Coupling of the Guanosine Glycosidic Bond Conformation and the Ribonucleotide Cleavage Reaction: Implications for Barnase Catalysis

To examine the possible relationship of guanine-dependent GpA conformations with ribonucleotide cleavage, two potential of mean force (PMF) calculations were performed in aqueous solution. In the first calculation, the guanosine glycosidic (Gχ) angle was used as the reaction coordinate, and computations were performed on two GpA ionic species: protonated (neutral) or deprotonated (negatively charged) guanosine ribose O2’. Similar energetic profiles were obtained for both ionic forms, with two minima (anti and syn Gχ). In both simulations the anti conformation was more stable than the syn, and barriers of ~4 kcal/mol for the anti → syn transition were obtained. Structural analysis showed a remarkable sensitivity of the phosphate moiety to Gχ rotation, suggesting a possible connection between Gχ orientation and the mechanism of ribonucleotide cleavage. This hypothesis was confirmed by the second PMF calculations, for which the O2’-P distance for the deprotonated GpA was used as reaction coordinate. The computations were performed from two selected starting points: the anti and syn minima determined in the first PMF study of the deprotonated guanosine ribose O2’. The simulations revealed that the O2’ attack along the syn Gχ was more favorable than that along the anti Gχ: energetically, significantly lower barriers were obtained in the syn than in the anti conformation for the O-P bond formation; structurally, a lesser O2’-P initial distance and a better suited orientation for an in-line attack was observed in the syn relative to the anti conformation. These results are consistent with the barnase-ribonucleotide catalytic interaction, for which a guanine syn conformation of the substrate is required to allow the abstraction of the ribose H2’ proton by the general base Glu73, thereby suggesting a coupling between reactive substrate conformation and enzyme structure and mechanis

Political cycles and risk aversion

Treball Final de Grau en Economia. Codi: EC1049. Curs acadèmic: 2018-2019This paper checks whether the main implications of the Pastor and Veronesi (2017) model of political cycles driven by time-varying risk aversion are valid for the Spanish case. In particular, we analyze whether the quarterly growth rate of the Spanish real GDP and the excess return behave in such a way as to support this theory. The conclusions obtained are contrary to the theory since we obtain that the economic growth of the country has been faster under the right wing party, and there are no significant differences in excess returns between mandates. These results suggest that this theory might not explain the Spanish political cycles

Simulating Enzyme Catalysis

Chemistry is about transformations between compounds as the result of forming and breaking bonds between their atoms. A detailed knowledge of these processes should open the door to one of the most desired goals in this field, which is the control of the rate constants that govern the time dependence of the concentrations of reactants and products. Changes in the concentration and preparation of the reactants, the nature of the solvents and external conditions (such as pressure and temperature) can be employed to speed up or slow down a chemical reaction. One of the major breakthroughs in the field of chemical kinetics was achieved when it was recognized that certain substances, the catalysts , were able to accelerate chemical reactions without being consumed during the process

Revealing the molecular mechanisms of proteolysis of SARS-CoV-2 Mpro by QM/MM computational methods

SARS-CoV-2 Mpro is one of the enzymes essential for the replication process of the virus responsible for the COVID-19 pandemic. This work is focused on exploring its proteolysis reaction by means of QM/MM methods. The resulting free energy landscape of the process provides valuable information on the species appearing along the reaction path and suggests that the mechanism of action of this enzyme, taking place in four steps, slightly differs from that of other cysteine proteases. Our predictions, which are in agreement with some recently published experimental data, can be used to guide the design of COVID-19 antiviral compounds with clinical potential

The influence of active site conformations on the hydride transfer step of the thymidylate synthase reaction mechanism

The hydride transfer from C6 of tetrahydrofolate to the reaction's exocyclic methylene–dUMP intermediate is the rate limiting step in thymidylate synthase (TSase) catalysis. This step has been studied by means of QM/MM molecular dynamics simulations to generate the corresponding free energy surfaces. The use of two different initial X-ray structures has allowed exploring different conformational spaces and the existence of chemical paths with not only different reactivities but also different reaction mechanisms. The results confirm that this chemical conversion takes place preferentially via a concerted mechanism where the hydride transfer is conjugated to thiol-elimination from the product. The findings also confirm the labile character of the substrate–enzyme covalent bond established between the C6 of the nucleotide substrate and a conserved cysteine residue. The calculations also reproduce and rationalize a normal H/T 2° kinetic isotope effect measured for that step. From a computational point of view, the results demonstrate that the use of an incomplete number of coordinates to describe the real reaction coordinate can render biased results

Actitudes frente a las familias homoparentales en el contexto escolar

Dotzenes Jornades de Foment de la Investigació de la FCHS (Any 2006-2007)Actualmente, en las escuelas conviven cada vez más, niños que provienen de contextos familiares muy diversos. En los últimos tiempos la inmigración ha sido uno de los fenómenos más investigados dentro del contexto escolar. Nuestra investigación hace un intento de abarcar otra parte de esa diversidad que convive en las aulas, los hijos/as de padres gays o lesbianas. Así pues, la presente investigación ha tenido como objeto indagar sobre que actitudes manifiesta la sociedad, y en especial, la comunidad escolar ante dichas familias. Para llevar a cabo dicho proyecto recogimos información de 406 personas relacionadas con el contexto escolar (estudiantes de magisterio, maestros en activo, padres, abuelos/as, etc.) en torno a sus creencias, conducta y norma subjetiva que manifiestan frente a la homoparentalidad. Algunos de los resultados obtenidos tras el análisis fundamentado de las variables nos desvelan como el sexo, la edad, el nivel de estudios, el conocer o no a una pareja homoparental, la profesión e incluso el tener o no tener hijos influyen en las actitudes que los sujetos presentan ante la homoparentalidad.Nowadays, it is becoming more common to see children from diverse family backgrounds in our schools. In recent times immigration has been one of the most studied phenomenon in the school context. However, our investigation tries to look at another aspect of classroom diversity and that is, children from gay or lesbian couples. Our investigation, therefore, looks to identify the attitudes not only that society has towards these families but more specifically the attitude of the school community towards them. To complete our project we collected information from 406 people involved in the school context (primary school teachers, students studying to be primary school teachers, parents, grandparents, etc.) and their beliefs, behaviour, and subjectivity towards single sex parents. Some of the results gained through this analysis showed us the variables like, gender, age , level of studies, knowing single sex parents, profession, having or not having children influenced the attitudes of the people questioned with regard to single sex parents

