Farafonov Vladimir S, Nerukh Dmitry
Department of Physical Chemistry, V. N. Karazin Kharkiv National University, 61022 Kharkiv, Ukraine.
Department of Mathematics, Systems Analytics Research Institute, Aston University, Birmingham B4 7ET, UK.
Interface Focus. 2019 Jun 6;9(3):20180081. doi: 10.1098/rsfs.2018.0081. Epub 2019 Apr 19.
The all-atom model of an MS2 bacteriophage particle without its genome (the capsid) was built using high-resolution cryo-electron microscopy (EM) measurements for initial conformation. The structural characteristics of the capsid and the dynamics of the surrounding solution were examined using molecular dynamics simulation. The model demonstrates the overall preservation of the cryo-EM structure of the capsid at physiological conditions (room temperature and ions composition). The formation of a dense anion layer near the inner surface and a diffuse cation layer near the outer surface of the capsid was detected. The flow of water molecules and ions across the capsid through its pores were quantified, which was considerable for water and substantial for ions.
利用高分辨率冷冻电子显微镜（EM）测量结果构建了不含基因组的MS2噬菌体颗粒（衣壳）的全原子模型，以确定其初始构象。使用分子动力学模拟研究了衣壳的结构特征和周围溶液的动力学。该模型表明，在生理条件（室温及离子组成）下，衣壳的冷冻电镜结构总体上得以保留。检测到在衣壳内表面附近形成了致密的阴离子层，在外表面附近形成了扩散的阳离子层。对穿过衣壳孔隙的水分子和离子流进行了量化，结果表明水的流量很大，离子的流量也相当可观。
