Technologies for Proteome-Wide Discovery of Extracellular Host-Pathogen Interactions

Martinez-Martin, Nadia

The plasma membrane constitutes a critical biological interface between the cytosol and the extracellular environment of the cell, and consequently membrane-tethered proteins and secreted molecules (collectively termed extracellular proteins) are essential regulators of cellular communication. From high affinity cytokine-receptor interactions to low affinity cell-cell adhesion contacts, extracellular protein-protein interactions (ePPIs) are key for information processing and coordination of virtually all processes in a living organism. Furthermore, given their fundamental functions and their accessibility to systemically delivered drugs, extracellular proteins are particularly suitable targets for therapeutic intervention. In fact, despite these proteins being encoded by approximately one-fourth of the human genes, at least two-thirds of the existing drugs target either secreted or membrane-bound proteins [1] . Thus, the elucidation of the ePPI networks on a global scale has become crucial for the biomedical research. However, in spite of their relevance and abundance, ePPIs are remarkably underrepresented in available large-scale datasets. This discrepancy is due to the low sensitivity and limited compatibility of current high throughput technologies to detect extracellular interactions because of the unusual biochemical nature of the membrane proteins and the intractability of their binding partners [2] [3] [4] . In particular, transmembrane domain-containing proteins are amphipathic, making it difficult to solubilize them in their native conformation, and often contain posttranslational modifications such as glycans and disulfide bonds, which are not properly added in common heterologous expression systems [5] . In addition, interactions between cell surface proteins are often characterized by fast dissociation rates and therefore weak binding affinities, and in consequence well-established PPI methods such as yeast-two-hybrid or affinity purification-mass spectrometry (AP/MS) largely fail to detect these interactions. Over the last decade, several innovative technologies have been developed to overcome the aforementioned technical challenges and allow for sensitive 2 Journal of Immunology Research detection of ePPIs [2, [6] [7] [8] [9] [10] . Nevertheless, the mapping of ePPIs remains a major challenge in biology.