Capturing coevolutionary signals in repeat proteins

The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural ensembles. Here we introduce a statistical coupling analysis for repeat proteins -- natural systems for which the identification of domains remains challenging. We show that the inherent translational symmetry of repeat protein sequences introduces a strong bias in the pair correlations at precisely the length scale of the repeat-unit. Equalizing for this bias reveals true co-evolutionary signals from which local native-contacts can be identified. Importantly, parameter values obtained for all other interactions are not significantly affected by the equalization. We quantify the robustness of the procedure and assign confidence levels to the interactions, identifying the minimum number of sequences needed to extract evolutionary information in several repeat protein families. The overall procedure can be used to reconstruct the interactions at long distances, identifying the characteristics of the strongest couplings in each family, and can be applied to any system that appears translationally symmetric

Detecting Repetitions and Periodicities in Proteins by Tiling the Structural Space

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association towards higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information we can identify structural units that can be encoded by a variety of distinct amino acid sequences

Negative effect of copper nanoparticles on the conjugation frequency of degradative catabolic plasmid

Due to their antimicrobial properties Copper nanoparticles (CuNps) have been proposed to be used in agriculture for pest control. Pesticides removal is mainly done by microorganisms, whose genes usually are found in degradative plasmids transferable by conjugation. Our objective was to evaluate if subinhibitory concentrations of CuNps affect the conjugation frequency (CF) of two degradative plasmids, pJP4 and pADP1. CuNps were characterized by scanning electron microscopy with X-ray detector, dynamic light scattering and atomic absorption spectrophotometry. Mating pairs were incubated in liquid media supplemented with subinhibitory concentrations of CuNps (nominal size 40-60 nm) or copper sulphate (CuSO4) as salt form. Transconjugants strains were checked for pesticide degradation and presence of plasmidial genes by PCR. CuNps dissolution in LB broth were quickly (less 3 h), meanwhile in saline medium without organic matter dissolution never pass over 20%. Neither nanoparticles nor copper salt modify the bacterial growth under subinhibitory concentrations assessed. However, under low concentrations of both copper forms (20 µg mL-1), the conjugation frequencies of degradative plasmids were reduced to 90 %. Therefore, our results indicate that ionic copper affect transference of catabolic plasmids as a subinhibitory consequence. The intentional or accidental release of copper to the environment would be affecting the biodegradative potential of microbial communities and inevitably producing as a result a decrease in the pesticides removal.Fil: Parra, Boris. Universidad de Concepcion; ChileFil: Tortella, Gonzalo R.. Universidad de La Frontera. Núcleo Científico y Tecnológico en Recursos Naturales; ChileFil: Cuozzo, Sergio Antonio. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Planta Piloto de Procesos Industriales Microbiológicos; ArgentinaFil: Martínez, Miguel. Universidad de Concepción; Chil

Highlights from the eleventh ISCB Student Council Symposium 2015

This report summarizes the scientific content and activities of the annual symposium organized by the Student Council of the International Society for Computational Biology (ISCB), held in conjunction with the Intelligent Systems for Molecular Biology (ISMB) / European Conference on Computational Biology (ECCB) conference in Dublin, Ireland on July 10, 2015

Cardiovascular magnetic resonance findings in a pediatric population with isolated left ventricular non-compaction

<p>Abstract</p> <p>Background</p> <p>Isolated Left Ventricular Non-compaction (LVNC) is an uncommon disorder characterized by the presence of increased trabeculations and deep intertrabecular recesses. In adults, it has been found that Ejection Fraction (EF) decreases significantly as non-compaction severity increases. In children however, there are a few data describing the relation between anatomical characteristics of LVNC and ventricular function. We aimed to find correlations between morphological features and ventricular performance in children and young adolescents with LVNC using Cardiovascular Magnetic Resonance (CMR).</p> <p>Methods</p> <p>15 children with LVNC (10 males, mean age 9.7 y.o., range 0.6 - 17 y.o.), underwent a CMR scan. Different morphological measures such as the Compacted Myocardial Mass (CMM), Non-Compaction (NC) to the Compaction (C) distance ratio, Compacted Myocardial Area (CMA) and Non-Compacted Myocardial Area (NCMA), distribution of NC, and the assessment of ventricular wall motion abnormalities were performed to investigate correlations with ventricular performance. EF was considered normal over 53%.</p> <p>Results</p> <p>The distribution of non-compaction in children was similar to published adult data with a predilection for apical, mid-inferior and mid-lateral segments. Five patients had systolic dysfunction with decreased EF. The number of affected segments was the strongest predictor of systolic dysfunction, all five patients had greater than 9 affected segments. Basal segments were less commonly affected but they were affected only in these five severe cases.</p> <p>Conclusion</p> <p>The segmental pattern of involvement of non-compaction in children is similar to that seen in adults. Systolic dysfunction in children is closely related to the number of affected segments.</p

ISCB Student Council Symposium 2021, a virtual global venue : challenges and lessons learned

Since 2004, the ISCB Student Council has been organizing different symposia worldwide, gathering together the community of young computational biologists. Due to the coronavirus disease 2019 (COVID-19) pandemic situation, the world scientific community was forced to cancel in-person meetings for almost two years, imposing the adoption of virtual formats instead. After the successful editions of our continental symposia in 2020 in the USA, Latin America, and Europe, we organized our flagship global event, the Student Council Symposium (SCS) 2021, trying to apply all previous lessons learned and to exploit the advantages that virtuality has to offer