Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, Chicago, IL 60637.
Department of Chemistry, Institute for Biophysical Dynamics, James Franck Institute, and Computation Institute, University of Chicago, Chicago, IL 60637
Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9396-401. doi: 10.1073/pnas.1401997111. Epub 2014 Jun 16.
The influenza A virus M2 channel (AM2) is crucial in the viral life cycle. Despite many previous experimental and computational studies, the mechanism of the activating process in which proton permeation acidifies the virion to release the viral RNA and core proteins is not well understood. Herein the AM2 proton permeation process has been systematically characterized using multiscale computer simulations, including quantum, classical, and reactive molecular dynamics methods. We report, to our knowledge, the first complete free-energy profiles for proton transport through the entire AM2 transmembrane domain at various pH values, including explicit treatment of excess proton charge delocalization and shuttling through the His37 tetrad. The free-energy profiles reveal that the excess proton must overcome a large free-energy barrier to diffuse to the His37 tetrad, where it is stabilized in a deep minimum reflecting the delocalization of the excess charge among the histidines and the cost of shuttling the proton past them. At lower pH values the His37 tetrad has a larger total charge that increases the channel width, hydration, and solvent dynamics, in agreement with recent 2D-IR spectroscopic studies. The proton transport barrier becomes smaller, despite the increased charge repulsion, due to backbone expansion and the more dynamic pore water molecules. The calculated conductances are in quantitative agreement with recent experimental measurements. In addition, the free-energy profiles and conductances for proton transport in several mutants provide insights for explaining our findings and those of previous experimental mutagenesis studies.
甲型流感病毒 M2 通道（AM2）在病毒生命周期中至关重要。尽管有许多先前的实验和计算研究，但质子渗透酸化病毒粒子以释放病毒 RNA 和核心蛋白的激活过程的机制仍未得到很好的理解。在此，我们使用多尺度计算机模拟系统地研究了 AM2 质子渗透过程，包括量子、经典和反应分子动力学方法。据我们所知，我们首次报道了在各种 pH 值下通过整个 AM2 跨膜结构域的质子传输的完整自由能谱，包括对过剩质子电荷离域和通过 His37 四联体穿梭的显式处理。自由能谱表明，过剩质子必须克服很大的自由能障碍才能扩散到 His37 四联体，在那里它稳定在一个深的最小值，反映了过剩电荷在组氨酸之间的离域和质子通过它们穿梭的成本。在较低的 pH 值下，His37 四联体的总电荷增加，从而增加了通道的宽度、水合作用和溶剂动力学，这与最近的 2D-IR 光谱研究一致。尽管由于排斥电荷增加，质子传输的势垒变小，但由于骨架扩张和更动态的孔水分子，质子传输的势垒变小。计算得到的电导率与最近的实验测量值定量一致。此外，质子在几种突变体中的传输自由能谱和电导率为解释我们的发现和先前的实验突变体研究提供了线索。
