Fries Jacques, Diaz Javier, Jardat Marie, Pagonabarraga Ignacio, Illien Pierre, Dahirel Vincent
Sorbonne Université, CNRS, Physico-Chimie des Electrolytes et Nanosystèmes Interfaciaux(PHENIX), 4 Place Jussieu, Paris 75005, France.
Departament de Física de la Matèria Condensada, Universitat de Barcelona, Carrer de Martí i Franqués 1, Barcelona 08028, Spain.
J R Soc Interface. 2025 May;22(226):20240803. doi: 10.1098/rsif.2024.0803. Epub 2025 May 7.
The formation of condensates is now considered a major organizing principle of eukaryotic cells. Several studies have recently shown that the properties of these condensates are affected by enzymatic reactions. We propose here a simple generic model to study the interplay between two enzyme populations and a two-state protein. In one state, the protein forms condensed droplets through attractive interactions, while in the other state, the proteins remain dispersed. Each enzyme catalyses the production of one of these two protein states only when reactants are in its vicinity. A key feature of our model is the explicit representation of enzyme trajectories, capturing the fluctuations in their local concentrations. The spatially dependent growth rate of droplets naturally arises from the stochastic motion of these explicitly modelled enzymes. Using two complementary numerical methods-(i) Brownian dynamics simulations and (ii) a hybrid method combining Cahn-Hilliard-Cook diffusion equations with Brownian dynamics for the enzymes-we investigate how enzyme concentration and dynamics influence the evolution with time and the steady-state number and size of droplets. Our results show that the concentration and diffusion coefficient of enzymes govern the formation and size-selection of biocondensates.
凝聚物的形成现在被认为是真核细胞的一个主要组织原则。最近的几项研究表明,这些凝聚物的性质会受到酶促反应的影响。我们在此提出一个简单的通用模型,以研究两种酶群体与一种双态蛋白质之间的相互作用。在一种状态下,蛋白质通过吸引相互作用形成凝聚液滴,而在另一种状态下,蛋白质保持分散状态。每种酶仅在反应物在其附近时才催化这两种蛋白质状态之一的产生。我们模型的一个关键特征是酶轨迹的明确表示,捕捉其局部浓度的波动。液滴的空间依赖性生长速率自然源于这些明确建模的酶的随机运动。使用两种互补的数值方法——(i)布朗动力学模拟和(ii)一种将Cahn-Hilliard-Cook扩散方程与酶的布朗动力学相结合的混合方法——我们研究了酶浓度和动力学如何随时间影响演化以及液滴的稳态数量和大小。我们的结果表明,酶的浓度和扩散系数控制着生物凝聚物的形成和尺寸选择。