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Theoretical Study on Electronic States and Electron Transfer Pathways in Proteins Containing Prosthetic Groups

含辅基蛋白质电子态和电子传递途径的理论研究

基本信息

批准号：
07640682
负责人：
KASHIWAGI Hiroshi
金额：
$ 1.41万
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：
1995
资助国家：
日本
起止时间：
1995 至 1996
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-07640682/
关键词：
PROTEINS DENSITY FUNCTIONAL THEORY OBJECT ORIENTED PROGRAMMING CYTOCHROME C_2 OBJECT ORIENTED CONCURRENCY AVS JAVA VRML チトクロムc_3 確率オートマトン GUI

项目摘要

In order to understand the structural and electronic Properties of proteins containing prosthetic groups, we developed a density functional thcory (DFT) program for all-electron calculations of proteins. In this study, we mainly focused on the computational efficicncies of the DFT-program. The results were summarized as follows :1.The parallel control of our DFT program has been implemented to makc calculations faster. The object oriented technology is useful to attain the safe and flexible parallel control of our program. The separation between scenario parts of the DFT,calculation parts, control parts of the message passing, and machine dependent parts was clearly achieved by the function of the object oriented programming. The timing data from an all-electron calculation of 20 residues peptides with 4 processor units suggests that all-electron calculations of proteins over thousand atoms are realizable with distributed and/or massively parallel computers.2.The electron density of both amino acids and a prosthetic group, heme, were calculated and stored to a database for effective estimation of the initial density of proteins.3.Data input of the DFT program and analyzes of results could be controlled through our original efficient graphical user interface. The former was coded in JAVE and VRML (Virtual Rcality Modeling Language) to designate the complicated electronic states of proteins, while the latter was based on AVS (Application Visualization System) to make efficient graphics with high quality.

为了了解含有辅基的蛋白质的结构和电子特性，我们开发了用于蛋白质全电子计算的密度泛函理论（DFT）程序。在本研究中，我们主要关注 DFT 程序的计算效率。结果总结如下： 1.我们的DFT程序的并行控制已经实现，使kc计算更快。面向对象技术有助于实现程序的安全、灵活的并行控制。面向对象编程的功能清楚地实现了DFT的场景部分、计算部分、消息传递的控制部分和机器相关部分之间的分离。使用 4 个处理器单元对 20 个残基肽进行全电子计算的计时数据表明，可以通过分布式和/或大规模并行计算机实现对数千个原子的蛋白质的全电子计算。2.计算氨基酸和辅基血红素的电子密度并将其存储到数据库中，以便有效估计蛋白质的初始密度。3.DFT 的数据输入程序和结果分析可以通过我们独创的高效图形用户界面进行控制。前者用JAVE和VRML（虚拟现实建模语言）编码，用于指定蛋白质的复杂电子状态，而后者基于AVS（应用可视化系统），以制作高质量的高效图形。