Theoretical study of primary reaction of Pseudozyma antarctica lipase B as the starting point to understand its promiscuity

Pseudozyma antarctica lipase B (PALB) is a serine hydrolase that catalyzes the hydrolysis of carboxylic acid esters in aqueous medium but it has also shown catalytic activity for a plethora of reactions. This promiscuous activity has found widespread applications. In the present paper, the primary reaction of PALB, its native hydrolytic activity, has been studied using hybrid quantum mechanical/molecular mechanical (QM/MM) potentials. Free energy surfaces, obtained from QM/MM Molecular Dynamics (MD) simulations, show that the reaction takes place by means of a multi-step mechanism where the first step, the activation of the carbonyl group of the substrate and the nucleophilic attack of Ser105 to the carbonyl carbon atom, presents the highest energy transition state. Our results, which are in good agreement with kinetic experimental data, suggest that the origin of the catalytic activity of the enzyme is due to favorable interactions established between the residues of the active site that create an oxyanion hole, Gln106 and Thr40, as well as the Asp187 that is capable of modulating the pKa of His224 to act as a base or an acid depending on the step of the catalytic process. Our results can be used to rationalize the design of an optimum biocatalyst to accelerate fundamental reactions in organic synthesis based on the protein scaffold of PALB

Computational Study of the Michaelis Complex Formation and the Effect on the Reaction Mechanism of Cruzain Cysteine Protease

Cruzain, a cysteine protease of the papain family, is essential in the development of the protozoan Trypanosoma cruzi, the etiologic agent of Chagas disease, making it an attractive target for developing new drugs. The present paper is aimed at the study of the catalytic mechanism of the cruzain by first exploring the different protonation states of the active site Cys25 and His159 in the Michaelis complex and the effect on the full catalytic mechanism of this enzyme. The exploration of the equilibrium between these two states has been performed with alchemical free energy perturbation methods with molecular mechanics (MM) force fields and by generating the free energy surfaces in terms of the potential of mean force computed at two levels of theory: AM1d/MM and M06-2X/6-31+G(d,p):AM1d/MM. Alternative mechanisms for the acylation step have been identified on the free energy surfaces and the results suggest the existence of three new reaction mechanisms starting from the peptide binding to the apoenzyme in its neutral Cys25S/His159 dyad state. The mechanism starting with the protonation of the nitrogen atom of the peptide followed by the attack of Cys25S– was revealed as the most favorable one, but it can be competitive with its counterpart mechanism initiated in the Cys25S–/His159H+ ion pair Michaelis complex. Analysis of energetic and average geometries will allow continuing improvement of our knowledge on this enzyme at the molecular level, which can be crucial to the design of new inhibitors based on the structures of the transition states (transition states analogues) or stable intermediates

El sistema de gestión de calidad (norma iso 9001:2000) en la Biblioteca de la Universitat Jaume I de Castellón

The library of the Universitat Jaume I in Castelló, Spain, has implemented a quality management system based on ISO 9001:2000. The aim of such system is to improve both the quality of services and users’ satisfaction. As a result ofgood practices, a number of improvements in the service has been achieved. Inthis article we describe the main procedures and methods that have led to a better management and excellence of the services offered by our library.La biblioteca de la Universitat Jaume I de Castellón implanta su sistema de gestión de la calidad en base a las normas ISO 9001:2000 con el propósito de mejorar los servicios prestados y la satisfacción de los usuarios. Los resultados obtenidos son consecuencia de las buenas prácticas consolidadas. Este trabajo describe los principales procedimientos y métodos que han constituido los factores clave para una mejor gestión y excelencia en los servicios de biblioteca

QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate

The environmental problems derived from the generalized plastic consumption and disposal could find a friendly solution in enzymatic biodegradation. Recently, two hydrolases from Ideonella sakaiensis 201-F6 and the metagenome-derived leaf-branch compost cutinase (LCC), more specially the improved ICCG variant, have revealed degradation activity toward poly ethylene terephthalate (PET). In the present study, the reaction mechanism of this polymer breakage is studied at an atomic level by multiscale QM/MM molecular dynamics simulations, using semiempirical and DFT Hamiltonians to describe the QM region. The obtained free energy surfaces confirmed a characteristic four-step path for both systems, with activation energies in agreement with the experimental observations. Structural analysis of the evolution of the active site along the reaction progress and the study of electrostatic effects generated by the proteins reveal the similarity in the behavior of the active site of these two enzymes. The origin of the apparent better performance of the LCC-ICCG protein over PETase must be due to its capabilities of working at higher temperature and its intrinsic relationship with the crystallinity grade of the polymer. Our results may be useful for the development of more efficient enzymes in the biodegradation of PET.Funding for open access charge: CRUE-Universitat Jaume