Computer Simulations of Electron Transfer Proteins

电子转移蛋白质的计算机模拟

• 批准号: 7932671
• 负责人: Toshiko Ichiye
• 金额: $ 10.52万
• 依托单位: GEORGETOWN UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2009
• 资助国家: 美国
• 起止时间: 2009-09-30 至 2009-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7932671
• 关键词: Affect; Anabolism; Area; Biodegradation; Bioinformatics; Biological Process; Computer Simulation; Data; Disease; Drug Design; Electron Transport; Electronics; Electrons; Electrostatics; Environment; Ferredoxin; Free Energy; Goals; Hydrogen Bonding; Iron-Sulfur Proteins; Knowledge; Metabolism; Metals; Methods; Modeling; Molecular; Mutation; Nature; Oxidation-Reduction; Photosynthesis; Play; Process; Property; Proteins; Quantum Mechanics; Research; Research Personnel; Respiration; Roentgen Rays; Role; Rubredoxins; Sequence Analysis; Side; Site; Solvents; Sorting - Cell Movement; Spectrum Analysis; Structure; Synchrotrons; Vertebral column; Work; analog; base; biotin synthase; computerized tools; density; driving force; electronic structure; molecular dynamics; molecular mechanics; mutant; programs; theories

One of the most intriguing questions about electron transfer proteins is how the protein modifies the electron transfer properties of its redox site. This knowledge is crucial in understanding the molecular basis of a variety of metabolic processes, diseases involving these processes, and drug design targeting these processes. The overall goal is to understand the properties of electron transfer proteins at a molecular level. The focus is on the iron-sulfur proteins, which are ubiquitous proteins involved in fundamental processes such as respiration, photosynthesis, biosynthesis, and biodegradation. Our approach uses electrostatic potential calculations, molecular dynamics simulations, electronic structure calculations, and sequence analysis. Our studies cover three essential areas: (1) the reduction potentials (E),which determine the driving force for electron transfer, (2) the protein reorganization energy, which must play a role in how proteins can move electrons so efficiently and quickly, and (3) cluster conversion, which is important in the function and formation of many Fe-Sproteins. Studies will be mainly on the 2[4Fe-4S] ferredoxins and biotin synthase. The specific aimsare: Aim 1. The origins of differences in E due to polar groups in Fe-Sproteins will be determined. Our working model is that hydrogen bonds to the redox site affect E mainly by the electrostatics of the hydrogen bond donor dipole rather than by electronic perturbation. Aim 2. The nature of the reorganization energy of Fe-Sproteins will be determined. Our working model is that sequence differences can affect the reorganization energy via hydrogen bonds. Aim 3. The mechanisms of cluster conversion in Fe-S analogs and proteins will be determined . Our working model is that spin delocalization and redox state are important.

关于电子转移蛋白最耐人寻味的问题之一是蛋白质如何改变电子。 其氧化还原位的转移性质。这一知识对于理解分子基础是至关重要的。 代谢过程的多样性，涉及这些过程的疾病，以及针对这些过程的药物设计 流程。总体目标是在分子水平上了解电子转移蛋白的性质。 重点放在铁硫蛋白上，这是一种参与基本过程的普遍存在的蛋白质。 如呼吸作用、光合作用、生物合成和生物降解。我们的方法是使用静电 势计算、分子动力学模拟、电子结构计算和序列 分析。我们的研究包括三个基本方面：(1)还原电位(E)，它决定了 电子传递的驱动力，(2)蛋白质重组能，它必须如何发挥作用 蛋白质可以如此高效和快速地移动电子，以及(3)团簇转换，这在 多种铁蛋白的功能和形成。研究将主要集中在2[4Fe-4S]铁氧还蛋白和生物素 合成酶。具体目标是： 目的1.确定Fe-S蛋白中极性基团导致E差异的原因。我们的工作 模型认为，氧化还原位上的氢键主要通过氢键的静电作用来影响E 施主偶极而不是电子微扰。 目的2.确定铁蛋白重组能的性质。我们的工作模式是 这种序列差异可以通过氢键影响重组能量。 目的3.确定铁-S类似物和蛋白质中的簇状转化机制。我们的 工作模型是自旋离域和氧化还原态是重要的。