Optimal cruciform specimen design using the direct multi-search method and design variable influence study

Nowadays the development of new testing machines and the optimization of new specimen geometries are two very demanding activities. In order to study complex material stress and strain distributions, as in-plane biaxial loading, one must develop new technical solutions. A new type of testing machine has been developed by the present authors, for the fatigue testing of cruciform specimens, but the low capacity of the testing machine requires the optimization of the specimen in order to achieve higher but uniform stress and strain distributions on the specimen center. In this paper, the authors describe the procedure to optimize one possible geometry for cruciform specimens, able to determine the fatigue initiation life of material subjected to out of phase in-plane biaxial fatigue loadings. The high number of design variables were optimized using the direct multi-search method, considering two objective functions, the stress level on the specimen center and the uniformity of the strain distribution on a 1.0 mm radius of the specimen center. Several Pareto Fronts were obtained for different material thickness, considering the commercially available sheet metal thickness. With the optimal solution, the influence of every design variable was studied in order to provide others with a powerful tool that allows selecting the optimal geometry for the desired application. The results are presented in the form of design equations considering that the main design variable, the material thickness, was chosen from a Renard series of preferred numbers. The end user is then able to configure the optimal specimen for the required fatigue test.info:eu-repo/semantics/publishedVersio

Trends in protein-based biosensor assemblies for drug screening and pharmaceutical kinetic studies

The selection of natural and chemical compounds for potential applications in new pharmaceutical formulations constitutes a time-consuming procedure in drug screening. To overcome this issue, new devices called biosensors, have already demonstrated their versatility and capacity for routine clinical diagnosis. Designed to perform analytical analysis for the detection of a particular analyte, biosensors based on the coupling of proteins to amperometric and optical devices have shown the appropriate selectivity, sensibility and accuracy. During the last years, the exponential demand for pharmacokinetic studies in the early phases of drug development, along with the need of lower molecular weight detection, have led to new biosensor structure materials with innovative immobilization strategies. The result has been the development of smaller, more reproducible biosensors with lower detection limits, and with a drastic reduction in the required sample volumes. Therefore in order to describe the main achievements in biosensor fields, the present review has the main aim of summarizing the essential strategies used to generate these specific devices, that can provide, under physiological conditions, a credible molecule profile and assess specific pharmacokinetic parameters.info:eu-repo/semantics/publishedVersio

Fibromyalgia: description of the syndrome in athletes and its implications

Fibromyalgia syndrome is a very common feature in the daily practice of rheumatologists. Therapy is based on the use of analgesics, anti-depressants, and other drugs. Many physicians indicate exercise, stretching, and relaxing programs as adjuvant therapies. It was surprising to find fibromyalgia in well-trained athletes. The syndrome, however, appears in athletes that reported recurrent tendon-muscle lesions. In this study, the authors analyzed a group of gymnastics and track and field athletes involved in competitive training. They found a significant incidence of the syndrome (7 in 20 subjects) in this group. This is an important finding, since fibromyalgia causes muscular pain and stiffness, and can predispose the athletes to muscle lesions and damage. Another important point regarding the syndrome is that some of its symptoms are related to overtraining and to the chronic fatigue syndrome. Therefore, the authors suggest that there is an important connection between those aspects.A fibromialgia é uma patologia de alta prevalência na população geral, cujo tratamento é feito por meio de medicamentos como antiinflamatórios, antidepressivos e miorrelaxantes, que pode ser complementado por medidas físicas como relaxamento, alongamento e exercícios físicos. A observação de fibromialgia entre atletas constatada em exames de rotina, em especial naqueles que apresentavam lesões musculares de repetição, levou os autores a pesquisar, de maneira prospectiva, um grupo de atletas praticantes de ginástica olímpica e atletismo, nos quais puderam confirmar alta incidência desta síndrome. Como a fibromialgia predispõe ao aparecimento de lesões por contratura muscular, sugerem que ela possa atuar como um mecanismo de indução ao surgimento de lesões musculares de repetição. Ainda devido às semelhanças dos sintomas encontrados na síndrome do supertreinamento, síndrome da fadiga crônica e fibromialgia, propõem uma possível ligação entre estes quadros.UNIFESP-EPMPMSP COTPUNIFESP-EPM Departamento de FisiologiaUSP Departamento de HistologiaUNIFESP, EPM, Depto. de FisiologiaSciEL

