VoroMQA: Assessment of protein structure quality using interatomic contact areas

In the absence of experimentally determined protein structure many biological questions can be addressed using computational structural models. However, the utility of protein structural models depends on their quality. Therefore, the estimation of the quality of predicted structures is an important problem. One of the approaches to this problem is the use of knowledge‐based statistical potentials. Such methods typically rely on the statistics of distances and angles of residue‐residue or atom‐atom interactions collected from experimentally determined structures. Here, we present VoroMQA (Voronoi tessellation‐based Model Quality Assessment), a new method for the estimation of protein structure quality. Our method combines the idea of statistical potentials with the use of interatomic contact areas instead of distances. Contact areas, derived using Voronoi tessellation of protein structure, are used to describe and seamlessly integrate both explicit interactions between protein atoms and implicit interactions of protein atoms with solvent. VoroMQA produces scores at atomic, residue, and global levels, all in the fixed range from 0 to 1. The method was tested on the CASP data and compared to several other single‐model quality assessment methods. VoroMQA showed strong performance in the recognition of the native structure and in the structural model selection tests, thus demonstrating the efficacy of interatomic contact areas in estimating protein structure quality. The software implementation of VoroMQA is freely available as a standalone application and as a web server at http://bioinformatics.lt/software/voromqa . Proteins 2017; 85:1131–1145. © 2017 Wiley Periodicals, Inc.     

Structural modeling of protein complexes: Current capabilities and challenges

Proteins frequently interact with each other, and the knowledge of structures of the corresponding protein complexes is necessary to understand how they function. Computational methods are increasingly used to provide structural models of protein complexes. Not surprisingly, community-wide Critical Assessment of protein Structure Prediction (CASP) experiments have recently started monitoring the progress in this research area. We participated in CASP13 with the aim to evaluate our current capabilities in modeling of protein complexes and to gain a better understanding of factors that exert the largest impact on these capabilities. To model protein complexes in CASP13, we applied template-based modeling, free docking and hybrid techniques that enabled us to generate models of the topmost quality for 27 of 42 multimers. If templates for protein complexes could be identified, we modeled the structures with reasonable accuracy by straightforward homology modeling. If only partial templates were available, it was nevertheless possible to predict the interaction interfaces correctly or to generate acceptable models for protein complexes by combining template-based modeling with docking. If no templates were available, we used rigid-body docking with limited success. However, in some free docking models, despite the incorrect subunit orientation and missed interface contacts, the approximate location of protein binding sites was identified correctly. Apparently, our overall performance in docking was limited by the quality of monomer models and by the imperfection of scoring methods. The impact of human intervention on our results in modeling of protein complexes was significant indicating the need for improvements of automatic methods.     

Extracellular superoxide dismutase protects cardiovascular syndecan-1 from oxidative shedding

The extracellular matrix is a complex system that regulates cell function within a tissue. The antioxidant enzyme extracellular superoxide dismutase (EC-SOD) is bound to the matrix, and previous studies show that a lack of EC-SOD results in increased cardiac injury, fibrosis, and loss of cardiac function. This study tests the hypothesis that EC-SOD protects against cardiac fibrosis mechanistically by limiting oxidative stress and oxidant-induced shedding of syndecan-1 in the extracellular matrix. Wild-type and EC-SOD null mice were treated with a single dose of doxorubicin, 15 mg/kg, and evaluated on day 15. Serum and left-ventricle tissue were collected for biochemical assays, including Western blot, mRNA expression, and immunohistochemical staining for syndecan-1. The loss of EC-SOD and doxorubicin-induced oxidative injury led to increases in shed syndecan-1 in the serum, which originates from the endothelium of the vasculature. The shed syndecan-1 ectodomain induces proliferation of primary mouse cardiac fibroblasts. This study suggests that one mechanism by which EC-SOD protects the heart against cardiac fibrosis is the prevention of oxidative shedding of cardiovascular syndecan-1 and its subsequent induction of fibroblast proliferation. This study provides potential new targets for understanding and altering fibrosis progression in the heart.     

Taxonomy and distribution of Poa carpatica in the Western Carpathians

We examined the taxonomic status and distribution of Poa populations from supramontane and subalpine belt of the central Western Carpathians, so far classified as P. nemoralis subsp. carpatica and P. nemoralis subsp. montana. Significant morphological differences from P. nemoralis s. str. as well as combination of shared vs distinct characters allow us to attribute the populations under study to the species P. carpatica (V. Jirásek) Chopyk with two subspecies: P. carpatica subsp. carpatica a P. carpatica subsp. supramontana subsp. nova.     

