Coupled Protons and Electrons in Biological Systems

项目概要/摘要 控制电子和质子的运动对于广泛的生物过程至关重要，包括 细胞呼吸、DNA 生物合成和用于光遗传学的光接收。其中许多过程是 由通过质子耦合电子转移（PCET）形成酪氨酸或色氨酸自由基物种驱动。安 基本的 PCET 反应涉及一个电子和一个质子的转移，但更复杂的 PCET 过程涉及多个电子和质子的转移。 Hammes-Schiffer 小组开发了一种 通用 PCET 理论能够计算速率常数，并将该理论应用于仿生模型 系统和酶中的基本PCET。模拟更复杂的生物 PCET 过程是 由于氢隧道效应和构象运动的重要性以及关键 来自多个时间和长度尺度的贡献。该提案的一个主要目标是开发一个多尺度 描述各个 PCET 步骤的建模方法，包括电子和核量子 效应，以及与之相关的关键构象变化。量子化学和分子动力学 方法将用于计算 PCET 理论的输入量。计算出的速率常数为 单个 PCET 反应和蛋白质构象变化将作为微动力学模型的输入 能够完整描述复杂的多电子、多质子生物过程。这种多尺度 建模方法将与实验数据紧密联系，依赖于原子级结构和 热力学和动力学测量。最初，这种方法将应用于 PCET 中明确定义的、 α3X 蛋白的受控蛋白质环境，由具有单个内部的三个 α 螺旋组成 可以被电化学氧化的酪氨酸或色氨酸。这种方法将被扩展以探索多种 核糖核苷酸还原酶（RNR）更复杂的蛋白质环境中的电子、多质子反应。 该酶催化核苷酸转化为脱氧核苷酸，从而维持核苷酸 有效的 DNA 合成、复制和修复所需的库平衡。除了其生化作用外 重要的是，RNR 可以作为多步骤生物 PCET 的原型。长程自由基易位 RNR 中的约 35 Å 被认为是通过一系列涉及酪氨酸和色氨酸残基的 PCET 步骤发生的，如 以及显着的构象变化。最近解决的活性复合物的冷冻电镜结构 整个PCET途径并提供了理论研究的机会。这项工作将阐明其影响 蛋白质静电环境、溶剂可及性和 PCET 上的构象运动。它还将 深入了解各个 PCET 步骤如何相互耦合以及如何与蛋白质构象运动耦合 以及什么决定了步骤的顺序和总体速率。发现影响生物的因素 PCET 对于理解和控制各种重要的生化过程至关重要。这些 基本见解也可能对蛋白质设计和光遗传学产生更广泛的影响。

Project Summary/Abstract Controlling the movement of electrons and protons is critical for a wide range of biological processes, including cellular respiration, DNA biosynthesis, and photoreception used for optogenetics. Many of these processes are driven by the formation of tyrosine or tryptophan radical species via proton-coupled electron transfer (PCET). An elementary PCET reaction involves the transfer of one electron and one proton, but more complex PCET processes involve the transfer of multiple electrons and protons. The Hammes-Schiffer group has developed a general PCET theory enabling the calculation of rate constants and has applied this theory to biomimetic model systems and to elementary PCET in an enzyme. Simulating more complex biological PCET processes is challenging because of the significance of hydrogen tunneling and conformational motions, as well as key contributions from multiple time and length scales. A major goal of this proposal is to develop a multiscale modeling approach that describes the individual PCET steps, including the electronic and nuclear quantum effects, as well as the key conformational changes coupled to them. Quantum chemistry and molecular dynamics methods will be used to compute the input quantities to the PCET theory. The calculated rate constants for individual PCET reactions and protein conformational changes will serve as input into microkinetic models to enable the complete description of complex multi-electron, multi-proton biological processes. This multiscale modeling approach will be closely connected to experimental data, relying on atomic-level structures and thermodynamic and kinetic measurements. Initially this approach will be applied to PCET in the well-defined, controlled protein environment of the α3X proteins, which consist of three alpha helices with a single interior tyrosine or tryptophan that can be oxidized electrochemically. This approach will be expanded to explore multi- electron, multi-proton reactions in the more complex protein environment of ribonucleotide reductase (RNR). This enzyme catalyzes the conversion of nucleotides to deoxynucleotides, thereby maintaining the nucleotide pool balance required for effective DNA synthesis, replication, and repair. In addition to its biochemical importance, RNR serves as a prototype for multi-step biological PCET. The long-range radical translocation over ~35 Å in RNR is proposed to occur via a series of PCET steps involving tyrosine and tryptophan residues, as well as significant conformational changes. A recently solved cryo-EM structure of the active complex resolves the entire PCET pathway and provides an opportunity for theoretical studies. This work will elucidate the impact of the protein electrostatic environment, solvent accessibility, and conformational motions on PCET. It will also provide insights into how individual PCET steps are coupled to each other and to protein conformational motions and what determines the order of the steps and the overall rate. Discovering the factors that impact biological PCET is vital for understanding and controlling a wide range of essential biochemical processes. These fundamental insights may also have broader implications for protein design and optogenetics.