Two-Metal Ion Catalysis in Enzymatic Acyl- and Phosphoryl-Transfer Reactions

Numerous studies, both in enzymatic and nonenzymatic catalysis, have been undertaken to understand the way by which metal ions, especially zinc ions, promote the hydrolysis of phosphate ester and amide bonds. Hydrolases containing one metal ion in the active site, termed mononuclear metallohydrolases, such as carboxypeptidase. A and thermolysin were among the first enzymes to have their structures unraveled by X-ray crystallography. In recent years an increasing number of metalloenzymes have been identified that use two or more adjacent metal ions in the catalysis of phosphoryl-transfer reactions (R-OPO₃ + R′-OH → R′-OPO₃ + R-OH; in the case of the phosphatase reaction R′-OH is a water molecule) and carbonyl-transfer reactions, for example, in peptidases or other amidases. These dinuclear metalloenzymes catalyze a great variety of these reactions, including hydrolytic cleavage of phosphomono-, -di- and -triester bonds, phosphoanhydride bonds as well as of peptide bonds or urea. In addition, the formation of the phosphodiester bond of RNA and DNA by polymerases is catalyzed by a two-metal ion mechanism. A remarkable diversity is also seen in the structures of the active sites of these di- and trinuclear metalloenzymes, even for enzymes that catalyze very similar reactions. The determination of the structure of a substrate, product, stable intermediate, or a reaction coordinate analogue compound bound to an active or inactivated enzyme is a powerful approach to investigate mechanistic details of enzyme action. Such studies have been applied to several of the metalloenzymes reviewed in this article; together with many other biochemical studies they provide a growing body of information on how the two (or more) metal ions cooperate to achieve efficient catalysis.     

Transition structure selectivity in enzyme catalysis: a QM/MM study of chorismate mutase

Two different transition structures (TSs) have been located and characterized for the chorismate conversion to prephenate in Bacillus subtilis chorismate mutase by means of hybrid quantum-mechanical/molecular-mechanical (QM/MM) calculations. GRACE software, combined with an AM1/CHARMM24/TIP3P potential, has been used involving full gradient relaxation of the position of ca. 3300 atoms. These TSs have been connected with their respective reactants and products by the intrinsic reaction coordinate (IRC) procedure carried out in the presence of the protein environment, thus obtaining for the first time a realistic enzymatic reaction path for this reaction. Similar QM/MM computational schemes have been applied to study the chemical reaction solvated by ca. 500 water molecules. Comparison of these results together with gas phase calculations has allowed understanding of the catalytic efficiency of the protein. The enzyme stabilizes one of the TSs (TS_OHout) by means of specific hydrogen bond interactions, while the other TS (TS_OHin) is the preferred one in vacuum and in water. The enzyme TS is effectively more polarized but less dissociative than the corresponding solvent and gas phase TSs. Electrostatic stabilization and an intramolecular charge-transfer process can explain this enzymatically induced change. Our theoretical results provide new information on an important enzymatic transformation and the key factors responsible for efficient selectivity are clarified. Received: 25 March 2000 / Accepted: 7 August 2000 / Published online: 23 November 2000     

Entropy,Binding Energy,and Enzymic Catalysis

Why are enzyme-catalyzed reactions so much faster than uncatalyzed reactions, and why are enzymes so specific? What is the effect of mere approximation of enzyme and substrate, and what is the influence of the strain energy? Attempts to answer these questions have led to comparisons between entropy changes in intermolecular and intramolecular reactions, and to determinations of the intrinsic energy of the bond arising by non-covalent interaction between enzyme and substrate.     

Tunable Chirality of Self-Assembled Dipeptides Mediated by Bipyridine Derivative

Supramolecular peptide assemblies have been widely used for the development of biomedical, catalytical, and optical materials with chiral nanostructures in view of the intrinsic chirality of peptides. However, the assembly pathway and chiral transformation behavior of various peptides remain largely elusive especially for the transient assemblies under out-of-equilibrium conditions. Herein, the N-fluorenylmethoxycarbonyl-protected phenylalanine-tyrosine dipeptide (Fmoc-FY) was used as a peptide assembly platform, which showed that the assembly proceeds multistep evolution. The original spheres caused by liquid-liquid phase separation (LLPS) can nucleate and elongate into the formation of right-handed helices which were metastable and easily converted into microribbons. Interestingly, a bipyridine derivative can be introduced to effectively control the assembly pathway and induce the formation of thermodynamically stable right-handed or left-handed helices at different stoichiometric ratios. In addition, the chiral assembly can also be regulated by ultrasound or enzyme catalysis. This minimalistic system not only broadens the nucleation-elongation mechanisms of protein aggregates but also promotes the controllable design and development of chiral biomaterials.     

