MD Predicted Structure of Full-length Src Kinase and Its Key Phosphorylated States

Src kinase is one of the key regulators of cellular metabolism dysregulated in numerous diseases, including cancer and neurodegenerative diseases, particularly, Alzheimer’s disease. Despite its therapeutic importance, its full-length structure has never been obtained before, as it contains an intrinsically disordered regulatory region SH4UD. The SH4UD is crucial for Src activation, functional dimerization and regulation by other kinases. In this study, we used REHT MD approach to obtain the conformational ensemble of full-length Src kinase in its non-phosphorylated state and in presence of its two key regulatory phosphorylations: pY419 and pY530. The representative structures and simulation trajectories of non-phosphorylated, pY419 and pY530 Src are available at Zenodo, DOI: 10.5281/zenodo.13237004. We demonstrate that pY419 phosphorylation, which is associated with Src activation, enhances its motility, whereas inhibited pY530 Src preserves relatively compact conformation. This study also provides insight into how SH4UD contributes to the Src substrate binding, dimerization and autophosphorylation, highlighting the putative role of 14-RRR-16 in this process. These findings will help to develop highly specific inhibitors to Src kinase and predict its interaction interfaces with its protein partners.