The ERM (ezrin, radixin,
and moesin) family of proteins and the
related protein merlin participate in scaffolding and signaling events
at the cell cortex. The proteins share an N-terminal FERM [band four-point-one
(4.1) ERM] domain composed of three subdomains (F1, F2, and F3) with
binding sites for short linear peptide motifs. By screening the FERM
domains of the ERMs and merlin against a phage library that displays
peptides representing the intrinsically disordered regions of the
human proteome, we identified a large number of novel ligands. We
determined the affinities for the ERM and merlin FERM domains interacting
with 18 peptides and validated interactions with full-length proteins
through pull-down experiments. The majority of the peptides contained
an apparent Yx[FILV] motif; others show alternative motifs. We defined
distinct binding sites for two types of similar but distinct binding
motifs (YxV and FYDF) using a combination of Rosetta FlexPepDock computational
peptide docking protocols and mutational analysis. We provide a detailed
molecular understanding of how the two types of peptides with distinct
motifs bind to different sites on the moesin FERM phosphotyrosine
binding-like subdomain and uncover interdependencies between the different
types of ligands. The study expands the motif-based interactomes of
the ERMs and merlin and suggests that the FERM domain acts as a switchable
interaction hub.