A Bioinformatics Study of Protein Conformational Flexibility and Misfolding: a Sequence, Structure and Dynamics Approach

This PhD Thesis titled "A Bioinformatics Study of Protein Conformational Flexibility and Misfolding: a Sequence, Structure and Dynamics Approach" comprises the results and conclusions obtained by us from the study of three different but somehow related research projects, covering aspects of the phenomenon of protein local conformational instability, its relationship with protein function, evolvability and aggregation, and the effect of genetic variations on protein conformational instability related to Conformational Diseases. These projects include the prediction of putative prion proteins in complete proteomes and the study of prion biology from a genomic perspective, the prediction of conformationally unstable protein regions and the existence of a structural framework for linking conformational instability to folding and function, and the establishment of a rationale for assessing the connection among mutations and disease phenotypes in Conformational Diseases.Esta tesis doctoral comprende los resultados y conclusiones obtenidos por nosotros a partir del estudio de tres proyectos de investigación diferentes pero de alguna manera relacionados, cubriendo los aspectos del fenómeno de la inestabilidad conformacional local de la proteína, su relación con la función de la proteína, la capacidad de evolución y agregación, y el efecto de las variaciones genéticas en la inestabilidad conformacional de la proteína relacionados con las enfermedades conformacionales. Estos proyectos incluyen la predicción de presuntas proteínas priónicas en proteomas complejos y el estudio de la biología de priones desde una perspectiva genómica, la predicción de las regiones de proteínas conformacionalmente inestables y la existencia de un marco estructural para la vinculación de la inestabilidad conformacional del plegado y la función, y el establecimiento de una razón fundamental para la evaluación de la relación entre las mutaciones y fenotipos de la enfermedad en enfermedades conformacionales

Structural (and sequence-based) analysis of transcriptional regulation

Most computational approaches to transcriptional regulation use sequence-based methodologies, that aim to discover regulatory motifs in genomic segments. Here we argue that the current content of the Protein Data Bank (PDB) can provide invaluable data that drive the prediction of regulatory interactions within genomes. First, we dissect protein-DNA interfaces and find atomic interactions that contribute to sequence-specific recognition, mainly hydrogen bonds and Van derWaals contacts. These specificity determinants can be expressed in terms of atomic weight matrices, that are shown to be robust in bootstrap experiments and yield scores that correlate with approximate measures of binding specificity. Second, using example transcription factors from Escherichia coli we find that some protein-DNA interfaces have sequence-dependent DNA geometries that constitute indirect readout mechanisms, in agreement with previous reports. Third, we are able to build structure-based position weight matrices that capture both types of recognition mechanisms and test them in genomic experiments, with results comparable to sequence-based methodologies. We conclude that the PDB can be further exploited in exploring transcriptional regulation and other biological processes mediated by protein-DNA interactions.Funded by CSIC grant number 200720I038Peer reviewe

ACOMPANHAMENTO DE PACIENTES PORTADORES DE HIPERTENSÃO ARTERIAL SISTÊMICA: PLANO DE AÇÃO

A Hipertensão Arterial Sistêmica ( HAS) é um problema grave de saúde pública no Brasil e no mundo.A prevalência de HAS é elevada estimando-se que cerca de 20% da população brasileira adulta possa ser rotulada como hipertensa. A hipertensão arterial sistêmica (HAS) é uma condição clinica multifatorial caracterizada por níveis elevados e sustentados de pressão arterial (PA). A Hipertensão Arterial é definida como pressão arterial sistólica maior ou igual a 140 mmhg e uma pressão diastólica maior ou igual a 90 mmhg, em indivíduos que não estão fazendo uso de medicação anti-hipertensiva. Com o intuito de organizar a assistência aos portadores de hipertensão arterial, o presente trabalho objetivou elaborar um plano de ação, que seria executado pela Equipe de Saúde Familiar 4(ESF 4) do Centro de Saúde da Mulher de Jaru/RO a partir de Janeiro 2015. Dentro das ações desenvolvidas elaborou-se uma agenda programada para a realização das atividades da equipe. Adotamos os Protocolos do Ministério de Saúde e trabalhamos para lograr o melhor preenchimento dos Prontuários e as Fichas. Nosso trabalho permitiu que a ESF 4 acompanhasse a totalidade dos pacientes hipertensos cadastrados por esta doença, com agendamento das consultas mensais .Implantou-se a Linha –Guia: Saúde do Adulto – hipertensão e diabetes e a coleta da informação nesse período foi superior ao passado

