Radiationless decay of red fluorescent protein chromophore models via twisted intramolecular charge-transfer states

Potential Energy Landscape of the Electronic States of the GFP Chromophore in Different Protonation Forms: Electronic Transition Energies and Conical Intersections

We present the results of quantum chemical calculations of the transition energies and conical intersection points for the two lowest singlet electronic states of the green fluorescent protein chromophore, 4'-hydroxybenzylidene-2,3-dimethylimidazolinone, in the vicinity of its cis conformation in the gas phase. Four protonation states of the chromophore, i.e., anionic, neutral, cationic, and zwitterionic, were considered. Energy differences were computed by the perturbatively corrected complete active space self-consistent field (CASSCF)-based approaches at the corresponding potential energy minima optimized by density functional theory and CASSCF (for the ground and excited states, respectively). We also report the EOM-CCSD and SOS-CIS(D) results for the excitation energies. The minimum energy S0/S1 conical intersection points were located using analytic state-specific CASSCF gradients. The results reproduce essential features of previous ab initio calculations of the anionic form of the chromophore and provide an extension for the neutral, cationic, and zwitterionic forms, which are important in the protein environment. The S1 PES of the anion is fairly flat, and the barrier separating the planar bright conformation from the dark twisted one as well as the conical intersection point with the S0 surface is very small (less than 2 kcal/mol). On the cationic surface, the barrier is considerably higher (∼13 kcal/mol). The PES of the S1 state of the zwitterionic form does not have a planar minimum in the Franck-Condon region. The S1 surface of the neutral form possesses a bright planar minimum; the energy barrier of about 9 kcal/mol separates it from the dark twisted conformation as well as from the conical intersection point leading to the cis-trans chromophore isomerization.

QM/MM studies of structural and energetic properties of the far-red fluorescent protein HcRed

The far-red fluorescent protein HcRed was investigated using molecular dynamics (MD) and combined quantum mechanics/molecular mechanics (QM/MM) calculations. Three models of HcRed (anionic chromophore) were considered, differing in the protonation states of nearby Glu residues (A: Glu214 and Glu146 both protonated; B: Glu214 protonated and Glu146 deprotonated; C: Glu214 and Glu146 both deprotonated). SCC-DFTB/MM MD simulations of model B yield good agreement with the available crystallographic data at ambient pH. Bond lengths in the QM region are well reproduced, with a root mean square (rms) deviation between experimental and average MD data of 0.079 A; the chromophore is almost co-planar, which is consistent with experimental observation; and the five hydrogen bonds involving the chromophore are conserved. QM/MM geometry optimizations were performed on representative snapshot structures from the MD simulations for each model. They confirm the structural features observed in the MD simulations. According to the DFT(B3LYP)/MM results, the cis-conformation of the chromophore is more stable than the trans-form by 9.1-12.9 kcal mol(-1) in model B, and by 12.4-19.9 kcal mol(-1) in model C, consistent with the experimental preference for the cis-isomer. However, in model A when both Glu214 and Glu146 are protonated, the stability is inverted with the trans-form being favored. The different protonation states of the titratable active-site residues Glu214 and Glu146 thus critically influence the manner in which the relative stability and degree of planarity of the cis- and trans-conformers vary with pH. Coupled with the known correlation of chromophore conformation with fluorescence efficiency, this work provides a detailed structural basis for the observed phenomenon that red fluorescent proteins such as HcRed, mKate and Rtms5 show bright fluorescence at high pH.

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

The emitting states of green fluorescent protein (GFP), monomeric Kusabira orange (mKO), and Discosoma red (DsRed) were studied using QM/MM and SAC-CI methods. By comparing the electronic structures among the green-, orange-, and red-emitting states as well as their electrostatic and quantum mechanical interactions within the protein cavity, the basic mechanisms for determining emission colors have been clarified. We found that the orange and red emissions of mKO and DsRed, respectively, result from cancellation between two effects, the pi skeleton extension (red shift) and protein electrostatic potential (blue shift). The extension of the pi skeleton enhances the intramolecular charge-transfer character of the transition, which makes the fluorescence energy more sensitive to the protein's electrostatic potential. On the basis of this mechanism, we predicted amino acid mutations that could red shift the emission energy of DsRed. A novel single amino acid mutation, which was examined computationally, reduced the DsRed emission energy from 2.14 (579 nm) to 1.95 eV (636 nm), which is approaching near-infrared fluorescence.

The 559-to-600 nm shift observed in red fluorescent protein eqFP611 is attributed to cis-trans isomerization of the chromophore in an anionic protein pocket

Fluorescent proteins are commonly used as molecular labels, noninvasive markers of gene expression, and reporters of environmental conditions in live cells. We investigate the structural and spectroscopic properties of the chromophore of a far-red fluorescent protein eqFP611. Both the cis and trans isomers of the chromophore are examined within the protein for which both anionic and neutral states of protonation are considered. Spectroscopic properties are examined using time-dependent density functional theory (TDDFT), employing the B3LYP, PBE and B3PW91 density functionals. Intermolecular and long-range contributions to the structure and spectroscopy were treated using the own n-layered integrated molecular orbital and molecular mechanics (ONIOM) approach. The results indicated that the chromophore before excitation is in an anionic, protonated state, with the long-range contributions inducing a blue shift in the absorption and fluorescence maxima of the chromophore. Moreover, the calculated changes of the lowest pi-pi* excitation energy upon isomerization match the observed shift from 559 to 600 nm in the absorption maximum of the system following prolonged irradiation. Furthermore, decomposition analysis of the electrostatic contributions from individual residues indicated that the interactions from four residues Arg92, Lys67, Glu145, and His197 to the chromophore play a key role in the absorption and fluorescence spectra of eqFP611, suggesting that mutations at these sites should provide very useful mechanistic information.

