Indigo stability: an ab initio study

This work shows that indigo's high stability can be attributed both to the large π conjugation inside the molecule and to intra- and intermolecular hydrogen bonds. The theoretical investigation of indigo's electronic structure has been performed using high-level methods. To understand the interactions in solid state, calculations of the dimer system with both molecules in the same plane was carried out. In the monomer, two intramolecular hydrogen bridges between amino and carbonyl groups occupy positions that would otherwise be the most reactive ones for nucleophilic and electrophilic attacks. In the dimer, amino and carbonyl groups on different monomers form intermolecular multicentred non-linear hydrogen bonds in six-member rings, protecting again the same reactive centres and explaining the limited solubility of indigo. The addition of the free radical OH breaks the central C = C double bond, the conjugation and the hydrogen bridges as a first step. The Gibbs energy calculation favours the addition of OH radical over C1.     

Serine proteases: an ab initio molecular dynamics study

In serine proteases (SPs), the H-bond between His57 and Asp102 and that between Gly193 and the transition state intermediate play a crucial role in enzymatic function. To shed light on the nature of these interactions, we have carried out ab initio molecular dynamics simulations on complexes representing adducts between the reaction intermediate and elastase (one protein belonging to the SP family). Our calculations indicate the presence of a low-barrier H-bond between His57 and Asp102, in complete agreement with NMR experiments on enzyme-transition state analogue complexes. Comparison with an ab initio molecular dynamics simulation on a model of the substrate-enzyme adduct indicates that the Gly193-induced strong stabilization of the intermediate is accomplished by charge/dipole interactions and not by H-bonding as previously suggested. Inclusion of the protein electric field in the calculations does not affect significantly the charge distribution.     

Structural phase transition of CdTe: an ab initio study

A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in zinc-blende CdTe. We found that CdTe undergoes a structural first-order phase transition to $ {\text{I}}\overline 4 {\text{m2}} $ (binary β-tin) tetragonal structure in the constant pressure molecular dynamics simulation at 20 GPa. When the pressure was increased to 50 GPa, the phase of tetragonal structure converted to a new Imm2 orthorhombic structure. These phase transformations were also calculated by using the enthalpy calculations. Transition phases, lattice parameters and bulk properties we attained are comparable with experimental and theoretical data.     

Pressure-induced phase transition in wurtzite ZnTe: an ab initio study

A constant pressure ab initio MD technique and density functional theory with a generalized gradient approximation (GGA) was used to study the pressure-induced phase transition in wurtzite ZnTe. A first-order phase transition from the wurtzite structure to a Cmcm structure was successfully observed in a constant-pressure molecular dynamics simulation. This phase transformation was also analyzed using enthalpy calculations. We also investigated the stability of wurtzite (WZ) and zinc-blende (ZB) phases from energy–volume calculations, and found that both structures show quite similar equations of state and transform into a Cmcm structure at 16 GPa using enthalpy calculations, in agreement with experimental observations. The transition phase, lattice parameters and bulk properties we obtained are comparable with experimental and theoretical data.     

Fructose production by chicory inulin enzymatic hydrolysis: A kinetic study and reaction mechanism

In this paper, a reaction scheme for fructose production by inulin enzymatic hydrolysis is proposed, taking into account the possibility of dealing with a mixture of enzymes acting on a mixture of polymers as substrate. The scheme is subsequently simplified to obtain a stoichiometric relationship between the fructose product and the reacted substrate. The former may be measured by HPLC, while the latter is the subject of kinetic investigations. Our proposed kinetic model is defined within temperature and substrate concentration ranges of industrial interest (40–60 °C and 3–60 g/L, respectively). Some assumptions were made in order to simplify the model, which is based on a minimum number of parameters. These hypotheses were always specified and assumed only on the basis of convenience and rational consideration. Eventually, the kinetic model was successfully validated by comparison with a vast set of experimental results.     

