ATP Binding and Aspartate Protonation Enhance Photoinduced Electron Transfer in Plant Cryptochrome

International audienceCryptochromes are flavoproteins encountered in most vegetal and animal species. They play a role of blue-light receptors in plants and in invertebrates. The putative resting state of the FAD cofactor in these proteins is its fully oxidized form, FADox. Upon blue-light excitation, the isoalloxazine ring (ISO) may undergo an ultrafast reduction by a nearby tryptophan residue W400. This primary reduction triggers a cascade of electron and proton transfers, ultimately leading to the formation of the FADH° radical. A recent experimental study has shown that the yield of FADH° formation in Arabidopsis cryptochrome can be strongly modulated by ATP binding and by pH, affecting the protonation state of D396 (proton donor to FAD°–). Here we provide a detailed molecular analysis of these effects by means of combined classical molecular dynamics simulations and time-dependent density functional theory calculations. When ATP is present and D396 protonated, FAD remains in close contact with W400, thereby enhancing electron transfer (ET) from W400 to ISO*. In contrast, deprotonation of D396 and absence of ATP introduce flexibility to the photoactive site prior to FAD excitation, with the consequence of increased ISO-W400 distance and diminished tunneling rate by almost two orders of magnitude. We show that under these conditions, ET from the adenine moiety of FAD becomes a competitive relaxation pathway. Overall, our data suggest that the observed effects of ATP and pH on the FAD photoreduction find their roots in the earliest stage of the photoreduction process; i.e., ATP binding and the protonation state of D396 determine the preferred pathway of ISO* relaxation

Energetics of Photoinduced Charge Migration within the Tryptophan Tetrad of an Animal (6–4) Photolyase

International audienceCryptochromes and photolyases are flavoproteins that undergo cascades of electron/hole transfers after excitation of the flavin cofactor. It was recently discovered that animal (6–4) photolyases, as well as animal cryptochromes, feature a chain of four tryptophan residues, while other members of the family contain merely a tryptophan triad. Transient absorption spectroscopy measurements on Xenopus laevis (6–4) photolyase have shown that the fourth residue is effectively involved in photoreduction but at the same time could not unequivocally ascertain the final redox state of this residue. In this article, polarizable molecular dynamics simulations and constrained density functional theory calculations are carried out to reveal the energetics of charge migration along the tryptophan tetrad. Migration toward the fourth tryptophan is found to be thermodynamically favorable. Electron transfer mechanisms are sought either through an incoherent hopping mechanism or through a multiple sites tunneling process. The Jortner–Bixon formulation of electron transfer (ET) theory is employed to characterize the hopping mechanism. The interplay between electron transfer and relaxation of protein and solvent is analyzed in detail. Our simulations confirm that ET in (6–4) photolyase proceeds out of equilibrium. Multiple site tunneling is modeled with the recently proposed flickering resonance mechanism. Given the position of energy levels and the distribution of electronic coupling values, tunneling over three tryptophan residues may become competitive in some cases, although a hopping mechanism is likely to be the dominant channel. For both reactive channels, computed rates are very sensitive to the starting protein configuration, suggesting that both can take place and eventually be mixed, depending on the state of the system when photoexcitation takes place

AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms

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Unexpected Ultrafast Silver Ion Reduction: Dynamics Driven by the Solvent Structure

Picosecond pulse radiolysis measurements have been performed in neutral and highly acidic aqueous solutions containing silver ions at different concentrations. Silver ion reduction is used to understand the ultrafast chemistry of irradiated water and aqueous solutions. The absorption band measured at the end of the 7-ps electron pulses has an intense band with a maximum at 360 nm due to the formation of silver atoms. Kinetics shows that the amount of silver atom formed at the end of the electron pulse in phosphoric acid solutions is greater than that in neutral water. This unexpectedly high yield of silver atom formation cannot be explained solely by the reaction between silver ions and solvated electrons in neutral solutions nor by the reaction with hydrogen atoms in phosphoric acid solutions. To explain the observed ultrafast reduction of silver ions, the presolvated electron, be it free or paired to the hydronium cation, must react very quickly with a silver ion, potentially competing with geminate recombination of the electron and its sibling radical cation

Water binding to FeIII hemes studied in a cooled ion trap: characterization of a strong ‘weak’ ligand

