Theoretical study of the phosphotriesterase reaction mechanism

Catalytic Redundancies and Conformational Plasticity Drives Selectivity and Promiscuity in Quorum Quenching Lactonases

Several enzymes from the metallo-β-lactamase-like family of lactonases (MLLs) degrade N- acyl-L-homoserine lactones (AHLs). In doing so, they play a role in a microbial communication system, quorum sensing, which contributes to pathogenicity and biofilm formation. There is currently great interest in designing quorum quenching ( QQ ) enzymes that can interfere with this communication and be used in a range of industrial and biomedical applications. However, tailoring these enzymes for specific targets requires a thorough understanding of their mechanisms and the physicochemical properties that determine their substrate specificities. We present here a detailed biochemical, computational, and structural study of the MLL GcL, which is highly proficient, thermostable, and has broad substrate specificity. Strikingly, we show that GcL does not only accept a broad range of substrates but is also capable of utilizing different reaction mechanisms that are differentially used in function of the substrate structure or the remodeling of the active site via mutations. Comparison of GcL to other lactonases such as AiiA and AaL demonstrates similar mechanistic promiscuity, suggesting this is a shared feature across lactonases in this enzyme family. Mechanistic promiscuity has previously been observed in the lactonase/paraoxonase PON1, as well as with protein tyrosine phosphatases that operate via a dual general-acid mechanism. The apparent prevalence of this phenomenon is significant from both a biochemical and an engineering perspective: in addition to optimizing for specific substrates, it is possible to optimize for specific mechanisms, opening new doors not just for the design of novel quorum quenching enzymes, but also of other mechanistically promiscuous enzymes.

Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set

We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.

Catalytic Reaction Mechanism of Glyoxalase II: A Quantum Mechanics/Molecular Mechanics Study

Methylglyoxal (MG) is a reactive and toxic compound produced in carbohydrate, lipid, and amino acid metabolism. The glyoxalase system is the main detoxifying route for MG and consists of two enzymes, glyoxalase I (GlxI) and glyoxalase II (GlxII). GlxI catalyzes the formation of S-d-lactoylglutathione from hemithioacetal, and GlxII converts this intermediate to d-lactate. A relationship between the glyoxalase system and some diseases like diabetes has been shown, and inhibiting enzymes of this system may be an effective means of controlling certain diseases. A detailed understanding of the reaction mechanism of an enzyme is essential to the rational design of competitive inhibitors. In this work, we use quantum mechanics/molecular mechanics (QM/MM) calculations and energy refinement utilizing the big-QM and QM/MM thermodynamic cycle perturbation methods to propose a mechanism for the GlxII reaction that starts with a nucleophilic attack of the bridging OH^- group on the substrate. The coordination of the substrate to the Zn ions places its electrophilic center close to the hydroxide group, enabling the reaction to proceed. Our estimated reaction energies are in excellent agreement with experimental data, thus demonstrating the reliability of our approach and the proposed mechanism. Additionally, we examined alternative protonation states of Asp-29, Asp-58, Asp-134, and the bridging hydroxide ion in the catalytic process. However, these give less favorable reactions, a poorer reproduction of the crystal structure geometry of the active site, and higher root-mean-squared deviations of the active site residues in molecular dynamics simulations.

Organophosphate pesticides an emerging environmental contaminant: Pollution, toxicity, bioremediation progress, and remaining challenges

Organophosphates (OPs) are an integral part of modern agriculture; however, due to overexploitation, OPs pesticides residues are leaching and accumulating in the soil, and groundwater contaminated terrestrial and aquatic food webs. Acute exposure to OPs could produce toxicity in insects, plants, animals, and humans. OPs are known for covalent inhibition of acetylcholinesterase enzyme in pests and terrestrial/aquatic organisms, leading to nervous, respiratory, reproductive, and hepatic abnormalities. OPs pesticides also disrupt the growth-promoting machinery in plants by inhibiting key enzymes, permeability, and trans-cuticular diffusion, which is crucial for plant growth. Excessive use of OPs, directly/indirectly affecting human/environmental health, raise a thoughtful global concern. Developing a safe, reliable, economical, and eco-friendly methods for removing OPs pesticides from the environment is thus necessary. Bioremediation techniques coupled with microbes or microbial-biocatalysts are emerging as promising antidotes for OPs pesticides. Here, we comprehensively review the current scenario of OPs pollution, their toxicity (at a molecular level), and the recent advancements in biotechnology (modified biocatalytic systems) for detection, decontamination, and bioremediation of OP-pesticides in polluted environments. Furthermore, the review focuses on onsite applications of OPs degrading enzymes (immobilizations/biosensors/others), and it also highlights remaining challenges with future approaches.

