RESUMEN
Glutathione S-transferases are a family of detoxifying enzymes that catalyze the conjugation of reduced glutathione (GSH) with different xenobiotic compounds using either Ser, Tyr, or Cys as a primary catalytic residue. We identified a novel GST in the genome of the shrimp pathogen V. parahaemolyticus FIM- S1708+, a bacterial strain associated with Acute Hepatopancreatic Necrosis Disease (AHPND)/Early Mortality Syndrome (EMS) in cultured shrimp. This new GST class was named Gtt2. It has an atypical catalytic mechanism in which a water molecule instead of Ser, Tyr, or Cys activates the sulfhydryl group of GSH. The biochemical properties of Gtt2 from Vibrio parahaemolyticus (VpGSTT2) were characterized using kinetic and crystallographic methods. Recombinant VpGSTT2 was enzymatically active using GSH and CDNB as substrates, with a specific activity of 5.7 units/mg. Low affinity for substrates was demonstrated using both Michaelis-Menten kinetics and isothermal titration calorimetry. The crystal structure showed a canonical two-domain structure comprising a glutathione binding G-domain and a hydrophobic ligand H domain. A water molecule was hydrogen-bonded to residues Thr9 and Ser 11, as reported for the yeast Gtt2, suggesting a primary role in the reaction. Molecular docking showed that GSH could bind at the G-site in the vicinity of Ser11. G-site mutationsT9A and S11A were analyzed. S11A retained 30% activity, while T9A/S11A showed no detectable activity. VpGSTT2 was the first bacterial Gtt2 characterized, in which residues Ser11 and Thr9 coordinated a water molecule as part of a catalytic mechanism that was characteristic of yeast GTT2. The GTT2 family has been shown to provide protection against metal toxicity; in some cases, excess heavy metals appear in shrimp ponds presenting AHPND/EMS. Further studies may address whether GTT2 in V. parahaemolyticus pathogenic strains may provide a competitive advantage as a novel detoxification mechanism.
Asunto(s)
Glutatión Transferasa/genética , Penaeidae/microbiología , Vibrio parahaemolyticus/genética , Animales , Genoma , Filogenia , Análisis de SecuenciaRESUMEN
The rate constants and H/D kinetic isotope effect for hydrogen abstraction reactions involving isotopomers of methyl formate by methyl radical are computed employing methods of the variational transition state theory (VTST) with multidimensional tunneling corrections. The energy paths were built with a dual-level method using the moller plesset second-order perturbation theory (MP2) method as the low-level and complete basis set (CBS) extrapolation as the high-level energy method. Benchmark calculations with the CBSD-T approach give an enthalpy of reaction at 0 K for R1 (-4.5 kcal/mol) and R2 (-4.2 kcal/mol) which are in good agreement with the experiment, that is, -4.0 and - 4.8 kcal/mol. For the reactional paths involving the isotopomers CH3 + CH3 OCOH â CH4 + CH3 OCO and CH3 + CH3 OCOD â CH3 D + CH3 OCO, the value of kH /kD (T = 455 K) using the canonical VTST/small-curvature tunneling approximation method is 6.7 in close agreement with experimental value (6.2). © 2019 Wiley Periodicals, Inc.
RESUMEN
We propose a scheme to estimate hydrogen isotope effects on molecular polarizabilities. This approach combines the any-particle molecular orbital method, in which both electrons and H/D nuclei are described as quantum waves, with the auxiliary density perturbation theory, to calculate analytically the polarizability tensor. We assess the performance of method by calculating the polarizability isotope effect for 20 molecules. A good correlation between theoretical and experimental data is found. Further analysis of the results reveals that the change in the polarizability of a X-H bond upon deuteration decreases as the electronegativity of X increases. Our investigation also reveals that the molecular polarizability isotope effect presents an additive character. Therefore, it can be computed by counting the number of deuterated bonds in the molecule.
RESUMEN
Se estudió el efecto de la sustitución isotópica de hidrógeno sobre la geometría, la estructura electrónica y la estabilidad del aducto borano-carbonilo, mediante el método de orbitales moleculares nucleares y electrónicos (OMNE) implementado en el paquete computacional APMO. Se encontró que el aumento de la masa isotópica acorta las distancias de enlace boro-isótopo y carbono-oxígeno, mientras que alarga la distancia boro-carbono. Se determinó además la estabilidad del aducto a partir de las energías de formación y las distancias de enlace B-C. Se encontró que el aumento de la masa isotópica debilita el enlace B-C. Una primera explicación de este fenómeno en términos del concepto de acidez de Lewis predijo resultados contrarios a los encontrados, mientras que un modelo de reactividad basado en las diferencias de las energías de los orbitales LUMO del borano permitió dar cuenta de este efecto.