International audienceThe interaction of a water molecule with ferric heme-iron protoporphyrin ([PP Fe III ] +) has been investigated in the gas phase in an ion trap and studied theoretically by density functional theory. It is found that the interaction of water with ferric heme leads to a stable [PP-Fe III-H 2 O] + complex in the intermediate spin state (S = 3/2), in the same state as its unligated [PP-Fe III ] + homologue, without spin crossing during water attachment. Using the Van't Hoff equation, the reaction enthalpy for the formation of a Fe-OH 2 bond has been determined for [PP-Fe III-H 2 O] + and [PP-Fe III-(H 2 O) 2 ] +. The corrected binding energy for a single Fe-H 2 O bond is À12.2 AE 0.6 kcal mol À1 , while DFT calculations at the OPBE level yield À11.7 kcal mol À1. The binding energy of the second ligation yielding a six coordinated Fe III atom is decreased with a bond energy of À9 AE 0.9 kcal mol À1 , well reproduced by calculations as À7.1 kcal mol À1. However, calculations reveal features of a weaker bond type, such as a rather long Fe-O bond with 2.28 Å for the [PP-Fe III-H 2 O] + complex and the absence of a spin change by complexation. Thus despite a strong bond with H 2 O, the Fe III atom does not show, through theoretical modelling, a strong acceptor character in its half filled 3d z 2 orbital. It is also observed that the binding properties of H 2 O to hemes seem strikingly specific to ferric heme and we have shown, experimentally and theoretically, that the affinity of H 2 O for protonated heme [H PP-Fe] + , an intermediate between Fe III and Fe II , is strongly reduced compared to that for ferric heme

Ultrafast flavin photoreduction in an oxidized animal (6-4) photolyase through an unconventional tryptophan tetrad

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Spin-driven activation of dioxygen in various metalloenzymes and their inspired models.

International audienceAlthough potentially powerful, molecular oxygen is an inert oxidant due to the triplet nature of its ground state. Therefore, many enzymesse various metal cations (M) to produce singlet active species M(n) O(2) . In this communication we investigate the topology of the Electron Localization Function (ELF) within five biomimetic complexes which are representative of the strategies followed by metalloenzymes to activate O(2) . Thanks to its coupling to the constrained DFT methods the ELF analysis reveals the tight connection between the spin state of the adduct and the spatial organization of the oxygen lone pairs. We suggest that enzymes could resort to spin state control to tune the regioselectivity of substrate oxidations

The surprisingly high ligation energy of CO to Ruthenium porphyrins

International audienceA combined theoretical and experimental approach has been used to investigate the binding energy of a ruthenium metalloporphyrin ligated with CO, ruthenium tetraphenyl porphyrin [Ru II TPP] in the Ru II oxidation degree. Measurements made by VUV ionization with the DESIRS beamline at Synchrotron SOLEIL lead to adiabatic ionization energies of [Ru II TPP] and its complex with CO, [Ru II TPP-CO], to be 6.48±0.03 eV and 6.60±0.03 eV, respectively while the ion dissociation threshold of [Ru II TPP-CO] + is measured at 8.36±0.03 eV. These experimental data are used to derive binding energies of the CO ligand in the neutral and cationic complex (1.88±0.06 eV and 1.76±0.06 eV, respectively) using a Born-Haber cycle. Density Functional Theory calculations, in very satisfactory agreement with the experimental results, help to get insights into the metal-ligand bond. Notably, the high ligation energies can be rationalized in terms of the ruthenium orbital structure, which is singular from that of the iron atom. Thus, beyond indications of a strengthening of the Ru-CO bond from the decrease in the CO vibrational frequency in the complex as compared to the Fe-CO bond, high level calculations are essential to describe accurately the metal ligand (CO) bond and show that the Ru-CO bond energy is strongly affected by the splitting of triplet and singlet spin states in uncomplexed [Ru TPP]

QM/MM with Auxiliary DFT

International audienceThis chapter describes the theoretical background of the quantum mechanical/molecular mechanical (QM/MM) implementation in deMon2k within the framework of auxiliary density functional theory (ADFT). It aims to give the reader an overview of the current state of the art of this QM/MM implementation and perspectives for its future development. To this end, we first derive the ADFT working equations for the QM and QM/MM energy and gradient expressions. Based on the joint QM/MM gradient expression, we present algorithms for QM/MM structure optimizations, transition-state searches and molecular dynamics simulations. The use of auxiliary density perturbation theory (ADPT) in the framework of QM/MM is discussed using illustrative implementations including analytic second-order ADFT energy derivatives, nuclear magnetic resonance chemical shift calculations and excited state calculations using time-dependent ADFT. The chapter closes with the description of a transformation program used to generate deMon2k QM/MM inputs