Theoretical Study of the Mechanism of Exemestane Hydroxylation Catalyzed by Human Aromatase Enzyme

Human aromatase (CYP19A1) aromatizes the androgens to form estrogens via a three-step oxidative process. The estrogens are necessary in humans, mainly in women, because of the role they play in sexual and reproductive development. However, these also are involved in the development and growth of hormone-dependent breast cancer. Therefore, inhibition of the enzyme aromatase, by means of drugs known as aromatase inhibitors, is the frontline therapy for these types of cancers. Exemestane is a suicidal third-generation inhibitor of aromatase, currently used in breast cancer treatment. In this study, the hydroxylation of exemestane catalyzed by aromatase has been studied by means of hybrid QM/MM methods. The Free Energy Perturbation calculations provided a free energy of activation for the hydrogen abstraction step (rate-limiting step) of 17 kcal/ mol. The results reveal that the hydroxylation of exemestane is not the inhibition stage, suggesting a possible competitive mechanism between the inhibitor and the natural substrate androstenedione in the first catalytic subcycle of the enzyme. Furthermore, the analysis of the interaction energy for the substrate and the cofactor in the active site shows that the role of the enzymatic environment during this reaction consists of a transition state stabilization by means of electrostatic effects

The rebirth of urban public space?

La actual crisis económica global parece haber devuelto el protagonismo al espacio público en la ciudad. Por una parte, renace el papel reivindicado del espacio público. Por otra, el uso cívico del mismo se ha intensificado frente a la realidad sesgada de los espacios colectivos privados, predominantes durante los últimos años. A partir de tres episodios recientes de la evolución del espacio público en la sociedad española, este artículo pone en evidencia tres enfoques sobre el mismo: el control político, la reivindicación social y el uso cívico. Tras un posterior periodo de decadencia y predominio de lo privado en la ciudad, la condición ciudadana ha vuelto a impulsar el espacio público como espacio social por excelencia. Se concluye destacando la oportunidad de recuperar el lugar urbano, así como la necesidad de potenciar el rol que el espacio público debe seguir representando en la complejidad de la ciudad.The current global economic crisis seems to have returned to the role of public space in the cities. First, the claimed role of public space is reborn. In addition, civic use of public space has been boosted in opposite to skewed perception of private collective spaces, prevalent in recent years. Using three recent episodes of the evolution of public space in Spanish society, this article presents three approaches about public space: political control, social claim and civic use. After a period of decline and subsequent dominance of the private in the city, the citizenship status has boosted again the public space as social space par excellence. It concludes by highlighting the opportunity to recover the urban place and the need to enhance the role that public space must continue to play in the complexity of the city

Modeling of Free Surface Flows with Elastic Bodies Interactions

In this paper, a series of new fluid and structure interactions test cases with strong free surface effects are presented and computations of such flows with the Particle Finite Element Method (PFEM) (Idelsohn, Oiiate, Del Pin and Calvo, 2006) are documented. The structures object of study are elastic cantilever bars clamped inside sloshing tanks subjected ro roll motion. The possibilities of PFEM for the coupled simulation of moderately violent free surface flows interacting with elastic bodies are investigated. The problem can be described as the coupling of a sloshing flow with an easily deformable elastic body. A series of experiments designed and executed specifically for these tests are also described. The experiments comprise cases with different liquid height and liquids of different viscosity. The aim is to identify canonical benchmark problems in FSI (Fluid and Structure Interactions), including free surfaces, for future comparisons between different numerical approaches

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

A QM/MM study on the origin of retro-aldolase activity of a catalytic antibody

The retro-aldolase mechanism of methodol catalysed by the catalytic antibody 33F12 is described based on the exploration of the free energy landscape obtained with QM/MM methods. The amino acids involved in the reaction have been identified, as well as their specific role played in the active site and in the flexibility of the loops. Finally, the comparison with a de novo enzyme RA95.5-8F provides a deeper understanding of catalytic differences between such different protein scaffolds

Understanding the Directed Evolution of De Novo Retro-Aldolases from QM/MM Studies

In an era in which climatic change puts the planet at risk, the study and development of alternative green chemistry which can help and improve our life can play an essential role. In this context, the use of artificial enzymes that are capable of substitute traditional industrial processes by environmental friendly routes is a challenge. Unfortunately, the complete understanding of the catalytic activity and selectivity of enzymes remains elusive, thus hampering creation and development of enzymatic proteins. In this paper, the molecular mechanism of the non-natural multistep retro-aldolase reaction catalyzed by a de novo biocatalyst, the RA95.5-5, has been investigated by means of multiscale QM/MM methods. The design of a retro-aldolase presents the difficulty to create an enzyme being able to stabilize several transition states, maintaining low-energy barriers along the overall reaction. The obtained QM/MM free-energy landscape has allowed defining the rate-determining step corresponding to the carbon–carbon bond scission of the substrate, which is in accordance with the experimental data. A deep analysis of the electrostatic interactions between the substrate and the different amino acid residues of the protein, as well as the estimation of the electrostatic potential generated on key atoms of the substrate, has been carried out for the key steps of the reaction. The results, compared with previous computational studies on the most efficient de novo retro-aldolase, the RA95.5-8F, explains the different activities achieved during the directed evolution process and provides insights for future developments of more efficient enzymes

