Computational Modeling Methods for Understanding the Interaction of Lignin and Its Derivatives with Oxidoreductases as Biocatalysts

This chapter will be presented as follow. First, a brief introduction to structure and characterization of lignin and its derivatives is presented, as well as their importance as chemical scaffolds for obtaining value-added products in chemical, food, pharmaceutical and agriculture industry. Second, an extensive review of different reports using computational modeling methods—like molecular dynamics simulations, quantum mechanics and hybrid calculation methods, among others—in the understanding of enzyme-substrate interaction and biocatalysis will be presented. Third, and as last part of chapter, some hand picked examples from literature will be chosen as successful cases where the interplay between experiment and computation has given as a result protein engineered oxidoreductases with improved catalytic capabilities

Modelação da força de adesão em válvulas de compressores considerando fenômenos interfaciais na película de óleo lubrificante

Tese (doutorado) - Universidade Federal de Santa Catarina, Centro Tecnológico, Programa de Pós-Graduação em Engenharia Mecânica, Florianópolis, 2014Em condições ideais, válvulas automáticas de sucção e descarga devem abrir ou fechar, de forma instantânea, no momento em que a pressão no interior do cilindro de compressão se iguala às pressões nas respectivas câmaras de sucção e descarga. Entretanto, na realidade, isto não acontece devido a efeitos como a inércia das válvulas, perdas viscosas e à existência de uma força de adesão provocada pela presença de uma película de óleo entre a válvula e o assento.A força de adesão é provocada pela deformação do filme de óleo que ingressa principalmente pela folga pistão cilindro e se deposita entre a válvula e o assento. A presença do óleo provoca um atraso na abertura das válvulas, tendo em vista que uma maior diferença de pressão é necessária entre o cilindro e as câmaras de sucção e descarga, reduzindo as eficiências volumétrica e isentrópica do compressor.Neste trabalho, é proposto um modelo matemático para investigar fenômenos de adesão provocados por um filme de óleo entre superfícies sólidas de geometrias planas e esféricas. O modelo foi aplicado para quantificar a força de adesão em válvulas de compressores e sua influência no comportamento dinâmico das válvulas durante a abertura. Parâmetros necessários para o fechamento do modelo, como o ângulo de contato entre a película de óleo e a superfície (com e sem a dissolução de fluido refrigerante no óleo) e a tensão interfacial foram obtidos por meio de experimentos em bancadas construídas especificamente para este estudo.De acordo com os resultados experimentais, a tensão interfacial óleo-refrigerante diminui com o aumento da solubilidade, gerando uma redução dos efeitos da força de capilaridade no fenômeno de adesão. Por outro lado, o ângulo de contato, independentemente da rugosidade das superfícies, do tipo de configuração geométrica utilizada e da solubilidade da mistura, apresenta um alto grau de molhabilidade na superfície, o que traz como resultado a intensificação dos efeitos das forças de tensão superficial.Por último, os resultados numéricos demonstraram que o sistema de sucção é mais sensível aos efeitos de adesão gerados pela presença da película de óleo entre a válvula e o assento.<br>Abstract: At ideal conditions, suction and discharge valves open and close instantaneously when the cylinder pressure becomes equal to the pressures in the suction and discharge chambers. However, in real systems, it does not occur because of viscous losses, valve inertia effects and due to an adhesion effect that is caused by the presence of an oil film between the valve and the seat. The adhesion force is caused by the deformation of the lubricating oil film that reaches the space between the valve and the film through the piston-cylinder gap. This causes a delay in the valve opening, since a larger pressure difference between the cylinder and the suction and discharge chambers is necessary to overcome the adhesion force. As a result, both the isentropic and the volumetric efficiencies of the compressor are reduced. In this work, a mathematical model is developed to investigate adhesion phenomena due to the presence of an oil film between solid surfaces of flat and spherical geometries. The model was applied to investigate the adhesion force in compressor valves and its influence on the dynamic behaviour of valves during the opening process. Input parameters needed to develop the model, such as the contact angle between the oil film and the surface (with and without considering refrigerant absorption in the oil) and the interfacial tension, have been determined via experimental apparatuses designed and built specifically for this purpose. According to the experimental results, the oil-refrigerant mixture interfacial tension decreases with the refrigerant solubility, which leads to a reduction of capillary effects and film adhesion. On the other hand, the contact angle measurements indicate a significant wettability of the surface, which was seen to be independent of surface roughness, geometric configuration and solubility. This increases the contribution of interfacial tension effects. Finally, the numerical results showed that suction systems are more sensitive to oil film adhesion phenomena than discharge systems

