Mechanistic Investigations of Green mEos4b Reveal a Dynamic Long-Lived Dark State.

Green-to-red photoconvertible fluorescent proteins (PCFPs) are key players in advanced microscopy schemes such as photoactivated localization microscopy (PALM). Whereas photoconversion and red-state blinking in PCFPs have been studied intensively, their green-state photophysical behavior has received less attention. Yet dark states in green PCFPs can become strongly populated in PALM schemes and exert an indirect but considerable influence on the quality of data recorded in the red channel. Furthermore, green-state photoswitching in PCFPs can be used directly for PALM and has been engineered to design highly efficient reversibly switchable fluorescent proteins (RSFPs) amenable to various nanoscopy schemes. Here, we demonstrate that green mEos4b efficiently switches to a long-lived dark state through cis-trans isomerization of its chromophore, as do most RSFPs. However, by combining kinetic crystallography, molecular dynamics simulations, and Raman spectroscopy, we find that the dark state in green mEos4b is much more dynamic than that seen in switched-off green IrisFP, a biphotochromic PCFP engineered from the common EosFP parent. Our data suggest that H-bonding patterns maintained by the chromophore in green PCFPs and RSFPs in both their on- and off-states collectively control photoswitching quantum yields. The reduced number of H-bonds maintained by the dynamic dark chromophore in green mEos4b thus largely accounts for the observed lower switching contrast as compared to that of IrisFP. We also compare the long-lived dark states reached from green and red mEos4b, on the basis of their X-ray structures and Raman signatures. Altogether, these data provide a unifying picture of the complex photophysics of PCFPs and RSFPs.

Chromophore twisting in the excited state of a photoswitchable fluorescent protein captured by time-resolved serial femtosecond crystallography.

Chromophores absorb light in photosensitive proteins and thereby initiate fundamental biological processes such as photosynthesis, vision and biofluorescence. An important goal in their understanding is the provision of detailed structural descriptions of the ultrafast photochemical events that they undergo, in particular of the excited states that connect chemistry to biological function. Here we report on the structures of two excited states in the reversibly photoswitchable fluorescent protein rsEGFP2. We populated the states through femtosecond illumination of rsEGFP2 in its non-fluorescent off state and observed their build-up (within less than one picosecond) and decay (on the several picosecond timescale). Using an X-ray free-electron laser, we performed picosecond time-resolved crystallography and show that the hydroxybenzylidene imidazolinone chromophore in one of the excited states assumes a near-canonical twisted configuration halfway between the trans and cis isomers. This is in line with excited-state quantum mechanics/molecular mechanics and classical molecular dynamics simulations. Our new understanding of the structure around the twisted chromophore enabled the design of a mutant that displays a twofold increase in its off-to-on photoswitching quantum yield.

Theoretical estimation of redox potential of biological quinone cofactors.

Redox potentials are essential to understand biological cofactor reactivity and to predict their behavior in biological media. Experimental determination of redox potential in biological system is often difficult due to complexity of biological media but computational approaches can be used to estimate them. Nevertheless, the quality of the computational methodology remains a key issue to validate the results. Instead of looking to the best absolute results, we present here the calibration of theoretical redox potential for quinone derivatives in water coupling QM + MM or QM/MM scheme. Our approach allows using low computational cost theoretical level, ideal for long simulations in biological systems, and determination of the uncertainties linked to the calculations. © 2017 Wiley Periodicals, Inc.

Electron and Hydrogen Atom Transfers in the Hydride Carrier Protein EmoB.

