Theoretical Modeling of Enzyme Reactions: The Thermodynamics of Formation of Compound 0 in Horseradish Peroxidase

Mechanistic insights into the chemistry of compound I formation in heme peroxidases: quantum chemical investigations of cytochrome c peroxidase

Peroxidases are heme containing enzymes that catalyze peroxide-dependant oxidation of a variety of substrates through forming key ferryl intermediates, compounds I and II. Cytochrome c peroxidase (Ccp1) has served for decades as a chemical model toward understanding the chemical biology of this heme family of enzymes. It is known to feature a distinctive electronic behaviour for its compound I despite significant structural similarity to other peroxidases. A water-assisted mechanism has been proposed over a dry one for the formation of compound I in similar peroxidases. To better identify the viability of these mechanisms, we employed quantum chemistry calculations for the heme pocket of Ccp1 in three different spin states. We provided comparative energetic and structural results for the six possible pathways that suggest the preference of the dry mechanism energetically and structurally. The doublet state is found to be the most preferable spin state for the mechanism to proceed and for the formation of the Cpd I ferryl-intermediate irrespective of the considered dielectric constant used to represent the solvent environment. The nature of the spin state has negligible effects on the calculated structures but great impact on the energetics. Our analysis was also expanded to explain the major contribution of key residues to the peroxidase activity of Ccp1 through exploring the mechanism at various in silico generated Ccp1 variants. Overall, we provide valuable findings toward solving the current ambiguity of the exact mechanism in Ccp1, which could be applied to peroxidases with similar heme pockets.

Discerning the feasibility of a no-water peroxidase mechanism in the doublet spin state irrespective of the environment surrounding the heme pocket.

The Nature and Reactivity of Ferryl Heme in Compounds I and II

Aerobic organisms have evolved to activate oxygen from the atmosphere, which allows them to catalyze the oxidation of different kinds of substrates. This activation of oxygen is achieved by a metal center (usually iron or copper) buried within a metalloprotein. In the case of iron-containing heme enzymes, the activation of oxygen is achieved by formation of transient iron-oxo (ferryl) intermediates; these intermediates are called Compound I and Compound II. The Compound I and II intermediates were first discovered in the 1930s in horseradish peroxidase, and it is now known that these same species are used across the family of heme enzymes, which include all of the peroxidases, the heme catalases, the P450s, cytochrome c oxidase, and NO synthase. Many years have passed since the first observations, but establishing the chemical nature of these transient ferryl species remains a fundamental question that is relevant to the reactivity, and therefore the usefulness, of these species in biology. This Account summarizes experiments that were conceived and conducted at Leicester and presents our ideas on the chemical nature, stability, and reactivity of these ferryl heme species. We begin by briefly summarizing the early milestones in the field, from the 1940s and 1950s. We present comparisons between the nature and reactivity of the ferryl species in horseradish peroxidase, cytochrome c peroxidase, and ascorbate peroxidase; and we consider different modes of electron delivery to ferryl heme, from different substrates in different peroxidases. We address the question of whether the ferryl heme is best formulated as an (unprotonated) Fe^IV═O or as a (protonated) Fe^IV-OH species. A range of spectroscopic approaches (EXAFS, resonance Raman, Mossbauer, and EPR) have been used over many decades to examine this question, and in the last ten years, X-ray crystallography has also been employed. We describe how information from all of these studies has blended together to create an overall picture, and how the recent application of neutron crystallography has directly identified protonation states and has helped to clarify the precise nature of the ferryl heme in cytochrome c peroxidase and ascorbate peroxidase. We draw comparisons between the Compound I and Compound II species that we have observed in peroxidases with those found in other heme systems, notably the P450s, highlighting possible commonality across these heme ferryl systems. The identification of proton locations from neutron structures of these ferryl species opens the door for understanding the proton translocations that need to occur during O-O bond cleavage.

