Tyrosine or Tryptophan? Modifying a Metalloradical Catalytic Site by Removal of the Cys-Tyr Cross-Link in the Galactose 6-Oxidase Homologue GlxA.

The concerted redox action of a metal ion and an organic cofactor is a unique way to maximize the catalytic power of an enzyme. An example of such synergy is the fungal galactose 6-oxidase, which has inspired the creation of biomimetic copper oxidation catalysts. Galactose 6-oxidase and its bacterial homologue, GlxA, possess a metalloradical catalytic site that contains a free radical on a covalently linked Cys-Tyr and a copper atom. Such a catalytic site enables for the two-electron oxidation of alcohols to aldehydes. When the ability to form the Cys-Tyr in GlxA is disrupted, a radical can still be formed. Surprisingly, the radical species is not the Tyr residue but rather a copper second-coordination sphere Trp residue. This is demonstrated through the introduction of a new algorithm for Trp-radical EPR spectra simulation. Our findings suggest a new mechanism of free-radical transfer between aromatic residues and that the Cys-Tyr cross-link prevents radical migration away from the catalytic site.

Effects of the protein environment on the spectral properties of tryptophan radicals in Pseudomonas aeruginosa azurin.

Many biological electron-transfer reactions involve short-lived tryptophan radicals as key reactive intermediates. While these species are difficult to investigate, the recent photogeneration of a long-lived neutral tryptophan radical in two Pseudomonas aeruginosa azurin mutants (Az48W and ReAz108W) made it possible to characterize the electronic, vibrational, and magnetic properties of such species and their sensitivity to the molecular environment. Indeed, in Az48W the radical is embedded in the hydrophobic core while, in ReAz108W it is solvent-exposed. Here we use density functional theory and multiconfigurational perturbation theory to construct quantum-mechanics/molecular-mechanics models of Az48W(•) and ReAz108W(•) capable of reproducing specific features of their observed UV-vis, resonance Raman, and electron paramagnetic resonance spectra. The results show that the models can correctly replicate the spectral changes imposed by the two contrasting hydrophobic and hydrophilic environments. Most importantly, the same models can be employed to disentangle the molecular-level interactions responsible for such changes. It is found that the control of the hydrogen bonding between the tryptophan radical and a single specific surface water molecule in ReAz108W(•) represents an effective means of spectral modulation. Similarly, a specific electrostatic interaction between the radical moiety and a Val residue is found to control the Az48W(•) excitation energy. These modulations appear to be mediated by the increase in nitrogen negative charge (and consequent increase in hydrogen bonding) of the spectroscopic D2 state with respect to the D0 state of the chromophore. Finally, the same protein models are used to predict the relaxed Az48W(•) and ReAz108W(•) D2 structures, showing that the effect of the environment on the corresponding fluorescence maxima must parallel that of D0 absorption spectra.

The nature of tryptophan radicals involved in the long-range electron transfer of lignin peroxidase and lignin peroxidase-like systems: Insights from quantum mechanical/molecular mechanics simulations.

A catalytically active tryptophan radical has been demonstrated to be involved in the long-range electron transfer to the heme cofactor of lignin peroxidase (LiP) from Phanerochaete chrysosporium although no direct detection by EPR spectroscopy of the tryptophan radical intermediate has been reported to date. An engineering-based approach has been used to manipulate the microenvironment of the redox-active tryptophan site in LiP and Coprinus cinereus Peroxidase (CiP), allowing the direct evidence of the tryptophan radical species. In light of the newly available EPR experimental data, we performed a quantum mechanical/molecular mechanics computational study to characterize the tryptophan radicals in the above protein matrices as well as in pristine LiP. The nature of the tryptophan radicals is discussed together with the analysis of their environment with the aim of understanding the different behavior of pristine LiP in comparison with that of LiP and CiP variants.

EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level.

Quantum mechanics/molecular mechanics (QM/MM) methods, employing density functional theory (DFT), have been used to compute the electron paramagnetic resonance (EPR) parameters of tryptophan and tyrosyl radical intermediates involved in the catalytic cycle of Pleurotus eryngii versatile peroxidase (VP) and its W164Y variant, respectively. These radicals have been previously experimentally detected and characterized both in the two-electron and one-electron activated forms of the enzymes. In this work, the well-studied W164 radical in VP has been chosen for calibration purposes because its spectroscopic properties have been extensively studied by multifrequency EPR and ENDOR spectroscopies. Using a B3LYP/CHARMM procedure, appropriately accounting for electrostatic, such as hydrogen bonding, and steric environmental interactions, a good agreement between the calculated and measured EPR parameters for both radicals has been achieved; g-tensors, hyperfine coupling constants (hfcc) and Mulliken spin densities have been correlated to changes in geometries, hydrogen bond networks and electrostatic environment, with the aim of understanding the influence of the protein surroundings on EPR properties. In addition, the present calculations demonstrate, for VP, the formation of a neutral tryptophan radical, hydrogen bonded to the nearby E243, via a stepwise electron and proton transfer with earlier involvement of a short-lived tryptophan cationic species. Instead, for W164Y, the QM/MM dynamics simulation shows that the tyrosine oxidation proceeds via a concerted electron and proton transfer and is accompanied by a significant reorganization of residues and water molecules surrounding the tyrosyl radical.

