A three-dimensional topology of complex I inferred from evolutionary correlations

More than 60% of the evolutionary correlation among the conserved seven subunits of the complex I matrix arm can be explained by the physical distance between the subunits. The three-dimensional evolutionary model of the eukaryotic conserved matrix arm has a striking similarity to the matrix arm quaternary structure in the bacterium Thermus thermophilus (rmsd=19 ？) and supports the previous finding that in eukaryotes the N-module is turned relative to the Q-module when compared to bacteria. By contrast, the evolutionary rates contained little information about the structure of the membrane arm. A large evolutionary model of 45 subunits and assembly factors allows to predict subunit positions and interactions (rmsd = 52.6 ？). The model supports an interaction of NDUFAF3, C8orf38 and C2orf56 during the assembly of the proximal matrix arm and the membrane arm. The model further suggests a tight relationship between the assembly factor NUBPL and NDUFA2, which both have been linked to iron-sulfur cluster assembly, as well as between NDUFA12 and its paralog, the assembly factor NDUFAF2.The physical distance between subunits of complex I is a major correlate of the rate of protein evolution in the complex I matrix arm and is sufficient to infer parts of the complex’s structure with high accuracy. The resulting evolutionary model predicts the positions of a number of subunits and assembly factors.NADH:ubiquinone oxidoreductase (complex I) is with about 1000 kDa [1,2] the largest of the five complexes of the oxidative phosphorylation (OXPHOS) and a major contributor to the proton motive force that drives the ATP production by ATP-synthase [3]. Complex I has an L-shape with a hydrophilic matrix arm that protrudes into the cytoplasm in bacteria or the mitochondrial matrix in eukaryotes and a hydrophobic membrane arm. The canonical “core” of complex I consists of 14 subunits that originate from three pre-existing evolutionary modules [4]. The N-module at the distal end of the m