How phosphorylation of peptides affects their interaction with 14‐3‐3η domains

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2022-02, Vol.90 (2), p.351-362
• Main Authors: Künzel, Nicolas, Helms, Volkhard
• Format: Article
• Language: English
• Subjects: Binding; Dimers; Domains; free energy calculation; Grooves; Humans; Molecular dynamics; molecular dynamics simulation; Peptides; Peptides - chemistry; peptide–protein complex; Phosphorylation; post translational modification; Protein Binding; Protein Conformation; Protein Domains; Proteins; Residues; Threonine
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.26224

Members of the 14‐3‐3 domain family have important functions as adapter domains. Via an amphipathic groove on their protein surface they typically bind to disordered C‐terminals of other proteins. Importantly, binding partners of 14‐3‐3 domains usually contain a phosphorylated serine or threonine residue at their binding interface and possess one of three different sequence motifs. Binding of the respective unphosphorylated versions of the peptides is typically strongly disfavored. There is a wealth of structural and thermodynamic data available for the phosphorylated forms but not for the unphosphorylated forms as the binding affinities seem to be too weak to be measurable experimentally. Here, we characterized the mechanistic details that govern the preference for the binding of phosphorylated peptides to 14‐3‐3η domains by means of molecular dynamics (MD) simulations. We found that the phosphate group is ideally coordinated in the binding pocket whereas the respective unphosphorylated side‐chain counterpart is not. Thus, the binding preference results from the tight coordination of the phosphorylated residue at the center of the binding interface. Furthermore, MD simulations of 14‐3‐3η dimers showed a preference for the simultaneous binding of two phosphorylated peptides in agreement with their experimentally observed cooperativity.