Incidentes críticos en los docentes de enfermería: descubriendo una nueva identidad / Incidentes críticos em docentes de enfermagem: descobrindo uma nova identidade / Critical incidents in nursing academics: discovering a new identity

RESUMEN Objetivo: estudio cualitativo que siguió los principios de la teoría fundamentada con el fin de analizar la identidad profesional de docentes de enfermería por medio del análisis de incidentes críticos que más las desestabilizaban. Método: entrevistas semi-estructuradas fueron realizadas a siete enfermeras que actúan como docentes e investigadoras en una universidad privada de Barcelona. Resultados: el material empírico resultante fue organizado en dos categorías: caracterización de los incidentes críticos y reacción de las enfermeras frente a ellos. Conclusión: se concluye que la identidad profesional de estas enfermeras en el campo académico está aún en construcción y que la inexperiencia es el mayor obstáculo que enfrentan para gestionar los incidentes críticos en el trabajo docente. .

RESUMO Objetivo: estudo qualitativo que seguiu os princípios da teoria fundamentada em dados com o objetivo de analisar a identidade profissional de docentes de enfermagem por meio da análise de incidentes críticos que mais as desestabilizaram. Método: entrevistas semiestruturadas foram realizadas com sete enfermeiras que atuam como docentes e pesquisadoras em uma universidade privada de Barcelona. Resultados: o material empírico resultante foi organizado em duas categorias: caracterização dos incidentes críticos e reação das enfermeiras frente a eles. Conclusão: concluiu-se que identidade profissional dessas enfermeiras no campo acadêmico está ainda em construção e a que inexperiência é o maior obstáculo que enfrentam para gerenciar incidentes críticos no trabalho docente. .

ABSTRACT Objective: a qualitative study that followed the principles of the grounded theory in order to analyze the professional identity of nursing academics through the analysis of the most disturbing critical incidents. Method: semi-structured interviews were conducted with seven nurses who worked as professors and researchers in a private university in Barcelona. Results: the resulting empirical material was organized into two categories: characterization of critical incidents and responsiveness to the incident. Conclusion: the professional identity of nurses regarding the academic area is still under construction and inexperience is the major obstacle in the management of critical incidents in the teaching career. .

Priorização de alvos para fármacos no combate a doenças tropicais negligenciadas causadas por protozoários / Prioritization of targets for drugs to fight neglected tropical diseases caused by protozoan

As doenças negligenciadas são doenças infecciosas que afetam principalmente a população mais pobre do mundo. Os fármacos existentes para o combate a essas doenças causam muitos efeitos colaterais aos pacientes e não são suficientes ou são inacessíveis à eles. Além disso, ainda há a resistência aos fármacos. Neste sentido, identificar alvos para a descoberta de novos fármacos se faz necessário. Este trabalho propõe uma metodologia para apoiar a priorização de alvos no combate a doenças tropicais negligenciadas causadas por cinco protozoários: Entamoeba histolytica, Leishmania major, Plasmodium falciparum, Trypanosoma brucei e T. cruzi, baseando-se nos conceitos de essencialidade e drogabilidade da proteína. A metodologia aproveita-se da vasta quantidade de dados e informações disponíveis publicamente em bases de dados genômicas, bioquímicas e farmacológicas, além da literatura biomédica, para buscar e integrar dados e informações de organismos modelo e proteínas alvo de fármaco para sugerir candidatos (proteínas alvo) essenciais e drogáveis para os protozoários, levantando assim, possíveis alvos para posteriores estudos e experimentosPara a obtenção destes dados foi utilizada a abordagem de anotação semântica baseada em ontologia para extrair dados a partir de artigos científicos e os conceitos de homologia e ortologia entre sequências de proteínas armazenadas em bases de dados semi-estruturadas de modo a levantar candidatos essenciais e drogáveis. Exemplos dos resultados gerados são mostrados, assim como algumas relações encontradas, e possíveis integrações entre os dados extraídos da literatura e dos resultados de homologia e ortologia...

Neglected diseases are infectious diseases that primarily affect the poorest people inthe world. The existing drugs to fight these diseases cause many side effects topatients and are not sufficient or inaccessible. Another problem is that there still isdrug resistance. Accordingly, it is very important to identify targets for new drugs.This study proposes a methodology to support the prioritization of targets to combatneglected tropical diseases caused by five protozoan Entamoeba histolytica,Leishmania Major, Plasmodium falciparum, Trypanosoma cruzi and T. brucei, basedon the concepts of protein essentiality and druggability. The methodology takesadvantage of the large amount of data and information publicly available on genomic,biochemical and pharmacological databases, and also the biomedical literature to seekand integrate data and information from model organisms and drug target proteins tosuggest essential and druggable candidates (target proteins) for protozoa, raising thepossibility of targets for future studies and experiments. To obtain these data we usedthe approach of ontology-based semantic annotation to extract data from scientificarticles and the concepts of homology and orthology between protein sequencesstored in semi-structured databases, in order to raise essential and drugablecandidates. Examples of the results generated are shown, as well as somerelationships found, and possible integration between the data extracted from theliterature and the results of homology and orthology...

