标题： 使用通用粗粒度模型 MARTINI 对细菌核糖体的计算机模拟 显示英文标题

标题： Computer simulations of the bacterial ribosome using a general purpose coarse-grained model MARTINI

摘要： 核糖体是所有已知生物体中负责蛋白质合成的关键生物分子纳米机器。 核糖体的功能和动态可以通过分子动力学计算机模拟来研究。 尽管在原子层面这一任务仍然具有挑战性，但已有几项研究报道了整个核糖体的全原子分子动力学模拟。 然而，由于可达到的模拟时间尺度有限，对于某些应用，原子级模拟并不实际。 在本研究中，我们探讨了粗粒度MARTINI模型在细菌核糖体模拟中的适用性。 经过测试几种模拟设置后，我们发现与参考实验结构相比，核糖体及其组件的结构通常得到了良好的表示。 与整个核糖体的全原子模拟相比，粗粒度模拟导致核糖体的灵活性较低且体积较小。 我们展示了如何修改模型的一些参数可以增强核糖体的动力学，使其更好地与原子模型对齐。 我们的工作提供了一个详细的核糖体粗粒度模拟协议，并指出了需要改进的模型方面。 显示英文摘要

摘要： Ribosomes are critical biomolecular nanomachines responsible for protein synthesis in all known organisms. The function and dynamics of ribosomes can be studied using molecular dynamics computer simulations. Although this task remains challenging at atomic level, several studies have reported all-atom molecular dynamics simulations of the entire ribosome. However, for certain applications, atomistic simulations are impractical due to the limited simulation timescales achievable. In this study, we investigate the applicability of the coarse-grained MARTINI model for simulations of the bacterial ribosome. After testing several simulation setups, we found that the structure of the ribosome and its components are generally well represented compared to the reference experimental structure. Compared with all-atom simulations of the entire ribosome, coarse-grained simulations result in a less flexible and smaller ribosome. We demonstrate how modifications of some parameters of the model can enhance the dynamics of the ribosome to better align with the atomistic model. Our work provides a detailed protocol for coarse-grained simulations of the ribosome and highlights aspects of the model that need improvements.