Quantum-mechanical study on the catalytic mechanism of alkaline phosphatases

Alkaline phosphatases (APs) catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The catalytic mechanism was examined by quantum-mechanical calculations using an active-site model based on the X-ray crystal structure of the human placental AP. Free energies of activation and of reaction for the catalytic steps were evaluated for a series of aryl and alkyl phosphate esters, and the computational results were compared with experimental values available in the literature. Mechanistic observations previously reported in experimental works were rationalized by the present theoretical study, particularly regarding the difference in the rate-determining step between aryl and alkyl phosphates. The formation rate of the covalent phosphoserine intermediate followed a linear free energy relationship (LFER) with the pKa of the leaving group. This LFER, which could be experimentally determined only for less reactive alkyl phosphates, was verified by the present calculations to apply for the entire set of aryl and alkyl phosphate substrates. (Chemical Equation Presented).Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentin

Computational study on the role of residue Arg166 in alkaline phosphatases

Quantum chemical calculations were performed with the goal of achieving a better understanding of the influence of Arg166 on the catalytic activity of alkaline phosphatases. The present results indicate that the active site Arg166 residue contributes to catalysis by orienting the phosphate monoester substrate in a favorable position for the rate-limiting nucleophilic attack. The stabilizing hydrogen bond interactions of the guanidinium group with two nonbridging oxygens of the phosphate decrease the barrier for the phosphoryl transfer process by attainment of a tighter and preorganized transition state.Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentin

Alkaline phosphatases: In silico study on the catalytic effect of conserved active site residues using human placental alkaline phosphatase (plap) as a model protein

The metalloenzymes from the alkaline phosphatase (AP) superfamily catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The role of several amino acids highly conserved in the active site of this family of enzymes was examined, using human placental AP (PLAP) as a model protein. By employing an active-site model based on the X-ray crystal structure of PLAP, mutations of several key residues were modeled by quantum mechanical methods in order to determine their impact on the catalytic activity. Kinetic and thermodynamic estimations were achieved for each reaction step of the catalytic mechanism by characterization of the intermediates and transition states on the reaction pathway, and the effects of mutations on the activation barriers were analyzed. A good accordance was observed between the present computational results and experimental measurements reported in the literature.Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentin

Mutagenicity of heteroaromatic amines: Computational study on the influence of methyl substituents

Quantum mechanical calculations were performed to elucidate the factors determining the variations in mutagenic activity within groups of isomeric heteroaromatic amines that differ in the position of methyl substituents. Formation energies for noncovalent complexes and covalent DNA adducts were evaluated by means of high level quantum chemical methods. According to the computational results in this work, covalent adduct stability is proposed to influence the relative mutagenicities of structurally related heterocyclic amines. The stability of covalent C8-dG DNA adducts was found to be mainly determined by π-stacking interactions between the fused ring system of the heteroaromatic amines and the flanking nucleobases. Relative mutagenicity of amines of very related structure is proposed to be regulated by both nitrenium ion and covalent adduct stabilities.Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentin

Catalytic Activity of Human Placental Alkaline Phosphatase (PLAP):Insights from a Computational Study

Alkaline phosphatases (APs) catalyze the hydrolysis and transphosphorylation of phosphate monoesters. Quantum-mechanical computational methods were employed to study the catalytic mechanism of human placental AP (PLAP). An active-site model was used, constructed on the basis of the X-ray crystal structure of the enzyme. Kinetic and thermodynamic evaluations were achieved foreach reaction step. Calculations shed light on the mechanistic differences that had been experimentally observed between aryl and alkyl phosphates, particularly regarding the rate-determining step. The functional implications of relevant residues in the active site were examined. The present theoretical study rationalizes experimental observations previously reported in the literature.Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentin

Quantum-chemical studies on mutagenicity of aromatic and heteroaromatic amines

With the prospect of potential treatments for Huntington's disease (HD), non-invasive markers of disease progression are needed. Cognitive impairment has long been recognised as one of the core symptoms of HD. The first aim of this review is to provide insight into the onset and nature of cognitive loss in the progressing stages of HD. The second aim is to provide an overview of the cognitive functions that have been examined in an attempt to identify those areas that have the most potential to yield a cognitive biomarker. Literature, consisting of 110 studies, since the implementation of genetic testing until the beginning of 2011 has been included in this review. The clinical features of premanifest HD include deficits in psychomotor speed, negative emotion recognition and to some extent in executive functioning. The clinical profile of manifest HD includes impairment in memory, psychomotor speed, negative emotion recognition and executive functioning. Furthermore, potential candidate biomarkers should be most expected from such domains as working memory, psychomotor speed, recognition of negative emotions, attentional and visuospatial executive functions.Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; Argentin

Computational modeling of the catalytic mechanism of human placental alkaline phosphatase (PLAP)