In this article, we investigate the mechanism of hydride transfer taking place within the EmoB protein of the Mesorhizobium species. The reaction involves the net transfer of one proton and two electrons from a reduced flavin mononucleotide (FMN) cofactor, which is anchored in the protein scaffold, to a diffusible oxidized FMN cofactor, both being held together by π-stacking interactions. To analyze the formal hydride transfer in terms of more elementary steps, electron transfer (ET), and hydrogen atom transfers (HAT), we employ a combination of classical molecular dynamics simulations and hybrid constrained Density Functional Theory/Molecular Mechanics (cDFT/MM) energy calculations to build the free energy profiles, for the ET before and after HAT occurs between the flavins. The main outcomes of our study are first to highlight the role of the protein in stabilizing the π-stacked FMN dimer and second to reveal the coupling between the ET and HAT. Before HAT has taken place, ET is unfavorable by 8 kcal/mol and become favorable by 8 kcal/mol after HAT. Our simulations show that such a coupling is not present for the analogous process in water (ET is almost athermal). This suggests a functional role for the protein matrix to ensure EmoB a role of hydride carrier in the Mesorhizobium species.

Structural evidence for a two-regime photobleaching mechanism in a reversibly switchable fluorescent protein.

Photobleaching, the irreversible photodestruction of a chromophore, severely limits the use of fluorescent proteins (FPs) in optical microscopy. Yet, the mechanisms that govern photobleaching remain poorly understood. In Reversibly Switchable Fluorescent Proteins (RSFPs), a class of FPs that can be repeatedly photoswitched between nonfluorescent and fluorescent states, photobleaching limits the achievable number of switching cycles, a process known as photofatigue. We investigated the photofatigue mechanisms in the protein IrisFP using combined X-ray crystallography, optical in crystallo spectroscopy, mass spectrometry and modeling approaches. At laser-light intensities typical of conventional wide-field fluorescence microscopy, an oxygen-dependent photobleaching pathway was evidenced. Structural modifications induced by singlet-oxygen production within the chromophore pocket revealed the oxidation of two sulfur-containing residues, Met159 and Cys171, locking the chromophore in a nonfluorescent protonated state. At laser-light intensities typical of localization-based nanoscopy (>0.1 kW/cm(2)), a completely different, oxygen-independent photobleaching pathway was found to take place. The conserved Glu212 underwent decarboxylation concomitantly with an extensive rearrangement of the H-bond network around the chromophore, and an sp(2)-to-sp(3) hybridization change of the carbon atom bridging the chromophore cyclic moieties was observed. This two-regime photobleaching mechanism is likely to be a common feature in RSFPs from Anthozoan species, which typically share high structural and sequence identity with IrisFP. In addition, our results suggest that, when such FPs are used, the illumination conditions employed in localization-based super-resolution microscopy might generate less cytotoxicity than those of standard wide-field microscopy at constant absorbed light-dose. Finally, our data will facilitate the rational design of FPs displaying enhanced photoresistance.

The single T65S mutation generates brighter cyan fluorescent proteins with increased photostability and pH insensitivity.

Cyan fluorescent proteins (CFP) derived from Aequorea victoria GFP, carrying a tryptophan-based chromophore, are widely used as FRET donors in live cell fluorescence imaging experiments. Recently, several CFP variants with near-ultimate photophysical performances were obtained through a mix of site-directed and large scale random mutagenesis. To understand the structural bases of these improvements, we have studied more specifically the consequences of the single-site T65S mutation. We find that all CFP variants carrying the T65S mutation not only display an increased fluorescence quantum yield and a simpler fluorescence emission decay, but also show an improved pH stability and strongly reduced reversible photoswitching reactions. Most prominently, the Cerulean-T65S variant reaches performances nearly equivalent to those of mTurquoise, with QY  = 0.84, an almost pure single exponential fluorescence decay and an outstanding stability in the acid pH range (pK(1/2) = 3.6). From the detailed examination of crystallographic structures of different CFPs and GFPs, we conclude that these improvements stem from a shift in the thermodynamic balance between two well defined configurations of the residue 65 hydroxyl. These two configurations differ in their relative stabilization of a rigid chromophore, as well as in relaying the effects of Glu222 protonation at acid pHs. Our results suggest a simple method to greatly improve numerous FRET reporters used in cell imaging, and bring novel insights into the general structure-photophysics relationships of fluorescent proteins.

New insights into the mechanism of electron transfer within flavohemoglobins: tunnelling pathways, packing density, thermodynamic and kinetic analyses.