Effect of pH on the influenza fusion peptide properties unveiled by constant-pH molecular dynamics simulations combined with experiment

© The Author(s) 2020. Open Access. This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.The influenza virus fusion process, whereby the virus fuses its envelope with the host endosome membrane to release the genetic material, takes place in the acidic late endosome environment. Acidification triggers a large conformational change in the fusion protein, hemagglutinin (HA), which enables the insertion of the N-terminal region of the HA2 subunit, known as the fusion peptide, into the membrane of the host endosome. However, the mechanism by which pH modulates the molecular properties of the fusion peptide remains unclear. To answer this question, we performed the first constant-pH molecular dynamics simulations of the influenza fusion peptide in a membrane, extending for 40 µs of aggregated time. The simulations were combined with spectroscopic data, which showed that the peptide is twofold more active in promoting lipid mixing of model membranes at pH 5 than at pH 7.4. The realistic treatment of protonation introduced by the constant-pH molecular dynamics simulations revealed that low pH stabilizes a vertical membrane-spanning conformation and leads to more frequent contacts between the fusion peptide and the lipid headgroups, which may explain the increase in activity. The study also revealed that the N-terminal region is determinant for the peptide's effect on the membrane.This work was financially supported by FCT—Fundação para a Ciência e a Tecnologia, Portugal, through projects PTDC/QUI-BIQ/114774/2009, PTDC/CCI-BIO/28200/2017 and Pest-OE/EQB/LA0004/2011. This work was also financially supported by Project LISBOA-01-0145-FEDER-007660 (Microbiologia Molecular, Estrutural e Celular) funded by FEDER funds through COMPETE2020—Programa Operacional Competitividade e Internacionalização (POCI) and by national funds through FCT—Fundação para a Ciência e a Tecnologia. DL was supported by FCT post-doc fellowship SFRH/BPD/92537/2013.info:eu-repo/semantics/publishedVersio

Programa Institucional de Bolsa de Iniciação à Docência (Pibid) e a Formação de Professores de Química – Subprojeto UnB/Ceilândia-DF

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Inter-domain Communication Mechanisms in an ABC Importer: A Molecular Dynamics Study of the MalFGK2E Complex

ATP-Binding Cassette transporters are ubiquitous membrane proteins that convert the energy from ATP-binding and hydrolysis into conformational changes of the transmembrane region to allow the translocation of substrates against their concentration gradient. Despite the large amount of structural and biochemical data available for this family, it is still not clear how the energy obtained from ATP hydrolysis in the ATPase domains is “transmitted” to the transmembrane domains. In this work, we focus our attention on the consequences of hydrolysis and inorganic phosphate exit in the maltose uptake system (MalFGK2E) from Escherichia coli. The prime goal is to identify and map the structural changes occurring during an ATP-hydrolytic cycle. For that, we use extensive molecular dynamics simulations to study three potential intermediate states (with 10 replicates each): an ATP-bound, an ADP plus inorganic phosphate-bound and an ADP-bound state. Our results show that the residues presenting major rearrangements are located in the A-loop, in the helical sub-domain, and in the “EAA motif” (especially in the “coupling helices” region). Additionally, in one of the simulations with ADP we were able to observe the opening of the NBD dimer accompanied by the dissociation of ADP from the ABC signature motif, but not from its corresponding P-loop motif. This work, together with several other MD studies, suggests a common communication mechanism both for importers and exporters, in which ATP-hydrolysis induces conformational changes in the helical sub-domain region, in turn transferred to the transmembrane domains via the “coupling helices”