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Receptor tyrosine kinases (RTKs) and protein phosphatases comprise protein families that play crucial roles in cell signaling. We used two protein-protein interaction (PPI) approaches, the Membrane Yeast Two-Hybrid (MYTH) and the Mammalian Membrane Two-Hybrid (MaMTH), to map the PPIs between human RTKs and phosphatases. The resulting RTK-phosphatase interactome reveals a considerable number of previously unidentified interactions and suggests specific roles for different phosphatase families. Additionally, the differential PPIs of some protein tyrosine phosphatases (PTPs) and their mutants suggest diverse mechanisms of these PTPs in the regulation of RTK signaling. We further found that PTPRH and PTPRB directly dephosphorylate EGFR and repress its downstream signaling. By contrast, PTPRA plays a dual role in EGFR signaling: besides facilitating EGFR dephosphorylation, it enhances downstream ERK signaling by activating SRC. This comprehensive RTK-phosphatase interactome study provides a broad and deep view of RTK signaling.

Our analysis examines the conservation of multiprotein complexes among metazoa through use of high resolution biochemical fractionation and precision mass spectrometry applied to soluble cell extracts from 5 representative model organisms Caenorhabditis elegans, Drosophila melanogaster, Mus musculus, Strongylocentrotus purpuratus, and Homo sapiens. The interaction network obtained from the data was validated globally in 4 distant species (Xenopus laevis, Nematostella vectensis, Dictyostelium discoideum, Saccharomyces cerevisiae) and locally by targeted affinity-purification experiments. Here we provide details of our massive set of supporting biochemical fractionation data available via ProteomeXchange (http://www.ebi.ac.uk/pride/archive/projects/PXD002319-http://www.ebi.ac.uk/pride/archive/projects/PXD002328), PPIs via BioGRID (185267); and interaction network projections via (http://metazoa.med.utoronto.ca) made fully accessible to allow further exploration. The datasets here are related to the research article on metazoan macromolecular complexes in Nature [1]. Keywords: Proteomics, Metazoa, Protein complexes, Biochemical, Fractionation

Connectivity webs mediate the unique biology of the mammalian brain. Yet, while cell circuit maps are increasingly available, knowledge of their underlying molecular networks remains limited. Here, we applied multi-dimensional biochemical fractionation with mass spectrometry and machine learning to survey endogenous macromolecules across the adult mouse brain. We defined a global "interactome" comprising over one thousand multi-protein complexes. These include hundreds of brain-selective assemblies that have distinct physical and functional attributes, show regional and cell-type specificity, and have links to core neurological processes and disorders. Using reciprocal pull-downs and a transgenic model, we validated a putative 28-member RNA-binding protein complex associated with amyotrophic lateral sclerosis, suggesting a coordinated function in alternative splicing in disease progression. This brain interaction map (BraInMap) resource facilitates mechanistic exploration of the unique molecular machinery driving core cellular processes of the central nervous system. It is publicly available and can be explored here https://www.bu.edu/dbin/cnsb/mousebrain/.

Connectivity webs mediate the unique biology of the mammalian brain. Yet while cell circuit maps are increasingly available, knowledge of the underlying molecular networks remains limited. Here, we applied multi-dimensional biochemical fractionation with precision mass spectrometry and machine learning to survey endogenous macromolecules in adult mouse brain. We defined a global ‘interactome’ of multi-protein complexes, most never reported before. These brain-selective assemblies have distinct physical and functional attributes and show regional- and cell-type specificity. A striking number are also linked to neurological disorders and disease variants with broad pathophysiological relevance. Using reciprocal pulldowns and a transgenic model, we validated a putative 15-member RNA-binding protein complex associated with amyotrophic lateral sclerosis, establishing regulatory functions in alternative splicing and disease progression. This Brain Interaction Map – or BraInMap – resource facilitates mechanistic exploration of the molecular machinery driving core processes and diseases of the central nervous system.

SummaryThe prevalence of autism spectrum disorders (ASDs) is rapidly growing, yet its molecular basis is poorly understood. Here, we sought to gain a systems-level understanding of ASD candidate genes by mapping them onto ubiquitous human protein complexes and characterizing the resulting complexes. These studies revealed the role of histone deacetylases (HDAC1/2) in regulating the expression of ASD orthologs in the embryonic mouse brain. Next, proteome-wide screens for subunits co-complexed with HDAC1 and six other key ASD proteins in human neuronal cells revealed a protein interaction network that displayed preferential expression in fetal brain development, exhibited increased deleterious mutations in ASD cases, and encompassed genes strongly regulated by FMRP and MECP2, mutations that are causal for fragile X and Rett syndromes, respectively. Overall, our study reveals molecular components in ASD, suggests a shared mechanism between the syndromic and idiopathic forms of ASDs, and provides a groundwork for analyzing complex human diseases.

The paper presents results of experimental investigation of concrete made with recycled concrete aggregate, low cement content and high content of different mineral supplements. Such concretes belong to “green” or “eco” concretes, since they have less impact on the environment, help in solving the problem of construction and industrial waste disposal, and contribute to the conservation of natural resources. For green recycled aggregate concrete (GRAC) production fine river aggregate and coarse recycled aggregate were used and 50% of cement by weight was replaced by a variety of inert, pozzolanic, and highly reactive mineral admixtures: milled limestone, fly ash, silica fume and metakaolin. Basic properties of ten different concrete mixtures were tested, compared and classified in terms of possible applications. Test results showed that the optimal combination of different mineral admixtures can reduce the basic disadvantage of concrete with high content of mineral supplements – the relatively low strength in the period up to 28-day age, which allows certain structural applications of this type of “green” concrete.