Better probes for the proteome Proteomics is the in-depth examination of protein behaviour. To advance research in this area, more sophisticated probes, binders, are needed to study health and disease. Fundamental Research Health © Promotive, Shutterstock Binders include antibody fragments and engineered scaffolds or aptamers (peptide molecules used to bind to a specific target molecule). Relevant applications for binders include microarrays for sorting and analysing information captured from analysis, multidimensional fluorescence imaging to study biological functioning, and proximity ligation, for observation of protein-protein interactions. The EU-funded AFFINITYPROTEOME (Advanced affinity tools and technologies for high throughput studies of the human proteome) project has developed recombinant methods for generating binders and enhancing applications for analysis of human proteome targets. Optimisation was achieved using high-throughput binder production and better binder-based application technologies for automation, cost and quality. AFFINITYPROTEOME work concentrated on developing a pipeline to define and produce targets, select binders and establish methods for their characterisation and adaptation to application systems. The researchers then honed in on specific technical applications, which were used in investigations of protein interactions in fixed and living cells. Researchers analysed MAP kinase and TGF-ß signal transduction pathways including receptors, scaffolds and transcription factors. Implicated in diseases such as cancer, high-quality binding reagents for these proteins are particularly needed for relevant research and drug development. Designed ankyrin repeat proteins (DARPins) are an alternative to antibodies for target binding in drug discovery and development. The team generated very high affinity DARPins and research results emphasise the great potential of DARPins as a novel class of highly specific intracellular inhibitors of distinct enzymes. As possible therapeutic lead molecules, DARPins are able to block specific cell signalling actions in living cells. A number of commercial opportunities were taken up and developed by the consortium SMEs. These include improved reagents for sale, technical advances and product accessories. The coordinator founded a new company specialising in protein arrays. 37 original papers and reviews have been published and several others are in preparation. There were more than 80 presentations at conferences and workshops. Helping both research and dissemination, partners worked closely with similar key initiatives in the United States. Binders generated in the AFFINITYPROTEOME study have applications in a range of diseases including infectious and autoimmune diseases, transplantation, wound healing and various types of cancer. Keywords Proteome, binder, AFFINITYPROTEOME, cancer, DARPins
