A protein affinity pipeline

The analysis of the human proteome, collectively known as proteomics, is of major significance in both basic and medical research. Proteomics applications continue to expand and in the near future would be an integral process in the biotechnology and pharmaceutical industries.

To realise the potential of proteomics, the development and availability of protein reagents and especially specific binding molecules is critical. A high-throughput production pipeline of binders is required to enable the investigation of the expression, modification and interaction of all genome-encoded proteins.

The scope of the EU-funded AFFINOMICS (Protein binders for characterisation of human proteome function: generation, validation, application) project was to actualise a high-throughput, automated pipeline for the production of proteomics binders. The AFFINOMICS consortium encompassed 19 leading European centres and one industrial partner and the main goal was to study signal transduction pathways and cancer-related proteins.

Apart from standard monoclonal and polyclonal antibodies, the consortium made significant technological improvements towards the production of recombinant binder molecules. In this context, they used molecular selection systems such as phage and ribosome display. To achieve the necessary properties for diverse applications, protein binders had to be carefully designed based on the structure of fully folded proteins, individual domains or specific modifications.

Overall, AFFINOMICS generated and characterised binders for over 1 400 kinases, phosphatases, proteins mutated in cancer and plasma biomarkers. Information on all the protein targets and binders produced is freely available here.

Implementation of the AFFINOMICS binder-based technologies and tools towards the proteomic analysis of signal transduction provided novel insight. This led to the delineation of how the signalling complexes assemble and integrate into larger networks and also revealed how they become dysfunctional. Collectively, the toolbox of AFFINOMICS binders offers unprecedented possibilities not only for basic research and healthcare but also for drug development.