COMPUTER SIMULATIONS OF ELECTRON TRANSFER PROTEINS

电子转移蛋白的计算机模拟

• 批准号: 6018823
• 负责人: Toshiko Ichiye
• 金额: $ 12.84万
• 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 2001-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6018823
• 关键词: Azotobacter vinelandii; Clostridium; Desulfovibrio; bacterial proteins; computer simulation; electrical potential; electron transport; ferredoxin; intermolecular interaction; ionic bond; iron sulfur protein; mathematical model; molecular dynamics; molecular energy level; molecular site; oxidation reduction reaction; protein structure function; rubredoxins; solvents

DESCRIPTION: One of the most intriguing questions about the electron transfer proteins is how the protein modifies the electron transfer properties of a given type of redox site. It is crucial to know, not only the structure of these proteins, but also the structural origins of their electron transfer properties, to gain an understanding of the molecular basis of disease and drug design. The overall goal of this research is to understand the electron transfer properties particularly the donor/acceptor energetic interactions, of electron transfer proteins at a molecular level using computer simulations and other theoretical methods. The focus is on the iron-sulfur proteins, especially the single (Fe) rubredoxins and the 2(Fe-4S) (and structurally related) ferredoxins. These ubiquitous proteins are involved in fundamental processes such as respiration and photosynthesis. In addition, the ferrodoxins are homologous to a variety of more complex enzymes. However, despite the rapidly growing number of crystal structures, the structural origins of the redox potentials for these proteins remain unclear. The premise is that they are mainly due to the electrostatic effects of the polar backbone, polar side chains and solvent. In particular, the changes in solvent accessibility upon reduction observed in MD simulations of rubredoxins can explain some of the puzzling data from mutational studies. Moreover, since the total electrostatics is the sum of many small contributions from both the protein and the solvent, rather than a few key interactions, these competing effects are often difficult to resolve from structural data alone. The approach of Dr. Ichiye is mainly based on MD simulations of the protein, which are crucial to understanding these complex phenomena, in conjunction with come supplementary electronic structure calculations of redox site analogs, thus giving a complete picture of the protein. The first two aims specific aims concern the rubredoxins and the ferredoxins and involve using MD methods to predict difference in redox potentials in mutated or homologous proteins and then to look for their structural origins, thus providing the crucial link between experimental and structures and redox potentials. The third specific aim involves using MD simulations to examine the contribution of nuclear polarization to intermolecular electron transfer in the ferrodoxins, which may be key to understanding the significance of the two redox sites, since there relatively little experimental data in this case. These three aims will lead to a fuller understanding of the proteins involved in electron transport chains and how they determine energy flow in processes such as respiration and photosynthesis.

描述：关于电子最有趣的问题之一 转移蛋白是蛋白质如何改变电子转移 给定类型的氧化还原位点的性质。 重要的是要知道，不仅 这些蛋白质的结构，以及它们的结构起源， 电子转移性质，以了解分子 疾病和药物设计的基础。 本研究的总体目标是 了解电子转移特性，特别是供体/受体 电子传递蛋白质在分子水平上的能量相互作用 使用计算机模拟和其他理论方法。 重点是 铁硫蛋白，特别是单一的（Fe）红蛋白和 2（Fe-4S）（和结构相关的）铁氧化还原蛋白。 这些无处不在的蛋白质 参与呼吸等基本过程， 光合作用 此外，铁氧蛋白与多种 更复杂的酶。 然而，尽管人数迅速增加， 晶体结构，这些氧化还原电位的结构起源 蛋白质仍不清楚。 前提是，它们主要是由于 极性主链、极性侧链和溶剂的静电效应。 特别是，观察到还原后溶剂可及性的变化 在分子动力学模拟的红蛋白可以解释一些令人困惑的数据， 突变研究 此外，由于总的静电是 蛋白质和溶剂的许多小贡献，而不是 一些关键的相互作用，这些竞争的影响往往很难 仅从结构数据中解决。 一叶博士的方法主要是 基于对蛋白质的MD模拟，这对于理解 这些复杂的现象，加上补充的电子 氧化还原位点类似物的结构计算，从而给出完整的图片 蛋白质。 前两个目标的具体目标涉及红蛋白 和铁氧化还原蛋白，并涉及使用MD方法来预测差异， 突变或同源蛋白质的氧化还原电位，然后寻找 它们的结构起源，从而提供了 实验和结构和氧化还原电位。 第三个具体目标 包括使用MD模拟来检查核的贡献， 极化到分子间电子转移的铁蛋白， 可能是理解这两个氧化还原位点重要性的关键， 在这种情况下，实验数据相对较少。 这三个目标 将导致对参与电子传递的蛋白质的更全面的理解。 运输链以及它们如何决定诸如 呼吸和光合作用。