Density functional theory explorations of parathion and paraoxon hydrolysis as a function of the underlying alkaline environment

Parathion, a once commonly used pesticide known for its potential toxicity, can follow several degradation mechanisms in the environment. Given the species stability and persistence, parathion can be washed into waterways from rain, and therefore an atomistic perspective of the hydrolysis of parathion, and its byproduct paraoxon, is required in order to understand its fate in the environment. Experimental studies have determined that pH plays an important role in the calculated hydrolysis rate constants of parathion degradation. In this work, the degradation of parathion into either paraoxon or 4-nitrophenol, and the degradation of paraoxon to 4-nitrophenol are explored through density functional theory using the M06-2X functional. How the level of basicity affects the reaction mechanism is explored through two different hydroxide/water environments. Our calculations support the anticipated mechanisms determined by previous experimental work that the formation of 4-nitrophenol is the predominant pathway in hydrolysis of parathion.

The His23 and Lys79 pair determines the high catalytic efficiency of the inorganic pyrophosphatase of the haloacid dehalogenase superfamily

Haloacid dehalogenase (HAD) superfamily members are mainly phosphomonoesterases, while BT2127 from Bacteroides thetaiotaomicron of the HAD superfamily is identified as an inorganic pyrophosphatase. In this study, to explore the roles of the Lys79 and His23 pair in the hydrolysis reaction of inorganic pyrophosphate (PP_i) catalyzed by BT2127, a series of models were designed. Calculations were performed by using the density functional theory (DFT) method with the dispersion energy D3-B3LYP. The His23 and Lys79 pair plays a key role in the high catalytic efficiency of BT2127 with PPi. First, the His23 and Lys79 pair prompts Asp13 to easily provide a proton to the leaving group, which remarkably reduces the energy barrier of the phospho-transfer step; then, Lys79 provides a proton to the first leaving phosphate group via His23, produces a more electrically stabilized phosphate (H₃PO₄), makes this step exothermal, and further promotes the subsequent phospho-enzyme intermediate hydrolysis. The results suggest that the Lys79-His23 pair helps BT2127 reach high catalytic efficiency by strengthening the acid catalysis. Our study provides detailed chemical insights into the evolution of the inorganic pyrophosphatase function of BT2127 from the phosphomonoesterase of the HAD superfamily and the biomimetic enzyme design.

Enzymes, Reacting with Organophosphorus Compounds as Detoxifiers: Diversity and Functions

Organophosphorus compounds (OPCs) are able to interact with various biological targets in living organisms, including enzymes. The binding of OPCs to enzymes does not always lead to negative consequences for the body itself, since there are a lot of natural biocatalysts that can catalyze the chemical transformations of the OPCs via hydrolysis or oxidation/reduction and thereby provide their detoxification. Some of these enzymes, their structural differences and identity, mechanisms, and specificity of catalytic action are discussed in this work, including results of computational modeling. Phylogenetic analysis of these diverse enzymes was specially realized for this review to emphasize a great area for future development(s) and applications.

