Study of molecular interaction between AGO protein and miRNA-mRNA duplex
The second round docking was performed between AGO protein and miRNA-mRNA duplexes (miR-106 and PTEN; miR-21 and TGFBR2; and miR-29b-2 and VEGFA) separately in PatchDock web server, and scores are reported (Table 8). Amino acids which are strong hydrophobic in nature and amino acids with aromatic rings which are relatively hydrophobic generally contribute a lot towards the stability of binding during molecular interaction between two macro molecules. Hence the molecular interaction between miRNA-mRNA duplexes and AGO protein was studied by inspecting close amino acid residues of AGO protein within a distant of 3.5 Å. Strong hydrophobic amino acids of AGO like VAL 152, LEU 153, VAL 264, LEU 265, LEU 267, LEU 277, ALA 278, LEU 279, ALA 414, ILE 434, ALA 479, VAL 663, and VAL 685 in miR-106a and PTEN duplex; LEU 45, LEU 46, ALA 47, VAL 49, ALA 50, ALA 80, ILE 173, LEU 265, LEU 267, LEU 277, ALA 278, LEU 279, LEU 281, ALA 479, ALA 644, ALA 648, LEU 652, and VAL 663 in miR-21 and TGFBR2 duplex; and ALA 80, LEU 132, VAL 152, LEU 153, ALA 170, ILE 173, VAL 264, ALA 479, VAL 606, ALA 644, ALA 648, VAL 663, and VAL 685 in miR-29b-2 and VEGFA duplex are observed within a distant of 3.5 Å. Similarly, amino acids like TYR 43, TRP 415, PHE 487, and TYR 642 in miR-106a and PTEN duplex; TYR 43, TRP 202, TRP 415, TYR 642, PHE 647, and PHE 649 in miR-21 and TGFBR2 duplex; and TYR 43, TYR 86, TYR 135, TRP 415, TYR 171, TYR 642, PHE 647, and PHE 649 in miR-29b-2 and VEGFA duplex, with aromatic ring are also found as participating in interaction within the binding pocket of AGO protein around distance of 3.5 Å (Table 9, Fig. 6).