The mitochondria in our cells are responsible for the conversion of energy from nutrients into ATP, the native fuel of the organism. However, occasional stray chemical reactions in the mitochondria lead to production of a small amount of reactive oxygen species (ROS), such as superoxide, which are harmful to cells and related to aging [Massaad et al. Aging 1:758. 2009, Brand. Exp. Gerontol 45:466. 2010]. As the metabolic energy conversion processes often involve a series of redox reactions, or electron transfers, and the enzymes involved therefore contain redox active cofactors or prosthetic groups, it is conceivable that occasional reactions with e.g. molecular oxygen could lead to small amounts of ROS formation as an unwanted byproduct. Computational modeling of processes, including binding and unbinding of oxygen molecules and electron transfer to O2, have been carried out for two important metabolic enzymes to shed light on possible ROS formation mechanisms in the metabolic pathways.
Cytochrome bc1 complex
The membrane-embedded cytochrome bc1 complex, also known as complex III in the electron transport chain is one of the central enzymes in the energy conversion machinery of mitochondria and is believed to produce small yields of superoxide through side reactions with molecular oxygen. The mechanism of such superoxide production in the bc1 complex is, however, still unclear.
The bc1 complex serves to transport protons across the membrane through a series of redox reactions with substrate molecules in the membrane to maintain a cross-membrane potential, which is used to power ATP synthesis. The net reactions and transport processes during the enzyme's complex reaction cycle, the Q-cycle, are depicted in Fig. 1. At intermediate stages, substrate quinol molecules become radical semiquinones, which conceivably could further lead to production of other radical species such as superoxide.
The proton transfers in the bc1 complex are coupled to a series of internal electron transfers as illustrated in Fig. 2 (see also Proton-coupled electron transfer in the cytochrome bc1 complex), involving several iron-containing prosthetic groups: Three heme groups and an iron-sulfur cluster (Fe2S2). The substrate QH2 at the Qo-site first transfers an electron the Fe2S2-cluster and briefly becomes a radical semiquinone before it is fully oxidized to Q through the second electron transfer to heme bL. An oxygen molecule, if present at the Qo-site, could conceivably "steal" the excess electron from the semiquinone and escape the bc1 complex as a radical superoxide, possibly leading to cell damage.
Molecular dynamics simulations show that oxygen molecules are indeed able to migrate into the bc1 complex and bind at the Qo-site, where it can stay bound for tens of nanoseconds at a time, while a semiquinone substrate is present (see Fig. 3) [Husen & Solov'yov. JACS 138:12150. 2016]. This makes the Qo-site a viable candidate as a center of superoxide production.
A follow-up study found the precise O2 binding modes and statistics depended strongly on mutations of a tyrosine amino acid (Y302) at the Qo-site [Husen & Solov'yov. J. Phys. Chem. B 121: 3308. 2016]. Fig. 4 shows different observed O2 binding sites as the tyrosine is replaced by alanine (A302), cysteine (C302) or serine (S302).
Further quantum chemical calculations on snapshots of the Qo-site with bound O2 and semiquinone reveal that several charge transfer mechanisms leading to superoxide are possible [Salo et al. J. Phys. Chem. B 121:1771. 2016]: essentially, the excess electron transferred to the oxygen molecule can either come from the Fe2S2 cluster or from the semiquinone as illustrated in Fig. 5.
The ETF enzyme
The ETF enzyme, which consists of two protein subunits (alpha and beta) and the cofactors flavin adenine dinucleotide (FAD/ FADH2) and adenosine monophosphate (AMP) facilitates elctron transport as part of the fatty acid metabolism in mitochondria [Rodrigues et al. Free Radical Biol. Med. 53, 12–19 (2012)]. The redox active nature of the protein, however, also makes it a potential source of reactive oxygen species as a byproduct.
Atomistic molecular dynamics simulations were employed [Husen et al. J. Chem. Inf. Model 59, 4868–4879 (2019)] to study the dynamics of oxygen molecules in the ETF enzyme and possible O2 binding modes near the FADH2 cofactor, which could serve as electron donor in a superoxide production mechanism.
In particular, extensive molecular dynamics simulations of the ETF enzyme in solution with a concentration of oxygen molecules were carried out to identify O2 binding sites and characterize binding modes. Five binding sites were identified near the enzyme’s FADH2 cofactor and were used for further modeling. Site 5 is particularly interesting for superoxide production, as the positively charged β-ARG12 stabilizes the superoxide anion. O2 binding was further characterized through 100 replicate binding event simulations for each of the 5 sites. The characteristic O2 binding time are in the range of 0.5-3 ns, but a subpopulation of simulated events at site 5 showed significantly longer binding.
Electron transfer from FADH2 to O2 would initially lead to formation of a radical pair, FADH• − O2•− [Imlay, J.A. Nat. Rev. Microbiol 11, 443–454 (2013)]. Interchange between the singlet and triplet states of the radical pair, which could be influenced by external magnetic fields or RF radiation, then decides the ultimate release of reactive oxygen species.