Flavohemoglobins (FlavoHb) are metalloenzymes catalyzing the reaction of nitric oxide dioxygenation. The iron cation of the heme group needs to be preliminarily reduced to the ferrous state to be catalytically competent. This reduction is triggered by a flavin adenine dinucleotide (FAD) prosthetic group which is localized in a distinct domain of the protein. In this paper we obtain new insights into the internal long range electron transfer (over ca. 12 Å) using a combination of experimental and computational approaches. Employing a time-resolved pulse radiolysis technique we report the first direct measurement of the FADH˙→ HemeFe(III) electron transfer rate. A rate constant of (6.8 ± 0.5) × 10(3) s(-1) is found. A large panel of computational approaches are used to provide the first estimation of the thermodynamic characteristics of the internal electron transfer step within flavoHb: both the driving force and the reorganization energy are estimated as a function of the protonated state of the flavin semi-quinone. We also report an analysis of the electron pathways involved in the tunnelling of the electron through the aqueous interface between the globin and the flavin domains.

Robust and Efficient Constrained DFT Molecular Dynamics Approach for Biochemical Modeling.

Constrained density functional theory (cDFT) is a powerful tool to investigate the dynamics of the electrons accompanying various physical-chemical processes. In this article we present our recent progresses in the implementation of the method in the parallelized version of the DFT program deMon2k. We take advantage of the possibility to express atomic densities in terms of linear combination of Hermite Gaussian functions to improve the computation of the cDFT integration weights within the Hirshfeld and Voronoi deformation density electronic population approaches. The efficiency of the method is illustrated on the computation of the average electronic coupling for an electron transfer (ET) through a glycine polypeptide of increasing length. The sampling is based on cDFT and hybrid cDFT/molecular mechanics molecular dynamics simulations. We also report the first estimations of quantum decoherence times from cDFT-based simulations for an ET reaction.

Low-temperature chromophore isomerization reveals the photoswitching mechanism of the fluorescent protein Padron.

Photoactivatable fluorescent proteins are essential players in nanoscopy approaches based on the super-localization of single molecules. The subclass of reversibly photoswitchable fluorescent proteins typically activate through isomerization of the chromophore coupled with a change in its protonation state. However, the interplay between these two events, the details of photoswitching pathways, and the role of protein dynamics remain incompletely understood. Here, by using a combination of structural and spectroscopic approaches, we discovered two fluorescent intermediate states along the on-switching pathway of the fluorescent protein Padron. The first intermediate can be populated at temperatures as low as 100 K and results from a remarkable trans-cis isomerization of the anionic chromophore taking place within a protein matrix essentially deprived of conformational flexibility. This intermediate evolves in the dark at cryotemperatures to a second structurally similar but spectroscopically distinct anionic intermediate. The final fluorescent state, which consists of a mixture of anionic and neutral chromophores in the cis configuration, is only reached above the glass transition temperature, suggesting that chromophore protonation involves solvent interactions mediated by pronounced dynamical breathing of the protein scaffold. The possibility of efficiently and reversibly photoactivating Padron at cryotemperatures will facilitate the development of advanced super-resolution imaging modalities such as cryonanoscopy.

Excited State Dynamics of the Green Fluorescent Protein on the Nanosecond Time Scale.

We have introduced a new algorithm in the parallel processing PMEMD module of the AMBER suite that allows MD simulations with a potential involving two coupled torsions. We have used this modified module to study the green fluorescent protein. A coupled torsional potential was adjusted on high accuracy quantum chemical calculations of the anionic chromophore in the first excited state, and several 15-ns-long MD simulations were performed. We have obtained an estimate of the fluorescence lifetime (2.2 ns) to be compared to the experimental value (3 ns), which is, to the best of our knowledge, the first theoretical estimate of that lifetime.

Relation between pH, structure, and absorption spectrum of Cerulean: a study by molecular dynamics and TD DFT calculations.

