Computational Study of Protein-Ligand Unbinding for Enzyme Engineering

The computational prediction of unbinding rate constants is presently an emerging topic in drug design. However, the importance of predicting kinetic rates is not restricted to pharmaceutical applications. Many biotechnologically relevant enzymes have their efficiency limited by the binding of the substrates or the release of products. While aiming at improving the ability of our model enzyme haloalkane dehalogenase DhaA to degrade the persistent anthropogenic pollutant 1,2,3-trichloropropane (TCP), the DhaA31 mutant was discovered. This variant had a 32-fold improvement of the catalytic rate toward TCP, but the catalysis became rate-limited by the release of the 2,3-dichloropropan-1-ol (DCP) product from its buried active site. Here we present a computational study to estimate the unbinding rates of the products from DhaA and DhaA31. The metadynamics and adaptive sampling methods were used to predict the relative order of kinetic rates in the different systems, while the absolute values depended significantly on the conditions used (method, force field, and water model). Free energy calculations provided the energetic landscape of the unbinding process. A detailed analysis of the structural and energetic bottlenecks allowed the identification of the residues playing a key role during the release of DCP from DhaA31 via the main access tunnel. Some of these hot-spots could also be identified by the fast CaverDock tool for predicting the transport of ligands through tunnels. Targeting those hot-spots by mutagenesis should improve the unbinding rates of the DCP product and the overall catalytic efficiency with TCP

Assembly of peptidoglycan fragments: a synthetic challenge

SFRH/BD/52207/2013 PTDC/BIA-MIC/30746/2017 UID/QUI/50006/2019 POCI-01-0145-FEDER-007265 UID/Multi/04378/2019Peptidoglycan (PGN) is a major constituent of most bacterial cell walls that is recognized as a primary target of the innate immune system. The availability of pure PGN molecules has become key to different biological studies. This review aims to (1) provide an overview of PGN biosynthesis, focusing on the main biosynthetic intermediates; (2) focus on the challenges for chemical synthesis posed by the unique and complex structure of PGN; and (3) cover the synthetic routes of PGN fragments developed to date. The key difficulties in the synthesis of PGN molecules mainly involve stereoselective glycosylation involving NAG derivatives. The complex synthesis of the carbohydrate backbone commonly involves multistep sequences of chemical reactions to install the lactyl moiety at the O-3 position of NAG derivatives and to control enantioselective glycosylation. Recent advances are presented and synthetic routes are described according to the main strategy used: (i) based on the availability of starting materials such as glucosamine derivatives; (ii) based on a particular orthogonal synthesis; and (iii) based on the use of other natural biopolymers as raw materials.publishersversionpublishe

DSP implementation of the multiple reference frames theory for the diagnosis of stator faults in a DTC induction motor drive

This paper deals with the use of a new diagnostic technique based on the multiple reference frames theory for the diagnosis of stator winding faults in a direct-torque-controlled (DTC) induction motor drive. The theoretical aspects underlying the use of this diagnostic technique are presented but a major emphasis is given to the integration of the diagnostic system into the digital-signal-processor (DSP) board containing the control algorithm. Taking advantage of the sensors already built in the drive for control purposes, it is possible to implement this diagnostic system at no additional cost, thus giving a surplus value to the drive itself. Experimental results show the effectiveness of the proposed technique to diagnose stator faults and demonstrate the possibility of its integration in the DSP boar

A Knack to Know an Honest Man

Alzheimer’s disease (AD) is a multifactorial disorder with several target proteins contributing to its etiology. In search for multifunctional anti-AD drug candidates, taking into account that the acetylcholinesterase (AChE) and beta-amyloid (Aβ) aggregation are particularly important targets for inhibition, the tacrine and benzothiazole (BTA) moieties were conjugated with suitable linkers in a novel series of hybrids. The designed compounds (7a–7e) were synthesized and in vitro as well as in ex vivo evaluated for their capacity for the inhibition of acetylcholinesterase (AChE) and Aβ self-induced aggregation, and also for the protection of neuronal cells death (SHSY-5Y cells, AD and MCI cybrids). All the tacrine–BTA hybrids displayed high in vitro activities, namely with IC50 values in the low micromolar to sub-micromolar concentration range towards the inhibition of AChE, and high percentages of inhibition of the self-induced Aβ aggregation. Among them, compound 7a, with the shortest linker, presented the best inhibitory activity of AChE (IC50 = 0.34 μM), while the highest activity as anti-Aβ42 self-aggregation, was evidenced for compound 7b (61.3%, at 50 μM. The docking studies demonstrated that all compounds are able to interact with both catalytic active site (CAS) and peripheral anionic site (PAS) of AChE. Our results show that compounds 7d and 7e improved cell viability in cells treated with Aβ42 peptide. Overall, these multi-targeted hybrid compounds appear as promising lead compounds for the treatment of Alzheimer’s disease

Contribuições acadêmicas para o metrô na cidade de Porto Alegre: experiência didática em ateliê colaborativo com o poder público