Alkaline phosphatases (APs) catalyze the hydrolysis and transphosphorylation of phosphate monoesters. Quantum mechanical, molecular dynamics, and molecular docking techniques were applied to computationally model the catalytic mechanism of human placental AP (PLAP). Kinetic and thermodynamic evaluations were performed for each reaction step. The functional significances of the more important residues within the active site were analyzed. The role of the metal ion at the metal binding site M3 was also examined. The calculated activation and reaction energy and free energy values obtained suggested the nucleophilic attack of the Ser92 alkoxide on the phosphorus atom of the substrate would be the rate-limiting step of the catalytic hydrolysis of alkyl phosphate monoesters by PLAP. The reactivities of the wild-type M3-Mg enzyme and the M3-Zn protein were compared, and the main difference observed was a change in the coordination number of the M3 metal for the M3-Zn enzyme. This modification in the active site structure lowered the free energy profile for the second chemical step of the catalytic mechanism (hydrolysis of the covalent phosphoserine intermediate). Consequently, a greater stabilization of the phosphoseryl moiety resulted in a small increment in the activation free energy of the phosphoserine hydrolysis reaction. These computational results suggest that the activation of APs by magnesium at the M3 site is caused by the preference of Mg2+ for octahedral coordination, which structurally stabilizes the active site into a catalytically most active conformation. The present theoretical results are in good agreement with previously reported experimental studies. © 2011 American Chemical Society.Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Lin, Susana. National Health Research Institutes; República de Chin

Oxidized metabolites from cyclopenta-fused polycyclic aromatic hydrocarbons (CP-PAHs). A DFT model study of their carbocations formed by epoxide ring opening

A density functional theory (DFT) study aimed at understanding structure-reactivity relationships in the oxidized metabolites of cyclopenta-fused polycyclic aromatic hydrocarbons (CP-PAHs) is reported. Epoxidation at various positions was examined in order to identify the most stable epoxide in each class of CP-PAHs. Relative energies of the carbocations resulting from O-protonation and epoxide ring opening were analyzed and compared, taking into account the available biological activity data on these compounds. Geometrical, electronic, and conformational issues were considered. Charge delocalization modes in the resulting carbocations were deduced via the natural population analysis (NPA)-derived changes in charges. Computational results pointed to the importance of the unsaturated cyclopenta ring on the reactivity of these compounds. The reported bioactivity of this highly mutagenic/carcinogenic family of PAHs was observed to parallel their relative carbocation stabilities. A different behavior was observed in crowded non-planar structures possessing a distorted aromatic system. A covalent adduct formed between a CP-PAH epoxide and a purine base was computed inside a DNA fragment employing the ONIOM method.Fil: Borosky, Gabriela Leonor. University of North Florida; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Laali, Kenneth K.. University of North Florida; Estados Unido

A computational study of SF5-substituted carbocations

The effect of the SF5 group as a substituent on various classes of carbocation was probed computationally employing DFT to examine geometrical changes, relative energies, and charge delocalization modes. Relative electron withdrawing power of the SF5 group was compared with CF3, NO2, CN, and SCF3 through isodesmic reactions. NPA charge densities were employed to gauge the influence of SF5 group on the charge delocalization modes in the carbocations.Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Córdoba. Instituto de Investigaciones en Físico-química de Córdoba. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Instituto de Investigaciones en Físico-química de Córdoba; ArgentinaFil: Laali, Kenneth K.. University of North Florida; Estados Unido

α-sulfur or α-fluorine ̶ Which is more stabilizing for a carbocation? A computational study of electrophilic addition to HFC=CH(SMe) and FC(R1)=CR2(SMe) and related model systems

Carbocations derived from protonation, methylation, and bromine addition to HFC55CH(SMe) (1) were studied by DFT [B3LYP/6-31G*, B3LYP/6-311G(3df,p), and B3LYP/aug-cc-pVTZ] and by MP2/6-31G* to examine relative carbocation stabilizing effects of a-SMe versus a-fluorine. The a-SMe carbocations 1aE+ and the unsymmetrical thiiranium ions 1cE+ were found to be considerably more stable than the corresponding a-fluorocarbenium ions 1bE+ . Study of protonation and methylation of FC(R1)55CR2(SMe) [R1 = H, R2 = SMe (2); R1 = F, R2 = H (3); R1 = F, R2 = SMe (4); R1 = Me, R2 = H (5); R1 = Me, R2 = SMe (6)] by B3LYP/6-31G* identified the corresponding unsymmetrical thiiranium cations as lowest energy minima, followed closely by the a-thiocarbenium ions. With 2, 4, and 6, skeletally rearranged a-thiocarbenium ions are formed by SMe migration. The a-SMe and the thiiranium cations are also favored relative to a- fluorocarbenium ions in protonation and methylation of the cyclic analogs 8 and 9. Computed NPA charges and the GIAO-derived 13C and 19F NMR chemical shifts underscore the significance of athiocarbocations and thiiranium ions in electrophilic addition to FC(R1)55CR2(SMe).Fil: Laali, Kenneth K.. University of North Florida. Department of Chemistry; Estados Unidos de América;Fil: Borosky, Gabriela Leonor. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto de Investigaciones en Físicoquímica de Córdoba; Argentina