On the nature of the transition state in catechol O-methyltransferase. A complementary study based on molecular dynamics and potential energy surface explorations

The way in which enzymes influence the rate of chemical processes is still a question of debate. The protein promotes the catalysis of biochemical processes by lowering the free energy barrier in comparison with the reference uncatalyzed reaction in solution. In this article we are reporting static and dynamic aspects of the enzyme catalysis in a bimolecular reaction, namely a methyl transfer from S-adenosylmethionine to the hydroxylate oxygen of a substituted catechol catalyzed by catechol O-methyltransferase. From QM/MM optimizations, we will first analyze the participation of the environment on the transition vector. The study of molecular dynamics trajectories will allow us to estimate the transmission coefficient from a previously localized transition state as the maximum in the potential of mean force profile. The analysis of the reactive and nonreactive trajectories in the enzyme environment and in solution will also allow studying the geometrical and electronic changes, with special attention to the chemical system movements and the coupling with the environment. The main result, coming from both analyses, is the approximation of the magnesium cation to the nucleophilic and the hydroxyl group of the catecholate as a result of a general movement of the protein, stabilizing in this way the transition state. Consequently, the free energy barrier of the enzyme reaction is dramatically decreased with respect to the reaction in solution.     

Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

A comparative theoretical study of a bimolecular reaction in aqueous solution and catalyzed by the enzyme catechol O-methyltransferase (COMT) has been carried out by a combination of two hybrid QM/MM techniques: statistical simulation methods and internal energy minimizations. In contrast to previous studies by other workers, we have located and characterized transition structures for the reaction in the enzyme active site, in water and in a vacuum, and our potential of mean force calculations are based upon reaction coordinates obtained from features of the potential energy surfaces in the condensed media, not from the gas phase. The AM1/CHARMM calculated free energy of activation for the reaction of S-adenosyl methionine (SAM) with catecholate catalyzed by COMT is 15 kcal mol(-1) lower the AM1/TIP3P free-energy barrier for the reaction of the trimethylsulfonium cation with the catecholate anion in water at 300 K, in agreement with previous estimates. The thermodynamically preferred form of the reactants in the uncatalyzed model reaction in water is a solvent-separated ion pair (SSIP). Conversion of the SSIP into a contact ion pair, with a structure resembling that of the Michaelis complex (MC) for the reaction in the COMT active site, is unfavorable by 7 kcal mol(-1), largely due to reorganization of the solvent. We have considered alternative ways to estimate the so-called "cratic" free energy for bringing the reactant species together in the correct orientation for reaction but conclude that direct evaluation of the free energy of association by means of molecular dynamics simulation with a simple standard-state correction is probably the best approach. The latter correction allows for the fact that the size of the unit cell employed with the periodic boundary simulations does not correspond to the standard state concentration of 1 M. Consideration of MC-like species allows a helpful decomposition of the catalytic effect into preorganization and reorganization phases. In the preorganization phase, the substrates are brought together into the MC-like species, either in water or in the enzyme active site. In the reorganization phase, the roles of the enzymic and aqueous environments may be compared directly because reorganization of the substrate is about the same in both cases. Analysis of the electric field along the reaction coordinate demonstrates that in water the TS is destabilized with respect to the MC-like species because the polarity of the solute diminishes and consequently the reaction field is also decreased. In the enzyme, the electric field is mainly a permanent field and consequently there is only a small reorganization of the environment. Therefore, destabilization of the TS is lower than in solution, and the activation barrier is smaller.     

Inhibition of the adsorption of cyclohexene over a Pd/sepiolite catalyst by acrylamide

Cyclohexene acts as a powerful hydrogen donor over supported Pd catalysts. On the basis of the theory of competitive hydrogenations, this paper aims at accounting for the fact that acrylamide cannot be reduced by hydrogen transfer using cyclohexene as donor, whereas methacrylamide can.

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Switching the Mechanism of NADH Photooxidation by Supramolecular Interactions

A series of three Ru(II) polypyridine complexes was investigated for the selective photocatalytic oxidation of NAD(P)H to NAD(P)⁺ in water. A combination of (time-resolved) spectroscopic studies and photocatalysis experiments revealed that ligand design can be used to control the mechanism of the photooxidation: For prototypical Ru(II) complexes a ¹O₂ pathway was found. Rudppz ([(tbbpy)₂Ru(dppz)]Cl₂, tbbpy=4,4'-di-tert-butyl-2,2'-bipyridine, dppz=dipyrido[3,2-a:2′,3′-c]phenazine), instead, initiated the cofactor oxidation by electron transfer from NAD(P)H enabled by supramolecular binding between substrate and catalyst. Expulsion of the photoproduct NAD(P)⁺ from the supramolecular binding site in Rudppz allowed very efficient turnover. Therefore, Rudppz permits repetitive selective assembly and oxidative conversion of reduced naturally occurring nicotinamides by recognizing the redox state of the cofactor under formation of H₂O₂ as additional product. This photocatalytic process can fuel discontinuous photobiocatalysis.     

Light-Activated Rhenium Complexes with Dual Mode of Action against Bacteria

New antibiotics and innovative approaches to kill drug-resistant bacteria are urgently needed. Metal complexes offer access to alternative modes of action but have only sparingly been investigated in antibacterial drug discovery. We have developed a light-activated rhenium complex with activity against drug-resistant S. aureus and E. coli. The activity profile against mutant strains combined with assessments of cellular uptake and synergy suggest two distinct modes of action.     

Tuning PtII-Based Donor–Acceptor Systems through Ligand Design: Effects on Frontier Orbitals,Redox Potentials,UV/Vis/NIR Absorptions,Electrochromism, and Photocatalysis

Asymmetric platinum donor–acceptor complexes [(pimp)Pt(Q²⁻)] are presented in this work, in which pimp=[(2,4,6-trimethylphenylimino)methyl]pyridine and Q²⁻=catecholate-type donor ligands. The properties of the complexes are evaluated as a function of the donor ligands, and correlations are drawn among electrochemical, optical, and theoretical data. Special focus has been put on the spectroelectrochemical investigation of the complexes featuring sulfonyl-substituted phenylendiamide ligands, which show redox-induced linkage isomerism upon oxidation. Time-dependent density functional theory (TD-DFT) as well as electron flux density analysis have been employed to rationalize the optical spectra of the complexes and their reactivity. Compound 1 ([(pimp)Pt(Q²⁻)] with Q²⁻=3,5-di-tert-butylcatecholate) was shown to be an efficient photosensitizer for molecular oxygen and was subsequently employed in photochemical cross-dehydrogenative coupling (CDC) reactions. The results thus display new avenues for donor–acceptor systems, including their role as photocatalysts for organic transformations, and the possibility to introduce redox-induced linkage isomerism in these compounds through the use of sulfonamide substituents on the donor ligands.     

Nonlinear wave interactions in patterned Silica and AlGaAs waveguides

We study nonlinear interactions between discrete optical solitons that propagate in different regimes of diffraction, and the nonlinear scattering of dispersive waves by local optical potentials. It is well known in optics that when linear coherent waves meet, they interfere without interactions. Linear waves also scatter through local optical structures not exchanging any power with the guided modes of these structures. As a focusing Kerr nonlinearity is present, such linearly-inhibited phenomena can exist. Our studies are performed in silica and AlGaAs nonlinear waveguides, excited by ultra-short pulses in the near infrared. Presented at 9-th International Workshop on Nonlinear Optics Applications, NOA 2007, May 17–20, 2007, Świnoujście, Poland