Theoretical modeling of enzyme catalytic power: analysis of "cratic" and electrostatic factors in catechol O-methyltransferase

A comparative theoretical study of a bimolecular reaction in aqueous solution and catalyzed by the enzyme catechol O-methyltransferase (COMT) has been carried out by a combination of two hybrid QM/MM techniques: statistical simulation methods and internal energy minimizations. In contrast to previous studies by other workers, we have located and characterized transition structures for the reaction in the enzyme active site, in water and in a vacuum, and our potential of mean force calculations are based upon reaction coordinates obtained from features of the potential energy surfaces in the condensed media, not from the gas phase. The AM1/CHARMM calculated free energy of activation for the reaction of S-adenosyl methionine (SAM) with catecholate catalyzed by COMT is 15 kcal mol(-1) lower the AM1/TIP3P free-energy barrier for the reaction of the trimethylsulfonium cation with the catecholate anion in water at 300 K, in agreement with previous estimates. The thermodynamically preferred form of the reactants in the uncatalyzed model reaction in water is a solvent-separated ion pair (SSIP). Conversion of the SSIP into a contact ion pair, with a structure resembling that of the Michaelis complex (MC) for the reaction in the COMT active site, is unfavorable by 7 kcal mol(-1), largely due to reorganization of the solvent. We have considered alternative ways to estimate the so-called "cratic" free energy for bringing the reactant species together in the correct orientation for reaction but conclude that direct evaluation of the free energy of association by means of molecular dynamics simulation with a simple standard-state correction is probably the best approach. The latter correction allows for the fact that the size of the unit cell employed with the periodic boundary simulations does not correspond to the standard state concentration of 1 M. Consideration of MC-like species allows a helpful decomposition of the catalytic effect into preorganization and reorganization phases. In the preorganization phase, the substrates are brought together into the MC-like species, either in water or in the enzyme active site. In the reorganization phase, the roles of the enzymic and aqueous environments may be compared directly because reorganization of the substrate is about the same in both cases. Analysis of the electric field along the reaction coordinate demonstrates that in water the TS is destabilized with respect to the MC-like species because the polarity of the solute diminishes and consequently the reaction field is also decreased. In the enzyme, the electric field is mainly a permanent field and consequently there is only a small reorganization of the environment. Therefore, destabilization of the TS is lower than in solution, and the activation barrier is smaller.     

Validation of a screening method for the simultaneous identification of fat-soluble and water-soluble vitamins (A,E, B<Subscript>1</Subscript>, B<Subscript>2</Subscript> and B<Subscript>6</Subscript>) in an aqueous micellar medium of hexadecyltrimethylammonium chloride

Simultaneous determination of the fat-soluble vitamins A and E and the water-soluble vitamins B₁, B₂ and B₆ has been carried using a screening method from fluorescence contour graphs. These graphs show different colour zones in relation to the fluorescence intensity measured for the pair of excitation/emission wavelengths. The identification of the corresponding excitation/emission wavelength zones allows the detection of different vitamins in an aqueous medium regardless of the fat or water solubility of each vitamin, owing to the presence of a surfactant which forms micelles in water at the used concentration (over the critical micelle concentration). The micelles dissolve very water insoluble compounds, such as fat-soluble vitamins, inside the aggregates. This approach avoids the use of organic solvents in determining these vitamins and offers the possibility of analysing fat- and water-soluble vitamins simultaneously. The method has been validated in terms of detection limit, cut-off limit, sensitivity, number of false positives, number of false negatives and uncertainty range. The detection limit is about g L^–1. The screening method was applied to different samples such as pharmaceuticals, juices and isotonic drinks.     