Modelación por homología de la proteína Luxs de Porphyromonas gingivalis cepa W83 / Modelling by homology of Luxs protein in Porphyromonas gingivalis strain W83

Antecedentes: En las proteínas no se logra siempre su cristalización, de buen tamaño y de buena calidad para someterla a difracción de rayos X. De tal manera que se abre un campo para el desarrollo de estudios teóricos moleculares y proteínicos, que permiten la representación de las moléculas en tres dimensiones, proporcionando una información espacial para estudiar la interacción entre ligandos y receptores macromoleculares. Materialesy Métodos: Estudio In silico, a partir del análisis de secuencias primarias de seis diferentes proteínas LuxS cristalizadas de diversas bacterias, se seleccionó la proteína 1J6X del Helicobacter pylori, por su similaridad con la secuencia de la proteína LuxS en Porphyromonas gingivalis (P. gingivalis) cepa W83, para producir un modelo por homología de esta proteína, utilizando los programas Sybyl y MOE. Se realizó un acoplamiento con el ligando natural para evaluar la reproducibilidad del modelo en un ambiente biológico. Resultados: Se desarrolló el modelado de la proteína LuxS de P. gingivalis cepa W83, que permite el acercamiento a una estructura que se propone, por la interacción entre la proteína y su ligando natural. El modelo generado con recursos computacionales logró una correcta estructura molecular que aceptó la realización de diversos cálculos. El acoplamiento demostró una cavidad donde se logran diversas posiciones del ligando con buenos resultados. Conclusiones: Se obtuvo un modelo 3D para la proteína LuxS en la P. gingivalis cepa W83 validado por diferentes métodos computacionales con una adecuada reproducibilidad biológica por medio del acoplamiento molecular.

Background: Crystallization is not always achieved for all proteins in a good size and a good quality for X-ray diffraction. So that condition opens a field for the development of theoretical molecular and protein studies allowing the representation of the molecules in 3D, providing spatial information to study the interaction between ligands and macromolecular receptors. Materials and Methods: In silico study from primary sequence analysis of six different proteins LuxS crystallized of several bacteria. 1J6X protein of Helicobacter pylori was selected for its similarity with the LuxS protein sequence in Porphyromonas gingivalis (P. gingivalis) strain W83 to produce a homology model of this protein, using the Sybyl and MOE software. A docking was performed to assess the reproducibility of the model in a biological environment. Results: The LuxS protein modelling of P. gingivalis strain W83 was developed, which allows the approach to a proposed structure for the interaction between the protein and its natural ligand. The model generated with computational resources achieved the correct position and biological behavior by means of developed calculations. The docking showed a cavity in which the ligand adopted several positions with good results. Conclusions: A LuxS protein model was obtained, validated by different methods. This generated a 3D model for LuxS protein in P. gingivalis strain W83 with biological reproducibility by means of molecular docking.

Predicted essential proteins of Plasmodium falciparum for potential drug targets

OBJECTIVE@#To identify novel drug targets for treatment of Plasmodium falciparum.@*METHODS@#Local BLASTP were used to find the proteins non-homologous to human essential proteins as novel drug targets. Functional domains of novel drug targets were identified by InterPro and Pfam, 3D structures of potential drug targets were predicated by the SWISS-MODEL workspace. Ligands and ligand-binding sites of the proteins were searched by Ef-seek.@*RESULTS@#Three essential proteins were identified that might be considered as potential drug targets. AAN37254.1 belonged to 1-deoxy-D-xylulose 5-phosphate reductoisomerase, CAD50499.1 belonged to chorismate synthase, CAD51220.1 belonged to FAD binging 3 family, but the function of CAD51220.1 was unknown. The 3D structures, ligands and ligand-binding sites of AAN37254.1 and CAD50499.1 were successfully predicated.@*CONCLUSIONS@#Two of these potential drug targets are key enzymes in 2-C-methyl-d-erythritol 4-phosphate pathway and shikimate pathway, which are absent in humans, so these two essential proteins are good potential drug targets. The function and 3D structures of CAD50499.1 is still unknown, it still need further study.

Crystal structure of the C-terminal domain of the ɛ subunit of human translation initiation factor eIF2B

Eukaryotic translation initiation factor eIF2B, the guanine nucleotide exchange factor (GEF) for eIF2, catalyzes conversion of eIF2·GDP to eIF2·GTP. The eIF2B is composed of five subunits, α, β, γ, δ and ɛ, within which the ɛ subunit is responsible for catalyzing the guanine exchange reaction. Here we present the crystal structure of the C-terminal domain of human eIF2Bɛ (eIF2Bɛ-CTD) at 2.0-Å resolution. The structure resembles a HEAT motif and three charge-rich areas on its surface can be identified. When compared to yeast eIF2Bɛ-CTD, one area involves highly conserved AA boxes while the other two are only partially conserved. In addition, the previously reported mutations in human eIF2Bɛ-CTD, which are related to the loss of the GEF activity and human VWM disease, have been discussed. Based on the structure, most of such mutations tend to destabilize the HEAT motif.

