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 highly reactive free radicals such as superoxide, which are harmful to cells and related to aging. In particular, the membrane-embedded cytochrome bc1 complex, one of the central enzymes in the energy conversion machinery of mitochondria, 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 between substrate molecules in the membrane and the the protein complex along with a number of internal electron transfer processes. 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 depicted in Fig. 2 (see also Proton-coupled electron transfer in the cytochrome bc1 complex), involving 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), making the Qo-site a viable candidate as a center of superoxide production.
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: essentially, the excess electron transferred to the oxygen molecule can either come from the Fe2S2 cluster or from the semiquinone as illustrated in Fig. 4.