Extended conformations of bifurcating electron transfer flavoprotein constitute up to half the population, possibly mediating conformational change

Abstract

Electron transfer bifurcation enables biological systems to drive unfavourable (endergonic) electron transfer by coupling it to favourable (exergonic) transfer of a second electron. In electron transfer flavoproteins (ETFs), a domain-scale conformational change is believed to sever the favourable pathway after a single electron has used it, thereby preventing the energy dissipation that would accompany exergonic transfer of the second electron. To understand the conformation change that participates in turnover, we have deployed small-angle neutron scattering (SANS) and computational techniques to characterize the bifurcating ETF from Acidaminococcus fermentans (AfeETF). SANS data reveal an overall radius of gyration (R_g) of 30.1 ± 0.2 Å and a maximum dimension (D_max) of 100 Å for oxidized AfeETF. These measurements are 4 Å and 30 Å larger, respectively, than those of any published bifurcating ETF structure. Thus, we find that none of the reported ETF structures can explain the observed scattering, nor can any individual conformation generated by either of our molecular dynamics protocols. To optimize ensembles best able to explain the SANS data, we adapted a genetic algorithm. Successful ensembles contained a compact conformation comparable to one of the crystallographically documented conformations, accompanied by a much more extended one, and these two conformations sufficed to account for the data. The extended conformations identified all have R_gs at least 4 Å larger than those of any currently published ETF structures. However, they are strongly populated, constituting 20% of the population of reduced ETF and over 50% of the population of oxidized AfeETF. Thus, the published (compact) structures provide a seriously incomplete picture of the conformation of AfeETF in solution. Moreover, because the composition of the conformational ensemble changes upon reduction of AfeETF's flavins, interconversion of the conformations may contribute to turnover. We propose that the extended conformations can provide energetically accessible paths for rapid interconversion of the open and closed compact conformations that are believed essential at alternating points in turnover.