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

• Published in: PLoS computational biology 2021-01, Vol.17 (1), p.e1008474-e1008474
• Main Authors: Jagannathan, N Suhas, Hogue, Christopher W V, Tucker-Kellogg, Lisa
• Format: Article
• Language: English
• Subjects: Adaptor Protein Complex 2 - chemistry; Adaptor Protein Complex 2 - metabolism; Adaptor Proteins, Vesicular Transport - chemistry; Adaptor Proteins, Vesicular Transport - metabolism; Allosteric properties; Alternative splicing; Amino acids; Binding; Binding sites; Biology and Life Sciences; Cell Membrane - chemistry; Cell Membrane - metabolism; Clathrin - chemistry; Clathrin - metabolism; Computer applications; Cooperative binding (Biochemistry); Endocytosis - physiology; Extreme environments; Fluorescence; Fluorescence spectroscopy; Genetic aspects; Humans; Hypotheses; Intrinsically Disordered Proteins - chemistry; Intrinsically Disordered Proteins - metabolism; Membrane proteins; Molecular Docking Simulation; NMR; Nuclear magnetic resonance; Pathogenesis; Phase separation; Physical Sciences; Physiological aspects; Polymers; Post-translation; Protein Binding; Protein Conformation; Proteins; Receptor-mediated endocytosis; Research and Analysis Methods; Self assembly; Small angle X ray scattering; Splicing; X ray scattering
• ISSN: 1553-7358; 1553-734X; 1553-7358
• DOI: 10.1371/journal.pcbi.1008474

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.