Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome
Complete Virion Simulated: All-Atom Model of an MS2 Bacteriophage with Native Genome
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完整的病毒颗粒模拟：具有天然基因组的 MS2 噬菌体的全原子模型
DOI：
10.1021/acs.jctc.3c00846
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发表时间：
2023
影响因子：
5.5
通讯作者：
Farafonov V
中科院分区：
文献类型：
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作者：
Farafonov V
第一次，一个完整的全原子分子动力学（MD）模型的病毒，噬菌体MS 2，在其整体，包括蛋白质外壳，天然基因组RNA与必要的二价离子，周围明确的水溶液与离子在生理浓度，建立。该模型是基于实验测量的冷冻EM结构，这是大大增强了重建缺失或低分辨率部分的测量密度（原子结构不能明确拟合）。该模型进行了测试的四分之一微秒MD运行，并获得和分析各种生物物理特性。当实验数据是碎片化的和/或分辨率不同时，建立模型的开发方法可用于重建其他大的生物分子结构，而模型本身可用于研究MS 2的生物学，包括其与宿主细菌相互作用的动力学。
For the first time, a complete all-atom molecular dynamics (MD) model of a virus, bacteriophage MS2, in its entirety, including a protein outer shell, native genomic RNA with necessary divalent ions, and surrounding explicit aqueous solution with ions at physiological concentration, was built. The model is based on an experimentally measured cryo-EM structure, which was substantially augmented by reconstructing missing or low-resolution parts of the measured density (where the atomistic structure cannot be fit unambiguously). The model was tested by a quarter of a microsecond MD run, and various biophysical characteristics are obtained and analyzed. The developed methodology of building the model can be used for reconstructing other large biomolecular structures when experimental data are fragmented and/or of varying resolution, while the model itself can be used for studying the biology of MS2, including the dynamics of its interaction with the host bacteria.