Evolutionary Co-variance Analysis of DsrAB
Because many of the non-conserved residues in DsrAB are found at subunit
interfaces, Evolutionary co-variance (EC) analysis on the EVCouplings
server (as described in Materials and Methods) (39) was used to reveal
how subunit contacts may have evolved with environment types or
taxonomic groups that are distributed across the DsrAB phylogeny. We
were particularly interested in False Positive Evolutionary Couplings
(FPEC), as these often correspond to inter-subunit contacts within
oligomers. They also can arise from long range allosteric pathways or
dynamic structural heterogeneity (26), although these types of FPECs
represent a small fraction of the total co-varying residues (48).
Numerous FPECs were identified as evolutionarily co-varying residues
that did not correspond to a contact in the 2D residue contact map of
the monomer and were separated in space (within the monomers) by greater
than 20 Å. Because the DsrA and DsrB subunits are highly homologous,
both in sequence and in structure (Figure S4), both subunits were
present in the multiple sequence alignments (MSAs) used in the
EVCouplings analysis (38, 39). Moreover, because DsrAB complexes are
hetero-tetramers, in principle, putative co-varying pairs of residues
could correspond to eight different possible residue pairs
(Res1A1-Res2A1, Res1B1-Res2B1, Res1A1-Res2B1, Res2A1-Res1B1,
Res1A1-Res2A2, Res1A1-Res2B2, Res2A1-Res1B2, and Res1B1-Res2B2).