Characterisation of the citrate synthase reaction with propionyl-CoA

Experiments with propionyl-CoA stereoselectively deuteriated in the propionyl moiety demonstrate that the formation of (2S,3S)-methylcitric acid (1) catalysed by citrate (si)-synthase occurs with inversion of configuration in the propionyl moiety; the absolute configurations of the methylcitric acids 1 and 2 indicate a si attack on oxaloacetate. Deuterium in the pro-S position is exchanged for protium 60 times faster than deuterium in the pro-R position. Experiments with (R,S)-(2-2H1)propionyl-CoA allowed the determination of isotope effects. For the enzymatic formation of 1, a primary deuterium isotope effect kH/kD = 1.8 and a secondary alpha-deuterium isotope effect kH/kD = 0.99 were calculated; both are effects on Vmax/KM.     

Chiral diamines 4: a computational study of the enantioselective deprotonation of Boc-pyrrolidine with an alkyllithium in the presence of a chiral diamine

The enantioselective deprotonation of N-Boc-pyrrolidine (1) with i-PrLi-(-)-sparteine has been studied at theoretical levels up through B3P86/6-31G. Four low-energy intermediate complexes involving i-PrLi-(-)-sparteine and 1 were located via geometry optimizations; two of these complexes would lead to abstraction of the pro-S hydrogen from 1, and the other two complexes would lead to loss of the pro-R hydrogen. The lowest-energy intermediate complex was found to lead to loss of the pro-S hydrogen as observed experimentally. Transition states for the deprotonations were located using the synchronous transit-guided quasi-Newton method. The calculated activation enthalpy for transfer of the pro-S hydrogen within the lowest-energy intermediate complex, 10.8 kcal/mol, is reasonable for a reaction that occurs at a relatively low temperature, and the calculated kinetic hydrogen isotope effect is in agreement with experimental data. The lower enantioselectivity observed experimentally for deprotonation of 1 using t-BuLi-(-)-sparteine is attributed to a transition-state effect due to increased steric interaction engendered by the bulky t-BuLi. Replacement of the tert-butoxycarbonyl group in 1 by a methoxycarbonyl is predicted to result in a slower deprotonation with somewhat decreased enantioselectivity. Asymmetric deprotonation of 1 using i-PrLi in combination with the C(2)-symmetric diamine, (S,S)-1,2-bis(N,N-dimethylamino)cyclohexane, was calculated to be much less selective than is the deprotonation mediated by (-)-sparteine as observed experimentally. The relative energies of the intermediate complexes were fairly well-reproduced by ONIUM calculations in which the sparteine ligand less its nitrogen atoms was treated by molecular mechanics and the remainder of the complex was treated by quantum mechanics.     

Mechanism of RNase T1: concerted triester-like phosphoryl transfer via a catalytic three-centered hydrogen bond

BACKGROUND: The microscopic events of ribonuclease (RNase) catalyzed phosphoryl transfer reactions are still a matter of debate in which the contenders adhere to either the classical concerted acid-base mechanism or a more sequential triester-like mechanism. In the case of RNase A, small thio-effects of the nonbridging oxygens have been invoked in favor of the classical mechanism. However, the RNase T1 catalyzed transphosphorylation of phosphorothioate RNA is highly stereoselective. R(P) thio-substituted RNA is depolymerized 60000 times faster than S(P) thio-substituted RNA by this enzyme, whereas the uncatalyzed cleavage of both substrates occurs at comparable rates. We combined site-directed mutagenesis in the RNase active site and stereospecific thio-substitution of an RNA substrate to probe the intermolecular interactions of the enzyme with the nonbridging pro-S(P) oxygen that bring about this stereoselectivity of RNase T1. RESULTS: Thio-substitution of the nonbridging pro-S(P) oxygen in the substrate afflicts chemical turnover but not ground state binding whereas thio-substitution of the nonbridging pro-R(P) oxygen does not affect the kinetics of RNase T1. Site-directed mutagenesis of the catalytic base Glu58 impairs the enzyme's ability to discriminate both phosphorothioate diastereomers. Glu58Ala RNase T1 cleaves R(P) and S(P) phosphorothioate RNA with similar rates. The dependence of the pro-S(P) thio-effect on the presence of the Glu58 carboxylate evidences a strong rate-limiting interaction between the nonbridging pro-S(P) oxygen and the catalytic base Glu58 in the wild type enzyme. CONCLUSIONS: Based on these results, we put forward a new triester-like mechanism for the RNase T1 catalyzed reaction that involves a three-centered hydrogen bond between the 2'-OH group, the nonbridging pro-S(P) oxygen and one of the carboxylate oxygens of Glu58. This interaction allows nucleophilic attack on an activated phosphate to occur simultaneously with general base catalysis, ensuring concerted phosphoryl transfer via a triester-like mechanism.     