Structural phase transition of BeTe: an ab initio molecular dynamics study

Beryllium telluride (BeTe) with cubic zinc-blende (ZB) structure was studied using ab initio constant pressure method under high pressure. The ab initio molecular dynamics (MD) approach for constant pressure was studied and it was found that the first order phase transition occurs from the ZB structure to the nickel arsenide (NiAs) structure. It has been shown that the MD simulation predicts the transition pressure P _T more than the value obtained by the static enthalpy and experimental data. The structural pathway reveals MD simulation such as cubic → tetragonal → orthorhombic → monoclinic → orthorhombic → hexagonal, leading the ZB to NiAs phase. The phase transformation is accompanied by a 10% volume drop and at 80 GPa is likely to be around 35 GPa in the experiment. In the present study, our obtained values can be compared with the experimental and theoretical results.

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Graphical abstract The energy-volume relation and ZB phase for the BeTe

     

A nucleophile activation dyad in ribonucleases. A combined X-ray crystallographic/ab initio quantum chemical study

Ribonucleases (RNases) catalyze the cleavage of the phosphodiester bond in RNA up to 10(15)-fold, as compared with the uncatalyzed reaction. High resolution crystal structures of these enzymes in complex with 3'-mononucleotide substrates demonstrate the accommodation of the nucleophilic 2'-OH group in a binding pocket comprising the catalytic base (glutamate or histidine) and a charged hydrogen bond donor (lysine or histidine). Ab initio quantum chemical calculations performed on such Michaelis complexes of the mammalian RNase A (EC ) and the microbial RNase T(1) (EC ) show negative charge build up on the 2'-oxygen upon substrate binding. The increased nucleophilicity results from stronger hydrogen bonding to the catalytic base, which is mediated by a hydrogen bond from the charged donor. This hitherto unrecognized catalytic dyad in ribonucleases constitutes a general mechanism for nucleophile activation in both enzymic and RNA-catalyzed phosphoryl transfer reactions.     

Using substrate analogues to probe the kinetic mechanism and active site of Escherichia coli MenD

MenD catalyzes the thiamin diphosphate-dependent decarboxylative carboligation of α-ketoglutarate and isochorismate. The enzyme is essential for menaquinone biosynthesis in many bacteria and has been proposed to be an antibiotic target. The kinetic mechanism of this enzyme has not previously been demonstrated because of the limitations of the UV-based kinetic assay. We have reported the synthesis of an isochorismate analogue that acts as a substrate for MenD. The apparent weaker binding of this analogue is advantageous in that it allows accurate kinetic experiments at substrate concentrations near K(m). Using this substrate in concert with the dead-end inhibitor methyl succinylphosphonate, an analogue of α-ketoglutarate, we show that MenD follows a ping-pong kinetic mechanism. Using both the natural and synthetic substrates, we have measured the effects of 12 mutations of residues at the active site. The results give experimental support to previous models and hypotheses and allow observations unavailable using only the natural substrate.     

A new mechanism and kinetic model for the enzymatic synthesis of short-chain fructooligosaccharides from sucrose

A kinetic model based on a ping-pong mechanism was developed under the steady-state hypothesis to account for the short-chain fructooligosaccharides (sc-FOS) synthesis using the commercial cellulolytic enzyme preparation, Rohapect CM. This new mechanism takes into account the interactions between the enzyme species and potential substrates (sucrose and sc-FOS) as a single complex reaction, allowing a better understanding of the reaction kinetics.The initial reaction rate laws appropriately describe the kinetic profiles of the examined substrates. Whereas sucrose exhibited Michaelis–Menten behavior with substrate inhibition, 1-kestose and nystose followed Michaelis–Menten and sigmoid enzyme kinetics. In addition, the enzyme was competitively inhibited by glucose and exhibited significant hydrolytic activity in the presence of nystose.The overall model was simultaneously fitted to experimental data from three initial sucrose concentrations (0.5, 1.5 and 2.1 M) using a multi-response regression with kinetic parameters that have biochemical relevance and are independent of the enzyme concentration. According to the model, sucrose acts almost exclusively as a fructosyl donor substrate. The mathematical development described herein is expected to be suitable for modeling similar enzymatic reaction systems.     