An artificial enzyme that catalyzes hydrolysis of aryl glycosides

Two cyclodextrin A,D-diacids were synthesized and found to catalyze the hydrolysis of nitrophenyl glycosides with k_cat/k_uncat of up to 35. The hydrolysis followed Michaelis-Menten kinetics, could be inhibited by compounds binding the cavity, and occurred optimally at pH 7.4.     

Artificial enzyme catalysis controlled and driven by light

Bio-inspired chemistry based on photoresponsive molecules is a rapidly developing new strategy to mimic the function of various biological systems. The interaction of electromagnetic radiation with molecular systems is ideally suited for the control and powering of dynamic processes at the speed of light. Besides typical applications in artificial photosynthesis, many other aspects, such as the catalytic turnover of substrates or the controlled release or uptake of small bioactive molecules, are readily verified with light-driven model systems. The potential of this novel approach in biomimetic chemistry is briefly explored in this concept article.     

Investigation of various synthetic protocols for self-assembled nanomaterials and their role in catalysis: progress and perspectives

Self-assembly is one of the most used strategies in the controlled synthesis and design of well-organized nanomaterials for various applications in diverse realms namely catalysis, sensors, microelectronics, energy storage, and energy conversion. It is quite common to see reports on the synthesis and design of several self-assembled nanomaterials for the application in the catalysis of various chemical, photochemical, and electrochemical reactions and processes. Nevertheless, a combined overview on the synthetic strategies for self-assembled nanomaterials has not been reported in any form in literature. Owing to the current interest shown and the future significance on the self-assembled nanomaterials, it is highly essential to have such an elaborated review on the progress and perspectives of synthesis of self-assembled nanomaterials and their subsequent application to catalysis of various chemical, photochemical, and electrochemical reactions and processes. In this review, we have highlighted various synthetic methodologies used so far for fabricating the self-assembled nanomaterials that includes Langmuir–Blodgett method, layer-by-layer assembly, amphiphilic (artificial and bio) self-assembly, and template-free approach. Nanomaterials derived from the above mentioned methods in various catalysis reactions are also highlighted in detail with an emphasis on confronts and prospects in the field of materials self-assembling and its concomitant application to catalysis.     

The effect of restricted intramolecular energy flow on the rate of one-substrate enzyme catalyzed reaction

We assume that the free intramolecular energy flow (intramolecular vibrational energy redistribution—IVR) between bonded substrate and enzyme can be restricted due to the presence of a metal atom near the binding site of enzyme. This restriction can represent one of the factors of enzyme catalysis. The concentration of energy evolved during the formation of enzyme-substrate complex in the bonded substrate enhances the reaction rate by several orders of magnitude in comparison with the case of free dissipation of evolved energy into the enzyme.     

Hydrolysis rates of alkyl and aryl sulfinamides: evidence of general acid catalysis

Sulfinamides are important in enantioselective synthesis, as rare post-translational modifications of proteins and as isosteres of the amide bond. Little is known about the rates of hydrolysis for aliphatic sulfinamides or the mechanism of hydrolysis. In this Letter, we show that sulfinamides hydrolyse by predominantly a non-specific acid/base catalysis with phosphate buffer but by varying the buffer concentration, it was possible to determine the hydrolysis rates of a range of sulfinamides with water through non-linear least squares regression.     