Modeling the Stiction Effect in Automatic Compressor Valves

The so-called stiction effect (or stiction force) is one of the sources of thermodynamic losses in compressor suction and discharge systems. The losses associated with the stiction effect are caused by a deformation of the lubricating oil film between the valve and the seat. This generates a delay in the valve opening, since larger pressure differencesbetween the cylinder and the discharge and/or suction chambers are needed to compensate for those effects. This paper advances a theoretical model for solving the dynamic behavior of a ring-shaped lubricant oil film between a discharge valve and the seat. The valve is allowed to move under the action of an external force due to the timedependent pressure difference between the cylinder and the discharge chamber. The main contributions of the model are the consideration of a finite amount of oil between the valve and the seat and mathematical relationships for calculating the initial condition for the oil film thickness. The model results are compared with those obtained with the Khalifa and Liu (1998) method. At conditions typical of discharge systems of domestic refrigeration compressors, viscous effects are the dominant component in the oil stiction force under dynamic conditions

Estudio jurídico de la extradición

Doctor en Jurisprudencia y Abogado de los Tribunales de Justicia de la RepúblicaCuenc

How a Second Mg2+ Ion Affects the Phosphoryl Transfer Mechanism in a Protein Kinase: A Computational Study

In this contribution, the phosphoryl transfer reaction in CDK2 has been studied in detail considering the presence of an additional Mg2+ ion in the active site. For this purpose, QM/MM (quantum mechanics/molecular mechanics) free energy calculations with the adaptive string method were performed, which showed that indeed the system containing two Mg2+ ions exhibits a lower activation free energy, corroborating the experimental observations.</div

Covalent adduct formation as strategy for efficient CO2 fixation in crotonyl-CoA carboxylases/reductases

Increasing levels of CO2 in the atmosphere have led to a growing interest into the various ways nature transforms this greenhouse gas into valuable organic compounds. Crotonyl-CoA carboxylases/reductases (Ccr\u27s) are the most efficient biocatalysts for CO2 fixation because of their oxygen tolerance, their high catalytic rate constants and their high fidelity. The reaction mechanism involving hydride transfer from the NADPH cofactor and addition of CO2 to the reactive enolate, however, is not completely understood. In this study, we use computer simulations in combination with high-level ab initio calculations to trace the free energy landscape along two possible reaction paths: In the direct mechanism hydride transfer is immediately followed by CO2 addition whereas in the C2 mechanism a thermodynamically stable covalent adduct between the substrate and the NADPH cofactor is formed. This C2 adduct, which has been previously characterized experimentally, serves as a stable intermediate avoiding the reduction side reaction of the reactive enolate species and it is able to react with CO2 with similar kinetics as the direct reaction mechanism as confirmed by measured kinetic isotope effects. Thus, our results show that nature\u27s most efficient CO2-fixing enzyme uses the formation of a covalent adduct as a strategy to store the reactive enolate species. The emerging microscopic picture of the CO2-fixing mechanism confirms previous experimental observations and provides new insights into how nature handles highly reactive intermediates to fix this inert greenhouse gas

Mechanistic insights into the phosphoryl transfer reaction in cyclin-dependent kinase 2: A QM/MM study.

Cyclin-dependent kinase 2 (CDK2) is an important member of the CDK family exerting its most important function in the regulation of the cell cycle. It catalyzes the transfer of the gamma phosphate group from an ATP (adenosine triphosphate) molecule to a Serine/Threonine residue of a peptide substrate. Due to the importance of this enzyme, and protein kinases in general, a detailed understanding of the reaction mechanism is desired. Thus, in this work the phosphoryl transfer reaction catalyzed by CDK2 was revisited and studied by means of hybrid quantum mechanics/molecular mechanics (QM/MM) calculations. Our results suggest that the base-assisted mechanism is preferred over the substrate-assisted pathway when one Mg2+ is present in the active site, in agreement with a previous theoretical study. The base-assisted mechanism resulted to be dissociative, with a potential energy barrier of 14.3 kcal/mol, very close to the experimental derived value. An interesting feature of the mechanism is the proton transfer from Lys129 to the phosphoryl group at the second transition state, event that could be helping in neutralizing the charge on the phosphoryl group upon the absence of a second Mg2+ ion. Furthermore, important insights into the mechanisms in terms of bond order and charge analysis were provided. These descriptors helped to characterize the synchronicity of bond forming and breaking events, and to characterize charge transfer effects. Local interactions at the active site are key to modulate the charge distribution on the phosphoryl group and therefore alter its reactivity

El juego en la clase de educación física, aplicada por profesores que se desempeñan en establecimientos educacionales privados, en dos comunas de la ciudad de Santiago.

