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     

A coupled two-compartment model for immobilized enzyme electrodes

The effect of stirring on the transient and pseudo steady-state behavior of potentiometric and amperometric immobilized enzyme electrodes is accurately modelled by a coupled two-compartment system of nonlinear differential equations. In the first compartment, the enzyme layer, the chemistry is governed by enzyme kinetics and diffusion. This is coupled to the second compartment, the bulk solution, which is controlled only by molecular diffusion. Several results of analytical significance can be obtained by using this model: for example, it is shown how the stirring rate can be used to increase the linear dynamic range.     

A model for the reaction mechanism of the transglutaminase 3 enzyme

Transglutaminase enzymes (TGases) catalyze the calcium dependent formation of an isopeptide bond between protein-bound glutamine and lysine substrates. Previously we have shown that activated TGase 3 acquires two additional calcium ions at site two and three. The calcium ion at site three results in the opening of a channel. At this site, the channel opening and closing could modulate, depending on which metal is bound. Here we propose that the front of the channel could be used by the two substrates for enzyme reaction. We propose that the glutamine substrate is directed from Trp236 into the enzyme, shown by molecular docking. Then a lysine substrate approaches the opened active site to engage Trp327, leading to formation of the isopeptide bond. Further, direct comparisons of the structures of TGase 3 with other TGases have allowed us to identify several residues that might potentially be involved in generic and specific recognition of the glutamine and lysine substrates.     

Observation of topical catalysis by sphingomyelinase coupled to microspheres

Sphingomyelinase, SMase (EC 3.1.4.12), was coupled onto amino-derivatized acrylate microspheres and was shown to retain its catalytic activity. The immobilized enzyme allows one to carry out topical enzymatic reaction in a controlled manner. Accordingly, these spheres were held with a micropipet and using micromanipulator brought into contact with a giant liposome membrane composed of phosphatidylcholine and sphingomyelin (SOPC/C16:0-SM, 0.75:0.25, molar ratio), representing the substrate for the immobilized enzyme. The macroscopic consequences of the enzyme reaction were visualized using fluorescence microscopy as well as differential interference contrast microscopy. The surface contact of the giant vesicle and immobilized enzyme causes membrane microdomain formation and domain clustering (capping) in the membrane and subsequent shedding of small vesicles from the membrane into the interior of the giant liposome. The method described represents a novel approach to study enzymatic reactions and allows manipulating giant vesicles as well as cultured cells in a spatially controlled manner.     

Protein motions are coupled to the reaction chemistry in coenzyme b(12) -dependent ethanolamine ammonia lyase

The role of protein dynamics in promoting catalysis is hotly debated. Infrared data from both ultrafast flash photolysis and stopped-flow studies show that not only does there appear to be vibrational coupling between the cofactor and protein in B(12) -dependent ethanolamine ammonia lyase, but also that there are significant protein motions coupled to the reaction that follows substrate binding.     

Chemical reactivity within a smectic B liquid crystalline phase: A model of enzyme catalysis?

The rearrangement of allyl p-dimethylaminobenzenesulphonate (ASE) to form a zwitterionic product has already been recognized as an effective probe for the study of reactivity within the smectic B phase [4, 5, 19]. We have used deuterium NMR, linear dichroism and X-ray diffraction techniques to investigate the phase diagram of the ASE-OS35 reaction system. The partitioning of the reactant molecules between coexisting smectic, nematic and/or isotropic phases and the structural organization of the smectic catalytic host at different temperatures and reactant guest concentrations have been characterized. On the basis of these measurements, a model of ASE reactivity in smectic solvents has been developed. The reaction takes place provided that coexisting isotropic or nematic phases are present to act as a reservoir for the ASE reactant molecules prior to their entering the smectic phase; they then react and leave the smectic phase as a zwitterionic product. The analogy between this model of reactivity within smectic phases and the Michaelis-Menten enzyme processes is discussed. This relationship opens up the intriguing possibility of designing new experiments with which to investigate further liquid crystalline models of enzyme catalysis.     

Efficiency and evolution of enzyme catalysis.