Solvolytic enolization of scytalone

[reaction--see text] The major conformation of scytalone has an envelope shape with C3 forming the flap and the C3 hydroxyl in the equatorial position as determined by quantum mechanical calculations and corroborated by NMR. The C2 axial pro-R is slower to exchange with solvent than the equatorial pro-S hydrogen. Modeling the transition state for enolate formation points to a deprotonation through the flipped envelope conformation in which the C3-hydroxyl and the C2 pro-S hydrogen are axial.     

Analysis of the 13C NMR spectra of molecules, chiral by isotopic substitution, dissolved in a chiral oriented environment: towards the absolute assignment of the pro-R/pro-S character of enantiotopic ligands in prochiral molecules

We examined and discuss the proton- and deuterium-decoupled carbon-13 1D spectrum of a molecule, chiral by virtue of the isotopic substitution, dissolved in a chiral oriented medium which simultaneously exhibits chiral discrimination, enantiomeric enrichment and isotope effect. Using the 1-deutero-(2',3',4',5',6'-pentadeuterophenyl)phenylmethanol orientationally ordered in a chiral nematic liquid crystal as illustrative example, we point out three important features. First, we demonstrate that the absolute assignment of the pro-R/pro-S character may be derived from the absolute configuration of the isotopically chiral analogue. Second, we report evidence that isotopic effect on (13)C chemical shift anisotropy is negligible in a weakly orienting solvent. Third, we definitely establish that the molecular orientation of prochiral C(s) symmetry molecules and their parent compounds that are chiral by virtue of the isotopic substitution is the same.     

Stereochemistry of the reduction step mediated by recombinant 1-deoxy-D-xylulose 5-phosphate isomeroreductase

[formula: see text] The stereochemistry of the 1-deoxy-D-xylulose 5-phosphate (DXP) isomeroreductase reduction step has been examined using the recombinant enzyme from Synechocystis sp. PCC6803. Using [3-2H]DXP and [4S-2H]NADPH, it has been determined that the C1 pro-S hydrogen in the 2-C-methyl-D-erythritol 4-phosphate product derives from C3 of DXP, indicating that hydride attack occurs on the re face of the intermediate aldehyde. The 4S-hydride from NADPH is delivered, assigning this enzyme as a class B dehydrogenase.     

A combined quantum mechanical and molecular mechanical study of the reaction mechanism and alpha-amino acidity in alanine racemase

Combined quantum mechanical/molecular mechanical simulations have been carried out to investigate the origin of the carbon acidity enhancement in the alanine racemization reaction catalyzed by alanine racemase (AlaR). The present study shows that the enhancement of carbon acidity of alpha-amino acids by the cofactor pyridoxal 5'-phosphate (PLP) with an unusual, unprotonated pyridine is mainly due to solvation effects, in contrast to the intrinsic electron-withdrawing stabilization by the pyridinium ion to form a quinonoid intermediate. Alanine racemase further lowers the alpha-proton acidity and provides an overall 14-17 kcal/mol transition-state stabilization. The second key finding of this study is that the mechanism of racemization of an alanine zwitterion in water is altered from an essentially concerted process to a stepwise reaction by formation of an external aldimine adduct with the PLP cofactor. Finally, we have used a centroid path integral method to determine the intrinsic kinetic isotope effects for the two proton abstraction reactions, which are somewhat greater than the experimental estimates.     

