Electronic structure calculations on K^+ ion channel protein

K^离子通道蛋白的电子结构计算

• 批准号: 14540482
• 负责人: KITAURA Kazuo
• 金额: $ 2.62万
• 依托单位: National Institute of Advanced Industrial Science and Technology (AIST)
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 2002
• 资助国家: 日本
• 起止时间: 2002 至 2003
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-14540482/
• 关键词: MO calculation of protein; channel protein; fragment MO method; potassium ion channel; large scale MO calculations; 大規模系の電子状態計算; カリウムイオンの透過機構

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.

我们发展了一种基于碎片的分子轨道方法（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，以阐明渗透机制。对于大规模计算，我们改进了FMO方法，以提高PC机群上的并行处理效率。在这个项目中开发的FMO代码与GAMESS接口。用该程序在RHF/STO-3G水平上对由5，902个原子组成的整个通道蛋白进行了FMO计算。在10台PentiumIV个人计算机上，用100个碱基的网络进行了13小时12分钟的计算，计算结果表明，通道中K ~+离子的净电荷由+1变为+0.54 ~+0.61，离子间的排斥作用大大降低。电荷转移主要发生在thr 75和tyr 78残基与K+之间。通过K+离子极化thy 75和tyr 78残基，并且在羰基氧原子上分别诱导-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。

项目成果

K.Nagayoshi, K.Kitaura, S.Koseki, S.Re, K.Kobayashi, Y-K.Choe, S.Nagase: "Calculation of packing structure of methanol solid using ab initio lattice energy at the MP2 level"Chem. Phys. Lett.. 369. 597-607 (2003)

K.Nagayoshi、K.Kitaura、S.Koseki、S.Re、K.Kobayashi、Y-K.Choe、S.Nagase：“使用 MP2 级别的从头晶格能计算甲醇固体的堆积结构”Chem。

The importance of three-body terms in the fragment molecular orbital method

• DOI: 10.1063/1.1687334
• 发表时间: 2004-04-15
• 期刊: JOURNAL OF CHEMICAL PHYSICS
• 影响因子: 4.4
• 作者: Fedorov, DG;Kitaura, K
• 通讯作者: Kitaura, K

Dmitri G.Fedorov, Kazuo Kitaura: "On the accuracy of the 3-body fragment molecular orbital method (FMO) applied to density functional theory"Chemical Physics Letters. in press.

Dmitri G.Fedorov、Kazuo Kitaura：“论三体碎片分子轨道法 (FMO) 应用于密度泛函理论的准确性”《化学物理快报》。

Dmitri G.Fedorov, Kazuo Kitaura: "A new hierarchical parallelization scheme : generalized distributed data interface (GDDI), and an application to the fragment molecular orbital method (FMO)"Journal of Computational Chemistry. 25. 872-880 (2004)

Dmitri G.Fedorov、Kazuo Kitaura：“一种新的分层并行化方案：广义分布式数据接口 (GDDI) 以及片段分子轨道方法 (FMO) 的应用”计算化学杂志。

Y.Komeiji, T.Nakano, K.Fukuzawa, Y.Ueno, Y.Inadomi, T.Nemoto, M.Uebayasi, D.G.Fedorov, K.Kitaura: "Fragment molecular orbital method : application to molecular dynamics simulation, "ab initio FMO-MD""Chem. Phys. Lett.. 372. 342-347 (2003)

Y.Komeiji、T.Nakano、K.Fukuzawa、Y.Ueno、Y.Inadomi、T.Nemoto、M.Uebayasi、D.G.Fedorov、K.Kitaura：“片段分子轨道方法：在分子动力学模拟中的应用”，从头开始