Dynamics of the Electron Transfer Reaction in Cytochrome b_5

细胞色素 b_5 中电子转移反应的动力学

基本信息

批准号：
06680650
负责人：
KITAO Akio
金额：
$ 1.41万
依托单位：
KYOTO UNIVERSITY
依托单位国家：
日本
项目类别：
Grant-in-Aid for General Scientific Research (C)
财政年份：
1994
资助国家：
日本
起止时间：
1994 至 1995
项目状态：
已结题

来源：
https://kaken.nii.ac.jp/en/grant/KAKENHI-PROJECT-06680650/
关键词：
Non-Adiabatic Electron Transfer Reaction Electronic Coupling Factor Frank-Condon Factor Normal Mode Solvent Effect Tanford-Kirkwood Model Cytochrome b5 Cytocrhome c 反応速度定数 Frank・Condon因子規準振動解析

项目摘要

Electron transfer is one of the most fundamental process in chemistry and biology. Theoretical frameworks describing non-adiabatic electron transfer process is well established through classical, semiclassical and quantum models. In all these theories, the basic assumption is that the electron transfer rate constant can be partitioned into two factors-the electronic coupling factor and the Frank-Condon factor.A new aproach is proposed in order to understand the relation between the protein modes and the electron transfer reaction, especially the Frank-Condon factor. We have presented a reduced spin-boson hamiltonian model where the bosonic bath is represented by the harmonic protein normal modes or the collective modes determined by the principal component analysis. Solvent effect is incorporated by the Tanford-Kirkwood model.The spin-boson model have been applied to the problem of electron transfer by others in previous studies. However, there are several new aspects that our work brings out. Our starting point is the normal mode analysis in the frequency domain. This allowed us to structurally identify all the bath modes in protein and solvent. This is important if one ones to correlate specific structural fluctuations of the protein to electron transfer coupling. Thus our model has all the advantages of a spin-boson model, with the added advantage that the individual bath modes are no more spatially anonymous. The present analysis is not just restricted to harmonic normal modes, but instead one can use data from a molecular dynamics run and through a principal component analysis.

电子转移是化学和生物学中最基本的过程之一。描述非绝热电子转移过程的理论框架已经通过经典、半经典和量子模型得到了很好的建立。在所有这些理论中，基本假设是电子转移速率常数可以分为两个因素——电子耦合因子和弗兰克-康登因子。为了理解蛋白质模式和分子间的关系，提出了一种新的方法。电子转移反应，尤其是弗兰克-康登因子。我们提出了一个简化的自旋玻色子哈密尔顿模型，其中玻色子浴由谐波蛋白质正常模式或由主成分分析确定的集体模式表示。 Tanford-Kirkwood 模型纳入了溶剂效应。自旋玻色子模型在之前的研究中已被其他人应用于电子转移问题。然而，我们的工作带来了几个新的方面。我们的出发点是频域中的简正模分析。这使我们能够从结构上识别蛋白质和溶剂中的所有浴模式。如果要将蛋白质的特定结构波动与电子转移耦合关联起来，这一点很重要。因此，我们的模型具有自旋玻色子模型的所有优点，还有一个额外的优点，即各个沐浴模式不再是空间匿名的。本分析不仅限于谐波简正模态，还可以使用来自分子动力学运行和主成分分析的数据。