Effect of microsolvation on zwitterionic glycine: an ab initio and density functional theory study

The effect of microsolvation on zwitterionic glycine, considering both (-NH3(+)) as proton donor and (-COO(-)) as proton acceptor at correlated ab initio (MP2) level and density functional methods (B3LYP, PW91, MPW1PW91 and PBE) using 6-311++G** basis set has been reported. DFT methods have been employed so as to compare the performance/quality of different gradient-corrected correlation functionals (PW91, PBE), hybrid functionals (B3LYP, MPW1PW91) and to predict the near quantitative structural and vibrational properties, at reduced computational cost. B3LYP method outperforms among the different DFT methods for the computed hydrogen bond distances and found closer to the value obtained by correlated MP2 level, whereas MPW1PW91 and PBE methods shows very similar values but approximately 0.03 A less, compared to B3LYP method. MP2 calculation and single point CCSD(T)//MP2 calculation have been considered to decompose the interaction energy, including corrections for basis set superposition error (BSSE). Moreover, charge distribution analysis has also been carried out to understand the long raised questions, how and why the two body energies have significant contribution to the total binding energy.     

The spontaneous and enzymatic reaction of N-acetyl-p-benzoquinonimine with glutathione: a stopped-flow kinetic study

The spontaneous and glutathione (GSH) transferase catalyzed reactions of GSH and N-acetyl-p-benzoquinonimine (NABQI) have been studied by stopped-flow kinetics. The spontaneous reaction was shown to be first order in NABQI, GSH and inversely proportional to the H+ concentration; e.g., at pH 7.0 and 25 degrees C the second-order rate constant was 3.2 X 10(4) M-1 s-1. Data for the enzymatic reaction gave values for Km of 27, 1.3, 7, and 7 microM and values for kappa cat of 90, 37, 5.1, and 165 s-1 for rat liver GSH transferases 1-1, 2-2, 3-3, and 7-7, respectively. Over a wide range of reactant concentrations and pH, the spontaneous reaction yields three products, namely a GSH conjugate, 3-(glutathion-S-yl)acetaminophen; a reduction product, acetaminophen; and an oxidation product, glutathione disulfide in the proportions 2:1:1. Analysis of products formed after enzymatic reaction showed that both GSH conjugation and the reduction of NABQI to acetaminophen were catalyzed to an extent characteristic of each isoenzyme. With respect to GSH conjugation, GSH transferase isoenzymes were effective in the order 7-7 greater than 2-2 greater than 1-1 greater than 3-3 greater than 4-4, and with respect to NABQI reduction these isoenzymes were effective in the order 1-1 greater than 2-2 greater than 7-7 the position of isoenzymes 3-3 and 4-4 being uncertain. Human GSH transferases delta, mu, and pi behave similarly to the homologous rat enzymes, i.e., toward conjugation in the order pi greater than delta greater than mu and the reduction delta greater than mu greater than pi (for nomenclature see W. B. Jakoby, B. Ketterer, and B. Mannervik, (1984) Biochem. Pharmacol. 33, 2539-2540). Possible mechanisms of the reaction and its effect on the toxicity of NABQI are discussed.     

Structural phase transition of SnSe under uniaxial stress and hydrostatic pressure: an ab initio study

We study the structural behavior of SnSe under the hydrostatic pressure using a constant pressure ab initio technique. We find SnSe undergoes a structural second order phase transition from the orthorhombic (Pnma) structure to orthorhombic (Cmcm) structure in the constant pressure simulation at 7 GPa which is in good agreement with the recent experimental study. The Cmcm structure is fivefold coordinated. This phase transition is also analyzed from the total energy calculations. Besides, we study the behavior of SnSe under uniaxial stress.     

Role of metal ions in catalysis by enolase: an ordered kinetic mechanism for a single substrate enzyme.