Mechanism and Inhibitor Exploration with Binuclear Mg Ketol-Acid Reductoisomerase: Targeting the Biosynthetic Pathway of Branched-Chain Amino Acids

Binuclear Mg ketol-acid reductoisomerase (KARI), which converts (S)-2-acetolactate into (R)-2,3-dihydroxyisovalerate, is responsible for the second step of the biosynthesis of branched-chain amino acids in plants and microorganisms and thus serves as a key inhibition target potentially without effects on mammals. Here, through the use of density functional calculations and a chemical model, the KARI-catalyzed reaction has been demonstrated to include the initial deprotonation of the substrate C2 hydroxy group, bridged by the two Mg ions, alkyl migration from the C2-alkoxide carbon atom to the C3-carbonyl carbon atom, and hydride transfer from a nicotinamide adenine dinucleotide phosphate [NAD(P)H] cofactor to C2. A dead-end mechanism with a hydride transferred to the C3 carbonyl group has been ruled out. The nucleophilicity (migratory aptitude) of the migrating carbon atom and the provision of additional negative charge to the di-Mg coordination sphere have significant effects on the steps of alkyl migration and hydride transfer, respectively. Other important mechanistic characteristics are also revealed. Inspired by the mechanism, an inhibitor (2-carboxylate-lactic acid) was designed and predicted by barrier analysis to be effective in inactivating KARI, hence probably enriching the antifungal and antibacterial library. Two types of slow substrate analogues (2-trihalomethyl acetolactic acids and 2-glutaryl lactic acid) were also found.

How does Mo-dependent perchlorate reductase work in the decomposition of oxyanions?

The mechanisms of Mo-dependent perchlorate reductase (PcrAB)-catalyzed decomposition of perchlorate, bromate, iodate, and nitrate were revealed by density functional calculations.

Theoretical Studies on Catalysis Mechanisms of Serum Paraoxonase 1 and Phosphotriesterase Diisopropyl Fluorophosphatase Suggest the Alteration of Substrate Preference from Paraoxonase to DFP

The calcium-dependent β-propeller proteins mammalian serum paraoxonase 1 (PON1) and phosphotriesterase diisopropyl fluorophosphatase (DFPase) catalyze the hydrolysis of organophosphorus compounds and enhance hydrolysis of various nerve agents. In the present work, the phosphotriesterase activity development between PON1 and DFPase was investigated by using the hybrid density functional theory method B3LYP. Based on the active-site difference between PON1 and DFPase, both the wild type and the mutant (a water molecule replacing Asn270 in PON1) models were designed. The results indicated that the substitution of a water molecule for Asn270 in PON1 had little effect on the enzyme activity in kinetics, while being more efficient in thermodynamics, which is essential for DFP hydrolysis. Structure comparisons of evolutionarily related enzymes show that the mutation of Asn270 leads to the catalytic Ca²⁺ ion indirectly connecting the buried structural Ca²⁺ ion via hydrogen bonds in DFPase. It can reduce the plasticity of enzymatic structure, and possibly change the substrate preference from paraoxon to DFP, which implies an evolutionary transition from mono- to dinuclear catalytic centers. Our studies shed light on the investigation of enzyme catalysis mechanism from an evolutionary perspective.

Impact of phenylalanines outside the dimer interface on phosphotriesterase stability and function

We explore the significance of phenylalanine outside of the phosphotriesterase (PTE) dimer interface through mutagenesis studies and computational modeling. Previous studies have demonstrated that the residue-specific incorporation of para-fluorophenylalanine (pFF) into PTE improves stability, suggesting the importance of phenylalanines in stabilization of the dimer. However, this comes at a cost of decreased solubility due to pFF incorporation into other parts of the protein. Motivated by this, eight single solvent-exposed phenylalanine mutants are evaluated viarosetta and good correspondence between experiments and these predictions is observed. Three residues, F304, F327, and F335, appear to be important for PTE activity and stability, even though they do not reside in the dimer interface region or active site. While the remaining mutants do not significantly affect structure or activity, one variant, F306L, reveals improved activity at ambient and elevated temperatures. These studies provide further insight into role of these residues on PTE function and stability.

