Kalita Monoj Mon, Fischer Wolfgang B
Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.
Institute of Biophotonics and Biophotonics and Molecular Imaging Research Center (BMIRC), School of Biomedical Science and Engineering, National Yang-Ming University, Taipei, Taiwan, ROC.
Biochim Biophys Acta. 2016 Jul;1858(7 Pt A):1462-70. doi: 10.1016/j.bbamem.2016.04.004. Epub 2016 Apr 11.
Protein p7 of hepatitis C virus (HCV) is a short 63 amino acid membrane protein which homo-oligomerises in the lipid membrane to form ion and proton conducting bundles. Two different genotypes (GTs) of p7, 1a and 5a, are used to simulate hexameric bundles of the protein embedded in a fully hydrated lipid bilayer during 400 ns molecular dynamics (MD) simulations. Whilst the bundle of GT 1a is based on a fully computational derived structure, the bundle of GT 5a is based on NMR spectroscopic data. Results of a full correlation analysis (FCA) reveal that albeit structural differences both bundles screen local minima during the simulation. The collective motion of the protein domains is asymmetric. No 'breathing-mode'-like dynamics is observed. The presence of divalent ions, such as Ca-ions affects the dynamics of especially solvent exposed parts of the protein, but leaves the asymmetric domain motion unaffected.
丙型肝炎病毒（HCV）的p7蛋白是一种由63个氨基酸组成的短膜蛋白，它在脂质膜中形成同源寡聚体，构成离子和质子传导束。在400纳秒的分子动力学（MD）模拟过程中，使用p7的两种不同基因型（GTs），即1a和5a，来模拟嵌入完全水合脂质双层中的该蛋白的六聚体束。虽然GT 1a的束基于完全通过计算得出的结构，但GT 5a的束基于核磁共振光谱数据。全相关分析（FCA）结果表明，尽管存在结构差异，但在模拟过程中两个束都筛选出局部最小值。蛋白质结构域的集体运动是不对称的。未观察到类似“呼吸模式”的动力学。二价离子（如钙离子）的存在会影响蛋白质尤其是溶剂暴露部分的动力学，但不会影响不对称结构域的运动。