A stationary‐wave model of enzyme catalysis

An expression for the external force driving a system of two coupled oscillators in the condensed phase was derived in the frame of the Debye theory of solids. The time dependence and amplitude of the force is determined by the size of the cell embedding the coupled oscillators and its Debye temperature (θ_D). The dynamics of the driven system of oscillators were followed in the two regimes of (a) low θ_D and cell diameter, as a model of liquid water, and (b) large θ_D and cell diameter, as a model of the core of a protein. The response in potential energy of the reference oscillator was computed for all possible values of the internal parameters of the system under investigation. For protein cores, the region in the parameter space of high maximum potential energy of the reference oscillator is considerably extended with respect to the corresponding simulation for water. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Supramolecular enzyme mimics by self-assembly

The development of supramolecular chemistry has led to a shift in the research focus from the structural design of supramolecules to developing functional systems, such as supramolecular enzyme models. The supramolecular enzyme mimics can be readily constructed by self-assembly which is an efficient strategy for generating highly-ordered structures with complex and hierarchical architectures to mimic the biopolymers. The study of supramolecular enzyme mimics has implications for understanding both the structure–function relationships of natural enzymes and the thermodynamic mechanism during catalysis. Additionally, they are potentially useful in many important applications, e.g., medicinal application and industrial biocatalysts and so on. This review is aimed at giving a brief overview of the synthesis of supramolecular enzyme mimics and their functions.     

Electrostatic effects in enzyme catalysis: a quantum mechanics/molecular mechanics study of the nucleophilic substitution reaction in haloalkane dehalogenase

Combined quantum mechanics/molecular mechanics molecular dynamics simulations have been carried out to study the cleavage of the carbon–chlorine bond in 1,2-dichloroethane catalysed by haloalkane dehalogenase from Xanthobacter Autotrophicus GJ10. The process has been compared with an adequate counterpart in aqueous solution, the nucleophilic attack of acetate anion on 1,2-dichloroethane. Within the limitations of the model, mainly due to the use of a semiempirical Hamiltonian, our results reproduce the magnitude and characteristics of the catalytic effect. Comparisons of the enzymatic and in solution potentials of mean force reveal that, irrespective of the reference state, the enzyme shows a larger affinity for the transition state. The origin of this increased affinity is found in the differences in the electrostatic pattern created by the environment in aqueous solution and in the enzyme.Proceedings of the 11th International Congress of Quantum Chemistry satellite meeting in honor of Jean-Louis Rivail     

Theoretical study of the role of low-barrier hydrogen bonds in enzyme catalysis: a model of proton transfer in serine protease

 A model of low-barrier hydrogen bonds (LBHBs) in enzymes has been studied by ab initio quantum mechanical calculations including the self-consistent reaction field solvent model. The hydrogen-bond strengths and the deprotonation energies for the hydrogen-bonded and non-hydrogen-bonded cis-urocanic acid were calculated at the HF/6-31 + G(d,p) level at various dielectric constants. The same calculations were performed for the α,β-dihydrourocanic acid to model the catalytic dyad of serine protease. The deprotonation energy of N^ɛ2 in α,β-dihydrourocanic acid is increased by formation of LBHBs and depends very much on the dielectric constant. This study suggests that the formation of LBHBs increases the basicity of the dyad, and the polarity change near the reaction center in the active site could help the proton abstraction from Ser 195 and the donation to the leaving group. Both the LBHBs and the environment can play crucial roles in the enzyme catalysis. Received: 8 March 2000 / Accepted: 3 January 2001 / Published online: 3 May 2001     

Release of enzyme strain during catalysis reduces the activation energy barrier

Several mechanisms have been considered as principal factors in enhancing the catalytic reaction velocity of enzymes: approximation, covalent catalysis, general acid-based catalysis, and strain. Among them, the strain on the substrate and/or the enzyme is often found to be brought about on association of the substrate and the enzyme. If this strain is released in the transition state, it contributes to enhancing the k(cat) value, although it does not change the k(cat)/K(m) value. In aspartate aminotransferase, however, we found by analysis of the Schiff base pK(a) values that the unliganded enzyme carries a strain in the protonated Schiff base formed between the coenzyme pyridoxal phosphate and a lysine residue. This bond is cleaved in most of the reaction intermediates, including the transition state. As a result, the activation energy between the free enzyme plus substrate and the transition state is decreased by 16 kJ/mol, equal to the value of the strain energy. The net effect of this strain is enhancement (10(3)-fold) of the catalytic efficiency in terms of k(cat)/K(m), the more important indicator of the catalytic efficiency at low concentration of the substrate.     

