Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York.
Biophys J. 2023 Nov 7;122(21):4144-4159. doi: 10.1016/j.bpj.2023.09.012. Epub 2023 Sep 23.
Liquid-liquid phase separation inside the cell often results in biological condensates that can critically affect cell homeostasis. Such phase separation events occur in multiple parts of cells, including the cell membranes, where the "lipid raft" hypothesis posits the formation of ordered domains floating in a sea of disordered lipids. The resulting lipid domains often have functional roles. However, the thermodynamics of lipid phase separation and their resulting mechanistic effects on cell function and dysfunction are poorly understood. Understanding such complex phenomena in cell membranes, with their diverse lipid compositions, is exceptionally difficult. For these reasons, simple model systems that can recapitulate similar behavior are widely used to study this phenomenon. Despite these simplifications, the timescale and length scales of domain formation pose a challenge for molecular dynamics (MD) simulations. Thus, most MD studies focus on spontaneous lipid phase separation-essentially measuring the sign (but not the amplitude) of the free-energy change upon separation-rather than directly interrogating the thermodynamics. Here, we propose a proof-of-concept pipeline that can directly measure this free energy by combining coarse-grained MD with enhanced sampling protocols using a novel collective variable. This approach will be a useful tool to help connect the thermodynamics of phase separation with the mechanistic insights already available from MD simulations.
细胞内的液-液相分离常常导致生物凝聚物的形成，这可能会严重影响细胞的内稳态。这种相分离事件发生在细胞的多个部位，包括细胞膜，其中“脂质筏”假说假设有序域在无序脂质的海洋中形成浮动。由此产生的脂质域通常具有功能作用。然而，脂质相分离的热力学及其对细胞功能和功能障碍的机械影响仍知之甚少。理解细胞膜中具有不同脂质组成的这种复杂现象非常困难。出于这些原因，广泛使用简单的模型系统来研究这种现象，以重现类似的行为。尽管进行了这些简化，但域形成的时间尺度和长度尺度对分子动力学 (MD) 模拟构成了挑战。因此，大多数 MD 研究都集中在自发的脂质相分离上——本质上是测量分离时自由能变化的符号（而不是幅度）——而不是直接探究热力学。在这里，我们提出了一个概念验证管道，该管道可以通过将粗粒度 MD 与使用新型集体变量的增强采样协议相结合，直接测量这种自由能。这种方法将是一种有用的工具，可以帮助将相分离的热力学与已经从 MD 模拟中获得的机械洞察力联系起来。