We have investigated the hydrogen isotope effect on the geometry, the electronic structure and the stability of the borane-carbonile adduct, by using the nuclear-electronic molecular orbital method (NEMO) which has been implemented in the APMO software. We have found that an increase of the mass of the hydrogen isotope reduces the boron-hydrogen and carbon-oxygen bond lengths while increasing the boron-carbon distance. In this study, the stability of the adduct has been analyzed in terms of formation energies and B-C bond distances. We have found that the increase of the isotope mass weakens the B-C bond. We tried to give an explaination to this phenomenon based on Lewis acidity concept but it predicted the wrong results. A reactivity model based on the energy differences of borane LUMO orbitais offered a correct explaination to this effect.
Temos estudado o efeito da substituição de isótopos de hidrogénio sobre a geometria, estrutura electrónica e da estabilidade do aduto Borana-carbonil, através do mêtodo de orbitais moleculares-core versões (OMNE) implementado no pacote computacional APMO. Descobrimos que um aumento da isótopo massa encurta as distâncias de ligação boro-carbono-isotópica de oxigênio e aumenta a distância, enquanto boro-carbono. Foi ainda determinada a estabilidade do aduto de as energias de formação e distâncias de ligação BC. Nós descobrimos que o aumento da massa isotópica minar a relação BC. Uma explicação para este fenômeno em termos de conceito de acidez de Lewis predita resultados contrários aos encontrados enquanto um modelo baseado em diferenças de reatividade nas energias dos orbitais LUMO do Borana autorizados a conta para este efeito.
RESUMEN
Se estudió teóricamente el efecto de isotópo de hidrógeno sobre la geometría, la distribución de carga electrónica, la estabilidad relativa y la energía de formación de complejos lineales tipo M-X-Y-F y todos sus isotopólogos de hidrógeno (M=Li, Na; X, Y= H, D, T). Estos estudios fueron realizados con el paquete computacional APMO a un nivel de teoría Hartree-Fock electrónico y nuclear. Los resultados obtenidos son acordes con resultados reportados por otros autores que usan métodos de estructura electrónica convencional.
We have carried out a theoretical investigacion of the hydrogen isotope effects on the geometry, the electronic charge distribution, the relative stability and the energy of formation of linear complexes of the type M-X-Y-F and all their hydrogen istopologues (M = Li, Na; X, Y= H, D, T). For this study we have utilized the APMO software at a nucleo-electronic Hartree-Fock level of theory. Our results are agreement with other reported theoretical data based on conventional electronic structure methods.
Foi estudado teoricamente o efeito do isótopo de hidrogênio sobre geometria, distribuição do carga eletrônica, a estabilidade relativa da energia e da formação do complexos lineares do tipo M-X-Y-F e todos os seus isotopólogos do hidrogênio (M = Li, Na, X, Y = H, D, T). Estes estudos foram realizados com o pacote computacional APMO para um nível da teoria Hartree-Fock eletrônica e nuclear. Os resultados são do acordo com os resultados relatados por outros autores que utilizam métodos do estrutura eletrônica convencionais.
RESUMEN
Con el fin de estudiar teóricamente fenómenos en donde los núcleos atómicos presentan comportamiento cuántico, hemos desarrollado el paquete computacional APMO (Any-Particle Molecular Orbital). Éste implementa el método de orbitales moleculares nucleares y electrónicos (OMNE) a un nivel de teoría Hartree- Fock (HF), en el que tanto núcleos como electrones se representan como funciones de onda. Para comprobar la correcta implementación del método se realizaron cálculos de estructura electrónica regular y núcleo- electrónica de las moléculas H2 y LiH. Las componentes de energía calculadas siguen las tendencias y están en el mismo orden de magnitud de cálculos similares reportados en la literatura. A diferencia de otros paquetes que implementan el método OMNE, el nuestro fue diseñado para estudiar sistemas con cualquier número de especies cuánticas.
With the aim of studying phenomena where atomic nuclei have a quantal behavior, we have developed the APMO (Any-Particle Molecular Orbital) software package. This implements the nuclear and electronic molecular orbital approach (NEMO) at a Hartree-Fock level of theory, where both nuclei and electrons are represented as wave functions. To verify the correct implementation of the method, a number of electronic and nuclear-electronic calculations were carried out on H2 and LiH molecules. The calculated energy components follow the trends and are of the same order of magnitude of similar calculations reported in the literature. In contrast to other packages that implement the NEMO approach, ours is designed to allow for studying systems with any number of quantum particles.
Com a finalidade de estudar teoricamente fenômenos cujos núcleos atômicos apresentam comportamento quântico, desenvolvemos o pacote computacional APMO (Any-Particle Molecular Orbital). Este implementa o método de orbitais moleculares nucleares e eletrônicos (OMNE) no nível da teoria Hartree-Fock (HF), onde tanto núcleos como elétrons se apresentam como funções de onda. Para comprovar a utilização correta do método, se realizaram cálculos da estrutura eletrônica regular e do núcleo eletrônico das moléculas H_2 y LiH. Os componentes de energia calculados seguem as tendências e estão na mesma ordem de magnitude de cálculos similares reportados na literatura. Diferentemente de outros pacotes que utilizam o método OMNE, o nosso foi desenhado para estudar sistemas de qualquer número de espécies quânticas.