Molecular dynamics (MD) and quantum mechanical calculations of the Cerulean green fluorescent protein (a variant of enhanced cyan fluorescent protein ECFP) at pH 5.0 and 8.0 are presented, addressing two questions arising from experimental results (Malo et al., Biochemistry 2007;46:9865-9873): the origin of the blue shift of absorption spectrum when the pH is decreased from 8.0 to 5.0, and the lateral chain orientation of the key residue Asp148. We demonstrate that the blue shift is reproduced assuming that a rotation around the single bond of the exocyclic ring of the chromophore takes place when the pH changes from 5.0 to 8.0. We find that Asp148 is protonated and inside the barrel at pH 5.0 in agreement with crystallographic data. However, the hydrogen bond pattern of Asp148 is different in simulations of the solvated protein and in the crystal structure. This difference is explained by a partial closing of the cleft between strands 6 and 7 in MD simulations. This study provides also a structure at pH 8.0: the Asp148 carboxylate group is exposed to the solvent and the chromophore is stabilized in the trans conformation by a tighter hydrogen bond network. This work gives some insight into the relationship between the pH and the chromophore conformation and suggests an interpretation of the very similar fluorescent properties of ECFP and ECFP/H148D. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Thermodynamics of water intrusion in nanoporous hydrophobic solids.

We report a joint experimental and molecular simulation study of water intrusion in silicalite-1 and ferrerite zeolites. The main conclusion of this study is that water condensation takes place through a genuine first-order phase transition, provided that the interconnected pores structure is 3-dimensional. In the extreme confinement situation (ferrierite zeolite), condensation takes place through a continuous transition, which is explained by a shift of both the first-order transition line and the critical point with increasing confinement. The present findings are at odds with the common belief that conventional phase transitions cannot take place in microporous solids such as zeolites. The most important features of the intrusion/extrusion process can be understood in terms of equilibrium thermodynamics considerations. We believe that these findings are very general for hydrophobic solids, i.e. for both nonwetting as well as wetting water-solid interface systems.

Anisotropic united-atoms (AUA) potential for alcohols.

An anisotropic united-atom (AUA4) intermolecular potential has been derived for the family of alkanols by first optimizing a set of charges to reproduce the electrostatic potential of the isolated molecules of methanol and ethanol and then by adjusting the parameters of the OH group to fit selected equilibrium properties. In particular, the proposed potential includes additional extra-atomic charges in order to improve the matching to the electrostatic field. Gibbs ensemble Monte Carlo simulations were performed to determine the phase equilibria, while the critical region was explored by means of grand canonical Monte Carlo simulations combined with histogram reweighting techniques. In order to increase the transferability of the model, only the parameters of the Lennard-Jones OH group have been fitted, the parameters of the other AUA groups are taken from previous works. Nevertheless, a good level of agreement was obtained for all compounds considered in this work. In particular, excellent results were obtained for the Henry constants calculation of different gases in alkanols.

2,2'-Biphosphinines and 2,2'-bipyridines in homoleptic dianionic Group 4 complexes and neutral 2,2'-biphosphinine Group 6 d(6) metal complexes: octahedral versus trigonal-prismatic geometries.

The geometric and electronic structure of formally d(6) tris-biphosphinine [M(bp)(3)](q) and tris-bipyridine [M(bpy)(3)](q) complexes were studied by means of DFT calculations with the B3LYP functional. In agreement with the available experimental data, Group 4 dianionic [M(bp)(3)](2-) complexes (1P-3P for M=Ti, Zr, and Hf, respectively) adopt a trigonal-prismatic (TP) structure, whereas the geometry of their nitrogen analogues [M(bpy)(3)](2-) (1N-3N) is nearly octahedral (OC), although a secondary minimum was found for the TP structures (1N'-3N'). The electronic factors at work in these systems are discussed by means of an MO analysis of the minima, MO correlation diagrams, and thermodynamic cycles connecting the octahedral and trigonal-prismatic limits. In all these complexes, pronounced electron transfer from the metal center to the lowest lying pi* ligand orbitals makes the d(6) electron count purely formal. However, it is shown that the bp and bpy ligands accommodate the release of electron density from the metal in different ways because of a change in the localization of the HOMO, which is a mainly metal-centered orbital in bp complexes and a pure pi* ligand orbital in bpy complexes. The energetic evolution of the HOMO allows a simple rationalization of the progressive change from the TP to the OC structure on successive oxidation of the [Zr(bp)(3)](2-) complex, a trend in agreement with the experimental structure of the monoanionic complex. The geometry of Group 6 neutral complexes [M(bp)(3)] (4P and 5P for M=Mo and W, respectively) is found to be intermediate between the TP and OC limits, as previously shown experimentally for the tungsten complex. The electron transfer from the metal center to the lowest lying pi* ligand orbitals is found to be significantly smaller than for the Group 4 dianionic analogues. The geometrical change between [Zr(bp)(3)](2-) and [W(bp)(3)] is analyzed by means of a thermodynamic cycle and it is shown that a larger ligand-ligand repulsion plays an important role in favoring the distortion of the tungsten complex away from the TP structure.