Syntaxonomy and ecology of plant communities of the Carici rupestris-Kobresietea bellardii in the western carpathians

We present a syntaxonomic account of the communities of the alliances of Oxytropido-Elynion Br.-Bl. 1949 and Festucion versicoloris Krajina 1933 from Western Carpathians. Both alliances comprise naked-rush, cushion form and dwarf-shrub heath communities typical of wind-exposed habitats occurring at the highest altitudes of the Tatra Mts. They represent a relic vegetation of the cold stages of the Pleistocene (probably Late Glacial Maximum) and they can be classified within the class of Carici rupestris-Kobresietea bellardii Ohba 1974. A set of relevés was subject to numerical-classification analysis. Floristics and ecology of the communities were characterised and the relationships to similar syntaxa were discussed. The Oxytropido-Elynion is restricted to the extreme ridge positions in the highest altitudes of the Belianske Tatry Mts. Five associations were distinguished, such as the Pyrolo carpaticae-Salicetum reticulatae, the Festuco versicoloris-Oreochloetum distichae, the Festucetum versicoloris, the Oxytropido carpaticae-Elynetum myosuroides and the Drabo siliquosae-Festucetum versicoloris. The Festucion versicoloris is limited to the mylonite zone of the alpine and subnival belt of the Vysoké Tatry and Západné Tatry Mts (and found as rare in the Nízke Tatry Mts). The stands of these communities prefer terraces of steep rocky faces and cliffs and stabilised small-grained screes below the cliffs. Within this alliance, three associations were described, including the Agrostio alpinae-Festucetum versicoloris, the Silenetum acaulis and the Salicetum kitaibelianae.     

Discriminating physiological from non-physiological interfaces in structures of protein complexes: A community-wide study

Reliably scoring and ranking candidate models of protein complexes and assigning their oligomeric state from the structure of the crystal lattice represent outstanding challenges. A community-wide effort was launched to tackle these challenges. The latest resources on protein complexes and interfaces were exploited to derive a benchmark dataset consisting of 1677 homodimer protein crystal structures, including a balanced mix of physiological and non-physiological complexes. The non-physiological complexes in the benchmark were selected to bury a similar or larger interface area than their physiological counterparts, making it more difficult for scoring functions to differentiate between them. Next, 252 functions for scoring protein-protein interfaces previously developed by 13 groups were collected and evaluated for their ability to discriminate between physiological and non-physiological complexes. A simple consensus score generated using the best performing score of each of the 13 groups, and a cross-validated Random Forest (RF) classifier were created. Both approaches showed excellent performance, with an area under the Receiver Operating Characteristic (ROC) curve of 0.93 and 0.94, respectively, outperforming individual scores developed by different groups. Additionally, AlphaFold2 engines recalled the physiological dimers with significantly higher accuracy than the non-physiological set, lending support to the reliability of our benchmark dataset annotations. Optimizing the combined power of interface scoring functions and evaluating it on challenging benchmark datasets appears to be a promising strategy.     

CAD‐score: A new contact area difference‐based function for evaluation of protein structural models

Evaluation of protein models against the native structure is essential for the development and benchmarking of protein structure prediction methods. Although a number of evaluation scores have been proposed to date, many aspects of model assessment still lack desired robustness. In this study we present CAD‐score, a new evaluation function quantifying differences between physical contacts in a model and the reference structure. The new score uses the concept of residue–residue contact area difference (CAD) introduced by Abagyan and Totrov (J Mol Biol 1997; 268:678–685). Contact areas, the underlying basis of the score, are derived using the Voronoi tessellation of protein structure. The newly introduced CAD‐score is a continuous function, confined within fixed limits, free of any arbitrary thresholds or parameters. The built‐in logic for treatment of missing residues allows consistent ranking of models of any degree of completeness. We tested CAD‐score on a large set of diverse models and compared it to GDT‐TS, a widely accepted measure of model accuracy. Similarly to GDT‐TS, CAD‐score showed a robust performance on single‐domain proteins, but displayed a stronger preference for physically more realistic models. Unlike GDT‐TS, the new score revealed a balanced assessment of domain rearrangement, removing the necessity for different treatment of single‐domain, multi‐domain, and multi‐subunit structures. Moreover, CAD‐score makes it possible to assess the accuracy of inter‐domain or inter‐subunit interfaces directly. In addition, the approach offers an alternative to the superposition‐based model clustering. The CAD‐score implementation is available both as a web server and a standalone software package at http://www.ibt.lt/bioinformatics/cad‐score/ . Proteins 2013. © 2012 Wiley Periodicals, Inc.