Maxwell Centre, Cavendish Laboratory, Department of Physics, University of Cambridge, J J Thomson Avenue, Cambridge, CB3 0HE, UK.
Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
Sci Rep. 2022 Mar 15;12(1):4390. doi: 10.1038/s41598-022-08130-2.
Biomolecular condensates formed by the process of liquid-liquid phase separation (LLPS) play diverse roles inside cells, from spatiotemporal compartmentalisation to speeding up chemical reactions. Upon maturation, the liquid-like properties of condensates, which underpin their functions, are gradually lost, eventually giving rise to solid-like states with potential pathological implications. Enhancement of inter-protein interactions is one of the main mechanisms suggested to trigger the formation of solid-like condensates. To gain a molecular-level understanding of how the accumulation of stronger interactions among proteins inside condensates affect the kinetic and thermodynamic properties of biomolecular condensates, and their shapes over time, we develop a tailored coarse-grained model of proteins that transition from establishing weak to stronger inter-protein interactions inside condensates. Our simulations reveal that the fast accumulation of strongly binding proteins during the nucleation and growth stages of condensate formation results in aspherical solid-like condensates. In contrast, when strong inter-protein interactions appear only after the equilibrium condensate has been formed, or when they accumulate slowly over time with respect to the time needed for droplets to fuse and grow, spherical solid-like droplets emerge. By conducting atomistic potential-of-mean-force simulations of NUP-98 peptides-prone to forming inter-protein [Formula: see text]-sheets-we observe that formation of inter-peptide [Formula: see text]-sheets increases the strength of the interactions consistently with the loss of liquid-like condensate properties we observe at the coarse-grained level. Overall, our work aids in elucidating fundamental molecular, kinetic, and thermodynamic mechanisms linking the rate of change in protein interaction strength to condensate shape and maturation during ageing.
液-液相分离(LLPS)过程形成的生物分子凝聚物在细胞内发挥着多种作用,从时空分隔到加速化学反应。凝聚物的液态特性是其功能的基础,随着成熟,这些特性逐渐丧失,最终导致具有潜在病理意义的固态。增强蛋白质之间的相互作用是引发固态凝聚物形成的主要机制之一。为了从分子水平上了解凝聚物内部蛋白质之间更强相互作用的积累如何影响生物分子凝聚物的动力学和热力学性质及其随时间的形状,我们开发了一种针对蛋白质的定制粗粒模型,该模型从建立弱相互作用转变为在凝聚物内部建立更强的蛋白质间相互作用。我们的模拟表明,在凝聚物形成的成核和生长阶段,快速积累具有强结合力的蛋白质会导致非球形固态凝聚物。相比之下,当强蛋白质间相互作用仅在形成平衡凝聚物之后出现,或者当它们相对于液滴融合和生长所需的时间以较慢的速度随时间积累时,会出现球形固态液滴。通过对易于形成蛋白质间[Formula: see text]-折叠的 NUP-98 肽进行原子力势能平均力模拟,我们观察到形成肽间[Formula: see text]-折叠会一致增加相互作用的强度,这与我们在粗粒水平观察到的液态凝聚物性质的丧失一致。总的来说,我们的工作有助于阐明将蛋白质相互作用强度变化率与凝聚物形状和老化过程中的成熟联系起来的基本分子、动力学和热力学机制。