El enfoque Ciencia Tecnología Sociedad desde el currículo propio: Género Salud y Sexualidad. Su intencionalidad formativa en la educación superior

El trabajo que se presenta aporta los sucesos más preponderantes en la historia de la sexualidad como fenómeno social y su vinculación con los estudios científicos realizados, respondiendo a las condicionantes en que este se comprende desde la antigüedad hasta los momentos actuales. Por otra parte, se abordan las consecuencias de la sexualidad desde el punto vista educativa a través del tratamiento de un enfoque Ciencia-Tecnología-Sociedad (CTS), desde la asignatura Género Salud y Sexualidad. Para ello, el trabajo se centra además en una metodología con enfoque ceteísta que accede a una mejor implementación de la asignatura, para los estudiantes de la carrera Licenciatura en Educación, Biología, de la facultad de Ciencias Agraria de la UCF Carlos Rafael Rodríguez. La metodología asume los procedimientos para cada una de las fases que llevan a la incorporación en los contenidos y los métodos, los adelantos de la ciencia y la tecnología en la sexualidad que repercuten en la sociedad

Melhoria da Atenção à Saúde da Pessoa com Hipertensão Arterial Sistêmica e/ou Diabetes Mellitus, na UBS Zona Sul, Pinheiro Machado/RS

A Hipertensão Arterial Sistêmica e o Diabetes Mellitus se constituem como as principais Doenças Crônicas Não-transmissíveis geradoras de possíveis complicações como infarto agudo do miocárdio e acidente vascular encefálico. Mediante a Análise Situacional realizada na UBS Zona Sul em Pinheiro Machado/RS, verificou-se a necessidade de melhorar a atenção ao hipertenso e diabético considerando-se para a intervenção os objetivos de aumento da cobertura e da adesão, qualificação da atenção, registro das informações, mapeamento dos usuários de risco cardiovascular e promoção saúde.Utilizaram-se indicadores para avaliar a evolução da intervenção ao longo de três meses que ocorreu entre fevereiro a junho de 2015, exceto nos meses de março e abril devido às férias. Utilizaram-se como referências os protocolos 36 e 37 do Ministério da Saúde (MS) e os instrumentos disponibilizados pelo curso que foram as fichas-espelho e as planilhas de coleta de dados. A ação programática voltada aos hipertensos e/ou diabéticos foi incorporada à rotina da UBS, ainda que, com limitações derivadas da infraestrutura e da demora no retorno dos resultados de exames, pois, foi possível observar melhorias no atendimento aos usuários, sugerindo-se, ainda maior engajamento público

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters

<p>Abstract</p> <p>Background</p> <p>The fine tuning of two features of the bacterial regulatory machinery have been known to contribute to the diversity of gene expression within the same regulon: the sequence of Transcription Factor (TF) binding sites, and their location with respect to promoters. While variations of binding sequences modulate the strength of the interaction between the TF and its binding sites, the distance between binding sites and promoters alter the interaction between the TF and the RNA polymerase (RNAP).</p> <p>Results</p> <p>In this paper we estimated the dissociation constants (<it>K</it>_<it>d</it>) of several <it>E. coli </it>TFs in their interaction with variants of their binding sequences from the scores resulting from aligning them to Positional Weight Matrices. A correlation coefficient of 0.78 was obtained when pooling together sites for different TFs. The theoretically estimated <it>K</it>_{<it>d </it>}values were then used, together with the dissociation constants of the RNAP-promoter interaction to analyze activated and repressed promoters. The strength of repressor sites -- i.e., the strength of the interaction between TFs and their binding sites -- is slightly higher than that of activated sites. We explored how different factors such as the variation of binding sequences, the occurrence of more than one binding site, or different RNAP concentrations may influence the promoters' response to the variations of TF concentrations. We found that the occurrence of several regulatory sites bound by the same TF close to a promoter -- if they are bound by the TF in an independent manner -- changes the effect of TF concentrations on promoter occupancy, with respect to individual sites. We also found that the occupancy of a promoter will never be more than half if the RNAP concentration-to-<it>K</it>_{<it>p </it>}ratio is 1 and the promoter is subject to repression; or less than half if the promoter is subject to activation. If the ratio falls to 0.1, the upper limit of occupancy probability for repressed drops below 10%; a descent of the limits occurs also for activated promoters.</p> <p>Conclusion</p> <p>The number of regulatory sites may thus act as a versatility-producing device, in addition to serving as a source of robustness of the transcription machinery. Furthermore, our results show that the effects of TF concentration fluctuations on promoter occupancy are constrained by RNAP concentrations.</p

