Short linear motif based interactions and dynamics of the ezrin, radixin, moesin and merlin FERM domains

Abstract

The ERMs (ezrin, radixin and moesin) and the closely related merlin (NF2) participate in signaling events at the cell cortex through interactions mediated by their conserved FERM domain. We systematically investigated the FERM domain mediated interactions with short linear motifs (SLiMs) by screening the FERM domains againsts a phage peptidome representing intrinsically disordered regions of the human proteome. We uncovered a diverse set of interacting partners with similar but distinct binding motifs (FYDF, xYxV, FY(D/E)L and LQE(I/L) that bind to distinct binding pockets. We validated interactions between moesin and merlin FERM domains and full-length FAM83G, HIF1A, LATS1, NOP53, PAK6, RRBP1 and ZNF622 through pull-down experiments. Using biophysical binding assays, we determined affinities of, and uncovered allosteric interdependencies between, different binding partners, suggesting that the FERM domain acts as a switchable interaction hub. Using Rosetta FlexPepDock computational peptide docking protocols, we investigated the energy landscapes of identified interactions, which provide a detailed molecular understanding of the binding of the distinct binding motifs, as well as possible allosteric interconnections. This study demonstrates how experimental and computational approaches together can unravel a complex system of protein-peptide interactions that includes a family of proteins with multiple binding sites that interact with similar but distinct binding motifs.HighlightsWe screened the human disorderome for motif-containing partners of the FERM domainsWe expand the ERM and merlin interactomes of the ERMs and merlinWe identify four distinct motif classes that bind the ERM and merlin FERM domains: FYDF, xYxV, FY(D/E)L and LQE(I/L)In-vitro and in-silico data suggest that the FYDF motif binds to the F3a site and that xYxV motif binds to the F3b siteIn-silico modelling sheds light on the underlying conformational changes responsible for ligand interdependenciesAbstract Figure

Matching protein surface structural patches for high-resolution blind peptide docking

“…4 B and D ). PFPD failed to place the peptide at the closed binding site at the rigid-body docking step, requesting an initial opening of the pocket for successful docking ( 28 ). This case demonstrates that PatchMAN is able to identify cryptic binding pockets, with its sampling approach that takes into account motifs with structural variability.…”

Analysis of NIS Plasma Membrane Interactors Discloses Key Regulation by a SRC/RAC1/PAK1/PIP5K/EZRIN Pathway with Potential Implications for Radioiodine Re-Sensitization Therapy in Thyroid Cancer

“…Although the participation of a PDZ-binding protein in NIS-EZRIN complex formation cannot be definitely excluded, these observations suggest that EZRIN might bind directly to NIS, possibly through an as yet unidentified FERM-binding domain in the symporter. While FERM-binding domains have highly heterogeneous sequences, Ali et al [82] recently characterized an xYxV motif that is present in many of EZRIN interacting partners, and mediates the interaction with the F3b site in its FERM domain. Interestingly, by analyzing the NIS protein sequence, we detected two putative FERM-interacting xYxV motifs near the interfaces between the second NIS cytoplasmic loop and the fourth transmembrane domain, and between the seventh NIS transmembrane domain and fourth cytoplasmic loop (see Figure S6B).…”

TMIGD1: Emerging functions of a tumor supressor and adhesion receptor

“…Similar clusters of positively charged AA have been found to interact with ERM proteins in binding assays with recombinant proteins in vitro [60], suggesting that this interaction is direct. Since TMIGD1 does not contain a canonical FERM domain-binding motiv (R/K/E-X-X-T-(Y/L)-X-X-A/G) [42,61], in vitro binding experiments with recombinant proteins will be needed to obtain further information on the nature of the interaction between TMIGD1 and moesin. Interestingly, ectopic expression of TMIGD1 in cultured epithelial cell lines impairs filopodia formation, stabilizes microtubules (MT) and slows down cell migration [22].…”