Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?

The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures

Homogeneously derived transit timings for 17 exoplanets and reassessed TTV trends for WASP-12 and WASP-4

We homogeneously analyse ∼3.2 × 105 photometric measurements for ∼1100 transit lightcurves belonging to 17 exoplanet hosts. The photometric data cover 16 years 2004–2019 and include amateur and professional observations. Old archival lightcurves were reprocessed using up-to-date exoplanetary parameters and empirically debiased limb-darkening models. We also derive self-consistent transit and radial-velocity fits for 13 targets. We confirm the nonlinear TTV trend in the WASP-12 data at a high significance, and with a consistent magnitude. However, Doppler data reveal hints of a radial acceleration about ( − 7.5 ± 2.2) m/s/yr, indicating the presence of unseen distant companions, and suggesting that roughly 10 per cent of the observed TTV was induced via the light-travel (or Roemer) effect. For WASP-4, a similar TTV trend suspected after the recent TESS observations appears controversial and model-dependent. It is not supported by our homogeneus TTV sample, including 10 ground-based EXPANSION lightcurves obtained in 2018 simultaneously with TESS. Even if the TTV trend itself does exist in WASP-4, its magnitude and tidal nature are uncertain. Doppler data cannot entirely rule out the Roemer effect induced by possible distant companions

Transit timing analysis of the exoplanet TrES-5 b. Possible existence of the exoplanet TrES-5 c

peer reviewedIn this work, we present transit timing variations detected for the exoplanet TrES-5b. To obtain the necessary amount of photometric data for this exoplanet, we have organized an international campaign to search for exoplanets based on the transit-timing variation (TTV) method and as a result of this we collected 30 new light curves, 15 light curves from the Exoplanet Transit Database (ETD) and 8 light curves from the literature for the timing analysis of the exoplanet TrES-5b. We have detected timing variations with a semi-amplitude of A≈ 0.0016 d and a period of P≈ 99 d. We carried out the N-body modelling based on the three-body problem. The detected perturbation of TrES-5b may be caused by a second exoplanet in the TrES-5 system. We have calculated the possible mass and resonance of the object: M ≈ 0.24MJup at a 1:2 Resonance. © 2018 The Author(s). Published by Oxford University Press on behalf of the Royal Astronomical Society.RSF: 14-50-0004

Predicting the protein-protein interactions using primary structures with predicted protein surface

<p>Abstract</p> <p>Background</p> <p>Many biological functions involve various protein-protein interactions (PPIs). Elucidating such interactions is crucial for understanding general principles of cellular systems. Previous studies have shown the potential of predicting PPIs based on only sequence information. Compared to approaches that require other auxiliary information, these sequence-based approaches can be applied to a broader range of applications.</p> <p>Results</p> <p>This study presents a novel sequence-based method based on the assumption that protein-protein interactions are more related to amino acids at the surface than those at the core. The present method considers surface information and maintains the advantage of relying on only sequence data by including an accessible surface area (ASA) predictor recently proposed by the authors. This study also reports the experiments conducted to evaluate a) the performance of PPI prediction achieved by including the predicted surface and b) the quality of the predicted surface in comparison with the surface obtained from structures. The experimental results show that surface information helps to predict interacting protein pairs. Furthermore, the prediction performance achieved by using the surface estimated with the ASA predictor is close to that using the surface obtained from protein structures.</p> <p>Conclusion</p> <p>This work presents a sequence-based method that takes into account surface information for predicting PPIs. The proposed procedure of surface identification improves the prediction performance with an <it>F-measure </it>of 5.1%. The extracted surfaces are also valuable in other biomedical applications that require similar information.</p

Simplified Method to Predict Mutual Interactions of Human Transcription Factors Based on Their Primary Structure

Background: Physical interactions between transcription factors (TFs) are necessary for forming regulatory protein complexes and thus play a crucial role in gene regulation. Currently, knowledge about the mechanisms of these TF interactions is incomplete and the number of known TF interactions is limited. Computational prediction of such interactions can help identify potential new TF interactions as well as contribute to better understanding the complex machinery involved in gene regulation. Methodology: We propose here such a method for the prediction of TF interactions. The method uses only the primary sequence information of the interacting TFs, resulting in a much greater simplicity of the prediction algorithm. Through an advanced feature selection process, we determined a subset of 97 model features that constitute the optimized model in the subset we considered. The model, based on quadratic discriminant analysis, achieves a prediction accuracy of 85.39 % on a blind set of interactions. This result is achieved despite the selection for the negative data set of only those TF from the same type of proteins, i.e. TFs that function in the same cellular compartment (nucleus) and in the same type of molecular process (transcription initiation). Such selection poses significant challenges for developing models with high specificity, but at the same time better reflects real-world problems. Conclusions: The performance of our predictor compares well to those of much more complex approaches for predicting TF and general protein-protein interactions, particularly when taking the reduced complexity of model utilisation into account