Spectroscopic and kinetic methods have been used to explore the roles of divalent metal ions in the enolase-catalyzed dehydration of 2-phosphoglycerate (2-PGA). Enolase requires 2 equiv of metal ion per active site for maximal activity. Previous crystallographic studies [Larsen, T. M., Wedekind, J. E., Rayment, I., and Reed, G. H. (1996) Biochemistry 35, 4349-4358] showed that both magnesium ions coordinated to the carboxylate group of the substrate/product-a scheme consistent with metal ion assistance in formation of the enolate intermediate. Electron paramagnetic resonance (EPR) data with 17O-labeled forms of phosphoenolpyruvate show that Mn(2+), bound at the lower affinity site, coordinates to one carboxylate oxygen and one phosphate oxygen of the substrate. These observations are fully consistent with the crystallographic data. Plots of activity versus log [metal ion] are bell-shaped, and the inhibitory phases of the profiles have been previously attributed to binding of metal ions at ancillary sites on the enzyme. However, the activation profiles and measurements of 2H kinetic isotope effects support an ordered kinetic mechanism wherein binding of 2-PGA precedes binding of the second metal ion, and release of the second metal ion occurs prior to departure of phosphoenolpyruvate. High concentrations of metal ion lead to inhibition in the ordered mechanism by interfering with product release. The 2H kinetic isotope effect is diminished in the inhibitory phases of the metal ion activation profiles in a manner that is consistent with the predominantly ordered mechanism. Zn(2+) gives lower maximal activity than Mg(2+), apparently due to slow release of Zn(2+) from the product complex. Addition of imidazole increases the maximal rate apparently by accelerating the release of Zn(2+) from the enzyme.     

An ab initio study of the guanidinium groups in saxitoxin

Quantum chemical (Hartree-Fock) calculations were performed on neutral and protonated saxitoxin in order to obtain optimum geometries, rotational energy barriers for the guanidinium ions and proton affinities. For comparison purposes, as model compounds, guanidinium systems in five and six membered rings were also investigated. In addition, DFT (B3LYP) calculations with the 6-31G** basis set were performed and the sodium affinities of the guanidinium groups in saxitoxin were obtained. It was concluded that the inhibition of the sodium channels by the saxitoxin is due to the interaction of the guanidinium group with carboxylate groups from the wall of the channel and not to the binding of the sodium ions. Figure Calculated structure of Compound 1, neutral saxitoxin. a Calculated structure of Compound 1a, saxitoxin protonated on the guanidine of the five-membered ring. b Calculated structure of Compound 1b, saxitoxin protonated on the guanidine of the six-membered ring     

The enzymatic mechanism of carboxypeptidase: A molecular dynamics study

An MD simulation of the system carboxypeptidase A (CPA) with the tetrapeptide Val-Leu-Phe-Phe has been performed in order to learn about the substrate disposition just prior to nucleophilic attack. We have explored the model in which the substrate does not substitute the zinc-coordinated water (the “water” mechanism). The simulations do suggest as feasible that the Zn-OH₂ group performs a nucleophilic attack on the Phe-Phe peptidic bond. We have also investigated the model in which the carbonyl oxygen displaces the zinc-coordinated water. In this case the substrate and Glu-270 orient themselves to allow an anhydride intermediate during the peptidic bond cleavage (the “anhydride” mechanism). Based on the results of the simulations, both “water” and “anhydride” mechanisms are structurally feasible, although the former model seems more probable on chemical grounds. © 1994 John Wiley & Sons, Inc.     

NADH interactions with WT- and S94A-acyl carrier protein reductase from Mycobacterium tuberculosis: an ab initio study

We present an ab initio molecular dynamics study of the complex between acyl carrier protein reductase InhA from M. tuberculosis and isonicotinic acid hydrazide-NADH. We focus on wild-type (WT) InhA and a mutant causing drug resistance (S94A) for which structural information is available (Rozwarski et al., 1998;279:98--102; Dessen et al., 1995;267:1638--1641). Our calculations suggest that the water-mediated H-bond interactions between Ser94 side chain and NADH, present in WT InhA X-ray structure, can be lost during the dynamics. This conformational change is accompanied by a structural rearrangement of Gly14. The calculated structure of WT is rather similar to the X-ray structure of the S94A mutant in terms of geometrical parameters and chemical bonding. Further evidence for the mobility of Ser94 is provided by a 1-ns-long classical molecular dynamics on the entire protein. The previously unrecognized high mobility of Ser94 can provide a rationale of the small change in free binding energies on passing from WT to S94A InhA.