A new function derived from kinetic data, the efficiency function, can be used to quantify the efficiency of a catalyst. For freely diffusing species the maximum efficiency is unity. The enzyme triose phosphate isomerase has an efficiency of 0.6 and is thus almost a perfect catalyst. The efficiency of the acetate ion as catalyst for the same reaction is 2.5 × 10^?11. This increase in catalytic efficiency is discussed in terms of three types of evolutionary improvement: the uniform binding of the substrate to the enzyme, changes in the internal thermodynamics of the bound states, and more effective catalysis of elementary steps. These concepts are illustrated for triose phosphate isomerase.     

Selenium-mediated micellar catalyst: an efficient enzyme model for glutathione peroxidase-like catalysis

Mimicking the properties of the selenoenzyme glutathione peroxidase (GPx) has inspired great interest. In this report, a selenium-containing micellar catalyst was successfully constructed by the self-assembly of the cationic surfactant hexadecyltrimethylammonium bromide (CTAB) with benzeneseleninic acid (PhSeO2H) through hydrophobic and electrostatic interaction in water. The selenium-containing micellar catalyst demonstrated substrate specificity for both 3-carboxy-4-nitrobenzenethiol (ArSH, 2) and cumene hydroperoxide (CUOOH), and their complexation was confirmed by UV and fluorescence spectra. More importantly, it demonstrated high GPx activity in two assay systems. It is about 126 times more effective than the well-known GPx mimic ebselen in the classical coupled reductase assay system; however, by using hydrophobic substrate ArSH (2) as an alternative of glutathione (GSH, 1), the micellar catalyst exhibited remarkable 500-fold and 94 500-fold rate enhancements compared with that of PhSeO2H and PhSeSePh.     

A mechanistic investigation of Biginelli reaction under base catalysis

The mechanism of the three component base mediated Biginelli dihydropyrimidines synthesis was investigated using Accurate Mass TOF LC-MS-ESI and Tandem TOF LC-MS-ESI. We suggest hemiaminal as a possible intermediate leading to the formation of Biginelli product. Under our current experimental conditions we did not observe any bis-ureide as reported by ji et al.     

A snapshot of enzyme catalysis using electrospray ionization mass spectrometry

Insights into the early molecular events involving protein-ligand/substrate interactions such as protein signaling and enzyme catalysis can be obtained by examining these processes on a very short, millisecond time scale. We have used time-resolved electrospray mass spectrometry to delineate the catalytic mechanism of a key enzyme in bacterial lipopolysaccharide biosynthesis, 3-deoxy-d-manno-2-octulosonate-8-phosphate synthase (KDO8PS). Direct real-time monitoring of the catalytic reaction under single enzyme turnover conditions reveals a novel hemiketal phosphate intermediate bound to the enzyme in a noncovalent complex that establishes the reaction pathway. This study illustrates the successful application of mass spectrometry to reveal transient biochemical processes and opens a new time domain that can provide detailed structural information of short-lived protein-ligand complexes.     

The role of large-scale motions in catalysis by dihydrofolate reductase

Dihydrofolate reductase has long been used as a model system to study the coupling of protein motions to enzymatic hydride transfer. By studying environmental effects on hydride transfer in dihydrofolate reductase (DHFR) from the cold-adapted bacterium Moritella profunda (MpDHFR) and comparing the flexibility of this enzyme to that of DHFR from Escherichia coli (EcDHFR), we demonstrate that factors that affect large-scale (i.e., long-range, but not necessarily large amplitude) protein motions have no effect on the kinetic isotope effect on hydride transfer or its temperature dependence, although the rates of the catalyzed reaction are affected. Hydrogen/deuterium exchange studies by NMR-spectroscopy show that MpDHFR is a more flexible enzyme than EcDHFR. NMR experiments with EcDHFR in the presence of cosolvents suggest differences in the conformational ensemble of the enzyme. The fact that enzymes from different environmental niches and with different flexibilities display the same behavior of the kinetic isotope effect on hydride transfer strongly suggests that, while protein motions are important to generate the reaction ready conformation, an optimal conformation with the correct electrostatics and geometry for the reaction to occur, they do not influence the nature of the chemical step itself; large-scale motions do not couple directly to hydride transfer proper in DHFR.     

