Cancer & Stem Cell Biology, and Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore.
Singapore-MIT Alliance, Computation and Systems Biology Program, National University of Singapore, Singapore.
PLoS Comput Biol. 2021 Jan 6;17(1):e1008474. doi: 10.1371/journal.pcbi.1008474. eCollection 2021 Jan.
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.
无定形区域（IDRs）在真核蛋白质组中普遍存在。IDRs 的常见功能包括形成灵活的连接子或在结合时进行变构折叠。最近的研究表明，IDRs 具有额外的功能作用：通过分子拥挤，在胞吞作用过程中对质膜产生空间压力。然而，为了实现有用的功能，这种拥挤需要在空间（例如，胞吞热点）和时间（例如，在囊泡形成过程中）上进行调节。在这项工作中，我们探讨了结合诱导的 IDR 位阻体积调节。我们模拟了网格蛋白介导的胞吞作用（CME）中的两种蛋白质的 IDR，以观察它们的构象空间是否通过结合诱导扩张来调节。我们使用排除体积的蒙特卡罗计算建模，为 Epsin 和 Eps15 的 IDR 生成了大量构象（300 万），并将构象对接至它们的 CME 结合伴侣，衔接蛋白 2（AP2α）的α亚基。我们的结果表明，随着结合的 AP2α 分子数量的增加，Epsin 衍生的集合显示出全局尺寸的显著增加，以回转半径（RG）和末端到末端距离（EED）来衡量。与 Epsin 不同，允许在一个基序处结合 AP2α 的 Eps15 衍生构象更有可能容纳 AP2α 在其他基序处的结合，这表明结合基序具有共可及性的趋势。在 Epsin 中没有观察到任何一对结合基序的共可及性。因此，我们推测 Epsin 和 Eps15 的无定形区域在 CME 中发挥不同的作用，Eps15 的可及性允许其充当 AP2α 分子的招募者，而 Epsin 无序区域的结合诱导扩张可能会在囊泡形成过程中对质膜产生空间压力并重塑质膜。
