Structuprint: a scalable and extensible tool for two-dimensional representation of protein surfaces

© 2016 Kontopoulos et al.Background: The term molecular cartography encompasses a family of computational methods for two-dimensional transformation of protein structures and analysis of their physicochemical properties. The underlying algorithms comprise multiple manual steps, whereas the few existing implementations typically restrict the user to a very limited set of molecular descriptors. Results: We present Structuprint, a free standalone software that fully automates the rendering of protein surface maps, given - at the very least - a directory with a PDB file and an amino acid property. The tool comes with a default database of 328 descriptors, which can be extended or substituted by user-provided ones. The core algorithm comprises the generation of a mould of the protein surface, which is subsequently converted to a sphere and mapped to two dimensions, using the Miller cylindrical projection. Structuprint is partly optimized for multicore computers, making the rendering of animations of entire molecular dynamics simulations feasible. Conclusions: Structuprint is an efficient application, implementing a molecular cartography algorithm for protein surfaces. According to the results of a benchmark, its memory requirements and execution time are reasonable, allowing it to run even on low-end personal computers. We believe that it will be of use - primarily but not exclusively - to structural biologists and computational biochemists

Limits to thermal adaptation in ectotherms

Climate change is expected to affect biological systems across multiple scales through its direct effects on the physiology of individual organisms. Therefore, to predict how communities and ecosystems will be impacted by changes in climate, it is key to understand the extent to which ectotherm physiology can change through thermal adaptation. In this thesis, we examine the influence of possible constraints on thermal adaptation, as predicted by the Metabolic Theory of Ecology. In Chapter 2 we describe the consequences of violating a key assumption of a model used for quantifying the thermal performance curve, i.e., the relationship of biological rates with temperature. We then proceed in Chapter 3 to evaluate the impact of thermodynamic constraints on the evolution of the thermal performance curves of phytoplankton. We show that thermodynamic constraints have a very weak effect on thermal adaptation, with phylogenetically structured variation being present across the entire thermal performance curve. Further support for such a conclusion is obtained in Chapter 4 through a phylogenetic comparative analysis of the evolution of thermal sensitivity across prokaryotes, phytoplankton, and plants. This reveals that thermal sensitivity is much more variable than expected, as it can change drastically within short amounts of evolutionary time. In Chapter 5, we finally investigate thermal adaptation at the molecular level, examining if changes in temperature can alter the effects of nonsynonymous mutations. We show that across prokaryotes, mutations become increasingly detrimental to the stability of proteins with temperature. In response, thermophile species evolve enzymes that are more robust to mutations and exhibit low substitution rates. Overall, these results further our understanding of how thermal physiology evolves and indicate areas where the theory – as it currently stands – may need to be modified.Open Acces

Migraine and Chronic Daily Headache: Quality of life in school children in Northern Greece

Primary headaches are very frequent in childhood. Migraine consists the majority of them. It appears in all ages of childhood. Chronic Daily Headache is the most recent category of primary headaches and can be divided into 4 categories. The aim of our study was to estimate the effect of these headaches in the quality of life of school children. 100 migraine and 39 Chronic Daily Headache children, 6 to 14 years old were studied.These children underwent neurological examination and in some cases MRI and laboratory tests. CHQ - Parent Form 50 was carried out in all of them. CHQ is a general instrument that counts the social, emotional and physical state of children. Two summary scores occur, a physical and a psychosocial score, through the answers of the 50 questions of the CHQ by the parents. The results were compared to 100 healthy children. According to the study’s results, migraine and Chronic Daily Headache caused a statistically significant adverse overall effect on all aspects of Quality of life in children. Furthermore, Chronic Daily Headache children had statistically significant lower CHQ scores in some aspects of quality of life and in psychosocial health summary score than migraine ones

Space constrained homology modelling: The paradigm of the RNA-dependent RNA polymerase of dengue (Type II) virus

Protein structure is more conserved than sequence in nature. In this direction we developed a novel methodology that significantly improves conventional homology modelling when sequence identity is low, by taking into consideration 3D structural features of the template, such as size and shape. Herein, our new homology modelling approach was applied to the homology modelling of the RNA-dependent RNA polymerase (RdRp) of dengue (type II) virus. The RdRp of dengue was chosen due to the low sequence similarity shared between the dengue virus polymerase and the available templates, while purposely avoiding to use the actual X-ray structure that is available for the dengue RdRp. The novel approach takes advantage of 3D space corresponding to protein shape and size by creating a 3D scaffold of the template structure. The dengue polymerase model built by the novel approach exhibited all features of RNA-dependent RNA polymerases and was almost identical to the X-ray structure of the dengue RdRp, as opposed to the model built by conventional homology modelling. Therefore, we propose that the space-aided homology modelling approach can be of a more general use to homology modelling of enzymes sharing low sequence similarity with the template structures. © 2013 Dimitrios Vlachakis et al