How does binuclear zinc amidohydrolase FwdA work in the initial step of methanogenesis: From formate to formyl-methanofuran

The initial step of methanogenesis is the fixation of CO₂ to formyl-methanofuran (formyl-MFR) catalyzed by formyl-MFR dehydrogenase, which can be divided into two half reactions. Herein, the second half reaction catalyzed by FwdA (formyl-methanofuran dehydrogenase subunit A), i.e., from formate to formyl-methanofuran, has been investigated using density functional theory and a chemical model based on the X-ray crystal structure. The calculations indicate that, compared with other well-known di-zinc hydrolases, the FwdA reaction employs a reverse mechanism, including the nucleophilic attack of MFR amine on formate carbon leading to a tetrahedral gem-diolate intermediate, two steps of proton transfer from amine to formate moieties assisted by the Asp385, and the CO bond dissociation to form the formyl-MFR product. The second step of proton transfer from the amine moiety to the Asp385 is rate-limiting with an overall barrier of 21.2 kcal/mol. The two zinc ions play an important role in stabilizing the transition states and intermediates, in particular the negative charge at the formate moiety originated from the nucleophilic attack of the MFR amine. The work here appends a crucial piece in the methanogenic mechanistics and advances the understanding of the global carbon cycle.

Challenges and advances in the computational modeling of biological phosphate hydrolysis

Phosphate ester hydrolysis is fundamental to many life processes, and has been the topic of substantial experimental and computational research effort. However, even the simplest of phosphate esters can be hydrolyzed through multiple possible pathways that can be difficult to distinguish between, either experimentally, or computationally. Therefore, the mechanisms of both the enzymatic and non-enzymatic reactions have been historically controversial. In the present contribution, we highlight a number of technical issues involved in reliably modeling these computationally challenging reactions, as well as proposing potential solutions. We also showcase examples of our own work in this area, discussing both the non-enzymatic reaction in aqueous solution, as well as insights obtained from the computational modeling of organophosphate hydrolysis and catalytic promiscuity amongst enzymes that catalyze phosphoryl transfer.

Active Site Hydrophobicity and the Convergent Evolution of Paraoxonase Activity in Structurally Divergent Enzymes: The Case of Serum Paraoxonase 1

Serum paraoxonase 1 (PON1) is a native lactonase capable of promiscuously hydrolyzing a broad range of substrates, including organophosphates, esters, and carbonates. Structurally, PON1 is a six-bladed β-propeller with a flexible loop (residues 70–81) covering the active site. This loop contains a functionally critical Tyr at position 71. We have performed detailed experimental and computational analyses of the role of selected Y71 variants in the active site stability and catalytic activity in order to probe the role of Y71 in PON1’s lactonase and organophosphatase activities. We demonstrate that the impact of Y71 substitutions on PON1’s lactonase activity is minimal, whereas the k_cat for the paraoxonase activity is negatively perturbed by up to 100-fold, suggesting greater mutational robustness of the native activity. Additionally, while these substitutions modulate PON1’s active site shape, volume, and loop flexibility, their largest effect is in altering the solvent accessibility of the active site by expanding the active site volume, allowing additional water molecules to enter. This effect is markedly more pronounced in the organophosphatase activity than the lactonase activity. Finally, a detailed comparison of PON1 to other organophosphatases demonstrates that either a similar “gating loop” or a highly buried solvent-excluding active site is a common feature of these enzymes. We therefore posit that modulating the active site hydrophobicity is a key element in facilitating the evolution of organophosphatase activity. This provides a concrete feature that can be utilized in the rational design of next-generation organophosphate hydrolases that are capable of selecting a specific reaction from a pool of viable substrates.

Metal–organic frameworks for the removal of toxic industrial chemicals and chemical warfare agents

Toxic gases can be captured or degraded by metal–organic frameworks.

Assembly of the active center of organophosphorus hydrolase in metal–organic frameworks via rational combination of functional ligands

Mimicking the total coordination sphere of the active center of organophosphorus hydrolase in MOFs to destruct nerve agents without co-catalysts.

Probing the mechanisms for the selectivity and promiscuity of methyl parathion hydrolase

