Department of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands; Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, the Netherlands.
Department of Applied Physics, Eindhoven University of Technology, Eindhoven, the Netherlands.
Biophys J. 2022 Jul 5;121(13):2583-2599. doi: 10.1016/j.bpj.2022.05.040. Epub 2022 May 30.
Inspired by recent experiments on the spontaneous assembly of virus-like particles from a solution containing a synthetic coat protein and double-stranded DNA, we put forward a kinetic model that has as main ingredients a stochastic nucleation and a deterministic growth process. The efficiency and rate of DNA packaging strongly increase after tiling the DNA with CRISPR-Cas proteins at predesignated locations, mimicking assembly signals in viruses. Our model shows that treating these proteins as nucleation-inducing diffusion barriers is sufficient to explain the experimentally observed increase in encapsulation efficiency, but only if the nucleation rate is sufficiently high. We find an optimum in the encapsulation kinetics for conditions where the number of packaging signal mimics is equal to the number of nucleation events that can occur during the time required to fully encapsulate the DNA template, presuming that the nucleation events can only take place adjacent to a packaging signal. Our theory is in satisfactory agreement with the available experimental data.
受最近关于在含有合成外壳蛋白和双链 DNA 的溶液中自组装类似病毒颗粒的实验的启发，我们提出了一个动力学模型，其主要成分是随机成核和确定性生长过程。在预定位置用 CRISPR-Cas 蛋白平铺 DNA 后，DNA 的包装效率和速度会大大提高，模拟了病毒中的组装信号。我们的模型表明，将这些蛋白质视为引发成核的扩散障碍足以解释实验观察到的封装效率的提高，但前提是成核速率足够高。我们发现，在封装动力学中存在一个最佳条件，即在包装信号模拟物的数量等于在完全封装 DNA 模板所需的时间内可以发生的成核事件的数量，假设成核事件只能发生在包装信号附近。我们的理论与现有的实验数据吻合良好。