Beauty Is in the Eye of the Beholder: Proteins Can Recognize Binding Sites of Homologous Proteins in More than One Way

Understanding the mechanisms of protein–protein interaction is a fundamental problem with many practical applications. The fact that different proteins can bind similar partners suggests that convergently evolved binding interfaces are reused in different complexes. A set of protein complexes composed of non-homologous domains interacting with homologous partners at equivalent binding sites was collected in 2006, offering an opportunity to investigate this point. We considered 433 pairs of protein–protein complexes from the ABAC database (AB and AC binary protein complexes sharing a homologous partner A) and analyzed the extent of physico-chemical similarity at the atomic and residue level at the protein–protein interface. Homologous partners of the complexes were superimposed using Multiprot, and similar atoms at the interface were quantified using a five class grouping scheme and a distance cut-off. We found that the number of interfacial atoms with similar properties is systematically lower in the non-homologous proteins than in the homologous ones. We assessed the significance of the similarity by bootstrapping the atomic properties at the interfaces. We found that the similarity of binding sites is very significant between homologous proteins, as expected, but generally insignificant between the non-homologous proteins that bind to homologous partners. Furthermore, evolutionarily conserved residues are not colocalized within the binding sites of non-homologous proteins. We could only identify a limited number of cases of structural mimicry at the interface, suggesting that this property is less generic than previously thought. Our results support the hypothesis that different proteins can interact with similar partners using alternate strategies, but do not support convergent evolution

Extending Levelt's Propositions to perceptual multistability involving interocular grouping.

Levelt's Propositions are central to understanding a wide range of multistable perceptual phenomena, but it is unclear whether they extend to perceptual multistability involving interocular grouping. We presented split-grating stimuli with complementary halves of the same color (either red or green) to human subjects. The subjects reported four percepts in alternation: the two stimuli presented to each eye (half red and half green), as well as the two single color (all red or all green), interocularly grouped percepts. Increasing color saturation lead to increased reports of the single color percept in most subjects, indicating increased predominance of grouped percepts (Levelt's Proposition I). This increase in predominance was due to a decrease in the average dominance duration of single-eye percepts, with grouped percept dominance largely unaffected. This agrees with a generalization of Levelt's Proposition II, as the average dominance duration of the stronger (in this case single-eye) percept was primarily affected by changes in stimulus strength. Moreover, in agreement with Levelt's Proposition III the alternation rate between percepts increased as the difference in the strength of the percepts decreased

The Physical Characterization of the Potentially Hazardous Asteroid 2004 Bl86: A Fragment of a Differentiated Asteroid

The physical characterization of potentially hazardous asteroids (PHAs) is important for impact hazard assessment and evaluating mitigation options. Close flybys of PHAs provide an opportunity to study their surface photometric and spectral properties that enable identification of their source regions in the main asteroid belt. We observed PHA (357439) 2004 BL86 during a close flyby of the Earth at a distance of 1.2 million km (0.0080 AU) on January 26, 2015, with an array of ground-based telescopes to constrain its photometric and spectral properties. Lightcurve observations showed that the asteroid was a binary and subsequent radar observations confirmed the binary nature and gave a primary diameter of 300 meters and a secondary diameter of 50-100 meters. Our photometric observations were used to derive the phase curve of 2004 BL86 in the V-band. Two different photometric functions were fitted to this phase curve, the IAU H-G model (Bowell et al. 1989) and the Shevchenko model (Shevchenko 1996). From the fit of the H-G function we obtained an absolute magnitude H=19.51+/-0.02 and a slope parameter G=0.34+/-0.02. The Shevchenko function yielded an absolute magnitude of H=19.03+/-0.07 and a phase coefficient b=0.0225+/-0.0006. The phase coefficient was used to calculate the geometric albedo (Ag) using the relationship found by Belskaya and Schevchenko (2000), obtaining a value of Ag=40+/-8% in the V-band. With the geometric albedo and the absolute magnitudes derived from the H-G and the Shevchenko functions we calculated the diameter (D) of 2004 BL86, obtaining D=263+/-26, and D=328+/-35 meters, respectively. 2004 BL86 spectral band parameters and pyroxene chemistry are consistent with non-cumulate eucrite meteorites.Comment: 27 pages, 8 figures, 4 tables. Accepted for publication in AP