Abstract
Using molecular dynamics simulations of the thermodynamic integration type, we study the energetics and kinetics of electron transfer through the nitrite reductase enzyme of Sulfurospirillum deleyianum, Wolinella succinogenes and Campylobacter jejuni. In all of these five-heme proteins, the storage of an even number of electrons within a monomeric chain is thermodynamically favoured. Kinetically, two of these electrons are usually transferred almost simultaneously towards the active site. Although the free energy landscape for charge transfer varies significantly from organism to organism, the heme cofactor closest to the interface of a protein dimer always exhibits a particularly low free energy, suggesting that protein dimerization is functional. Interheme electron interaction effects do not play a significant role.
Highlights
Despite the abundance of nitrogen in the earth’s atmosphere, biological growth processes are frequently limited by the availability of this element in a biologically suitable form.[1]
Little is known about the details underlying the thermodynamics and kinetics of the interheme charge transfer processes, apart from arguments based on the geometrical arrangements of the cofactors
The distances r13, r23, r34 and r45 are always close to a value chacteristic of p-stacking between aromatic molecules (B3.4 Å), while r14 varies between 4.8 Å (NrfA from W. succinogenes) and 5.6 Å (NrfA from C. jejuni)
Summary
Despite the abundance of nitrogen in the earth’s atmosphere, biological growth processes are frequently limited by the availability of this element in a biologically suitable form.[1]. The two perimeter hemes exhibit a small separation, a feature that has been attributed to promoting fast charge transfer.[20,21] As the exact orientation of the protein chains with respect to the membrane is not known, it should be kept in mind that these assignments of sites to functions are tentative, in particular that of the entry site. The NrfA active site heme of the systems investigated here is either linked to a single histidine (C. jejuni) or a single lysine residue (W. succinogenes, S. deleyianum) via the Nz atom of this residue.
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