Additional file 2.

Prediction of PKR interacting residues in NS5A 1b. (1) Alignment of PKR dimerisation region with ISDR (Interferon sensitivity determining region) of NS5A. (a) Dimer interface residues are colored in magenta in PKR sequence. The residues in NS5A 1b, 3a equivalent to the dimer interface residues of PKR are colored in cyan and yellow respectively. (b) Dimer interface residues are colored in magenta in PKR sequence. The residues in NS5A 1b, 2a equivalent to the dimer interface residues of PKR are colored in cyan and green respectively. (2) Trace residues are identified when NS5A from genotype 1b which interacts and inhibits PKR is compared with NS5A 3a and NS5A 2a which are unable to bind and inhibit PKR efficiently in few representative sequences. All the trace residues highlighted are highly conserved (> 80%) in the entire dataset. (a) Trace residues picked when MSA of genotype 1b Vs 3a is compared. (b) Trace residues picked when MSA of genotype 1b Vs 2a is compared. (c) Trace residues picked when MSA of genotype 1b Vs 3a and 2a are compared.

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Sudha et al. BMC Structural Biology 2012 12:28   doi:10.1186/1472-6807-12-28