Diverse organophosphate hydrolases have convergently evolved the ability to hydrolyse man-made organophosphates. Thus, these enzymes are attractive model systems for studying the factors shaping enzyme functional evolution. Methyl parathion hydrolase (MPH) is an enzyme from the metallo-β-lactamase superfamily, which hydrolyses a wide range of organophosphate, aryl ester and lactone substrates. In addition, MPH demonstrates metal-ion-dependent selectivity patterns. The origins of this remain unclear, but are linked to open questions about the more general role of metal ions in functional evolution and divergence within enzyme superfamilies. Here, we present detailed mechanistic studies of the paraoxonase and arylesterase activities of MPH complexed with five different transition metal ions, and demonstrate that the hydrolysis reactions proceed via similar pathways and transition states. However, while it is possible to discern a clear structural origin for the selectivity between different substrates, the selectivity between different metal ions appears to lie instead in the distinct electrostatic properties of the metal ions themselves, which causes subtle changes in transition state geometries and metal-metal distances at the transition state rather than significant structural changes in the active site. While subtle, these differences can be significant for shaping the metal-ion-dependent activity patterns observed for this enzyme.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

Towards a barrier height benchmark set for biologically relevant systems

We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory, we then benchmark PM6, PM7, PM7-TS, and DFTB3 and discuss the influence of system size, bulk solvation, and geometry re-optimization on the error. The mean absolute differences (MADs) observed for these five enzyme model systems are similar to those observed for PM6 and PM7 for smaller systems (10-15 kcal/mol), while DFTB results in a MAD that is significantly lower (6 kcal/mol). The MADs for PMx and DFTB3 are each dominated by large errors for a single system and if the system is disregarded the MADs fall to 4-5 kcal/mol. Overall, results for the condensed phase are neither more or less accurate relative to B3LYP than those in the gas phase. With the exception of PM7-TS, the MAD for small and large structural models are very similar, with a maximum deviation of 3 kcal/mol for PM6. Geometry optimization with PM6 shows that for one system this method predicts a different mechanism compared to B3LYP/6-31G(d,p). For the remaining systems, geometry optimization of the large structural model increases the MAD relative to single points, by 2.5 and 1.8 kcal/mol for barriers and reaction energies. For the small structural model, the corresponding MADs decrease by 0.4 and 1.2 kcal/mol, respectively. However, despite these small changes, significant changes in the structures are observed for some systems, such as proton transfer and hydrogen bonding rearrangements. The paper represents the first step in the process of creating a benchmark set of barriers computed for systems that are relatively large and representative of enzymatic reactions, a considerable challenge for any one research group but possible through a concerted effort by the community. We end by outlining steps needed to expand and improve the data set and how other researchers can contribute to the process.

μ3-Oxo stabilized by three metal cations is a sufficient nucleophile for enzymatic hydrolysis of phosphate monoesters

Diverse species have previously been proposed to be effective nucleophiles in the enzymatic hydrolysis of phosphate esters. A novel penta-metal cluster (two Fe(3+) and three Ca(2+)) was recently discovered in the active site of PhoX alkaline phosphatase, with the revelation of the architecture of μ3-oxo bridging one Ca(2+) and two antiferromagnetically coupled Fe(3+). In this work, using density functional theory calculations, the μ3-oxo stabilized by three cations has been demonstrated to be a new type of effective nucleophile. The calculations give strong support to the "ping-pong" mechanism involving the nucleophilic attack of the μ3-oxo on the substrate phosphor and the subsequent hydrolysis of the covalent phospho-enzyme intermediate. A base mechanism with the μ3-oxo acting as a general base to activate an additional water molecule has further been demonstrated to be inaccessible. The results advance the understanding of the enzymatic hydrolysis of phosphate esters and may give important inspiration for the exploration of multinuclear biomimetic catalysts.

Quantum Chemical Modeling of the Dehalogenation Reaction of Haloalcohol Dehalogenase

The dehalogenation reaction of haloalcohol dehalogenase HheC from Agrobacterium radiobacter AD1 was investigated theoretically using hybrid density functional theory methods. HheC catalyzes the enantioselective conversion of halohydrins into their corresponding epoxides. The reaction is proposed to be mediated by a catalytic Ser132-Tyr145-Arg149 triad, and a distinct halide binding site is suggested to facilitate halide displacement by stabilizing the free ion. We investigated the HheC-mediated dehalogenation of (R)-2-chloro-1-phenylethanol using three quantum chemical models of various sizes. The calculated barriers and reaction energies give support to the suggested reaction mechanism. The dehalogenation occurs in a single concerted step, in which Tyr145 abstracts a proton from the halohydrin substrate and the substrate oxyanion displaces the chloride ion, forming the epoxide. Characterization of the involved stationary points is provided. Furthermore, by using three different models of the halide binding site, we are able to assess the adopted modeling methodology.

