Guanidinylation of the cold shock protein YB-1: Molecular basis, structural changes and Notch-3 receptor binding

Posttranslational modifications of Y-box binding protein (YB)-1 are the prerequisite for its very different protein functions. Here, we investigate the underlying molecular mechanisms of YB-1 guanidinylation and link increased serum urea levels as well as the activity of glycine amidinotransferase (GATM) with guanidinylation. Computer simulations show changes in stability and conformation of the YB-1 protein induced by these modifications. In particular, the secondary structure of the doubly guanidinylated YB-1 (YB-1-2G) shows a reduced tendency to form β-sheets, and the modified cold shock domain is more exposed to the solvent. Protein-protein docking techniques in conjunction with molecular dynamics simulations confirm the binding between YB-1 and its receptor Notch-3 at EGF domains 17-24 but show no significant differences in the binding behavior of YB-1 and YB-1-2G. This is confirmed in two different types of receptor-ligand binding assays. In addition, we demonstrate for the first time a high-affinity binding of YB-1 to another ligand binding site on the Notch-3 receptor, thereby achieving effective displacement of the canonical ligand Jagged. In conclusion, we identified molecular processes that lead to the guanidinylation of YB-1 and revealed their effects on the structure and binding to receptor Notch-3.