Este artigo tem como objetivo apresentar a experiência didática desenvolvida na disciplina Projeto Arquitetônico V do curso de Arquitetura da Universidade Federal do Rio Grande do Sul. Tendo a implantação do metrô na cidade de Porto Alegre como tema de projeto, os alunos são desafiados a realizar trabalhos de pesquisa, estudo e modelagem das estações e dos espaços urbanos de entorno, atendendo ao que está estabelecido no Convênio entre a Universidade e as instituições públicas responsáveis pela implantação do metrô.Dessa maneira, as pesquisas e projetos urbanístico-arquitetônicos desenvolvidos pelos acadêmicos servem como subsídio para discussões acerca das potencialidades e fragilidades de cada caso, objetivando ampliar os estudos exploratórios para que os técnicos municipais possam produzir parâmetros e diretrizes tanto para os critérios de escolha dos projetos técnicos definitivos quanto para a elaboração dos próprios. A experiência, em curso há mais de dois anos, tem contribuído para o alto nível de qualidade dos trabalhos produzidos pelos alunos, além de permitir a simulação de uma experiência com um cliente real, enfrentando os desafios da vida profissional de forma simulada. Os procedimentos e metodologia empregados na construção do processo ensino-aprendizagem são discutidos no presente trabalho.Área temática 1: Proyecto Arquitectónico y Urbano - Eje EnseñanzaFacultad de Arquitectura y Urbanism

Contribuições acadêmicas para o metrô na cidade de Porto Alegre: experiência didática em ateliê colaborativo com o poder público

Este artigo tem como objetivo apresentar a experiência didática desenvolvida na disciplina Projeto Arquitetônico V do curso de Arquitetura da Universidade Federal do Rio Grande do Sul. Tendo a implantação do metrô na cidade de Porto Alegre como tema de projeto, os alunos são desafiados a realizar trabalhos de pesquisa, estudo e modelagem das estações e dos espaços urbanos de entorno, atendendo ao que está estabelecido no Convênio entre a Universidade e as instituições públicas responsáveis pela implantação do metrô.Dessa maneira, as pesquisas e projetos urbanístico-arquitetônicos desenvolvidos pelos acadêmicos servem como subsídio para discussões acerca das potencialidades e fragilidades de cada caso, objetivando ampliar os estudos exploratórios para que os técnicos municipais possam produzir parâmetros e diretrizes tanto para os critérios de escolha dos projetos técnicos definitivos quanto para a elaboração dos próprios. A experiência, em curso há mais de dois anos, tem contribuído para o alto nível de qualidade dos trabalhos produzidos pelos alunos, além de permitir a simulação de uma experiência com um cliente real, enfrentando os desafios da vida profissional de forma simulada. Os procedimentos e metodologia empregados na construção do processo ensino-aprendizagem são discutidos no presente trabalho.Área temática 1: Proyecto Arquitectónico y Urbano - Eje EnseñanzaFacultad de Arquitectura y Urbanism

sMolBoxes: Dataflow Model for Molecular Dynamics Exploration

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus, biochemists rely to a large extent only on quantitative analysis of geometric and physico-chemical properties. However, the usage of abstract methods to study inherently spatial data hinders the exploration and poses a considerable workload. sMolBoxes link quantitative analysis of a user-defined set of properties with interactive 3D visualizations. They enable visual explanations of molecular behaviors, which lead to an efficient discovery of biochemically significant parts of the MD simulation. sMolBoxes follow a node-based model for flexible definition, combination, and immediate evaluation of properties to be investigated. Progressive analytics enable fluid switching between multiple properties, which facilitates hypothesis generation. Each sMolBox provides quick insight to an observed property or function, available in more detail in the bigBox View. The case study illustrates that even with relatively few sMolBoxes, it is possible to express complex analyses tasks, and their use in exploratory analysis is perceived as more efficient than traditional scripting-based methods.Comment: 10 pages, 9 figures, IEEE VIS, TVC

IOP variations in the sitting and supine positions

Purpose: The aim of this study was to assess the influence of the position (upright vs. supine) in the intraocular pressure (IOP) measured with a non-contact portable tonometer. Methods: Fifty university students with a mean age of 22.3±4.2 years (mean±SD) were recruited to participate in this study. IOP was measured with the non-contact tonometer Keeler, Pulsair EasyEye. Measurements in upright and supine positions were randomly obtained. In the upright position, 2 series of 3 measures (UP1 and UP2) and a series of 3 measures in the supine position were performed. Results: The values obtained in the positions UP1 and UP2 were compared, as well as the values of the upright and supine positions. No statistically significant differences were found when comparing the values obtained in the upright position (P>0.05). Instead, when the subjects were in the supine position, IOP increased 2.47±2.12mm Hg (mean±SD), as opposed to the value obtained in the upright position (P<0.001). Conclusions: Results from this study showed that IOP increased when measured in the supine position and that the Pulsair EasyEye tonometer can determine those variations in a healthy young population

Bioatividade antimicrobiana e antitumoral do veneno de serpentes

Os venenos de serpentes são secreções com uma diversa composição de toxinas com características estruturais e funcionais particularmente interessantes. Embora possam ser letais, os venenos exibem potentes constituintes cuja a atividade e especificidade os tornam excelentes modelos para o desenvolvimento de novos fármacos. O estudo da bioatividade destas toxinas permite evidenciar a sua utilidade para o tratamento de diversas patologias que afetam a saúde humana. Desta forma, nesta revisão abordamos os principais constituintes dos venenos e os seus mecanismos no processo de envenenamento. Elucidamos relativamente às suas bioatividades antimicrobiana e antitumoral, focando, neste âmbito, o seu enorme potencial terapêutico.publishe