Factors Governing the Bridging Water Protonation State in Polynuclear Mg(2+) Proteins

An aqua ligand bridges metal cations in a wide variety of enzymes, many of which are drug targets for various diseases. However, the factors affecting its protonation state and thus biological roles remain elusive. By computing the free energy for replacing the bridging H2O by OH(-) in various model Mg(2+) sites, we have evaluated how the nature of an aqua bridge depends on the site's net charge (i.e., the number of charged ligands in the first and second shell and the number of metal cations), the site's solvent exposure, the ligand's charge-donating ability, the bridging oxygen's hydrogen-bonding interactions, intramolecular proton transfer from the bridging H2O to a nearby carboxylate, and the metal coordination number. The results reveal the key factors dictating the protonation state of bridging H2O and provide guidelines in predicting whether H2O or OH(-) bridges two Mg(2+) in polynuclear sites. This helps to elucidate the nucleophile in the enzyme-catalyzed reaction and the net charge of the metal complex (metal cation and first-shell ligands), which plays a critical role in binding.

Fundamentals of phosphate transfer

Historically, the chemistry of phosphate transfer-a class of reactions fundamental to the chemistry of Life-has been discussed almost exclusively in terms of the nucleophile and the leaving group. Reactivity always depends significantly on both factors; but recent results for reactions of phosphate triesters have shown that it can also depend strongly on the nature of the nonleaving or "spectator" groups. The extreme stabilities of fully ionised mono- and dialkyl phosphate esters can be seen as extensions of the same effect, with one or two triester OR groups replaced by O(-). Our chosen lead reaction is hydrolysis-phosphate transfer to water: because water is the medium in which biological chemistry takes place; because the half-life of a system in water is an accepted basic index of stability; and because the typical mechanisms of hydrolysis, with solvent H2O providing specific molecules to act as nucleophiles and as general acids or bases, are models for reactions involving better nucleophiles and stronger general species catalysts. Not least those available in enzyme active sites. Alkyl monoester dianions compete with alkyl diester monoanions for the slowest estimated rates of spontaneous hydrolysis. High stability at physiological pH is a vital factor in the biological roles of organic phosphates, but a significant limitation for experimental investigations. Almost all kinetic measurements of phosphate transfer reactions involving mono- and diesters have been followed by UV-visible spectroscopy using activated systems, conveniently compounds with good leaving groups. (A "good leaving group" OR* is electron-withdrawing, and can be displaced to generate an anion R*O(-) in water near pH 7.) Reactivities at normal temperatures of P-O-alkyl derivatives-better models for typical biological substrates-have typically had to be estimated: by extended extrapolation from linear free energy relationships, or from rate measurements at high temperatures. Calculation is free from these limitations, able to handle very slow reactions as readily as very fast ones, and capable of predicting rate constants with levels of accuracy acceptable to the experimentalist. We present an updated overview of phosphate transfer, with particular reference to the mechanisms of the reactions of alkyl derivatives and triesters. The intention is to present a holistic (not comprehensive!) overview of the reactivity of typical phosphate esters, in terms familiar to the working chemist, at a level sufficient to support informed predictions of reactivity for structures of interest.

Destruction of chemical warfare agents using metal-organic frameworks

Chemical warfare agents containing phosphonate ester bonds are among the most toxic chemicals known to mankind. Recent global military events, such as the conflict and disarmament in Syria, have brought into focus the need to find effective strategies for the rapid destruction of these banned chemicals. Solutions are needed for immediate personal protection (for example, the filtration and catalytic destruction of airborne versions of agents), bulk destruction of chemical weapon stockpiles, protection (via coating) of clothing, equipment and buildings, and containment of agent spills. Solid heterogeneous materials such as modified activated carbon or metal oxides exhibit many desirable characteristics for the destruction of chemical warfare agents. However, low sorptive capacities, low effective active site loadings, deactivation of the active site, slow degradation kinetics, and/or a lack of tailorability offer significant room for improvement in these materials. Here, we report a carefully chosen metal-organic framework (MOF) material featuring high porosity and exceptional chemical stability that is extraordinarily effective for the degradation of nerve agents and their simulants. Experimental and computational evidence points to Lewis-acidic Zr(IV) ions as the active sites and to their superb accessibility as a defining element of their efficacy.

