Bastug Turgut, Kuyucak Serdar
School of Physics, University of Sydney, NSW 2006, Australia.
Eur Biophys J. 2005 Jul;34(5):377-82. doi: 10.1007/s00249-005-0463-2. Epub 2005 Feb 12.
The force fields commonly used in molecular dynamics simulations of proteins are optimized under bulk conditions. Whether the same force fields can be used in simulations of membrane proteins is not well established, although they are increasingly being used for such purposes. Here we consider ion permeation in the gramicidin A channel as a test of the AMBER force field in a membrane environment. The potentials of mean force for potassium ions are calculated along the channel axis and compared with the one deduced from the experimental conductance data. The calculated result indicates a rather large central barrier similar to those obtained from other force fields, which are incompatible with the conductance data. We suggest that lack of polarizability is the most likely cause of this problem, and, therefore, urge development of polarizable force fields for simulations of membrane proteins.
常用于蛋白质分子动力学模拟的力场是在本体条件下优化的。尽管这些力场越来越多地用于膜蛋白模拟，但同样的力场是否能用于膜蛋白模拟尚未得到充分证实。在这里，我们将短杆菌肽A通道中的离子渗透作为膜环境中AMBER力场的一个测试。沿着通道轴计算钾离子的平均力势，并与从实验电导数据推导得到的平均力势进行比较。计算结果表明存在一个相当大的中心势垒，这与从其他力场得到的结果类似，与电导数据不相符。我们认为缺乏极化率是这个问题最可能的原因，因此，敦促开发用于膜蛋白模拟的可极化力场。