Structural basis for prokaryotic calcium-mediated regulation by a Streptomyces coelicolor calcium binding protein

The important and diverse regulatory roles of Ca(2+) in eukaryotes are conveyed by the EF-hand containing calmodulin superfamily. However, the calcium-regulatory proteins in prokaryotes are still poorly understood. In this study, we report the three-dimensional structure of the calcium-binding protein from Streptomyces coelicolor, named CabD, which shares low sequence homology with other known helix-loop-helix EF-hand proteins. The CabD structure should provide insights into the biological role of the prokaryotic calcium-binding proteins. The unusual structural features of CabD compared with prokaryotic EF-hand proteins and eukaryotic sarcoplasmic calcium-binding proteins, including the bending conformation of the first C-terminal α-helix, unpaired ligand-binding EF-hands and the lack of the extreme C-terminal loop region, suggest it may have a distinct and significant function in calcium-mediated bacterial physiological processes, and provide a structural basis for potential calcium-mediated regulatory roles in prokaryotes.

Analysis on sliding helices and strands in protein structural comparisons: a case study with protein kinases.

Protein structural alignments are generally considered as 'golden standard' for the alignment at the level of amino acid residues. In this study we have compared the quality of pairwise and multiple structural alignments of about 5900 homologous proteins from 718 families of known 3-D structures. We observe shifts in the alignment of regular secondary structural elements (helices and strands) between pairwise and multiple structural alignments. The differences between pairwise and multiple structural alignments within helical and beta-strand regions often correspond to 4 and 2 residue positions respectively. Such shifts correspond approximately to "one turn" of these regular secondary structures. We have performed manual analysis explicitly on the family of protein kinases. We note shifts of one or two turns in helix-helix alignments obtained using pairwise and multiple structural alignments. Investigations on the quality of the equivalent helix-helix, strand-strand pairs in terms of their residue side-chain accessibilities have been made. Our results indicate that the quality of the pairwise alignments is comparable to that of the multiple structural alignments and, in fact, is often better. We propose that pairwise alignment of protein structures should also be used in formulation of methods for structure prediction and evolutionary analysis.

SURF'S UP! - protein classification by surface comparisons.

Large-scale genome sequencing and structural genomics projects generate numerous sequences and structures for 'hypothetical' proteins without functional characterizations. Detection of homology to experimentally characterized proteins can provide functional clues, but the accuracy of homology-based predictions is limited by the paucity of tools for quantitative comparison of diverging residues responsible for the functional divergence. SURF'S UP! is a web server for analysis of functional relationships in protein families, as inferred from protein surface maps comparison according to the algorithm. It assigns a numerical score to the similarity between patterns of physicochemical features(charge, hydrophobicity) on compared protein surfaces. It allows recognizing clusters of proteins that have similar surfaces, hence presumably similar functions. The server takes as an input a set of protein coordinates and returns files with "spherical coordinates" of proteins in a PDB format and their graphical presentation, a matrix with values of mutual similarities between the surfaces, and the unrooted tree that represents the clustering of similar surfaces, calculated by the neighbor-joining method. SURF'S UP! facilitates the comparative analysis of physicochemical features of the surface, which are the key determinants of the protein function. By concentrating on coarse surface features, SURF'S UP! can work with models obtained from comparative modelling. Although it is designed to analyse the conservation among homologs, it can also be used to compare surfaces of non-homologous proteins with different three-dimensional folds, as long as a functionally meaningful structural superposition is supplied by the user. Another valuable characteristic of our method is the lack of initial assumptions about the functional features to be compared. SURF'S UP! is freely available for academic researchers at http://asia.genesilico.pl/surfs_up/.

Comparison of sequence-based and structure-based phylogenetic trees of homologous proteins: Inferences on protein evolution.

Several studies based on the known three-dimensional (3-D) structures of proteins show that two homologous proteins with insignificant sequence similarity could adopt a common fold and may perform same or similar biochemical functions. Hence, it is appropriate to use similarities in 3-D structure of proteins rather than the amino acid sequence similarities in modelling evolution of distantly related proteins. Here we present an assessment of using 3-D structures in modelling evolution of homologous proteins. Using a dataset of 108 protein domain families of known structures with at least 10 members per family we present a comparison of extent of structural and sequence dissimilarities among pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the structure-based dissimilarity measures and the sequence-based dissimilarity measures is usually good if the sequence similarity among the homologues is about 30% or more. For protein families with low sequence similarity among the members, the correlation coefficient between the sequence-based and the structure-based dissimilarities are poor.In these cases the structure-based dendrogram clusters proteins with most similar biochemical functional properties better than the sequence-similarity based dendrogram. In multi-domain protein families and disulphide-rich protein families the correlation coefficient for the match of sequence-based and structure-based dissimilarity (SDM) measures can be poor though the sequence identity could be higher than 30%. Hence it is suggested that protein evolution is best modelled using 3-D structures if the sequence similarities (SSM) of the homologues are very low.