Chwastyk Mateusz, Cieplak Marek
Institute of Physics, Polish Academy of Sciences, Warsaw, Poland.
Front Mol Biosci. 2021 Jun 7;8:692230. doi: 10.3389/fmolb.2021.692230. eCollection 2021.
We study the nascent behavior of three model coarse-grained proteins in six rigid all-atom structures representing ribosomes that come from three domains of life. The synthesis of the proteins is implemented as a growth process. The geometry of the exit tunnel is quantified and shown to differ between the domains of life: both in volume and the size of constriction sites. This results in different characteristic times of capture within the tunnel and various probabilities of the escape. One of the proteins studied is the bacterial YibK which is knotted in its native state. A fraction of the trajectories results in knotting and the probability of doing so is largest for the bacterial ribosomes. Relaxing the condition of the rigidness of the ribosomes should result in a better avoidance of trapping and better proper folding.
我们研究了三种模型粗粒化蛋白质在代表来自生命三个域的核糖体的六个刚性全原子结构中的新生行为。蛋白质的合成被实现为一个生长过程。对出口通道的几何形状进行了量化，结果表明不同生命域的出口通道在体积和收缩位点大小方面存在差异。这导致了通道内捕获的不同特征时间和不同的逃逸概率。所研究的蛋白质之一是细菌的YibK，它在天然状态下是打结的。一部分轨迹会导致打结，并且在细菌核糖体中打结的概率最大。放宽核糖体刚性的条件应该会更好地避免被困并实现更好的正确折叠。
