFP and its mutants provide an ideal basis due to mPlum's flexible binding pocket and extended dynamic Stokes shift. We found a large number of structural species with red-shifted emission that differ in rotamer states and H-bonds between key amino acid residues in the binding pocket. By analyzing their spectral and structural features, we derive guidelines for future rational genetic design strategies.

Rational designing of 8-hydroxyquinolin-imidazolinone-based fluorescent protein mutants with dramatically red shifted emission: A computational study

Engineering fluorescent proteins to be the customized in vivo labels for monitoring cellular dynamic events is critical in biochemical and biomedical studies. The design and development of novel red fluorescent proteins is one of the most important fronts in this field due to their potential of imaging the entire organism. A recent fluorescent protein mutant eqFP650-67-HqAla with the 8-hydroxyquinolin-imidazolinone (HQI) chromophore has the plausible bathochromic shift of ~30 nm in its emission spectrum wavelength comparing to the parent fluorescent protein eqFP650. However, molecular mechanism of this significant shift remains somewhat obscure. In this study, we carefully benchmarked our computational methods and performed extensive calculations to investigate various structural components' effect on the chromophore's emission energy and decipher the molecular origin of the spectral shift. The influences of conjugation size, substituent group, substituent site as well as the number of substituents have been examined by elaborately designed chromophore derivatives. Accordingly, we proposed several chromophore mutants with dramatic bathochromic shift of up to ~60 nm in their emission spectra. We further evaluated their structural stability in the protein using molecular dynamics simulations. Present theoretical study connects the structural feature of chromophore derivatives in red fluorescent proteins with their splendid performances in shifting the emission frequency and offer the molecular insight. The computational protocol and successive examination procedure to extract the structural effect utilized herein can also be widely applied to other fluorescent proteins in general. © 2018 Wiley Periodicals, Inc.

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.

Modifications of the chromophore of Spinach aptamer based on QM:MM calculations

Spinach aptamer was developed as an RNA analog of the green fluorescent protein. The aptamer interacts with its ligand and modifies its electronic spectrum so that it fluoresces brightly at the wavelength of 501 nm. Song et al. investigated modifications of the ligand in their experimental study and found a molecule emitting at 523 nm upon creating a complex with the Spinach aptamer. The crystal structure of the aptamer in complex with its original ligand has been published, which enabled us to study the system computationally. In this article, we suggest several new modifications of the ligand that shift the emission maximum of the complex to even longer wavelengths. Our results are based on combined quantum mechanical/molecular mechanical calculations with DFT method used for geometry optimization and TD-DFT for calculations of absorption and emission energies.

Structure-guided wavelength tuning in far-red fluorescent proteins

In recent years, protein engineers have succeeded in tuning the excitation spectra of natural fluorescent proteins from green wavelengths into orange and red wavelengths, resulting in the creation of a series of fluorescent proteins with emission in the far-red portions of the optical spectrum. These results have arisen from the synergistic combination of structural knowledge of fluorescent proteins, chemical intuition, and high-throughput screening methods. Here we review structural features found in autocatalytic far-red fluorescent proteins, and discuss how they add to our understanding of the biophysical mechanisms of wavelength tuning in biological chromophores.

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.

Quantum mechanical molecular interactions for calculating the excitation energy in molecular environments: a first-order interacting space approach

Intermolecular interactions regulate the molecular properties in proteins and solutions such as solvatochromic systems. Some of the interactions have to be described at an electronic-structure level. In this study, a commutator for calculating the excitation energy is used for deriving a first-order interacting space (FOIS) to describe the environmental response to solute excitation. The FOIS wave function for a solute-in-solvent cluster is solved by second-order perturbation theory. The contributions to the excitation energy are decomposed into each interaction and for each solvent.

Hydrogen bond flexibility correlates with Stokes shift in mPlum variants

Fluorescent proteins have revolutionized molecular biology research and provide a means of tracking subcellular processes with extraordinary spatial and temporal precision. Species with emission beyond 650 nm offer the potential for deeper tissue penetration and lengthened imaging times; however, the origin of their extended Stokes shift is not fully understood. We employed spectrally resolved transient grating spectroscopy and molecular dynamics simulations to investigate the relationship between the flexibility of the chromophore environment and Stokes shift in mPlum. We examined excited state solvation dynamics in a panel of strategic point mutants of residues E16 and I65 proposed to participate in a hydrogen-bonding interaction thought responsible for its red-shifted emission. We observed two characteristic relaxation constants of a few picoseconds and tens of picoseconds that were assigned to survival times of direct and water-mediated hydrogen bonds at the 16-65 position. Moreover, variants of the largest Stokes shift (mPlum, I65V) exhibited significant decay on both time scales, indicating the bathochromic shift correlates with a facile switching between a direct and water-mediated hydrogen bond. This dynamic model underscores the role of environmental flexibility in the mechanism of excited state solvation and provides a template for engineering next-generation red fluorescent proteins.

Spectral "Fine" Tuning in Fluorescent Proteins: The Case of the GFP-Like Chromophore in the Anionic Protonation State

Fluorescent proteins (FPs), featuring the same chromophore but different chromophore-protein interactions, display remarkable spectral variations even when the same chromophore protonation state, i.e. the anionic state, is involved. We examine the mechanisms behind this tuning by means of structural analysis, molecular dynamics simulations, and vertical excitation energy calculations using QM/MM Time-Dependent Density Functional Theory (TD-DFT), CASPT2/CASSCF, and SAC-CI. The proteins under investigation include the structurally similar, though spectrally distinct, Dronpa and mTFP0.7, with absorption peaks at 453 and 503 nm, respectively. We extend our analysis to two Green Fluorescent Protein variants, GFP-S65T (absorption peak at 484 nm), for comparison with previous computational studies, and GFP-S65G/V68L/S72A/T203Y, a yellow fluorescent protein (514 nm), in order to include one of the most red-shifted FPs containing a GFP-like chromophore. We compare different choices of the QM system, and we discuss how molecular dynamics simulations affect the calculation of excitation energies, with respect to X-ray structures. We are able to partially reproduce the spectral tuning of the FPs and correlate it to the chromophore bond-length variations, as determined by specific interactions with the chromophore environment.

