Darwin at the molecular scale: selection and variance in electron tunnelling proteins including cytochrome c oxidase

Abstract

Biological electron transfer is designed to connect catalytic clusters by chains of redox cofactors. A review of the characterized natural redox proteins with a critical eye for molecular scale measurement of variation and selection related to physiological function shows no statistically significant differences in the protein medium lying between cofactors engaged in physiologically beneficial or detrimental electron transfer. Instead, control of electron tunnelling over long distances relies overwhelmingly on less than 14 Å spacing between the cofactors in a chain. Near catalytic clusters, shorter distances (commonly less than 7 Å) appear to be selected to generate tunnelling frequencies sufficiently high to scale the barriers of multi-electron, bond-forming/-breaking catalysis at physiological rates. We illustrate this behaviour in a tunnelling network analysis of cytochrome c oxidase. In order to surmount the large, thermally activated, adiabatic barriers in the 5–10 kcal mol ⁻¹ range expected for H ⁺ motion and O ₂ reduction at the binuclear centre of oxidase on the 10 ³ –10 ⁵ s ⁻¹ time-scale of respiration, electron access with a tunnelling frequency of 10 ⁹ or 10 ¹⁰ s ⁻¹ is required. This is provided by selecting closely placed redox centres, such as haem a (6.9 Å) or tyrosine (4.9 Å). A corollary is that more distantly placed redox centres, such as Cu _A , cannot rapidly scale the catalytic site barrier, but must send their electrons through more closely placed centres, avoiding direct short circuits that might circumvent proton pumping coupled to haems a to a ₃ electron transfer. The selection of distances and energetic barriers directs electron transfer from Cu _A to haem a rather than a ₃ , without any need for delicate engineering of the protein medium to ‘hard wire’ electron transfer. Indeed, an examination of a large number of oxidoreductases provides no evidence of such naturally selected wiring of electron tunnelling pathways.