Biswas Subhadip, Potoyan Davit A
Department of Chemistry, Iowa State University, Ames, Iowa 50011, USA.
Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, Iowa 50011, USA.
PRX Life. 2024 Jun;2(2). doi: 10.1103/prxlife.2.023011. Epub 2024 Jun 6.
Biomolecular condensates are dynamic intracellular entities defined by their sequence- and composition-encoded material properties. During aging, these properties can change dramatically, potentially leading to pathological solidlike states, the mechanisms of which remain poorly understood. Recent experiments reveal that the aging of condensates involves a complex interplay of solvent depletion, strengthening of sticker links, and the formation of rigid structural segments such as beta fibrils. In this study, we use various coarse-grained models to investigate how solvent expulsion, biopolymer chain rigidity, and the lifetimes of sticker contacts influence the viscoelastic properties and aging dynamics of condensates. We find that the rigidity of the biopolymer backbone is essential for replicating the predominant elastic behavior observed in experiments. In contrast, models using fully flexible chains-an assumption common in simulations of intrinsically disordered proteins-fail to exhibit a dominant elastic regime. We also demonstrate that altering the solvent content within condensates affects the crossover between storage and loss moduli. This suggests that desolvation plays a significant role in condensate aging by promoting the transition from a viscous to an elastic state. Furthermore, the lifetime of sticker pairs profoundly influences the mature state of the condensates; short-lived stickers lead to a Maxwell fluid behavior, while longer-lived, irreversibly cross-linked stickers result in solidlike properties, consistent with the Kelvin-Voigt model. Finally, by incorporating the chain rigidification, desolvation, and sticker pair formation into a nonequilibrium dynamic aging simulation, we show the molecular mechanism of forming solid shells around the condensate surfaces observed in a recent experimental report.
生物分子凝聚物是由其序列和组成编码的物质特性所定义的动态细胞内实体。在衰老过程中,这些特性会发生显著变化,可能导致病理性的固态状态,但其机制仍知之甚少。最近的实验表明,凝聚物的老化涉及溶剂耗尽、粘性连接增强以及β-纤维等刚性结构段形成的复杂相互作用。在本研究中,我们使用各种粗粒度模型来研究溶剂排出、生物聚合物链刚性以及粘性接触的寿命如何影响凝聚物的粘弹性特性和老化动力学。我们发现生物聚合物主链的刚性对于复制实验中观察到的主要弹性行为至关重要。相比之下,使用完全柔性链的模型(这是内在无序蛋白质模拟中常见的假设)无法表现出主导的弹性区域。我们还证明,改变凝聚物中的溶剂含量会影响储能模量和损耗模量之间的转变。这表明去溶剂化通过促进从粘性状态到弹性状态的转变在凝聚物老化中起重要作用。此外,粘性对的寿命对凝聚物的成熟状态有深远影响;短寿命的粘性导致麦克斯韦流体行为,而寿命更长、不可逆交联的粘性则导致固态特性,这与开尔文 - 沃伊特模型一致。最后,通过将链刚性化、去溶剂化和粘性对形成纳入非平衡动态老化模拟,我们展示了最近一份实验报告中观察到的在凝聚物表面形成固体壳的分子机制。