Study of PKA binding sites in cAMP-signaling pathway using structural protein-protein interaction networks

Backgroud: Protein-protein interaction, plays a key role in signal transduction in signaling pathways. Different approaches are used for prediction of these interactions including experimental and computational approaches. In conventional node-edge protein-protein interaction networks, we can only see which proteins interact but ‘structural networks’ show us how these proteins interact which can give us so much information about the network. Structural networks help us understand the molecular basis of cellular functions and regulatory mechanisms in signaling pathways. In this study, we aimed to construct a structural network for a part of cAMP signaling pathway which has PKA (cAMP-dependent protein kinase catalytic subunit alpha) as the hub. A part of cAMP signaling pathway was selected from kegg database and interactions of PKA as hub protein with some of its partners were achieved using Hex8.00 software. The interfaces of the resulted complexes were predicted by KFC2 server. Hex8.00, as a docking software, gave us the complexes from the interaction of PKA with 15 proteins of its partners. For each complex, the KFC2 server gave us the amino acid composition of the interfaces. Using this amino acid composition, we draw a structural network which shows the binding sites on PKA surface. We have constructed a structural network for cAMP signaling pathway which shows how PKA interacts with its partners. This network can be used for understanding the mechanisms of signal transduction and also for drug design purposes.