Exploiting parameter space in MOFs: a 20-fold enhancement of phosphate-ester hydrolysis with UiO-66-NH2

The hydrolysis of nerve agents is of primary concern due to the severe toxicity of these agents. Using a MOF-based catalyst (UiO-66), we have previously demonstrated that the hydrolysis can occur with relatively fast half-lives of 50 minutes. However, these rates are still prohibitively slow to be efficiently utilized for some practical applications (e.g., decontamination wipes used to clean exposed clothing/skin/vehicles). We thus turned our attention to derivatives of UiO-66 in order to probe the importance of functional groups on the hydrolysis rate. Three UiO-66 derivatives were explored; UiO-66-NO2 and UiO-66-(OH)2 showed little to no change in hydrolysis rate. However, UiO-66-NH2 showed a 20 fold increase in hydrolysis rate over the parent UiO-66 MOF. Half-lives of 1 minute were observed with this MOF. In order to probe the role of the amino moiety, we turned our attention to UiO-67, UiO-67-NMe2 and UiO-67-NH2. In these MOFs, the amino moiety is in close proximity to the zirconium node. We observed that UiO-67-NH2 is a faster catalyst than UiO-67 and UiO-67-NMe2. We conclude that the role of the amino moiety is to act as a proton-transfer agent during the catalytic cycle and not to hydrogen bond or to form a phosphorane intermediate.

Human 3-hydroxyanthranilate 3,4-dioxygenase () dynamics and reaction, a multilevel computational study

3-Hydroxyanthranilate 3,4-dioxygenase () is a non-heme iron dependent enzyme. It catalyses the cleavage of the benzene ring of 3-hydroxyanthranilic acid (3-Ohaa), an intermediate in the kynurenine pathway, and therefore represents a potential target in treating numerous disorders related to the concentration of quinolinic acid (QUIN), the kynurenine pathway product, in tissues. The stability and behaviour of the enzyme in nearly physiological conditions, studied by the empirical molecular modelling methods enabled us to determine the influence of several, for the enzyme activity relevant, point mutations (Arg43Ala, Arg95Ala and Glu105Ala) on the protein structure, particularly on the active site architecture and the metal ion environment, as well as on the substrate, 3-Ohaa, binding. Besides, the water population of the active site, and the protein flexibility as well as the amino acid residues interaction networks relevant for the enzyme activity were determined for the 3-Ohaa complexes with the native and mutated enzyme variants. Finally, using the hybrid quantum-mechanics/molecular-mechanics (QM/MM) calculations the catalysed 3-Ohaa oxidation into 2-amino-3-carboxymuconic acid semialdehyde was elucidated.

Simulating the catalytic effect of a designed mononuclear zinc metalloenzyme that catalyzes the hydrolysis of phosphate triesters

One of the greatest challenges in biotechnology and in biochemistry is the ability to design efficient enzymes. In fact, such an ability would be one of the most convincing manifestations of a full understanding of the origin of enzyme catalysis. Despite some progress on this front, most of the advances have been made by placing the reacting fragments in the proper places rather than by optimizing the preorganization of the environment, which is the key factor in enzyme catalysis. A rational improvement of the preorganization and a consistent assessment of the effectiveness of different design options require approaches capable of evaluating reliably the actual catalytic effect. In this work we examine the ability of the empirical valence bond (EVB) to reproduce the results of directed evolution improvements of the catalysis of diethyl 7-hydroxycoumarinyl by a designed mononuclear zinc metalloenzyme. Encouragingly, our study reproduced the catalytic effect obtained by directed evolution and offers a good start for further studies of this system.

