Theoretical Studies of Biological Charge Transfer

细胞色素氧化酶（Cytochrome oxidase， COX）是线粒体呼吸系统电子传递链的末端组分，是细胞内负责能量生成的关键酶之一。COX是质子泵。提出的研究的总体目标是提高对这种酶和质子泵的能量转化的原理和分子机制的理解。本文将研究发生在COX中的电子和氧化还原耦合质子转移反应；在前一个资助期内发展的电子和质子转移的计算和理论方法将得到应用和进一步发展。具体项目如下：1)计算酶的四个氧化还原位点链上的电子转移速率和路径；隧道电流法的应用、测试及进一步发展。蛋白质中ET的音素模型分析（何时和乳清适用于蛋白质）。COX的动力学模拟及其对电子转移的动力学影响评价。2)计算酶在催化循环中各步骤的质子化状态作为其氧化还原状态的函数；发展非均质蛋白质的计算模型。关键可质子氨基酸突变效应的鉴定与研究。3) D-和k -通道中氧化还原耦合质子转移的研究。模拟酶中的水。电子耦合质子转移反应自由能率的研究。研究控制电子和质子转移反应速率的因素，以及酶的整体循环。4)建立质子泵的动力学模型，研究质子泵的效率、动力学要求和一般热力学原理。这些研究将有助于对生物能量转化的分子理解，并将为氧化还原蛋白的研究提供新的计算工具。

Cytochrome oxidase (COX) is the terminal component of electron transport chain of the respiratory system in mitochondria, and one of the key enzymes responsible for energy generation in cells. COX is a proton pump. The general goal of the proposed studies is to advanced understanding of the principles and molecular mechanisms of energy transformations in this enzyme and proton pumping. In the proposed work the electron and redox coupled proton transfer reactions occurring in COX will be investigated; the computational and theoretical methods for electron and proton transfer developed in the previous grant period will be applied and further advanced. The following specific projects will be undertaken: 1)Calculation of electron transfer rates and pathways along the chain of four redox sites of the enzyme; Application, test and further advancement of the Tunneling Current Method developed in the previous grant period. Analysis of phonemenological models of ET in proteins (when and whey they are applicable to proteins). Simulation of dynamics of COX and evaluation of the dynamic effects on electron transfer. 2) Calculation of the protonation state of the enzyme as a function of its redox state for various steps along the catalytic cycle; development of in homogenous protein computational models for such calculations. Identification and studies of the effects of mutations of key protonable amino acids. 3) Studies of the redox coupled proton transfer in D- and K-channels. Simulation of water in the enzyme. Studies of the free energy rates of electron coupled proton transfer reactions. Investigation of the factors that control rates of electron and proton transfer reactions, and the overall cycle of the enzyme. 4) Development of phenomenological kinetic models of proton pumps, investigation of their efficiency, kinetic requirements, and general thermodynamic principles. These studies will contribute to molecular understanding of biological energy transformations, and will result in new computational tools for investigation of redox proteins.