Phenylalanine ammonia-lyase: the use of its broad substrate specificity for mechanistic investigations and biocatalysis--synthesis of L-arylalanines

Several fluoro- and chlorophenylalanines were found to be good substrates of phenylalanine ammonia-lyase (PAL/EC 4.3.1.5) from parsley. The enantiomerically pure L-amino acids were obtained in good yields by reaction of the corresponding cinnamic acids with 5M ammonia solution (buffered to pH 10) in the presence of PAL. The kinetic constants for nine different fluoro- and chlorophenylalanines do not provide a rigorous proof for but are consistent with the previously proposed mechanism comprising an electrophilic attack of the methylidene-imidazolone cofactor of PAL at the aromatic nucleus as a first chemical step. In the resulting Friedel-Crafts-type sigma complex the beta-protons are activated for abstraction and consequently the pro-S is abstracted by an enzymic base. Results from semi-empirical calculations combined with a proposed partial active site model showed a correlation between the experimental kinetic constants and the change in polarization of the pro-S Cbeta-H bond and heat of formation of the sigma complexes, thus making the electrophilic attack at the neutral aromatic ring plausible. Furthermore, while 5-pyrimidinylalanine was found to be a moderately good substrate of PAL, 2-pyrimidinylalanine was an inhibitor.     

Stereochemical and mechanistic aspects of dioxygenase-catalysed benzylic hydroxylation of indene and chromane substrates

Toluene dioxygenase (TDO)-catalysed benzylic hydroxylation of indene substrates (8, 16 and 17), using whole cell cultures of Pseudomonas putida UV4, was found to yield inden-1-ol (14 and 22) and indan-1-one bioproducts (15 and 23). The formation of these bioproducts is consistent with the involvement of carbon-centred radical intermediates. TDO-catalysed oxidation of indenes 8 and 16 also gave cis-diols 13 and 18 respectively. TDO and naphthalene dioxygenase (NDO), used as both whole-cell preparations and as purified enzymes, were found to catalyse the benzylic hydroxylation of chromane 30, deuteriated (+/-)-chromane 30D and enantiomers (4S)-30D and (4R)-30D to yield (4R)- and (4S)-chroman-4-ols 31/31D respectively. The mechanism of benzylic hydroxylation of chromane 30/30D involves the stereoselective abstraction of a pro-R (with TDO) or a pro-S (with NDO) hydrogen atom at C-4 and a marked preference for retention of configuration.     

Selective kinetic determination of pyridoxal-5'-phosphate with an ammonia gas-sensing electrode

The coenzyme pyridoxal-5'-phosphate (PLP) is deiermined by in situ measurement of the rate of ammonia production using a potentiometric gas-sensing membrane electrode. It is shown that the initial rate of ammonia liberation from L-tryptophan by action of tryptophanase apoenzyme and the coenzyme can be linearly related to PLP levels in the nanogram range with minimal interference from related compounds. Calibration data for the 1 × 10^-7–2.5 × 10^-6 M range for PLP yielded a least-squares equation of rate (mV min^-1) = (0.64 ± 0.01) C — 0.01 ± 0.02 with a standard error of 0.02 mV min^-1, where concentration, C, is expressed in units of 10^-7 mol l^-1.     

Determination of the rates of formation and hydrolysis of the Schiff bases formed by pyridoxal 5′-phosphate and hydrazinic compounds

The macroscopic rate constants of formation (k₁) and hydrolysis (k₂) for the reactions of pyridoxal 5′-phosphate (PLP) with hydrazine (PLP-HY system), carbidopa (-hydrazino--methyl-β-(3,4-dihydroxyphenyl)propionic acid, PLP-CD system), hydralazine (1-hydrazinophthalazine, PLP-HL system) and isoniazid (4-pyridinecarboxylic acid hydrazide, PLP-ISO system) were fitted to a kinetic scheme that considers the different ionic species present in the medium, their protonation constants, and their individual rates of formation (k₁ⁱ) and hydrolysis (k₂ⁱ). The results obtained for the molecules bearing the hydrazine group are compared with those for the reactions of PLP with n-hexylamine (PLP-NHA system) and poly- -lysine (PLP-LYS system). Some structural effects on the individual rate constants are also examined.     

