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Abstract：
Cofilin, a key actin-binding protein, orchestrates the dynamics of the actomyosin network through its actin-severing activity and by promoting the recycling of actin monomers. Recent experiments suggest that cofilin forms functionally distinct oligomers via thiol post-translational modifications (PTMs) that promote actin nucleation and assembly. Despite these advances, the structural conformations of cofilin oligomers that modulate actin activity remain elusive because there are combinatorial ways to oxidize thiols in cysteines to form disulfide bonds rapidly. This study employs molecular dynamics simulations to investigate human cofilin 1 as a case study for exploring cofilin dimers via disulfide bond formation. Utilizing a biasing scheme in simulations, we focus on analyzing dimer conformations conducive to disulfide bond formation. Additionally, we explore potential PTMs arising from the examined conformational ensemble. Using the free energy profiling, our simulations unveil a range of probable cofilin dimer structures not represented in current Protein Data Bank entries. These candidate dimers are characterized by their distinct population distributions and relative free energies. Of particular note is a dimer featuring an interface between cysteines 139 and 147 residues, which demonstrates stable free energy characteristics and intriguingly symmetrical geometry. In contrast, the experimentally proposed dimer structure exhibits a less stable free energy profile. We also evaluate frustration quantification based on the energy landscape theory in the protein-protein interactions at the dimer interfaces. Notably, the 39-39 dimer configuration emerges as a promising candidate for forming cofilin tetramers, as substantiated by frustration analysis. Additionally, docking simulations with actin filaments further evaluate the stability of these cofilin dimer-actin complexes. Our findings thus offer a computational framework for understanding the role of thiol PTM of cofilin proteins in regulating oligomerization, and the subsequent cofilin-mediated actin dynamics in the actomyosin network.
摘要：
Cofilin,一种关键的肌动蛋白结合蛋白，通过肌动蛋白切断活性和促进肌动蛋白单体的回收来协调肌动球蛋白网络的动力学。最近的实验表明，cofilin通过促进肌动蛋白成核和组装的硫醇翻译后修饰（PTM）形成功能上不同的寡聚物。尽管取得了这些进展,调节肌动蛋白活性的cofilin寡聚体的结构构象仍然难以捉摸，因为存在氧化半胱氨酸中的硫醇以快速形成二硫键的组合方式。本研究采用分子动力学模拟来研究人类cofilin1，作为通过二硫键形成探索cofilin二聚体的案例研究。在模拟中利用偏置方案，重点分析有利于二硫键形成的二聚体构象。此外,我们探索了由检查的构象集合产生的潜在PTM。使用自由能剖面，我们的模拟揭示了当前蛋白质数据库条目中未显示的一系列可能的cofilin二聚体结构。这些候选二聚体的特征在于其不同的群体分布和相对自由能。特别值得注意的是具有半胱氨酸139和147个残基之间的界面的二聚体，这证明了稳定的自由能特性和有趣的对称几何。相比之下,实验提出的二聚体结构表现出较不稳定的自由能分布。我们还根据二聚体界面的蛋白质-蛋白质相互作用中的能量景观理论评估了挫折量化。值得注意的是,39-39二聚体构型成为形成cofilin四聚体的有希望的候选者，由挫折分析证实。此外,与肌动蛋白丝的对接模拟进一步评估了这些cofilin二聚体-肌动蛋白复合物的稳定性。因此，我们的发现为理解cofilin蛋白的硫醇PTM在调节寡聚化方面的作用提供了一个计算框架。以及随后的肌动球蛋白网络中的cofilin介导的肌动蛋白动力学。
