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.
Bibliographical noteFunding Information:
This study was funded by grants from the Swedish research council (2016-04965 to Y.I.), the Carl Trygger foundation (Y.I., CTS14:209), the Israel Science Foundation, founded by the Israel Academy of Science and Humanities (grant numbers 717/2017 and 311/2021 to O.S.F.), and the US-Israel Binational Science Foundation 2015207 (to O.S.F.). M.A. was the recipient of a PhD fellowship from the Sven and Lilly Lawski foundation. Sequencing was performed by the SNP&SEQ Technology Platform in Uppsala. The facility is part of the National Genomic Infrastructure (NGI) Sweden and Science for Life Laboratory. The SNP&SEQ Platform is also supported by the Swedish Research Council and the Knut and Alice Wallenberg Foundation. The authors acknowledge the kind support of Norman Davey and Izabella Krystkowiak related to annotation of peptides and Leandro Simonetti for managing the NGS data.
© 2023 The Authors. Published by American Chemical Society.