How the Reorganization Free Energy Affects the Reduction Potential of Structurally Homologous Cytochromes

Differences in the reduction potential E(0) among structurally similar metalloproteins cannot always be fully explained on the basis of their 3-D structures. We investigate the molecular determinants to E(0) using the mixed quantum mechanics/molecular mechanics approach named perturbed matrix method (PMM); after comparison with experimental values to assess the reliability of our calculations, we investigate the relationship between the change in free energy upon reduction ΔA(0) and the reorganization energy. We find that the reduction potential of cytochromes can be regarded as the result of the sum of two terms, one being mostly dependent on the energy fluctuations within a limited range around the mean transition energy and the second being mostly dependent linearly on the difference Δλ = λred - λox of the reorganization free energies for the ox → red (λred) and for the red → ox (λox) relaxations.

The reversible opening of water channels in cytochrome c modulates the heme iron reduction potential

Dynamic protein-solvent interactions are fundamental for life processes, but their investigation is still experimentally very demanding. Molecular dynamics simulations up to hundreds of nanoseconds can bring to light unexpected events even for extensively studied biomolecules. This paper reports a combined computational/experimental approach that reveals the reversible opening of two distinct fluctuating cavities in Saccharomyces cerevisiae iso-1-cytochrome c. Both channels allow water access to the heme center. By means of a mixed quantum mechanics/molecular dynamics (QM/MD) theoretical approach, the perturbed matrix method (PMM), that allows to reach long simulation times, changes in the reduction potential of the heme Fe(3+)/Fe(2+) couple induced by the opening of each cavity are calculated. Shifts of the reduction potential upon changes in the hydration of the heme propionates are observed. These variations are relatively small but significant and could therefore represent a tool developed by cytochrome c for the solvent driven, fine-tuning of its redox functionality.

A single-site mutation (F429H) converts the enzyme CYP 2B4 into a heme oxygenase: a QM/MM study

The intriguing deactivation of the cytochrome P450 (CYP) 2B4 enzyme induced by mutation of a single residue, Phe429 to His, is explored by quantum mechanical/molecular mechanical calculations of the O-OH bond activation of the (Fe(3+)OOH)(-) intermediate. It is found that the F429H mutant of CYP 2B4 undergoes homolytic instead of heterolytic O-OH bond cleavage. Thus, the mutant acquires the following characteristics of a heme oxygenase enzyme: (a) donation by His429 of an additional NH---S H-bond to the cysteine ligand combined with the presence of the substrate retards the heterolytic cleavage and gives rise to homolytic O-OH cleavage, and (b) the Thr302/water cluster orients nascent OH(•) and ensures efficient meso hydroxylation.

A general theoretical model for electron transfer reactions in complex systems

In this paper we present a general theoretical-computational model for treating electron transfer reactions in complex atomic-molecular systems. The underlying idea of the approach, based on unbiased first-principles calculations at the atomistic level, utilizes the definition and the construction of the Diabatic Perturbed states of the involved reactive partners (i.e. the quantum centres in our perturbation approach) as provided by the interaction with their environment, including their mutual interaction. In this way we reconstruct the true Adiabatic states of the reactive partners characterizing the electron transfer process as the fluctuation of the electronic density due to the fluctuating perturbation. Results obtained by using a combination of Molecular Dynamics simulation and the Perturbed Matrix Method on a prototypical intramolecular electron transfer (from 2-(9,9'-dimethyl)fluorene to the 2-naphthalene group separated by a steroidal 5-α-androstane skeleton) well illustrate the accuracy of the method in reproducing both the thermodynamics and the kinetics of the process.

Multireference and multiconfiguration ab initio methods in heme-related systems: what have we learned so far?

