Baştuğ Turgut, Patra Swarna M, Kuyucak Serdar
School of Physics, University of Sydney, NSW, Australia.
Chem Phys Lipids. 2006 Jun;141(1-2):197-204. doi: 10.1016/j.chemphyslip.2006.02.012. Epub 2006 Mar 20.
Molecular dynamics simulations of membrane proteins have become a popular tool for studying their dynamic features, which are not easily accessible by experiments. Whether the force fields developed for globular proteins are adequate this purpose is an important question that is often glossed over. Here we determine the permeation properties of potassium ions in the gramicidin A channel in a lipid bilayer from free energy simulations, and compare the results to experimental data. In particular, we check the dependence of the free energy barriers ions face at the channel center on the membrane size. The results indicate that there is a serious problem with the current rigid force fields independent of the membrane size, and new, possibly polarizable, force fields need to be developed to resolve this problem.
膜蛋白的分子动力学模拟已成为研究其动态特征的常用工具，而这些特征通过实验难以获得。为球状蛋白开发的力场是否适用于此目的是一个常被忽视的重要问题。在此，我们通过自由能模拟确定了脂双层中短杆菌肽A通道内钾离子的渗透特性，并将结果与实验数据进行比较。特别是，我们检查了离子在通道中心所面临的自由能垒对膜大小的依赖性。结果表明，当前与膜大小无关的刚性力场存在严重问题，需要开发新的、可能具有极化性的力场来解决这一问题。