Chemical Properties that Determine Boron Availability in Sugar Cane Soils

Context: Several factors are limiting the behavior and dynamics of boron (B) in the soil. Few results on assimilable B contents in the soil and its relation to other chemical properties have been published. Objective: To determine the contents of assimilable B and the chemical properties that condition its availability in three of the main soil types where sugar cane is cultivated. Methods: The samples were taken at random from the surface (0-20 cm) of three of the main soil types where sugar cane is cultivated in Cuba. Soil assimilable B was determined by extraction with hot water. Classification of assimilable boron concentration relied on category ranges set up by Agrolab, (2005): low (˂0.5 mg kg-1), mid (0.5 a 2.0 mg kg-1), and high (˃2.0 mg kg-1). Results: The concentration of assimilable B varied according to the soil type, with a high dependence on chemical properties. Conclusions: The B contents was highly dependent on variables K2O, P2O5, Mg+ and Na+. The average B concentration was within mid-range values in vertisols and low in brown and ferralitic soils, with high variability. The contents of assimilable B should be further studied, along with the effect of limiting chemical, physical, and biological factors on the soil

Discovering putative prion sequences in complete proteomes using probabilistic representations of Q/N-rich domains

Background: prion proteins conform a special class among amyloids due to their ability to transmit aggregative folds. Prions are known to act as infectious agents in neurodegenerative diseases in animals, or as key elements in transcription and translation processes in yeast. It has been suggested that prions contain specific sequential domains with distinctive amino acid composition and physicochemical properties that allow them to control the switch between soluble and β-sheet aggregated states. Those prion-forming domains are low complexity segments enriched in glutamine/asparagine and depleted in charged residues and prolines. Different predictive methods have been developed to discover novel prions by either assessing the compositional bias of these stretches or estimating the propensity of protein sequences to form amyloid aggregates. However, the available algorithms hitherto lack a thorough statistical calibration against large sequence databases, which makes them unable to accurately predict prions without retrieving a large number of false positives.- Results: here we present a computational strategy to predict putative prion-forming proteins in complete proteomes using probabilistic representations of prionogenic glutamine/asparagine rich regions. After benchmarking our predictive model against large sets of non-prionic sequences, we were able to filter out known prions with high precision and accuracy, generating prediction sets with few false positives. The algorithm was used to scan all the proteomes annotated in public databases for the presence of putative prion proteins. We analyzed the presence of putative prion proteins in all taxa, from viruses and archaea to plants and higher eukaryotes, and found that most organisms encode evolutionarily unrelated proteins with susceptibility to behave as prions. - Conclusions: to our knowledge, this is the first wide-ranging study aiming to predict prion domains in complete proteomes. Approaches of this kind could be of great importance to identify potential targets for further experimental testing and to try to reach a deeper understanding of prions' functional and regulatory mechanism

Identifying potential novel drugs against Helicobacter pylori by targeting the essential response regulator HsrA

The increasing antibiotic resistance evolved by Helicobacter pylori has alarmingly reduced the eradication rates of first-line therapies. To overcome the current circulating resistome, we selected a novel potential therapeutic target in order to identify new candidate drugs for treating H. pylori infection. We screened 1120 FDA-approved drugs for molecules that bind to the essential response regulator HsrA and potentially inhibit its biological function. Seven natural flavonoids were identified as HsrA binders. All of these compounds noticeably inhibited the in vitro DNA binding activity of HsrA, but only four of them, apigenin, chrysin, kaempferol and hesperetin, exhibited high bactericidal activities against H. pylori. Chrysin showed the most potent bactericidal activity and the most synergistic effect in combination with clarithromycin or metronidazole. Flavonoid binding to HsrA occurs preferably at its C-terminal effector domain, interacting with amino acid residues specifically involved in forming the helix-turn-helix DNA binding motif. Our results validate the use of HsrA as a novel and effective therapeutic target in H. pylori infection and provide molecular evidence of a novel antibacterial mechanism of some natural flavonoids against H. pylori. The results further support the valuable potential of natural flavonoids as candidate drugs for novel antibacterial strategies

A differential network analysis approach for lineage specifier prediction in stem cell subpopulations

10.1038/npjsba.2015.12npj Systems Biology and Applications11501