Division of Physical Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296, Gothenburg, Sweden ; Present address: School of Chemistry, University of Southampton, Highfield, SO17 1BJ, Southampton, UK.
Division of Physical Chemistry, Department of Chemistry and Molecular Biology, University of Gothenburg, SE-41296, Gothenburg, Sweden.
Comput Struct Biotechnol J. 2013 Dec 15;6:e201303022. doi: 10.5936/csbj.201303022. eCollection 2013.
We report a study of the interaction between internalin A (inlA) and human or murine E-cadherin (Ecad). inlA is used by Listeria monocytogenes to internalize itself into host cell, but the bacterium is unable to invade murine cells, which has been attributed to the difference in sequence between hEcad and mEcad. Using molecular dynamics simulations, MM/GBSA free energy calculations, hydrogen bond analysis, water characterization and umbrella sampling, we provide a complete atomistic picture of the binding between inlA and Ecad. We dissect key residues in the protein-protein interface and analyze the energetics using MM/GBSA. From this analysis it is clear that the binding of inlA-mEcad is weaker than inlA-hEcad, on par with the experimentally observed inability of inlA to bind to mEcad. However, extended MD simulations of 200 ns in length show no destabilization of the inlA-mEcad complex and the estimation of the potential of mean force (PMF) using umbrella sampling corroborates this conclusion. The binding strength computed from the PMFs show no significant difference between the two protein complexes. Hence, our study suggests that the inability of L. monocytogenes to invade murine cells cannot be explained by processes at the nanosecond to sub-microsecond time scale probed by the simulations performed here.
我们报告了内蛋白 A (inlA) 与人或鼠 E-钙黏蛋白 (Ecad) 相互作用的研究。李斯特菌利用 inlA 将自身内化进入宿主细胞，但由于 hEcad 和 mEcad 序列的差异，细菌无法入侵鼠细胞。我们通过分子动力学模拟、MM/GBSA 自由能计算、氢键分析、水特征和伞状采样，提供了 inlA 与 Ecad 结合的完整原子图像。我们剖析了蛋白质-蛋白质界面中的关键残基，并使用 MM/GBSA 分析了其能量。从该分析中可以清楚地看出，inlA-mEcad 的结合比 inlA-hEcad 弱，与实验观察到的 inlA 无法与 mEcad 结合的结果一致。然而，200 ns 长度的扩展 MD 模拟显示 inlA-mEcad 复合物没有失稳，使用伞状采样估计平均力势 (PMF) 也证实了这一结论。从 PMFs 计算出的结合强度在两个蛋白质复合物之间没有显著差异。因此，我们的研究表明，李斯特菌无法入侵鼠细胞的现象不能仅用这里进行的模拟探测到的纳秒到亚微秒时间尺度上的过程来解释。
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