title: Electron transfer in ferredoxin: are tunneling pathways evolutionarily conserved?
abstract: A theoretical study of electron transfer (ET) pathways in a recently crystallized Clostridium acidurici ferredoxin is reported. The electronic structure of the protein complex is treated at the semiempirical extended Hückel level, and the tunneling pathways are calculated with the rigorous quantum mechanical method of tunneling currents. The model predicts two pathways between the two [4Fe-4S] cubanes: a strong one running directly from Cys(14) to Cys(43) and a weaker one from Cys(14) via Ile(23) to Cys(18), whereas other amino acids do not play a significant role in the electron tunneling. The cysteine ligands conduct almost all of the current when Ile(23) is mutated to valine in silico, so that there is no appreciable change in the ET rate. The calculated value of the transfer matrix element is consistent with the experimentally determined rate of transfer. Results of the sequence analysis performed on this ferredoxin reveal that Ile(23) is a highly variable amino acid compared with the cubane-ligating cysteine amino acids, even though Ile(23) lies directly between the donor and acceptor complexes. We further argue that the homologous proteins with a [3Fe-4S] cofactor, which does not have one of the four cysteine ligands, use the same tunneling pathways as those in this ferredoxin, on the basis of the high homology as well as the absolute conservation of Cys(14) and Cys(43) which serve as the main tunneling conduit. Our results explain why mutation of amino acids around and between the donor and acceptor cubane clusters, including that of Ile(23), does not appreciably affect the rate of transfer and add support to the proposal that there exist evolutionarily conserved electron tunneling pathways in biological ET reactions.
authors.affiliation: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.
authors.forename: Iraj
authors.initials: I
authors.lastname: Daizadeh
authors.forename: Dmitry M
authors.initials: DM
authors.lastname: Medvedev
authors.forename: Alexei A
authors.initials: AA
authors.lastname: Stuchebrukhov
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000378:metabolism; D017124:Conserved Sequence; D004579:Electron Transport / Q000502:physiology*; D019143:Evolution, Molecular; D005288:Ferredoxins / Q000378:metabolism*; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D011487:Protein Conformation; D017386:Sequence Homology, Amino Acid; D013816:Thermodynamics
chemical_list: D000596:Amino Acids; D005288:Ferredoxins