A coupled hartree-fock calculation of the paramagnetic contribution to the cotton-mouton constant of helium

The perturbation equations necessary for the evaluation of the paramagnetic part of the Cotton-Mouton constant of helium are derived as an example of coupled Hartree-Fock theory for a double perturbation and the ensuing integro-differential equations solved numerically. A comment is made on the errors in the numerical solution of such equations.     

Preorganization and protein dynamics in enzyme catalysis

Recently, an alternative has been offered to the concept of transition state (TS) stabilization as an explanation for rate enhancements in enzyme-catalyzed reactions. Instead, most of the rate increase has been ascribed to preorganization of the enzyme active site to bind substrates in a geometry close to that of the TS, which then transit the activation barrier impelled by motions along the reaction coordinate. The question as to how an enzyme achieves such preorganization and concomitant TS stabilization as well as potential coupled motions along the reaction coordinate leads directly to the role of protein dynamic motion. Dihydrofolate reductase (DHFR) is a paradigm in which the role of dynamics in catalysis continues to be unraveled by a wealth of kinetic, structural, and computational studies. DHFR has flexible loop regions adjacent to the active site whose motions modulate passage through the kinetically preferred pathway. The participation of residues distant from the DHFR active site in enhancing the rate of hydride transfer, however, is unanticipated and may signify the importance of long range protein motions. The general significance of protein dynamics in understanding other biological processes is briefly discussed.     

Supercomputer technologies for structural-kinetic study of mechanisms of enzyme catalysis: A quantum-chemical description of aspartoacylase catalysis

The results of modeling of the complete catalytic cycle of aspartoacylase-catalyzed N-acetylaspartate hydrolysis by the combined quantum mechanics/molecular mechanics method and with the use of umbrella sampling replica-exchange molecular dynamics simulations are reported. It has been shown that the decrease in the high-energy barriers of rate-limiting stages is achieved through the preceding equilibrium stages, such as proton transfer and conformational changes. General features of the catalytic behavior of enzymes have been formulated.     

A dendritic active site: catalysis of the Henry reaction

[reaction: see text] Dendrimers containing an encapsulated tertiary amine were prepared by coupling tris(2-aminoethyl)amine with dendritic branches derived from L-lysine. These dendrimers were used as catalysts in the Henry (nitroaldol) reaction between 4-nitrobenzaldehyde and nitroethane, and their catalytic performance was compared with that of triethylamine. Attachment of the dendritic shell alters the rate of reaction and influences the syn:anti ratio of products. It is proposed that the dendritic shell generates an encapsulated catalytically active site, mimicking the behavior of a protein superstructure.     

Molecular approach to catalysis of electrochemical reaction in porous films

Current attempts to bridge the fields of what is conventionally called ‘electrocatalysis’ and of molecular catalysis of electrochemical reactions are surveyed and discussed. It amounts in many cases to ‘heterogenize’ molecular catalytic systems. Information on the meso- to nanostructures of the resulting catalytic films forms the basis of the understanding of new modes of transport of the reactants (catalysts, substrates and cosubstrates, products) that may govern the mechanistic competitions and consequently selectivity. Efforts to adapt benchmarking procedures developed in homogeneous molecular catalysis (catalytic Tafel plots) should be encouraged, taking into account, as additional factors, the transport of electrons and reacting species (including gases) through the catalytic system.     

Kinetic analysis of arginase-urease coupled reaction with a surface acoustic wave enzyme sensor system

An extended set of equations which describe coupled arginase-urease reactions is presented. The mathematical treatment leads to the development of new equations which relate the lag-time required for the concentration of urea to reach a defined fraction of its steady-state concentration to the kinetic parameters of the enzymes, when the steady-state concentration of urea is small compared to its Michaelis constant value, the coupled arginase-urease reaction was monitored with a surface acoustic wave (SAW) enzyme sensor system, to couple the biochemical selectivity of enzymes with the sensitivity of SAW sensors. The proposed theoretical expressions were verified experimentally. The kinetic parameters of urease and arginase (extracted directly from bovine liver) were examined under theoretical guidance. Dependence of the lag-time of the coupled enzyme reaction on the concentrations of urease and arginase is also described.