Are Heme-Dependent Enzymes Always Using a Redox Mechanism? A Theoretical Study of the Kemp Elimination Catalyzed by a Promiscuous Aldoxime Dehydratase

The design of biocatalysts is a goal to improve the rate, selectivity and environmental friendship of chemical processes in biotechnology. In this regard, the use of computational techniques has provided valuable assistance in the design of enzymes with remarkable catalytic activity. In this paper, hybrid QM/MM simulations have allowed getting an insight into the mechanism of a promiscuous aldoxime dehydratase (OxdA) for the Kemp elimination. We first demonstrate that, based on the use of linear response approximation (LRA) methods, the lowest energy electronic state of the benzisoxazole placed in the active sit of OxdA corresponds to a singlet state, being the triplet and the quintet state higher in energy. The presence of a heme group in the active site of the OxdA promiscuous enzyme opens the possibility of exploring a redox mechanism, similar to the one proposed in other reactions catalysed by heme-dependent enzymes. In addition, according to the geometrical analysis of the active site of this aldoxime dehydratase, the presence of a good base in the active site, His320, the proper pose of the substrate assisted by the porphyrin and an adequate electrostatic environment to stabilize the negative charge developed in the oxygen leaving group, makes available an acid/base mechanism. Comparison of the results derived from the exploration of both acid/base and redox mechanisms at B3LYP(Def2-TZVP)/MM level, shows how the later render the most favourable reaction path within the quintet state. The obtained activation free energy is in good agreement with the activation energy that can be deduced from the experimentally measured rate constant

Graphic resources for urban planning: international standardization proposals

Los recursos de expresión gráfica empleados por los urbanistas de diversas culturas presentan divergencias derivadas de las distintas concepciones y tradiciones formativas del planeamiento urbano, pero también del diferente enfoque cultural y disciplinar de la expresión gráfica del mismo. No obstante, pueden apreciarse ciertos recursos universales que nos informan sobre la oportunidad de investigar alternativas de estandarización gráfica y, al mismo tiempo, que respeten las normativas particulares de cada lugar. Tras una introducción sobre los recursos gráficos del planeamiento urbano, este artículo compila y expone algunas propuestas internacionales –tanto europeas como norteamericanas, sin olvidar alguna iniciativa de países emergentes– de normalización gráfica del planeamiento urbano. Se concluye apoyando las bases de una potencial homogeneización en el uso de los diferentes recursos gráficos que requiere el planeamiento urbanístico, sobre la coyuntura que supone el potencial de los actuales sistemas de información geográfica.Graphic resources used by urban planners from diverse cultural backgrounds, differ not only on urban planning tradition but also, on specific cultural and professional approaches. However, certain universal graphic resources clearly reveal the opportunity to investigate the standardization alternatives which, in turn, respect each local regulation. After an introduction about graphic resources for urban planning, this paper complies and presents several international proposals ―from both Europe and North America, without forgetting some initiatives from emerging economies― for graphic standardization. It can be concluded that the implementation of current GIS offers a potential possibility to homogenize the graphic resources for urban planning

Historical background and proposals for the standardisation of graphic expression in urban planning

El presente artículo tiene como objetivo analizar la expresión gráfica como herramienta de transmisión de la información contenida en los instrumentos de ordenación urbanística y abrir potenciales investigaciones sobre su normalización. Para ello, el planteamiento inicial se centra en identificar algunos de los mecanismos de expresión gráfica empleados por dos hitos de referencia en la historia del planeamiento urbano: los planes de ensanche de mediados del siglo XIX y el movimiento moderno del primer tercio del siglo XX, ambos selectivamente ejemplarizados. Se desvela cómo estas propuestas anuncian posibles criterios de homogeneización en la expresión gráfica del urbanismo. Finalmente, se expone una línea de investigación actual sobre normalización gráfica y cromática en el planeamiento urbano, centrada en un estudio inductivo del que se expone, a modo de conclusión, un ejemplo de potencial propuesta de normalización.This article analyses graphic expression as a tool for the transmission of the information contained in urban planning instruments and aims to open a line of research on its standardisation. To this end, this work identifies some of the tools of graphic expression used in two milestone events in the history of urban planning: the Spanish expansion plans for population centres in the mid-19th century and the Modern Movement of the first third of the 20th century. The article exemplifies how these proposals included criteria for the possible standardisation of graphic expression in urban planning. As a way of conclusion, the article presents an example of a recent line of research advocating for the standardisation of graphics and colour use in urban planning, based on an inductive study