Table 3

Dimer interface residues in PKR that are mimicked by the residues in HCV NS5A
Nature of interaction Dimer interface residues of PKR Equivalent residues in NS5A
D266 (Ionic interaction) R262 S249
R262 (Ionic interaction) D266 D253
C326 (Hydrogen bond : NE2 of His with O of Cys ) H286 T270
Y300, V309 (Hydrophobic interaction) I288 V272
Y323 (Hydrogen bond: OD2 of Asp with OH of Tyr) D289 E273
I288, V309 (Hydrophobic interaction) Y300 F284

The equivalent residues in NS5A to the PKR dimer interface residues are obtained from the pairwise alignment as shown in the Figure 6. The equivalent residues in NS5A which are capable of interacting with PKR mimics the binding of PKR protomer to the other PKR protomer due to the shared binding region of NS5A and PKR protomer with another PKR protomer [14].

Sudha et al.

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

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