The evolutionary history of topological variations in the CPA/AT transporters
Fig 9
An example showing the annotation of the topology of DUF819 family using our integrated pipeline.
The main steps involved in the pipeline are shown. (a) Evolution guided topology annotation: Topology predictions are mapped onto the seed MSA to obtain a multiple topology alignment. The phylogenetic tree from seed MSA is used to reorder the multiple topology alignment into a “Reordered topology alignment”. This evolution guided topology prediction is used to infer initial topologies for a family. Generation of the final topology and annotation of core and scaffold subdomains is obtained by comparing to the known structure of sodium-citrate symporter (PDB id: 5A1S). The TM helices (in-out) and TM helices (out-in) are colored dark red/grey and light red/grey, respectively. Reentrant helices (in-in) and (out-out) are colored yellow and blue respectively. The inside and outside loops are colored yellow and blue respectively. The vertical bar is colored based on the taxonomy of the sequences (Bacteria: Purple, Archaea: Dark blue Eukaryotes: Green). Scaffold subdomains and reentrant core subdomains are colored brown and green, respectively. N- and C-terminal repeats are shown as black trapezoids. ΔG values describing the hydrophobicity [65] are obtained for the representative sequence and are plotted to the aligned residues in the representative sequence. (b) Validation of broken/reentrant transporters by using the KRbias for the DUF819 family. KRbias or positive inside rule is the enrichment of inside loops compared to the outside loops of a transmembrane protein[36, 46, 47]. The number of Lys (K) and Arg(R) amino acids in the inside and outside loops are compared. The expected correct topology would show a higher KR-bias in one of the two topology models (Broken/Reentrant). The KR-bias plot is shown as a 2D scatter plot. (c) Homology modelling of the representative sequence (d) Contact prediction modelling pipeline.