Electronic structure calculations on K^+ ion channel protein

我们开发了一种基于片段的分子轨道方法（FMO），用于蛋白质等大分子的电子结构计算。我们将这种方法应用于K+离子通道蛋白来阐明其渗透机制。对于大规模计算，我们改进了FMO方法，以提高PC集群并行处理的效率。本项目开发的FMO代码与GAMESS接口。利用该程序，我们在RHF/STO-3G水平上对由5902个原子组成的整个通道蛋白进行了FMO计算。在连接100基网络的10台Pentium IV个人计算机上，计算时间（运行时间）为13小时12分钟。计算结果表明，通道中K+离子的净电荷由+1变为+0.54 ~ +0.61，离子间的斥力大大降低。电荷转移主要发生在thr75和tyr78残基到K+离子上。thy75和tyr78残基被K+离子极化，羰基氧原子上分别产生-0.09和-0.04电荷。基于FMO方法的相互作用能分析表明，诱导电荷也稳定了通道中的K+离子。

We have developed a fragment-based molecular orbital method(FMO) for electronic structure calculations of large molecules such as proteins. We applied this method to K+ ion channel proteins to elucidate the permeation mechanism. For large scale calculations, we improved the FMO method to improve efficiency of parallel processing on PC clusters. The FMO codes developed in this project was interfaced with GAMESS. Using the program we performed the FMO calculations of the whole channel protein consisting of 5,902 atoms at the RHF/STO-3G level. The computational time (elapsed time) was 13 hours and 12 minutes on a ten Pentium IV personal computers connected with 100-base network.The calculated result showed that the net charge of K+ ions in the channel was changed from +1 to +0.54-+0.61 and the repulsion between the ions was largely reduced. The charge transfers mainly occurred form the thr75 and tyr78 residues to the K+ ions. The thy75 and tyr78 residues were polarized by the K+ ions and -0.09 and -0.04 charges were induced on the carbonyl oxygen atoms, respectively. An interaction energy analysis based on the FMO method revealed that the induced charges also stabilize the K+ ions in the channel.