New dirhenium(III) compounds bridged by carboxylate ligands: N(C(4)H(9))(4)[Re(2)(OOCCF(3))Cl(6)] and Re(2)(OOCCCHCo(2)(CO)(6))(4)Cl(2)

The solvothermal reaction of (N(C(4)H(9))(4))(2)[Re(2)Cl(8)] with trifluoroacetic acid and acetic anhydride leads to the new rhenium trifluoroacetate dimer N(C(4)H(9))(4)[Re(2)(OOCCF(3))Cl(6)] (1) and to the rhenium carbonyl dimer Re(2)(mu(2)-Cl)(2)(CO)(8) as the rhenium-reduced byproduct. The reaction of the precursor complex, N(C(4)H(9))(4)[Re(2)(OOCCF(3))Cl(6)] (1), with the organometallic carboxylic acid (CO)(6)Co(2)HCCCOOH leads to the cluster of clusters compound Re(2)(OOCCCHCo(2)(CO)(6))(4)Cl(2) (2), which has the dimer structure of Re(2)(OOCR)(4)Cl(2). Cyclic voltammetric measurements show that Re(2)(OOCCCHCo(2)(CO)(6))(4)Cl(2) (2) has one reduction centered on the dirhenium core and a reduction centered on the cobalt atoms. DFT calculations have been used to rationalize the observed displacements of the voltammetric signals in Re(2)(OOCCCHCo(2)(CO)(6))(4)Cl(2) (2) compared to the parent ligand (CO)(6)Co(2)HCCCOOH and rhenium pivalate.     

Stereoselective conjugate addition of benzyl phenylsulfonyl carbanions to enoates derived from d-mannitol

The conjugate addition of benzylic phenylsulfonyl carbanions (2a'-d') to enoates derived from d-(+)-mannitol (E- or Z-1a-c) was studied using THF and THF/HMPA as solvent. Under kinetic conditions (-78 degrees C), enoate E-1a,b led to a mixture of syn-(R,S) and anti-(S,S) adducts (55/45), and syn-(R,S) adducts were the main product obtained ( approximately 90/10) from enoate Z-1a. Under thermodynamic conditions (-78 degrees C to room temperature) syn-(R,S) adducts were also preferentially formed ( approximately 90/10), despite the geometry at the double bond in the acceptor. Enoate 1c (E/Z = 57/43), bearing an additional benzyl group at the alpha-position, also reacted with carbanions 2'a,b, under thermodynamic conditions, leading to syn-adducts in excellent de (control at the three newly generated stereogenic centers). The adducts were quantitatively transformed into the corresponding beta-gamma-disubstituted gamma-butyrolactones and alpha,beta,gamma-trisubstituted gamma-butyrolactones. (1)H NMR studies (NOE and J-coupling) of these lactones allowed us to determine their configuration at the newly generated chiral centers. The reduction of the C-S bond in adducts syn-(R,S) with Na/Hg, followed by treatment of the resulting products in aqueous acid media, led to enantioenriched beta-benzyl-gamma-hydroxymethyl-gamma-butyrolactones. The conformational equilibrium of enoates E- and Z-1b was evaluated by theoretical calculations (ab initio, MP2/6-31G), and a mechanistic rationale was proposed to explain the observed stereoselectivities.     

Sublimation enthalpy of dye molecules measured using fluorescence

We present an in-flight fluorescence detection scheme for molecular beams which is applied to determine the enthalpy of sublimation of dye molecules. We investigate tetraphenylporphyrin (TPP), porphine, and nile red, which are believed to be suitable candidates for molecular de Broglie wave interferometry. The measured values are H(sub)(TPP)=142+/-3 kJ/mol, H(sub)(porphine)=87+/-3 kJ/mol, and H(sub)(nile red)=66+/-2 kJ/mol. For TPP, sublimation enthalpies differ in the literature by more than a factor of 2. Our measurements confirm a value at the lower end of this scale. We discuss changes in the character of the molecular flow with the source temperature as a prime reason for discrepancies in the published data.     