Fluorous biphase catalysis

The evolution and future prospects for the fluorous biphase approach to homogeneous catalysis are discussed.     

Enantioselective transesterification catalysis by nanosized serine protease subtilisin Carlsberg particles in tetrahydrofuran

Enzyme catalysis in organic solvents is a powerful tool for stereo-selective synthesis but the enantioselectivity is still hard to predict. To overcome this obstacle, we employed a nanoparticulate formulation of subtilisin Carlsberg (SC) and designed a series of 14 structurally related racemic alcohols. They were employed in the model transesterification reaction with vinyl butyrate and the enantioselectivities were determined. In general, short alcohol side chains led to low enantioselectivties, while larger and bulky side chains caused better discrimination of the enantiomers by the enzyme. With several bulky substrates high enantioselectivities with E>100 were obtained. Computational modeling highlighted that key to high enantioselectivity is the discrimination of the R and S substrates by the sole hydrophobic binding pocket based on their size and bulkiness. While bulky S enantiomer side chains could be accommodated within the binding pocket, bulky R enantiomer side chains could not. However, when also the S enantiomer side chain becomes too large and does not fit into the binding pocket anymore, enantioselectivity accordingly drops.     

Some chelating C-donor ligands in hydrogen transfer and related catalysis

Recent work is discussed that throws light on synthetic, steric, and electronic aspects of NHC complexes as well as on outer sphere effects in their reactivity. The chemistry of the NHC ligand is much more complex than the more traditional phosphines and provides much greater possibilities for altering steric and electronic properties for tuning reactivity. In synthetic work the Lin Ag₂O method is shown to be inapplicable to the synthesis of abnormal NHCs bound via C-4(5) where the C2 position is blocked with CH₃, because Ag(I) oxidizes the CH₃ group to formate with formation of the normal C-2 bound Ag-NHC. Linker effects on the behavior of chelating NHCs depend on the linker locking the azole rings into a conformation that depends on linker length. This gives rise to different complexes being formed when different linker lengths are employed. The failure of M-NHC bonds to reversibly dissociate can prevent potentially chelating bis and tris NHC precursors from forming the desired products but instead being trapped in a kinetic nonchelate form. Imidazolium carboxylates prove to be synthetically useful in that they can act as excellent NHC transfer agents to a variety of transition metals. The Tolman electronic parameter of NHCs can be determined by a variety of experimental and computational methods. Anion dependent chemistry can give rise to a switching of the product of imidazolium salt metallation from normal (C-2) to abnormal (C-4(5)) forms.     

Gold catalysis

Catalysis by gold has rapidly become a hot topic in chemistry, with a new discovery being made almost every week. Gold is equally effective as a heterogeneous or a homogeneous catalyst and in this Review we attempt to marry these two facets to demonstrate this new found and general efficacy of gold. The latest discoveries are placed within a historical context, but the main thrust is to highlight the new catalytic possibilities that gold-catalyzed reactions currently offer the synthetic chemist, in particular in redox reactions and nucleophilic additions to pi systems. Indeed gold has proved to be an effective catalyst for many reactions for which a catalyst had not been previously identified, and many new discoveries are still expected.     

Directed evolution of enantioselective hybrid catalysts: a novel concept in asymmetric catalysis

The concept of directed evolution of enantioselective hybrid catalysts was proposed in 2001/2002 and implemented experimentally for the first time in a proof-of-concept study in 2006. The idea is based on directed evolution, which comprises repeating cycles of random gene mutagenesis/expression/screening in a Darwinistic sense for the purpose of improving the catalytic profile of enzymes. In the case of hybrid catalysts, mutagenesis/expression of a protein is first performed with formation of a library of mutants, which are then modified chemically en masse with the introduction of an appropriate achiral ligand system harboring a transition metal. Screening these mutant hybrid catalysts in a given transition metal-catalyzed reaction then leads to an improved catalyst, so that the corresponding gene can be used to start another evolutionary cycle. This process can be repeated as often as needed until the desired catalytic profile has been reached, e.g., enhanced enantioselectivity.