Tesis (Profesor de Educación Física para la Enseñanza Básica, Licenciado en Educación)La presente tesis tiene como objetivo principal analizar la implementación del juego en la parte principal de la clase de educación física, considerando sus propósitos, duración y tipos, aplicado por profesores que se desempeñan en establecimientos educacionales particulares de la comuna de Las Condes y Lo Barnechea de la ciudad de Santiago, y las divergencias y coincidencias que presentan dichos profesores respecto a lo declarado y lo observado en clases. Iniciada y aplicada a profesores de Educación Física, titulares en colegios Lincoln International Academy, Saint Gabriel y Bertait College de las comunas de Las Condes y Lo Barnechea. En cursos de 1 °Basico a 4° Básico. La investigación se efectuó a través de dos instrumentos de evaluación, siendo estos una pauta de entrevista y un Guion de Observación que nos ayudó a recopilar datos para mostrar los siguientes resultados. De acuerdo al presente estudio, se afirma que, se obtuvo como resultado, una mayor coincidencia que divergencia de acuerdo a lo declarado y observado por profesores, sobre la utilización del juego en la parte principal de la clase de educación física.The present thesis has as main objective to analyze the implementation of the game in the main part of the physical education class, considering its purposes, duration and types, applied by teachers who work in particular educational establishments of the commune of Las Condes and Lo Barnechea Of the city of Santiago, and the divergences and coincidences that these professors present with respect to the declared and the observed in classes. Initiated and applied to teachers of Physical Education, holders at Lincoln International Academy, Saint Gabriel and Bertait College of the communes of Las Condes and Lo Barnechea. In courses from 1 O Basic to 4 ° Basic. The research was carried out through two evaluation instruments, these being an interview guideline and Observation Cuide that helped us to collect data to show the following results. According to the present study, it is stated that, as a result, a greater coincidence

Binding and catalytic mechanisms of Veratryl alcohol oxidation by lignin peroxidase: A theoretical and experimental study

9 p.-3 fig.-4 tab.Lignin peroxidase (LiP) and its natural substrate veratryl alcohol (VA) play a crucial role in lignin degradation by white-rot fungi. Understanding the molecular determinants for the interaction of this enzymewith its substrates is essential in the rational design of engineered peroxidases for biotechnological application. Here, we combine computational and experimental approaches to analyze the interaction of Phanerochaete chrysosporium LiP (isoenzyme H8)with VA and its radical cation (VA•+, resulting fromsubstrate oxidation by the enzyme). Interaction energy calculations at semiempirical quantum mechanical level (SQM) between LiP and VA/VA•+ enabled to identify those residues at the acidic environment of catalytic Trp171 involved in the main interactions. Then, a battery of variants, with single and multiple mutations at these residues (Glu168, Asp165, Glu250, Asp264,and Phe267), was generated by directed mutagenesis, and their kinetics parameters were estimated on VA and two additional substrates. The experimental results show that Glu168 and Glu250 are crucial for the binding of VA, with Glu250 also contributing to the turnover of the enzyme. The experimental resultswere further rationalized through new calculations of interaction energies between VA/VA•+ and LiP with each of the single mutations.Finally, the delocalization of spin density was determined with quantum mechanics/molecular mechanics calculations (QM/MM), further supporting the contribution of Glu250 to VA oxidation at Trp171.J.A.M. and F.A.S. acknowledge the financial support from FONDECYT projects 1140618 and 3170909, respectively. R.R. and J.O.R acknowledge support from the doctoral fellowships CONICYT-PFCHA/Folios 21130949, and 21160905, respectively. A.T.M. thanks the financial support of the EnzOx2 (H2020-BBI-PPP-2015-2-720297, https://www.enzox2.eu) EU project.Peer reviewe