COMPUTER SIMULATIONS OF ELECTRON TRANSFER PROTEINS

电子转移蛋白的计算机模拟

• 批准号: 2183059
• 负责人: Toshiko Ichiye
• 金额: $ 8.01万
• 依托单位: WASHINGTON STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 1992
• 资助国家: 美国
• 起止时间: 1992-02-01 至 1997-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2183059
• 关键词: computer data analysis; computer program /software; computer simulation; electrical potential; electron density; electron transport; intermolecular interaction; iron sulfur protein; molecular dynamics; molecular energy level; oxidation reduction reaction; protein structure function; quantum chemistry; rubredoxins; solutions; solvents

Electron transport is the essential mechanism for energy flow in respiration and photosynthesis. The mechanisms for electron transfer by proteins are still the subject of much debate. The research proposed here is to study electron transfer proteins by computational techniques such as molecular dynamics simulations. In these methods, the motions of individual atoms in a protein are modeled. This research is aimed at simulations of iron-sulfur proteins, which are a class of electron transfer proteins which are well characterized experimentally but not by simulations. Most of the initial studies will focus on the rubredoxins, which have a single iron. Preliminary steps will involve simple studies of the structure and dynamics of rubredoxin via molecular dynamics simulations. The next step will be to study how the protein environment influences the iron-sulfur site. The magnitudes and fluctuations of the distances the electron must travel and the polarization field at the active site can be calculated from the simulation. Comparison with simulations of analogs of the active site in solution can provide insight into how the protein environment alters the transfer process from what it would be for a simple compound with the same iron-sulfur site. Also, simulations of homologous rubredoxins, for which there are x-ray structures, can be used to determine how specific amino acid changes can influence the transfer. The eventual goal will be to develop methods for studying the quantum mechanical phenomena of electron transfer. One study will involve using path integral simulations of the transfer electron in the environment of the protein. Another approach will be to consider electron transfer as a two-level system. In this case, an important quantity to calculate is the interaction energy between the protein environment and the electron density (in the wavefunction representation of the electron) in the oxidized and reduced states.

电子输运是能量流动的基本机制， 呼吸和光合作用。 电子转移的机制， 蛋白质仍然是许多争论的主题。 这里提出的研究 是通过计算技术来研究电子转移蛋白， 分子动力学模拟 在这些方法中， 蛋白质中的单个原子被建模。 本研究的目的是 铁硫蛋白的模拟，这是一类电子转移 这些蛋白质在实验上得到了很好的表征，但没有被 模拟 大多数最初的研究将集中在红蛋白， 只有一个铁。 初步的步骤将涉及结构和动力学的简单研究 rubredoxin的分子动力学模拟。 下一步将 研究蛋白质环境如何影响铁硫位点。 的 电子必须行进的距离的大小和波动， 在活性位点处的极化场可以由 仿真 与活性位点类似物的模拟比较， 解决方案可以深入了解蛋白质环境如何改变 从简单化合物的转移过程， 铁硫部位 此外，模拟同源rubredoxins，其中 有x射线结构，可以用来确定具体的氨基 酸的变化会影响转移。 最终目标是 发展研究电子的量子力学现象的方法 转移 一项研究将涉及使用路径积分模拟的 在蛋白质的环境中传递电子。 另一种方法将 将电子转移视为两能级系统。 在本例中， 要计算的重要量是， 蛋白质环境和电子密度（在波函数中 在氧化和还原状态下的电子的表示）。