A novel biomimetic photochemical switch at work: design of a photomodulable peptide.

We report the outcomes of our recent computational and experimental work for the development of a novel biomimetic molecular switch. Furthermore, we present the new results on the design and computational characterization of a "functional" cyclic peptidomimetic formed by the switch conjugated to a biologically active peptide: the RGD sequence involved in the control of cell adhesion. Structural properties of the construct are investigated in aqueous solution using molecular dynamics (MD) simulations. Analysis of MD trajectories reveals that, for each diastereoisomer of the switch (E or Z), different conformations are stabilized. Electrostatic and spectroscopic properties of such conformers are evaluated by means of ab initio multiconfiguration quantum chemical method implemented in a quantum-mechanical/molecular-mechanic (CASPT2//CASSCF/6-31G*/AMBER) scheme.

In silico spectroscopy of tryptophan and tyrosine radicals involved in the long-range electron transfer of cytochrome c peroxidase.

Cytochrome c peroxidase (CcP) is a heme-containing enzyme that catalyzes the oxidation of the ferrocytochrome c to ferricytochrome c with concomitant reduction of H2O2 to H2O. Its catalytic cycle involves the formation of a double oxidized species (compound I) consisting of an oxoferryl center (Fe(IV)═O) and an amino acid radical (R(•)). Here we use a quantum-mechanics/molecular-mechanics (QM/MM) computational protocol based on density functional theory (DFT) and multiconfigurational perturbation theory (CASPT2) methods to reproduce specific features of compound I EPR and UV-vis spectra. The results show that the employed QM/MM models can correctly predict the magnetic, electronic and vibrational properties of the observed amino acid radicals of compound I. Furthermore, we have been able to confirm that the principal radical species of compound I is a tryptophan cationic radical located on residue 191 (Trp191(•+)) and that three tyrosine residues (Tyr203, Tyr236, and Tyr251), located along two possible ET pathways involving Trp191(•+), are possible candidates to host the secondary radical species.

Excited State Geometries and Vertical Emission Energies of Solvated Dyes for DSSC: A PCM/TD-DFT Benchmark Study.

The ability of Time-Dependent Density Functional Theory (TD-DFT) to provide excited state geometries and reproduce emission energies of organic D-π-A dyes designed for DSSC applications is evaluated. The performance of six functionals (CAM-B3LYP, MPW1K, ωB97X-D, LC-BLYP, LC-ωPBE, and M06-HF) in combination with three basis sets (cc-pVDZ, 6-31+G(d,p), and 6-311+G(2d,p)) has been analyzed. Solvent effects have been taken into account by means of a Polarizable Continuum Model in both LR and SS formalisms. Our LR-PCM/TD-DFT results show that accurate emission energies are obtained only when solvent effects are included in the computation of excited state geometries and when a range separated hybrid functional is used. Vertical emission energies are reproduced with a mean absolute error of at most 0.2 eV. The accuracy is further improved using the SS-PCM formalism.

Synthesis, spectroscopic and DFT structural characterization of two novel ruthenium(III) oxicam complexes. In vivo evaluation of anti-inflammatory and gastric damaging activities.

The reactions of ruthenium(III) chloride trihydrate with piroxicam (H2PIR) and tenoxicam (H2TEN), two widely used non-steroidal anti-inflammatory drugs, afforded [Ru(III)Cl2(H2PIR)(HPIR)],·1, and [Ru(III)Cl2(H2TEN)(HTEN)],·2. Both compounds were obtained as pure green solids through purification via flash column chromatography. Characterizations were accomplished through UV-vis and IR spectroscopy, potentiometry and HPLC. Quantum mechanics and density functional computational methods were applied to investigate their respective molecular structures. The experimental and computational results are in agreement with a pseudo-octahedral coordination where the two chlorido ligands are in trans positions (apical) and the two trans-N,O chelating oxicam ligands occupy the equatorial sites. Both compounds revealed an acceptable solubility and stability profile upon dissolution in a standard buffer at physiological pH. Nonetheless, the addition of biologically occurring reducing agents caused spectral changes. The two complexes manifested a poor reactivity with the model proteins cytochrome c and lysozyme: no evidence for adduct formation was indeed obtained based on a standard ESI MS analysis; in contrast, some significant reactivity with serum albumin was proved spectrophotometrically. Remarkably, both study compounds revealed pronounced anti-edema effects in vivo suggesting that the pharmacological actions of the ligands are mostly retained; in addition, they were less irritating than piroxicam on the gastric mucosa when the coordination compounds and free oxicam were administered at the same overall molar concentration of the ligand. Overall, the present results point out that ruthenium coordination may represent an effective strategy to improve the pharmacological properties of oxicam drugs reducing their undesired side effects.

Insights into the homocoupling reaction of 4-methylamino benzoic acid mediated by Trametes versicolor laccase.

Spectroscopic measurements combined with Density Functional Theory calculations were applied to the characterization of the homocoupling reaction of 4-methylamino benzoic acid mediated by laccase.