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Activation of O2 and NO in Heme-Copper Oxidases – Chem Soc Rev View Article Online REVIEW ARTICLE View Journal | View Issue Activation of O2 and NO in heme-copper oxidases – mechanistic insights from Cite this: Chem. Soc. Rev., 2020, 49,7301 computational modelling Margareta R. A. Blomberg 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 Creative Commons Attribution-NonCommercial 3.0 Unported Licence. 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 This article is licensed under a 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 Received 9th July 2020 molecules. At the same time, the low reduction potentials lead to endergonic reduction steps with high Open Access Article. Published on 02 October 2020. Downloaded 10/4/2021 2:47:52 AM. DOI: 10.1039/d0cs00877j 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 rsc.li/chem-soc-rev explains why there is no energy conservation in cNOR. 1. Introduction The NORs are found in denitrifying bacteria and reduce nitric oxide to nitrous oxide as one of the steps in the nitrogen An important group of enzymes involved in cellular energy cycle. The best characterized NORs use electrons from soluble conservation is the superfamily of heme-copper oxidases. The cytochrome c (cNOR), with a reduction reaction described in superfamily is defined by amino acid sequence homology in a eqn (2): core subunit, and it contains both cytochrome c oxidases (CcO) 1 + À and the divergent nitric oxide reductases (NOR). The CcOs are 2NO + 2H +2ecytc - N2O+H2O (2) found in mitochondria and bacteria, and use electrons from soluble cytochrome c to reduce molecular oxygen to water as One of the most intriguing issues in the field of bioenergetics the last step in the respiratory chain in aerobic organisms concerns when and how the free energy released in exergonic according to eqn (1): reactions is conserved, to be used at a later stage by the organisms. The overall exergonicities of the reduction processes O +4H+ +4e À - 2H O (1) 2 cytc 2 described above are determined by the difference in reduction potential (midpoint potential) between the electron donor, soluble Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, cytochrome c, and the electron acceptor, molecular oxygen or nitric SE-106 91, Stockholm, Sweden. E-mail: [email protected]; Tel: +46-816-2616 oxide. The reduction potential of soluble cytochrome c is 0.25 V, This journal is © The Royal Society of Chemistry 2020 Chem. Soc. Rev., 2020, 49, 7301--7330 | 7301 View Article Online Review Article Chem Soc Rev Fig. 2 Sketch of the redox-active cofactors in the BNC active sites of the heme-copper oxidase subfamilies, indicating the type of high-spin heme group (a3 or b3) and the type of non-heme metal (CuB or FeB)ineach subfamily. The tyrosine in the CcOs is cross-linked to one of the histidine ligands on CuB. The A, B and C families are denoted by the CcO subindices. Fig. 1 Overview of the overall main reactions in CcO (left, showing the situation in the A family) and cNOR (right), with the binuclear active site (BNC) and the other redox-active cofactors indicated. The electron and metal. The CcOs have a copper ion as the non-heme metal, CuB, proton uptake to the BNC is indicated with arrows, as well as the proton and in the cNORs the copper ion is replaced by a non-heme pumping across the membrane in CcO. The figure is reprinted from ref. 12. iron, FeB, see Fig. 1 and 2. The reduced soluble cytochrome c, Copyright (2018), with permission from Elsevier. located on the positive side of the membrane, delivers the electrons to the BNC via a number of cofactors, which are the potential for the reduction of molecular oxygen to water is 0.8 V Cu-complexes and/or low-spin heme groups. Regarding the (per electron) and the reduction of nitric oxide to nitrous oxide and protons needed for the chemistry there is an important difference water has a potential of 1.177 V (per electron). This means that between the types of heme-copper oxidases. In the CcOs the both reactions are quite exergonic, eqn (1) by 50.7 kcal molÀ1 chemical protons are taken from the opposite side of the membrane, À1 Creative Commons Attribution-NonCommercial 3.0 Unported Licence. (2.2 V), and eqn (2) by 42.8 kcal mol (1.854 V). A significant part compared to the electrons, the negative side, which means that the of the free energy in the oxygen reduction process is conserved as chemical process corresponds to a charge separation across the an electrochemical gradient across the mitochondrial or bacterial membrane, referred to as an electrogenic reaction. In the cNORs, on membrane, in which the CcO enzymes are located.2 The gradient the other hand, the protons are taken from the same side of the isusedbytheenzymeATP-synthasetomakeATP,theenergy membrane as the electrons, the positive side, the chemistry is currency of the cell. In contrast, it has been found that none of non-electrogenic. In the CcOs there is also a second process that the free energy is conserved in the reduction of nitric oxide contribute to the charge separation, the chemistry is coupled to taking place in the bacterial membrane.3–5 An interesting a translocation of protons across the entire membrane, referred 2 observation is that in some of the heme-copper oxidases there to as proton pumping. Thus, in the CcOs there are two processes This article is licensed under a is a cross-reactivity, which means that they can reduce both contributing to the energy conservation in terms of building up 6–11 substrates, O2 and NO. an electrochemical gradient across the membrane, electrogenic In Fig. 1 an overview is given of the two types of heme-copper chemistry and proton pumping. In the cNORs there is neither Open Access Article. Published on 02 October 2020. Downloaded 10/4/2021 2:47:52 AM. oxidases to be discussed in the present review, CcO and cNOR. electrogenic chemistry nor proton pumping, i.e. no energy conserva- The active site, where the reduction chemistry takes place, tion, compare Fig. 1. The most essential questions concerning the is similar in all heme-copper oxidases, and it is referred to heme-copper oxidases include how the proton pumping is achieved, as the binuclear center (BNC). The BNC is composed of two i.e. how one electron can trigger the uptake of two protons, but also redox-active metal ions: a high-spin heme iron and a non-heme why there is no energy conservation in the cNOR enzymes. A large amount of knowledge about the structure and function of the heme-copper oxidases has been obtained from experimental Margareta R. A. Blomberg received investigations, both for the CcOs1,13–16 and the cNORs.17–19 her PhD in the field of quantum However, many questions regarding the details of the reaction chemistry at the Department of mechanisms and the energetics of particular reaction steps are Physics, Stockholm University in better answered by computational studies, or rather by a combi- 1983. After a postdoctoral period nation of experimental and computational data. Quantum at the IBM San Jose research mechanical calculations (using hybrid density functional theory) laboratory with Bowen Liu, she on cluster models of the BNC active site in the heme-copper returned to Stockholm University. oxidases are well suited for investigation of the mechanisms for Most of her scientific work has cleavage or formation of covalent bonds, the structure of different been devoted to the elucidation of intermediates and the energetics of individual steps in the the reaction mechanisms of catalytic cycles, but also certain aspects of the mechanisms for transition-metal systems. In recent the coupling between electron and proton transfer. In this review, Margareta R. A. Blomberg years her research has focused on results from such studies will be discussed. The purpose is to biochemical systems, in particular illustrate how quantum chemical studies can contribute to a redox-active metalloenzymes.
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