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

为了研究含辅基蛋白质的结构和电子性质，我们开发了一个用于蛋白质全电子计算的密度泛函（DFT）程序。在这项研究中，我们主要集中在DFT程序的计算效率。主要结果如下：1.对DFT程序进行了并行控制，提高了计算速度。采用面向对象技术，可以实现程序的安全、灵活的并行控制。通过面向对象编程的功能，明确实现了DFT的场景部分、计算部分、消息传递的控制部分和机器依赖部分之间的分离。用4个处理器单元对20个残基的肽进行全电子计算得到的计时数据表明，用分布式和/或大规模并行计算机可以实现对上千个原子的蛋白质的全电子计算。计算并存储到数据库中，以有效地估计蛋白质的初始密度。3. DFT程序的数据输入和结果分析可以通过我们独创的高效图形用户界面。前者用JAVA和VRML（虚拟现实建模语言）实现对蛋白质复杂电子状态的描述，后者基于AVS（应用可视化系统）实现高效、高质量的图形绘制。

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.