This work reviews the recent applications of ab initio multireference/multiconfiguration (MR/MC) electronic structure methods to heme-related systems, involving tetra-, penta-, and hexa-coordinate species, as well as the high-valent iron-oxo species. The current accuracy of these methods in the various systems is discussed, with special attention to potential sources of systematic errors. Thus, the review summarizes and tries to rationalize the key elements of MR/MC calculations, namely, the choice of the employed active space, especially the so-called double-shell effect that has already been recognized to be important in transition-metal-containing systems, and the impact of these elements on the spin-state energetics of heme species, as well as on the bonding mechanism of small molecules to the heme. It is shown that expansion of the MC wave function into one based on localized orbitals provides a compact and insightful view on some otherwise complex electronic structures. The effects of protein environment on the MR/MC results are summarized for the few available quantum mechanical/molecular mechanical (QM/MM) studies. Comparisons with corresponding DFT results are also made wherever available. Potential future directions are proposed.

On the role of water in peroxidase catalysis: a theoretical investigation of HRP compound I formation

We have investigated the dynamics of water molecules in the distal pocket of horseradish peroxidase to elucidate the role that they may play in the formation of the principal active species of the enzymatic cycle (compound I, Por(o+)-Fe(IV)=O) upon reaction of the resting Fe(III) state with hydrogen peroxide. The equilibrium molecular dynamics simulations show that, in accord with experimental evidence, the active site access channel is hydrated with an average of two to three water molecules within 5 A from the bound hydrogen peroxide. Although the channel is always hydrated, the specific conformations in which a water molecule bridges H(2)O(2) and the distal histidine, which were found (Derat; et al. J. Am. Chem. Soc. 2007, 129, 6346.) to display a low-energy barrier for the initial acid-base step of the reaction, occur with low probability but are relevant within the time scale of catalysis. Metadynamics simulations, which were used to reconstruct the free-energy landscape of water motion in the access channel, revealed that preferred interaction sites within the channel are separated by small energy barriers (<1.5 kcal/mol). Most importantly, water-bridged conformations lie on a shoulder just 1 kcal/mol above one local minimum and thus are easily accessible. Such an energy landscape appears as a requisite for the effectiveness of compound I formation, whereby the H-bonding pattern involving reactants and catalytic residues (including the intervening water molecule) has to rearrange to deliver the proton to the distal OH moiety of the hydrogen peroxide and thereby lead to heterolytic O-O cleavage. Our study provides an example of a system for which the "reactive configurations" (i.e., structures characterized by a low barrier for the chemical transformation) correspond to a minor population of the system and show how equilibrium molecular dynamics and free-energy calculations may conveniently be used to ascertain that such reactive conformations are indeed accessible to the system. Once again, the MD and QM/MM combination shows that a single water molecule acts as a biocatalyst in the cycle of HRP.

The dynamic role of distal side residues in heme hydroperoxidase catalysis. Interplay between X-ray crystallography and ab initio MD simulations

The enzymatic cycle of hydroperoxidases involves the resting Fe(III) state of the enzyme and the high-valent iron intermediates Compound I and Compound II. These states might be characterized by X-ray crystallography and the transition pathways between each state can be investigated using atomistic simulations. Here we review our recent work in the modeling of two key steps of the enzymatic reaction of hydroperoxidases: the formation of Cpd I in peroxidase and the reduction of Cpd I in catalase. It will be shown that small conformational motions of distal side residues (His in peroxidases and His/Asn in catalases), not,or only partially, revealed by the available X-ray structures, play an important role in the catalytic processes examined.

Charge transfer equilibria of aqueous single stranded DNA

The charge transfer thermodynamics of a simple model of DNA, a single stranded 10-mer poly-adenine oligonucleotide, in water is investigated by means of a computational/theoretical procedure, in which all the relevant environmental effects are considered. Our data indicate that water and counterions ultimately dominate the DNA reduction and oxidation free energies, which are also strongly influenced by the base position along the strand. In fact, we estimated that reduction free energies are large and negative, particularly for the bases close to the 5' and 3' positions, whereas the electron detachment is thermodynamically unfavoured all along the strand, but with a higher free energy cost in the central region of the molecule. Further investigation on double charging, i.e. one nucleobase is oxidized and one is reduced within the strand, predicts that charge-separated states are possible and thermodynamically largely stable when the ionic forms are separated by several nucleobases.