Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037, USA.
Biomolecules. 2023 Jan 11;13(1):151. doi: 10.3390/biom13010151.
Biomolecular condensation and phase separation are increasingly understood to play crucial roles in cellular compartmentalization and spatiotemporal regulation of cell machinery implicated in function and pathology. A key aspect of current research is to gain insight into the underlying physical mechanisms of these processes. Accordingly, concepts of soft matter and polymer physics, the thermodynamics of mixing, and material science have been utilized for understanding condensation mechanisms of multivalent macromolecules resulting in viscoelastic mesoscopic supramolecular assemblies. Here, we focus on two topological concepts that have recently been providing key mechanistic understanding in the field. First, we will discuss how percolation provides a network-topology-related framework that offers an interesting paradigm to understand the complex networking of dense 'connected' condensate structures and, therefore, their phase behavior. Second, we will discuss the idea of entanglement as another topological concept that has deep roots in polymer physics and important implications for biomolecular condensates. We will first review some historical developments and fundamentals of these concepts, then we will discuss current advancements and recent examples. Our discussion ends with a few open questions and the challenges to address them, hinting at unveiling fresh possibilities for the modification of existing knowledge as well as the development of new concepts relevant to condensate science.
生物分子凝聚和相分离在细胞区室化和细胞机制的时空调节中起着至关重要的作用,这些细胞机制涉及功能和病理学。当前研究的一个关键方面是深入了解这些过程的潜在物理机制。因此,软物质和高分子物理的概念、混合的热力学以及材料科学已被用于理解多价大分子的凝聚机制,从而导致粘弹性介观超分子组装。在这里,我们关注两个最近在该领域提供关键机制理解的拓扑概念。首先,我们将讨论如何渗滤提供了一个与网络拓扑相关的框架,为理解密集“连接”凝聚结构的复杂网络及其相行为提供了一个有趣的范例。其次,我们将讨论缠结作为另一个拓扑概念的想法,它在高分子物理中有很深的根源,对生物分子凝聚物有重要的影响。我们将首先回顾这些概念的一些历史发展和基础,然后讨论当前的进展和最近的例子。我们的讨论以一些未解决的问题和挑战结束,这些问题和挑战暗示着对现有知识进行修改以及发展与凝聚物科学相关的新概念的可能性。