Theoretical Study on Electronic States and Electron Transfer Process in Proteins Containing Some Pigments

含色素蛋白质电子态及电子转移过程的理论研究

• 批准号: 09640611
• 负责人: KASHIWAGI Hiroshi
• 金额: $ 2.05万
• 依托单位: KYUSHU INSTITUTE OF TECHNOLOGY
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for Scientific Research (C)
• 财政年份: 1997
• 资助国家: 日本
• 起止时间: 1997 至 1999
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-09640611/
• 关键词: DENSITY FUNCTIONAL THEORY; PROTEINS; ALL-ELECTRON CALCULATIONS; LARGE SYSTEMS COMPUTATION; CONVERGENCE METHOD; BDS-I; PARALLEL CONTROL; オブジェクト指向による並列化; 非局所補正法; タンパク質内電子トンネリング; シトクロムc; オブジェクト指向プログラミング; ROKS法; シトクロムc_3; 大次元行列対角化の並列化; 大次元逆行列計算

In order to understand the electronic properties of whole proteins, we developed a density functional (DF) theory program for all-electron calculations of proteins. In this study, we achieved all-electron calculation of small protein and developed system to investigate electron tunneling mechanism in proteins. The results were summarized as follows :1. The parallel control of our DF program has been implemented to make calculations faster. The object oriented technology is useful to attain the safe and flexible parallel control of our program. The efficiency of parallel control with dozens of workstation clusters was over 80%.2. We added the function removing the linear dependence of calculations into our DF program.3. We newly introduced the restricted open-shell Kohn Sham (ROKS) method and adopted to the calculation of 4 active centers of cytochrome cィイD23ィエD2.4. We improved the computational accuracies of electron tunneling calculations in proteins by using Feynman's path integral method.5. The fast algorism to estimate non-local exchange-correlation potential, BLYP, was originally developed, and introduced into our DF program.6. The electron transfer pathways in Ru-modified cytochrome c were simulated under model potential, and 3 main pathways were observed.7. Some convergence techniques were originally developed for attaining the all-electron calculations of small proteins.8. We achieved all-electron calculation of BDS-I which is 43 residues proteins. This is the first all-electron calculation of protein with DF method.

为了了解整个蛋白质的电子性质，我们开发了一个用于蛋白质全电子计算的密度泛函（DF）理论程序。本研究实现了小分子蛋白质的全电子计算，开发了研究蛋白质电子隧穿机制的系统。主要研究结果如下：1.我们的DF程序的并行控制已经实现，使计算速度更快。采用面向对象技术，可以实现程序的安全、灵活的并行控制。在数十台工作站机群上并行控制效率达到80%以上.我们在DF程序中加入了去除计算线性相关的功能。本文引入了限制性开壳层Kohn Sham（ROKS）方法，并将其应用于细胞色素c的4个活性中心的计算。利用费曼路径积分方法提高了蛋白质电子隧穿计算的计算精度.提出了一种计算非定域交换关联势的快速算法BLYP，并将其引入到我们的DF程序中.在模型电位下模拟了钌修饰细胞色素c的电子传递途径，得到了3条主要的电子传递途径.一些收敛技术最初是为了实现小分子蛋白质的全电子计算而开发的。我们对43个残基的蛋白质BDS-I进行了全电子计算。这是首次用DF方法对蛋白质进行全电子计算。

项目成果

I.Okazaki,F.Sato,T.Yoshihiro,T.Ueno,and H.Kashiwagi: "Development of a Restricted Open Shell Kohn-Sham Program and its Application to a Model Heme Complex" THEOCHEM. 451. 109-119 (1998)

I.Okazaki、F.Sato、T.Yoshihiro、T.Ueno 和 H.Kashiwagi：“受限开壳 Kohn-Sham 程序的开发及其在血红素复合物模型中的应用”THEOCHEM。

F.Sato et al.: "Development of A New Density Functional Program for All Electron Calculation of Proteins" Int.J.Quant.Chem.63. 245-256 (1997)

F.Sato 等人：“开发用于蛋白质全电子计算的新密度泛函程序”Int.J.Quant.Chem.63。

F. Sato, T. Yoshihiro, I. Okazaki, H. Kashiwagi: "An all-electron calculation of an antihypertensive protein with the Gaussian-based density functional method"Chem. Phys. Lett.. 310. 523-529 (1999)

F. Sato、T. Yoshihiro、I. Okazaki、H. Kashiwagi：“使用基于高斯的密度泛函方法对抗高血压蛋白质进行全电子计算”Chem。

F.Sato,T.Yoshihiro,I.Okazaki and H.Kashiwagi: "Recent Progress in Computational Methods of Electronic States in Proteins with Density Functional Method"Proc.of the 195th Meeting of the Elecrochem.Soc.. 99(1). 937-937 (1999)

F.Sato、T.Yoshihiro、I.Okazaki 和 H.Kashiwagi：“用密度泛函方法计算蛋白质电子态方法的最新进展”Proc.of the 195th Meeting of the Elecrochem.Soc.. 99(1)。

I.Okazaki,F.Sato,and H.Kashiwagi: "A Theoretical Evaluation of the Ionization Potentials for One-Electron Oxidized States of Cytochrome c" THEOCHEM. (in press). (1998)

I.Okazaki、F.Sato 和 H.Kashiwagi：“细胞色素 c 的单电子氧化态电离势的理论评估”THEOCHEM。