Isolation and structure determination of the cembranoid eunicin from a new genus of octocoral, Pseudoplexaura

The known cembranoid diterpene eunicin (1) was isolated from a new genus of octocoral, Pseudoplexaura, collected in the Caribbean. The complete assignment of the 13C and 1H NMR spectra, including differentiation of pro-R and pro-S hydrogens and elucidation of all J values, was accomplished with the aid of TOCSY, HSQC, and HMBC data, and a consideration of three low-energy conformations using SYBYL.     

Determination of pyridoxal‐5′‐phosphate (PLP)‐bonding sites in proteins: a peptide mass fingerprinting approach based on diagnostic tandem mass spectral features of PLP‐modified peptides

Peptides modified by pyridoxal‐5′‐phosphate (PLP), linked to a lysine residue via reductive amination, exhibit distinct spectral characteristics in the collision‐induced dissociation (CID) tandem mass (MS/MS) spectra that are described here. The MS/MS spectra typically display two dominant peaks whose m/z values correspond to neutral losses of [H₃PO₄] (?98 Da) and the PLP moiety as [C₈H₁₀NO₅P] (?231 Da) from the precursor peptide ion, respectively. Few other peaks are observed. Recognition of this distinct fragmentation behavior is imperative since determining sequences and sites of modifications relies on the formation of amide backbone cleavage products for subsequent interpretation via proteome database searching. Additionally, PLP‐modified peptides exhibit suppressed precursor ionization efficiency which diminishes their detection in complex mixtures. Presented here is a protocol which describes an enrichment strategy for PLP‐modified peptides combined with neutral loss screening and peptide mass fingerprinting to map the PLP‐bonding site in a known PLP‐dependent protein. This approach represents an efficient alternative to site‐directed mutagenesis which has been the traditional method used for PLP‐bonding site localization in proteins. Copyright © 2009 John Wiley & Sons, Ltd.     

Density functional study of the in-line mechanism of methanolysis of cyclic phosphate and thiophosphate esters in solution: insight into thio effects in RNA transesterification

Density functional calculations of thio effects on the in-line mechanism of methanolysis of ethylene phosphate (a reverse reaction model for RNA phosphate transesterification) are presented. A total of 12 reaction mechanisms are examined using the B3LYP functional with large basis sets, and the effects of solvation were treated using the PCM, CPCM, and SM5 solvation models. Single thio substitutions at all of the distinct phosphoryl oxygen positions (2', 3', 5', pro-R) and a double thio substitution at the nonbridging (pro-R/pro-S) positions were considered. Profiles for each reaction were calculated in the dianionic and monoanionic/monoprotic states, corresponding to reaction models under alkaline and nonalkaline conditions, respectively. These models provide insight into the mechanisms of RNA transesterification thio effects and serve as a set of high-level quantum data that can be used in the design of new semiempirical quantum models for hybrid quantum mechanical/molecular mechanical simulations and linear-scaling electronic structure calculations.     

Kinetic isotope effects of L-Dopa decarboxylase

A mixed centroid path integral and free energy perturbation method (PI-FEP/UM) has been used to investigate the primary carbon and secondary hydrogen kinetic isotope effects (KIEs) in the amino acid decarboxylation of L-Dopa catalyzed by the enzyme L-Dopa decarboxylase (DDC) along with the corresponding uncatalyzed reaction in water. DDC is a pyridoxal 5'-phosphate (PLP) dependent enzyme. The cofactor undergoes an internal proton transfer between the zwitterionic protonated Schiff base configuration and the neutral hydroxyimine tautomer. It was found that the cofactor PLP makes significant contributions to lowering the decarboxylation barrier, while the enzyme active site provides further stabilization of the transition state. Interestingly, the O-protonated configuration is preferred both in the Michaelis complex and at the decarboxylation transition state. The computed kinetic isotope effects (KIE) on the carboxylate C-13 are consistent with that observed on decarboxylation reactions of other PLP-dependent enzymes, whereas the KIEs on the α carbon and secondary proton, which can easily be validated experimentally, may be used as a possible identification for the active form of the PLP tautomer in the active site of DDC.     

