Dual recognition of negative charge by pleckstrin homology (PH) domains

Pleckstrin homology (PH) domains are generally believed to act as phosphoinositide-binding modules, yet many do not exhibit strong lipid specificity and their wider ligand range remains unclear. Researchers have discovered that numerous yeast PH domains bind Nsr1p, the yeast counterpart of nucleolin, which acts as a PH domain ligand as well. This finding implies that various proteins with negatively charged regions are frequently recognized by PH domains.

The phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2)-binding PLC{delta}1 PH domain also interacts with a highly phosphorylated area of IRBIT via the same site that recognizes PtdIns(4,5)P2. To investigate the binding patterns of PH domains in mammalian sequences, the scientists employed high-throughput integrated phosphopeptide (Hi-P) screening on 38,624 mammalian sequences that contained three documented phosphoserines.

PLC{delta}1-PH domain displayed a propensity to bind both phosphorylated and unphosphorylated acidic peptides, and phosphorylation tended to reinforce existing interactions rather than impose strict specificity. Importantly, the interactions did not necessitate a fixed phosphoserine spacing. Instead, the most favorable phosphopeptides included a key phosphoserine alongside upstream acidic residues.

Structural modeling revealed that the phosphoserine resides within the customary inositol phosphate binding pocket, while the neighboring acidic residues establish delocalized electrostatic contacts.

In summary, PH domains are capable of identifying diverse patterns of protein negative charge, broadening their scope of regulatory roles beyond membrane targeting.