Fragment molecular orbital calculations on red fluorescent proteins (DsRed and mFruits)

We have performed a series of fragment molecular orbital (FMO) calculations for a family of red fluorescent proteins, DsRed and mFruits. The electronic transition energies were evaluated by the method of configuration interaction singles with perturbative doubles [CIS(D)] including higher-order corrections. The calculated values were in good agreement with the corresponding experimental peak values of spectra. Additionally, the chromophore environment was systematically analyzed in terms of the interaction energies between the pigment moiety and neighboring residues. It was theoretically revealed that the electrostatic interactions play a dominant role in the DsRed chromophore, whereas the color tunings in mFruits are controlled in a more delicate fashion.

Chromophore protonation state controls photoswitching of the fluoroprotein asFP595

Fluorescent proteins have been widely used as genetically encodable fusion tags for biological imaging. Recently, a new class of fluorescent proteins was discovered that can be reversibly light-switched between a fluorescent and a non-fluorescent state. Such proteins can not only provide nanoscale resolution in far-field fluorescence optical microscopy much below the diffraction limit, but also hold promise for other nanotechnological applications, such as optical data storage. To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements to their properties requires a detailed understanding of the molecular switching mechanism, which is currently unknown. Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 at the atomic level by multiconfigurational ab initio (CASSCF) calculations and QM/MM excited state molecular dynamics simulations with explicit surface hopping. Our simulations explain measured quantum yields and excited state lifetimes, and also predict the structures of the hitherto unknown intermediates and of the irreversibly fluorescent state. Further, we find that the proton distribution in the active site of the asFP595 controls the photochemical conversion pathways of the chromophore in the protein matrix. Accordingly, changes in the protonation state of the chromophore and some proximal amino acids lead to different photochemical states, which all turn out to be essential for the photoswitching mechanism. These photochemical states are (i) a neutral chromophore, which can trans-cis photoisomerize, (ii) an anionic chromophore, which rapidly undergoes radiationless decay after excitation, and (iii) a putative fluorescent zwitterionic chromophore. The overall stability of the different protonation states is controlled by the isomeric state of the chromophore. We finally propose that radiation-induced decarboxylation of the glutamic acid Glu215 blocks the proton transfer pathways that enable the deactivation of the zwitterionic chromophore and thus leads to irreversible fluorescence. We have identified the tight coupling of trans-cis isomerization and proton transfers in photoswitchable proteins to be essential for their function and propose a detailed underlying mechanism, which provides a comprehensive picture that explains the available experimental data. The structural similarity between asFP595 and other fluoroproteins of interest for imaging suggests that this coupling is a quite general mechanism for photoswitchable proteins. These insights can guide the rational design and optimization of photoswitchable proteins.

Proteins whose fluorescence can be reversibly switched on and off hold great promise for applications in high-resolution optical microscopy and nanotechnology. To systematically exploit the potential of such photoswitchable proteins and to enable rational improvements of their properties requires a detailed understanding of the molecular switching mechanism. Here, we have studied the photoswitching mechanism of the reversibly switchable fluoroprotein asFP595 by atomistic molecular dynamics simulations. Our simulations explain measured quantum yields and excited state lifetimes, and also predict the structures of the hitherto unknown intermediates and of the irreversibly fluorescent state. Further, we find that the proton distribution in the active site of the asFP595 controls the photochemical conversion pathways of the chromophore in the protein matrix. Our results show that a tight coupling between trans-cis isomerization of the chromophore and proton transfer is essential for the function of asFP595. The structural similarity between asFP595 and other fluoroproteins suggests that this coupling is a quite general mechanism for photoswitchable proteins. These insights can guide the rational design and optimization of photoswitchable proteins.

Electronic excitations of green fluorescent proteins: modeling solvatochromatic shifts of red fluorescent protein chromophore model compound in aqueous solutions

While green fluorescent proteins (GFPs) have been widely used as tools in biochemistry, cell biology, and molecular genetics, novel red fluorescent proteins (RFPs) with red fluorescence emission have also been identified, as complements to the existing GFP technology. The unusual spectrophotometric and fluorescence properties of GFPs and RFPs are controlled by the protonation states and possibly cis/trans isomerization within their chromophores. In this work, we have investigated the electronic structures, liquid structures, and solvent shifts of the possible neutral and anionic protonated states and the cis/trans isomerization of a RFP chromophore model compound HBMPI in aqueous solutions. The calculations reproduced the experimental absorption solvatochromatic shifts of dilute HBMPI in water under neutral and anionic conditions. Unlike the GFP chromophore, the RFP chromophore model compound HBMPI in basic solution can only adopt a conformation where the C=C bond between the bridge group and the imidazolinone ring and the C-C bond between the imidazolinone and ethylene groups exist in cis and trans conformations, respectively. Moreover, the solvent-solute hydrogen-bonding interactions are found to contribute significantly to the total solvent shifts of pi-pi* excitations of aqueous HBMPI solutions, signifying the importance of protein environment in the determination of the conformation of the chromophores in red fluorescent proteins.