Evolutionary Co-variance and Anisotropic Network Analysis
Evolutionary covariance (EC) analysis (25, 26, 38) was performed using
the EV Couplings server (https://evcouplings.org/ (39)) to
identify instances of False Positive Evolutionary Covariance (FPEC),
defined as significant covariance between residues that are too distant
(>20 Å) to be in direct contact within the monomeric
subunits. Given the strong homology between DsrA and DsrB subunits that
are suspected to have originated from gene duplication, it was not
possible to use the EV Complex Couplings option to identify co-varying
residues at subunit interfaces in the oligomers. Instead, EC analysis
was carried out using the monomeric sequences of the DsrA and DsrB
subunits of A. fulgidus , D. vulgaris, and MV2-Eury
separately as input. The values of Neff (number of
non-redundant sequences in the alignment normalized to the number of
residues) was between 1.16 and 2.84, depending upon the query, with the
number of non-redundant sequences was between 481 and 2786. Queries were
made by separately submitting the A and B subunits from the A.
fulgidus and MV2-Eury sequences. Recovered coupling probabilities were
between 80 and 94%. To model the possible dynamic fluctuations that
might be associated with the putative allosteric pathway that was
identified through EC analysis, we carried out Anisotropic Network
Modeling (ANM) (40) using the webserver from the Bahar group
(http://anm.csb.pitt.edu/cgi-bin/anm2/anm2.cgi; (41)).