Phosphate monoester hydrolysis by trinuclear alkaline phosphatase; DFT study of transition States and reaction mechanism

Alkaline phosphatase (AP) is a trinuclear metalloenzyme that catalyzes the hydrolysis of a broad range of phosphate monoesters to form inorganic phosphate and alcohol (or phenol). In this paper, by using density functional theory with a model based on a crystal structure, the AP-catalyzed hydrolysis of phosphate monoesters is investigated by calculating two substrates, that is, methyl and p-nitrophenyl phosphates, which represent alkyl and aryl phosphates, respectively. The calculations confirm that the AP reaction employs a "ping-pong" mechanism involving two chemical displacement steps, that is, the displacement of the substrate leaving group by a Ser102 alkoxide and the hydrolysis of the phosphoseryl intermediate by a Zn2-bound hydroxide. Both displacement steps proceed via a concerted associative pathway no matter which substrate is used. Other mechanistic aspects are also studied. Comparison of our calculations with linear free energy relationships experiments shows good agreement.

A dominant homolytic O-Cl bond cleavage with low-spin triplet-state Fe(IV)=O formed is revealed in the mechanism of heme-dependent chlorite dismutase

Chlorite dismutase (Cld) is a heme-dependent enzyme that catalyzes the decomposition of toxic chlorite (ClO2(-)) into innocuous chloride and O2. In this paper, using the hybrid B3LYP density functional theory (DFT) method including dispersion interactions, the Cld reaction mechanism has been studied with a chemical model constructed on the X-ray crystal structure. The calculations indicate that the reaction proceeds along a stepwise pathway in the doublet state, i.e. a homolytic O-Cl bond cleavage of the substrate leading to an O-Fe(heme) species and a ClO˙ radical, followed by a rebinding O-O bond formation between them. The O-Fe(heme) species is demonstrated to be a low-spin triplet-state Fe(IV)=O diradicaloid. A low-spin singlet-state Fe(IV)=O is much less stable than the former, with an energy difference of 9.2 kcal mol(-1). The O-Cl bond cleavage is rate-limiting with a barrier of 10.6 kcal mol(-1), in good agreement with the experimental reaction rate of 2.0 × 10(5) s(-1). Furthermore, a heterolytic O-Cl bond dissociation in the initial step is shown to be unreachable, which ensures the high efficiency of the Cld enzyme by avoiding the generation of chlorate byproduct observed in the reactions of synthetic Fe porphyrins. Also, the pathways in the quartet and sextet states are unfavorable for the Cld reaction. The present results reveal a detailed mechanism III (defined in the text) including an interesting di-radical intermediate composed of a low-spin triplet-state Fe(IV)=O and a ClO˙ radical. Compared to a competitive heterolytic Cl-O cleavage in synthetic Fe porphyrins, the revelation of the domination of homolysis in Cld indicates not only the high efficiency of enzyme, but also the sensitivity of a heme and the significance of the enzymatic active-site surroundings (the His170 and Arg183 residues in the present case), which gives more insights into heme chemistry.

Cellobiose dehydrogenase modified electrodes: advances by materials science and biochemical engineering

The flavocytochrome cellobiose dehydrogenase (CDH) is a versatile biorecognition element capable of detecting carbohydrates as well as quinones and catecholamines. In addition, it can be used as an anode biocatalyst for enzymatic biofuel cells to power miniaturised sensor-transmitter systems. Various electrode materials and designs have been tested in the past decade to utilize and enhance the direct electron transfer (DET) from the enzyme to the electrode. Additionally, mediated electron transfer (MET) approaches via soluble redox mediators and redox polymers have been pursued. Biosensors for cellobiose, lactose and glucose determination are based on CDH from different fungal producers, which show differences with respect to substrate specificity, pH optima, DET efficiency and surface binding affinity. Biosensors for the detection of quinones and catecholamines can use carbohydrates for analyte regeneration and signal amplification. This review discusses different approaches to enhance the sensitivity and selectivity of CDH-based biosensors, which focus on (1) more efficient DET on chemically modified or nanostructured electrodes, (2) the synthesis of custom-made redox polymers for higher MET currents and (3) the engineering of enzymes and reaction pathways. Combination of these strategies will enable the design of sensitive and selective CDH-based biosensors with reduced electrode size for the detection of analytes in continuous on-site and point-of-care applications.