基于反应平衡的细胞内蛋白模式分类
Classification of Intracellular Protein Patterns from Reactive Equilibria
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中文总结 AI 辅助
该研究开发了基于守恒结构的几何分类框架，将多组分反应-扩散网络的稳定性分析简化，可预测模式形成不稳定性，应用于原核与真核生物系统，为非平衡系统模式形成研究提供了可解释的实验可行框架。
中文摘要 AI 辅助
自组织空间模式是非平衡物理学与细胞生物学的核心内容，但多组分反应-扩散网络中不稳定性的定位仍具挑战性，因为标准特征值分析的计算量随生化状态数增加而增大，且依赖于实验中往往难以精确约束的反应动力学。利用蛋白反应动力学共有的质量守恒结构，以及非线性反馈通常局限于膜反应、而膜侧向扩散可忽略的事实，我们开发了一种几何分类方法，可从反应平衡预测稳态模式形成不稳定性，也可近似预测振荡模式形成不稳定性。所开发的判据将稳定性分析从全组分空间简化为守恒物种的空间。在该简化空间中，斜率矩阵（描述平衡态胞质密度随总物种密度的变化）主导不稳定性的 onset。基于化学平衡密度，该方法消除了实验系统中常缺失的全面动力学知识的要求。因此，广泛的不稳定性可被理解为质量再分布不稳定性——由局部平衡移动引发的自增强质量再分布。我们将这些判据应用于大肠杆菌 Min 系统和秀丽隐杆线虫极性系统的模型，表明该简化方法可扩展至耦合体相胞质动力学与边界膜动力学的混合维度动力学。综上，这些结果提供了一种可解释、适用范围广且可通过实验验证的框架，用于基于守恒定律诊断和设计多组分非平衡系统中的模式形成。
英文摘要
Self-organized spatial patterns are central to nonequilibrium physics and cell biology, yet locating instabilities in multi-component, reaction-diffusion networks remains challenging because standard eigenvalue analyses scale with the number of biochemical states and rely on reaction kinetics often poorly constrained by experiments. Exploiting the common mass-conserving structure of protein reaction kinetics and the fact that nonlinear feedback is typically confined to membrane reactions while lateral membrane diffusion is negligible, we develop a geometric classification that predicts stationary, and approximately also oscillatory, pattern-forming instabilities from reactive equilibria. The developed criteria reduce the stability analysis from the full component space to the space of conserved species. On this reduced space, slope matrices---describing the change of equilibrium cytosolic densities with respect to total species densities---govern onset. Based on densities in chemical equilibrium, this approach eliminates the requirement of comprehensive kinetic knowledge frequently lacking in experimental systems. Thus, a broad range of instabilities can be understood as mass-redistribution instabilities---self-amplifying mass redistribution caused by shifting local equilibria. We apply these criteria to models for the Escherichia coli Min system and the Caenorhabditis elegans polarity system and show that the reduction extends to the mixed-dimensional dynamics in systems coupling bulk cytosolic dynamics with membrane dynamics on the boundary. Together, these results provide an interpretable, broadly applicable, and experimentally accessible framework for diagnosing and designing pattern formation in multicomponent nonequilibrium systems on the basis of conservation laws.