Molecular simulation studies of water physisorption in zeolites.

We report a series of Grand Canonical Monte Carlo simulations of water adsorption in NaY and NaX faujasite, as well as in silicalite-1. Computed adsorption isotherms and heats of adsorption were in good agreement with the available experiments. The existence of cyclic water hexamers in NaX located in the 12-ring windows, recently disclosed by neutron diffraction experiments (Hunger et al., J. Phys. Chem. B, 2006, 110, 342-353) was reproduced in our simulations. Interestingly enough, such cyclic hexamer clusters were also observed in the case of NaY, in which no stabilizing cation is present in the 12-ring window. We also report cation redistribution upon water adsorption for sodium faujasite with varying cation contents (Si ratio Al ratio in the range 1.53-3). A simple and transferable forcefield was used, that enabled to reproduce the different aspects of water physisorption in stable zeolites. The high pressure water condensation in hydrophobic silicalite-1 was reproduced without any parameter readjustment. The method and forcefield used here should be useful for engineering oriented applications such as the prediction of multi-component mixture adsorptive separations in various stable zeolites. It allows to address the issue of the effect of the small amounts of water that are almost inevitably present in zeolite-based separation processes.

Water condensation in hydrophobic silicalite-1 zeolite: a molecular simulation study.

We report grand canonical Monte Carlo simulations of the gas and liquid phase adsorption of water in silicalite-1 zeolite. Simple but effective models and simulation methods, found useful for studying gas adsorption in nanoporous materials, have been extended to describe the intrusion/extrusion cycle of water in this hydrophobic solid. The picture of water confined to hydrophobic spaces of nanoscopic dimensions that emerges from this study is one of a strongly depleted and highly inhomogeneous fluid.

Cyan fluorescent protein: molecular dynamics, simulations, and electronic absorption spectrum.

The dynamics and electronic absorption spectrum of enhanced cyan fluorescent protein (ECFP), a mutant of green fluorescent protein (GFP), have been studied by means of a 1 ns molecular dynamics (MD) simulation. The two X-ray conformations A' and B' of ECFP were considered. The chromophore was assumed to be neutral, and all titratable residues were taken in their standard protonation state at neutral pH. The protein was embedded in a box of water molecules (and counterions). The first result is that the two conformations A' and B' are found to be stable all along the simulation. Then, an analysis of the hydrogen-bond networks shows strong differences between the two conformations in the surroundings of the nitrogen atom of the indolic part of the chromophore. This is partly due to the imperfection in the beta barrel near the His148 residue, which allows the access of one solvent molecule inside the protein in conformation A'. Finally, quantum mechanical calculations of the electronic transition energies of the chromophore in the charge cloud of the protein and solvent water molecules were performed using the TDDFT method on 160 snapshots extracted every 5 ps of the MD trajectories. It is found that conformations A' and B' exhibit very similar spectra despite different H-bond networks involving the chromophore. This similarity is related to the weak charge transfer involved in the electronic transition and the weak electrostatic field created by ECFP near the chromophore, within the hypotheses made in the present simulation.

Why [CpW(CO)3]+ reduces H2 to dihydride.

The [CpW(CO)3]+ complex, with three pi acceptor ligands and a positive charge, is shown to have an unexpected reducing ability towards H2 because of a low lying triplet state energy.