Preparation of trout liver microsomes for iron speciation in P-450 enzymes by AE–FPLC with ICP–(ORS)MS detection

Cytochromes P-450 are members of a superfamily of hemoproteins involved in the oxidative metabolism of various physiological and xenobiotic compounds in eukaryotes and prokaryotes. The multiplicity of this group of enzymes has been widely studied by chromatographic techniques, mainly high-performance liquid chromatography (HPLC). Because these enzymes are membrane-bound proteins, sample preparation for chromatographic separation of P-450 enzymes requires a solubilization step. The sample-preparation procedures are critical, because detergents affect not only the efficiency of protein solubilization but also their further chromatographic resolution. Trout liver microsomes have been taken here as a model sample to investigate iron speciation in cytochrome P-450. Trouts were treated intraperitoneally with -naphthoflavone, a potent inducer of some P-450 enzymes, and a microsomal suspension containing 7.4±0.1 nmol mL^–1 P-450 enzymes was obtained by ultracentrifugation. Lubrol PX was selected as detergent for solubilization, resulting in about 90% solubilization recovery. The solubilized cytochromes P-450 were further separated by AE–FPLC, with UV detection, or coupled to ICP–MS with an octapole reaction system, ICP–(ORS)MS (monitoring Fe signals at masses 54, 56, and 57). A sampling procedure and chromatographic conditions are developed and were successfully applied to iron speciation in trout liver P-450 enzymes. ICP–(ORS)MS detection of P-450 enzymes is Fe-specific and so will give accurate information on the prosthetic group of the protein, which can constitute an advantageous alternative to classical methods for detection of these hemoproteins.     

Comprehensive photokinetic and NMR study of a biphotochromic supermolecule involving two naphthopyrans linked to a central thiophene unit through acetylenic bonds

A photophysical and photochemical study of a biphotochromic compound where two naphthopyran units are linked by an acetylene-thiophene-acetylene bridge has been carried out in toluene. Both fluorescence and intersystem crossing to the triplet manifold were found to compete with the photocoloration process. Two photoproducts (transoid-trans and transoid-cis stereoisomers), absorbing at approximately 480 nm and corresponding to the opening of a single photochromic unit, were detected by spectrophotometric analysis after short irradiation time in diluted solution and identified by 1H-nuclear magnetic resonance (NMR) spectroscopy. After prolonged irradiation at 228 K of highly concentrated solutions (up to 3 x 10(-3) mol dm(-3)), two additional isomers, absorbing at approximately 550 nm, were formed. Their NMR spectra indicate the opening of both photochromic units. An interesting effect of selective vibronic excitation was found, showing that the photoreaction is favored at excited vibronic levels to the detriment of the radiative relaxation.     

Ru(TAP)2(dppz)]2+: a DNA intercalating complex, which luminesces strongly in water and undergoes photo-induced proton-coupled electron transfer with guanosine-5'-monophosphate

The lowest excited state of [Ru(TAP)2(dppz)]2+ (TAP = 1,4,5,8-tetraazaphenanthrene, dppz = dipyrido[3,2-a:2',3'-c]phenazine) 1 is strongly luminescent, even in water, and very oxidizing. Therefore it is able to oxidise not only guanosine-5'-monophosphate (GMP), as demonstrated by laser flash photolysis, but also guanine-containing polynucleotides such as calf thymus DNA and [poly(dG-dC)]2. The luminescence quenching was found to be faster in H2O than in D2O, as is the back reaction, indicating that both processes probably proceed by proton-coupled electron transfer. These properties, that are controlled by the triplet MLCT state in which the charge has been transferred from the Ru to a TAP ligand, contrast with those of the well known [Ru(phen)2(dppz)]2+ 2.     

The effect of engineered disulfide bonds on the stability of Drosophila melanogaster acetylcholinesterase

Background  

Acetylcholinesterase is irreversibly inhibited by organophosphate and carbamate insecticides allowing its use in biosensors for detection of these insecticides. Drosophila acetylcholinesterase is the most sensitive enzyme known and has been improved by in vitro mutagenesis. However, its stability has to be improved for extensive utilization.