Kinetic Study on Stability of Schiff Base of Pyridoxal 5′-Phosphate and Leucine in Water Media with Cationic Surfactants

We studied the stability of the Schiff bases formed between pyridoxal 5′-phosphate (PLP) and leucine in the presence of (hexadecyl)trimethylammonium bromide (CTAB) over a wide pH range by determining the kinetic constants of formation and hydrolysis of these compounds. The results show that the stability of the Schiff bases is increased by the presence of CTAB as a result of increased rates of formation and decreased hydrolysis rate constants. The ionic head groups of CTAB favour the formation of the bases, while its hydrophobic rests protect the imine double bond from hydrolysis. This model system permits one to obtain partially hydrophobic media with no need for any non-aqueous solvents.     

Alanine racemase free energy profiles from global analyses of progress curves

Free energy profiles for alanine racemase from Bacillus stearothermophilus have been determined at pH 6.9 and 8.9 from global analysis of racemization progress curves. This required a careful statistical design due to the problems in finding the global minimum in mean square for a system with eight adjustable parameters (i.e., the eight rate constants that describe the stepwise chemical mechanism). The free energy profiles obtained through these procedures are supported by independent experimental evidence: (1). steady-state kinetic constants, (2). solvent viscosity dependence, (3). spectral analysis of reaction intermediates, (4). equilibrium overshoots for progress curves measured in D(2)O, and (5). the magnitudes of calculated intrinsic kinetic isotope effects. The free energy profiles for the enzyme are compared to those of the uncatalyzed and the PLP catalyzed reactions. At pH 6.9, PLP lowers the free energy of activation for deprotonation by 8.4 kcal/mol, while the inclusion of apoenzyme along with PLP additionally lowers it by 11 kcal/mol.     

Stability of pyridoxal-5-phosphate semicarbazone: applications in plasma vitamin B6 analysis and population surveys of vitamin B6 nutritional status

The determination of pyridoxal-5-phosphate (PLP) and pyridoxal (PL) in plasma requires the availability of dark room facilities, due to the photosensitivity of these vitamin B6 vitamers. The fact that the semicarbazone forms of PL and PLP are more strongly fluorescent than the underivatized B6 vitamers has been exploited in plasma analyses, but it was not previously realised that these semicarbazone forms are also very stable even under conditions that lead to rapid decomposition of free PL and PLP. The stabilisation of PLP and PL obtained in this manner is sufficient and fully adequate to meet the practical requirements of clinical field studies. We report a high-performance liquid chromatographic method for plasma PLP and PL determinations based on precolumn semicarbazone formation and fluorescence detection. The method is sensitive enough for quantitative plasma PLP determinations even in B6-deficient patients.     

Enzymatic synthesis of chiral organophosphothioates from prochiral precursors

The phosphotriesterase from Pseudomonas diminuta has been shown to selectively cleave the pro-R p-nitrophenolate substituent from bis-p-nitrophenyl alkyl phosphothioate esters. When the alkyl substituent is methyl, ethyl, or isopropyl the enantiomeric excess of the product is >/=99%. Manipulation of the active site through mutagenesis has enabled the preparation of protein variants that preferentially hydrolyze the pro-S substituent of the target substrates. This methodology thus permits the preparation of chiral products from prochiral precursors.     

Etude des Dérivés de la Vitamine B6. Conformation des Complexes de Lanthanides avec le Pyridoxal-5′-phosphate et la Pyridoxamine-5′-phosphate en Phase Aqueuse à pD = 1,3

A suitable procedure is described for establishing the conformational analysis of flexible molecules coordinated to lanthanide cations from ¹H and ¹³C NMR paramagnetic shift data. The examples of pyridoxal 5′-phosphate (PLP) and pyridoxamine 5′-phosphate (PMP) in aqueous solution at pD = 1.3 values are discussed. In the two cases, a hindered rotation around P? O-5′, with Gaussian distribution is proposed. The values of angles and distances between rare earth cations and ligand nuclei are determined.