COMPUTER SIMULATIONS OF ELECTRON TRANSFER PROTEINS

电子传递是能量流动的基本机制 呼吸作用和光合作用。电子转移的机制 蛋白质仍然是许多争论的主题。在这里提出的这项研究 是通过计算技术研究电子转移蛋白质，例如 分子动力学模拟。在这些方法中，运动的 蛋白质中的单个原子被建模。这项研究的目的是 一类电子转移的铁硫蛋白的模拟 蛋白质在实验上有很好的特性，但不是 模拟。大多数最初的研究将集中在Rubredoxins上， 它们只有一个熨斗。 初步步骤将包括对结构和动力学的简单研究 通过分子动力学模拟对Rubredoxin进行了研究。下一步将是 研究蛋白质环境如何影响铁硫结合部位。这个 电子必须行进的距离的大小和波动 有源位的偏振场可以从 模拟。活性中心类似物模拟的比较 解决方案可以洞察蛋白质环境如何改变 转移过程从简单化合物的转移过程 铁硫点。此外，还对同源Rubredoxins进行了模拟，对于 还有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。最终目标将是 发展研究电子量子力学现象的方法 调职。其中一项研究将涉及使用路径积分模拟 在蛋白质的环境中传递电子。另一种方法将 把电子转移看作是一个二能级系统。在本例中，一个 要计算的重要数量是相互作用能 蛋白质环境和电子密度(在波函数中 电子的表示)处于氧化和还原状态。

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.