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 A spacing between the cofactors in a chain. Near catalytic clusters, shorter distances (commonly less than 7 A) 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 O2 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 A) or tyrosine (4.9 A). A corollary is that more distantly placed redox centres, such as CuA, 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 a3 electron transfer. The selection of distances and energetic barriers directs electron transfer from CuA to haem a rather than a3, 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.

Nanosecond electron tunneling between the hemes in cytochrome bo 3

“…This result is in excellent agreement with the observed rate of 8 ϫ 10 8 s Ϫ1 . In the refined version, a of 0.82 was suggested for cytochrome c oxidase [instead of the generic value of 0.76 (14,42)]. With the observed rate constant, the value for would then become 0.72 eV, again in good agreement with the Moser-Dutton treatment.…”

Heme–copper oxidases use tunneling pathways

“…The heme iron separations differ in the two proteins by less than 0.5 Å, and the nearby methyl groups distances differ by 0.8 Å, based on the x-ray structures [differences well within the range of thermal fluctuations (19)]; the coupling pathway structure is nearly the same in the two proteins, involving the bonded His-Phe-His path linking irons and the direct methyl-tomethyl through-space contact. Taking a minimum donor-acceptor distance of 7.8 Å, a (generic) packing density value (2,14), and a typical ET reorganization energy (0.7 eV) places rates computed with packing analysis in agreement with experimental rates (20). However, recent studies have found a reorganization energy for cytochrome bo 3 of Ͻ0.2 eV, so the kinetics cannot be accommodated with the packing density reported by Dutton and coworkers (20).…”

“…Taking a minimum donor-acceptor distance of 7.8 Å, a (generic) packing density value (2,14), and a typical ET reorganization energy (0.7 eV) places rates computed with packing analysis in agreement with experimental rates (20). However, recent studies have found a reorganization energy for cytochrome bo 3 of Ͻ0.2 eV, so the kinetics cannot be accommodated with the packing density reported by Dutton and coworkers (20).…”

“…Dutton and coworkers (20) have argued that ''[a]ny variance in the packing density of the tunnelling medium appears unrelated to function. .…”

“…If the rate of heme-to-heme electron transfer in the heme copper oxidases is of consequence to evolution, evolution has confronted the atomicscale features of the tunneling barrier structure in evolving the electrontunneling kinetics. At least in electrontransfer proteins, ''Darwin at the molecular scale'' (20) cannot escape the rich and grainy atomic structure of matter.…”