Molecular Dynamics Analysis of 4E-BP2 Protein Fold Stabilization Induced by Phosphorylation

Protein phosphorylation can affect the interaction with partner proteins but can also induce conformational transitions. In case of the eukaryotic translation initiation factor 4E-binding protein 2 (4E-BP2) threonine (Thr) phosphorylation at two turn motifs results in transition from a disordered to a folded structure. In order to elucidate the stabilizing mechanism we employed comparative molecular dynamics (MD) free energy simulations on the turn motifs indicating that Thr-phosphorylation favors a folded whereas dephosphorylation or substitution by Glu residues destabilizes the turn structure. In multiple unrestrained MD simulations at elevated temperature of the 4E-BP2 domain only the double phosphorylated variant remained close to the folded structure in agreement with experiment. Three surface Arg residues were identified as additional key elements for the tertiary structure stabilization of the whole phosphorylated domain. In addition to the local turn structure double phosphorylation also leads to an overall electrostatic stabilization of the folded form compared to wild type and other investigated variants of 4E-BP2. The principles of phosphorylation mediated fold stabilization identified in the present study may also be helpful for identifying other structural motifs that can be affected by phosphorylation or provide a route to design such motifs.