Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91, Stockholm, Sweden.
Chem Soc Rev. 2020 Oct 19;49(20):7301-7330. doi: 10.1039/d0cs00877j.
Heme-copper oxidases are transmembrane enzymes involved in aerobic and anaerobic respiration. The largest subgroup contains the cytochrome c oxidases (CcO), which reduce molecular oxygen to water. A significant part of the free energy released in this exergonic process is conserved as an electrochemical gradient across the membrane, via two processes, electrogenic chemistry and proton pumping. A deviant subgroup is the cytochrome c dependent NO reductases (cNOR), which reduce nitric oxide to nitrous oxide and water. This is also an exergonic reaction, but in this case none of the released free energy is conserved. Computational studies applying hybrid density functional theory to cluster models of the bimetallic active sites in the heme-copper oxidases are reviewed. To obtain a reliable description of the reaction mechanisms, energy profiles of the entire catalytic cycles, including the reduction steps have to be constructed. This requires a careful combination of computational results with certain experimental data. Computational studies have elucidated mechanistic details of the chemical parts of the reactions, involving cleavage and formation of covalent bonds, which have not been obtainable from pure experimental investigations. Important insights regarding the mechanisms of energy conservation have also been gained. The computational studies show that the reduction potentials of the active site cofactors in the CcOs are large enough to afford electrogenic chemistry and proton pumping, i.e. efficient energy conservation. These results solve a conflict between different types of experimental data. A mechanism for the proton pumping, involving a specific and crucial role for the active site tyrosine, conserved in all CcOs, is suggested. For the cNORs, the calculations show that the low reduction potentials of the active site cofactors are optimized for fast elimination of the toxic NO molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high barriers. To prevent even higher barriers, which would lead to a too slow reaction, when the electrochemical gradient across the membrane is present, the chemistry must occur in a non-electrogenic manner. This explains why there is no energy conservation in cNOR.
血红素铜氧化酶是参与需氧和厌氧呼吸的跨膜酶。最大的亚组包含细胞色素 c 氧化酶（CcO），它将分子氧还原为水。在这个放能过程中，大部分自由能通过两个过程——电生成化学和质子泵——以电化学梯度的形式储存在膜内。一个异常的亚组是细胞色素 c 依赖的一氧化氮还原酶（cNOR），它将一氧化氮还原为一氧化二氮和水。这也是一个放能反应，但在这种情况下，释放的自由能没有被储存。综述了应用杂化密度泛函理论对血红素铜氧化酶中双金属活性位点团簇模型进行的计算研究。为了获得反应机制的可靠描述，必须构建整个催化循环的能量曲线，包括还原步骤。这需要仔细结合计算结果和某些实验数据。计算研究阐明了反应的化学部分的机制细节，包括共价键的断裂和形成，这些细节无法从纯实验研究中获得。关于能量守恒机制的重要见解也已经获得。计算研究表明，CcO 中活性位点辅因子的还原电位足够大，可以进行电生成化学和质子泵，即有效的能量储存。这些结果解决了不同类型的实验数据之间的冲突。提出了一种质子泵机制，涉及所有 CcO 中保守的活性位点酪氨酸的特定和关键作用。对于 cNOR，计算表明，活性位点辅因子的低还原电位优化了快速消除有毒的 NO 分子。同时，低还原电位导致具有高势垒的吸能还原步骤。为了防止当膜内存在电化学梯度时，即使更高的势垒导致反应过慢，化学必须以非电生成的方式发生。这解释了为什么 cNOR 中没有能量储存。
