Computational modeling suggests binding-induced expansion of Epsin disordered regions upon association with AP2.

N Suhas Jagannathan,Christopher W V Hogue,Lisa Tucker-Kellogg,Wei Li

doi:10.1371/journal.pcbi.1008474

Abstract

Intrinsically disordered regions (IDRs) are prevalent in the eukaryotic proteome. Common functional roles of IDRs include forming flexible linkers or undergoing allosteric folding-upon-binding. Recent studies have suggested an additional functional role for IDRs: generating steric pressure on the plasma membrane during endocytosis, via molecular crowding. However, in order to accomplish useful functions, such crowding needs to be regulated in space (e.g., endocytic hotspots) and time (e.g., during vesicle formation). In this work, we explore binding-induced regulation of IDR steric volume. We simulate the IDRs of two proteins from Clathrin-mediated endocytosis (CME) to see if their conformational spaces are regulated via binding-induced expansion. Using Monte-Carlo computational modeling of excluded volumes, we generate large conformational ensembles (3 million) for the IDRs of Epsin and Eps15 and dock the conformers to the alpha subunit of Adaptor Protein 2 (AP2α), their CME binding partner. Our results show that as more molecules of AP2α are bound, the Epsin-derived ensemble shows a significant increase in global dimensions, measured as the radius of Gyration (RG) and the end-to-end distance (EED). Unlike Epsin, Eps15-derived conformers that permit AP2α binding at one motif were found to be more likely to accommodate binding of AP2α at other motifs, suggesting a tendency toward co-accessibility of binding motifs. Co-accessibility was not observed for any pair of binding motifs in Epsin. Thus, we speculate that the disordered regions of Epsin and Eps15 perform different roles during CME, with accessibility in Eps15 allowing it to act as a recruiter of AP2α molecules, while binding-induced expansion of the Epsin disordered region could impose steric pressure and remodel the plasma membrane during vesicle formation.

Highlights

Cells typically internalize surface or external cargo through processes that remodel the plasma membrane into cargo-containing vesicles
Clathrin-mediated endocytosis (CME) is one such cellular mechanism in which cell-surface cargo is internalized within a Clathrin-coated vesicle (CCV) that forms at the plasma membrane [1]
Our results show that the energetically-favorable subset of Epsin-iDR ensembles that allow increasing numbers of AP2α to bind, show a corresponding increase in dimensions, suggesting binding-induced expansion of the Epsin-iDR

Summary

Introduction

Cells typically internalize surface or external cargo through processes (e.g., endocytosis, phagocytosis, pinocytosis) that remodel the plasma membrane into cargo-containing vesicles. Clathrin-mediated endocytosis (CME) is one such cellular mechanism in which cell-surface cargo (typically membrane proteins and/or ligands) is internalized within a Clathrin-coated vesicle (CCV) that forms at the plasma membrane [1]. The overall CME process can be split into distinct temporal phases– 1) nucleation and initiation of the Clathrin-coated pit (CCP), 2) selection and binding of the cargo to the CCP, 3) growth and maturation of the CCV, 4) membrane scission and 5) cytoplasmic uncoating. During phases 1, 2 and 3, participating proteins are believed to generate forces required to overcome membrane stiffness and surface tension, to form a membrane vesicle. Given that CME is tightly regulated and crucial for cell physiology, it is very likely that conserved CME-IDRs are functionally relevant, and exertion of steric pressure through molecular crowding is one way they could be functionally relevant

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