Molecular-Level Insight into the Spectral Tuning Mechanism of the DsRed Chromophore

We present a detailed study of the protein environmental effects on the one- and two-photon absorption (1PA and 2PA, respectively) properties of the S0-S1 transition in the DsRed protein using the polarizable embedding density functional theory formalism. We find that steric factors and chromophore-protein interactions act in concert to enhance the 2PA activity inside the protein while adversely blue-shifting the 1PA maximum. A two-state model reveals that the 2PA intensity gain is primarily governed by the increased change in the permanent dipole moment between the ground and the excited states acquired inside the protein. Our results indicate that this mainly is attributable to counter-directional contributions stemming from Lys163 and the conserved Arg95 with the former additionally identified as a key residue in the color tuning mechanism. The results provide new insight into the tuning mechanism of DsRed and suggest a possible strategy for simultaneous improvement of its 1PA and 2PA properties.

Red fluorescent proteins: chromophore formation and cellular applications

In the last decade, a number of red fluorescent proteins (RFPs) that emit orange, red, and far-red fluorescence have been isolated from anthozoans (corals), and developed through directed molecular evolution. An attractive property possessed by some RFPs is that their red fluorescence can be turned on or modulated by illumination at specific wavelengths. Recent progress in the development of RFPs has been accompanied with detailed studies of chromophore chemistry. A thorough understanding of the molecular mechanisms involved in the post-translational modifications of red chromophores would enable scientists to design RFPs with the desired properties to advance imaging applications. This article provides a broad perspective on the chemistry and applications of RFPs.

Interpolated mechanics-molecular mechanics study of internal rotation dynamics of the chromophore unit in blue fluorescent protein and its variants

The excited state dynamics of the blue fluorescent protein (BFP) and its variants, azurite, EBFP1.2, and EBFP2.0, are studied using molecular dynamics (MD) simulations on potential energy surfaces (PESs) generated with the interpolated mechanics-molecular mechanics (IM/MM) scheme. This IM/MM strategy adopts the interpolated PES for an important area of the complex and the conventional force field for the remaining part. We focus on the internal rotation dynamics of the chromophore unit, which is directly related to its fluorescence property, and analyze the time evolutions of the nonrotated chromophore fractions based on trajectories over 10 μs of aggregate simulation time. The characteristics obtained from the calculated time progresses of the nonrotated chromophore fractions in BFP and other variants agree well with experimentally observed properties. The results show that the MD simulation with an IM/MM potential is an attractive approach for studying excited state dynamics of fluorescent proteins in consideration of its efficiency and reliability. We also attempt to investigate the detailed roles that the mutated residues play in delaying the excited state chromophore twisting and thus improving the fluorescence property, and discuss the contributions by the Coulombic and the steric interactions between the chromophore and the mutated residues.

Color tuning in photofunctional proteins

Depending on protein environment, a single photofunctional chromophore shows a wide variation of photoabsorption/emission energies. This photobiological phenomenon, known as color tuning, is observed in human visual cone pigments, firefly luciferase, and red fluorescent protein. We investigate the origin of color tuning by quantum chemical calculations on the excited states: symmetry-adapted cluster-configuration interaction (SAC-CI) method for excited states and a combined quantum mechanical (QM)/molecular mechanical (MM) method for protein environments. This Minireview summarizes our theoretical studies on the above three systems and explains a common feature of their color-tuning mechanisms. It also discuss the possibility of artificial color tuning toward a rational design of photoabsorption/emission properties.

Green fluorescent protein: a perspective

A brief personal perspective is provided for green fluorescent protein (GFP), covering the period 1994-2011. The topics discussed are primarily those in which my research group has made a contribution and include structure and function of the GFP polypeptide, the mechanism of fluorescence emission, excited state protein transfer, the design of ratiometric fluorescent protein biosensors and an overview of the fluorescent proteins derived from coral reef animals. Structure-function relationships in photoswitchable fluorescent proteins and nonfluorescent chromoproteins are also briefly covered.

Molecular mechanism of a green-shifted, pH-dependent red fluorescent protein mKate variant

Fluorescent proteins that can switch between distinct colors have contributed significantly to modern biomedical imaging technologies and molecular cell biology. Here we report the identification and biochemical analysis of a green-shifted red fluorescent protein variant GmKate, produced by the introduction of two mutations into mKate. Although the mutations decrease the overall brightness of the protein, GmKate is subject to pH-dependent, reversible green-to-red color conversion. At physiological pH, GmKate absorbs blue light (445 nm) and emits green fluorescence (525 nm). At pH above 9.0, GmKate absorbs 598 nm light and emits 646 nm, far-red fluorescence, similar to its sequence homolog mNeptune. Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation that was confirmed by quantum chemical calculations. Crystal structures reveal potential hydrogen bond networks around the chromophore that may facilitate the protonation switch, and indicate a molecular basis for the unusual bathochromic shift observed at high pH. This study provides mechanistic insights into the color tuning of mKate variants, which may aid the development of green-to-red color-convertible fluorescent sensors, and suggests GmKate as a prototype of genetically encoded pH sensors for biological studies.