Great interactions: How binding incorrect partners can teach us about protein recognition and function

Protein–protein interactions play a key part in most biological processes and understanding their mechanism is a fundamental problem leading to numerous practical applications. The prediction of protein binding sites in particular is of paramount importance since proteins now represent a major class of therapeutic targets. Amongst others methods, docking simulations between two proteins known to interact can be a useful tool for the prediction of likely binding patches on a protein surface. From the analysis of the protein interfaces generated by a massive cross‐docking experiment using the 168 proteins of the Docking Benchmark 2.0, where all possible protein pairs, and not only experimental ones, have been docked together, we show that it is also possible to predict a protein's binding residues without having any prior knowledge regarding its potential interaction partners. Evaluating the performance of cross‐docking predictions using the area under the specificity‐sensitivity ROC curve (AUC) leads to an AUC value of 0.77 for the complete benchmark (compared to the 0.5 AUC value obtained for random predictions). Furthermore, a new clustering analysis performed on the binding patches that are scattered on the protein surface show that their distribution and growth will depend on the protein's functional group. Finally, in several cases, the binding‐site predictions resulting from the cross‐docking simulations will lead to the identification of an alternate interface, which corresponds to the interaction with a biomolecular partner that is not included in the original benchmark. Proteins 2016; 84:1408–1421. © 2016 The Authors Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.     

Discriminating healthy from tumor and necrosis tissue in rat brain tissue samples by Raman spectral imaging

The purpose of this study was to investigate molecular changes associated with glioma tissues by Raman microspectroscopy in order to develop its use in clinical practice. Spectroscopic markers obtained from C6 glioma tissues were compared to conventional histological and histochemical techniques. Cholesterol and phospholipid contents were highest in corpus callosum and decreased gradually towards the cortex surface as well as in the tumor. Two different necrotic areas have been identified: a fully necrotic zone characterized by the presence of plasma proteins and a peri-necrotic area with a high lipid content. This result was confirmed by Nile Red staining. Additionally, one structure was detected in the periphery of the tumor. Invisible with histopathological hematoxylin and eosin staining, it was revealed by immunohistochemical Ki-67 and MT1-MMP staining used to visualize the proliferative and invasive activities of glioma, respectively. Hierarchical cluster analysis on the only cluster averaged spectra showed a clear distinction between normal, tumoral, necrotic and edematous tissues. Raman microspectroscopy can discriminate between healthy and tumoral brain tissue and yield spectroscopic markers associated with the proliferative and invasive properties of glioblastoma. Development of in vivo Raman spectroscopy could thus accurately define tumor margins, identify tumor remnants, and help in the development of novel therapies for glioblastoma.     

Genotype by environment interactions in relation to growth traits in slow growing chickens

Since feed conversion ratio (FCR) is higher in slow-growing "Label Rouge" chickens than in broiler chickens, it is important to work on its improvement in this breed. However, this involves rearing animals in cages (C), an environment very different from that used for selection (in floor pens, S) and production (outdoor, E). The aim of this study was to evaluate the importance of genotype by environment (G × E) interactions between S, C, and E environments, to find the best way to select for FCR, using 2002 related animals. Growth curve parameters were estimated and body composition measured. Individual feed conversion ratios (FCR) were recorded between 8 and 10 weeks in C. The presence of G × E interactions was assessed by the genetic correlations between the same trait recorded in different environments. Moderate but significant G × E interactions were detected for carcass traits, a significant one was observed between E and S or C for growth curve parameters but none between C and S. If G × E interactions are set aside, i.e. selecting on traits recorded in C, abdominal fatness is the best indirect selection criterion for FCR but if they are taken in account then leg yield or growth curve parameters in S and growth curve parameters in E are better.     

Developmentally regulated expression of a 78 kDa erythroblast membrane glycoprotein immunologically related to the platelet thrombospondin receptor.

We have previously described a monoclonal antibody (FA6-152), obtained by immunizing mice with fetal human erythrocytes [Edelman, Vinci, Villeval, Vainchenker, Henri, Miglierina, Rouger, Reviron, Breton-Gorius, Sureau & Edelman (1986) Blood 67, 56-63]. The antibody labelled fetal, but not adult, erythrocytes and bound to both fetal and adult platelets and monocytes. In the present study we have characterized the antigen recognized by FA6-152 on human platelets and on cells of the erythroid lineage at different stages of maturation. FA6-152 precipitated a chymotrypsin-resistant 88 kDa sialoglycoprotein from both iodinated and periodate/NaB3H4-surface-labelled platelets which corresponds to glycoprotein IV, the platelet thrombospondin (TSP) receptor. After neuraminidase treatment, a shift of the apparent molecular mass from 88 kDa to 85 kDa was observed. Scatchard analysis revealed that 125I-FA6-152 bound saturably with high affinity to a single class of platelet binding sites (Kd 6.4 +/- 0.6 nM). The number of FA6-152 IgG molecules bound per platelet was 25,400 +/- 8,800 (n = 4) and did not change upon thrombin activation of platelets. At low doses of alpha-thrombin (0.025 unit), FA6-152 inhibited platelet aggregation as well as endogenous TSP binding to the platelet surface. Immunofluorescence labelling of bone-marrow cells and of cultures in vitro of burst-forming units-erythroid (BFU-E) and colony-forming units-erythroid (CFU-E) revealed that that FA6-152 antigen is a very early marker of erythroid differentiation and that its expression declines during maturation. Immunochemical identification of the FA6-152 antigen on fetal erythroblasts and fetal mature erythrocytes revealed a 78 kDa glycoprotein migrating just in front of the glycophorin A dimer. The antigen, which was absent from adult mature erythrocytes, was also detected in human erythroleukaemic (HEL) cells where FA6-152 precipitated two bands of molecular mass 85 and 88 kDa. Our data establish the existence of a previously unidentified 78 kDa erythroblast cell-surface glycoprotein whose expression is developmentally regulated during erythroid differentiation and which is immunologically related to the 88 kDa platelet TSP receptor.     

Elevated Ras/protein kinase A activity in Saccharomyces cerevisiae reduces proliferation rate and lifespan by two different reactive oxygen species-dependent routes

Cells with overactive RAS /protein kinase A (PKA) signaling, such as RAS2^Val19 cells, exhibit reduced proliferation rates and accelerated replicative senescence. We show here that the extended generation time of RAS2^Val19 cells is the result of abrogated ATP/ADP carrier activity of the mitochondria. Both PKA-dependent and independent routes are responsible for inhibiting ATP/ADP exchange in the RAS -overactive cells. The reduced carrier activity is due, at least in part, to elevated levels of reactive oxygen species (ROS), which also cause a proteolysis-dependent fragmentation of the Aac2p carrier both in vivo and on isolated mitochondria. Attenuated carrier activity is suppressed by overproducing the superoxide dismutase, Sod1p, and this enhances both the proliferation rate and the replicative longevity of RAS2^Val19 cells. In contrast, overproducing functional Aac2p restored proliferation but not longevity of RAS2^Val19 cells. Thus, Ras signaling affects proliferation rate and replicative lifespan by two different, ROS-dependent, routes. While the reduction in generation time is linked to the inactivation, specifically, of the mitochondrial nucleotide carrier, longevity is affected by other, and hitherto unknown, target(s) of ROS attack.