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

TL;DR

This study explores how a modification called guanidinylation affects the structure and function of the YB-1 protein and its interaction with the Notch-3 receptor.

Contribution

The study reveals molecular mechanisms of YB-1 guanidinylation and identifies a new high-affinity binding site on the Notch-3 receptor.

Findings

Guanidinylation of YB-1 reduces β-sheet formation and increases solvent exposure of its cold shock domain.

YB-1 and its guanidinylated form bind similarly to Notch-3 receptor domains.

YB-1 displaces the canonical ligand Jagged by binding to a new site on Notch-3.

Abstract

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.

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