Study of molecular interaction between miRNAs and AGO protein
The AGO protein is a key player in the formation of the RNA-induced silencing complex, a major component of RNA interference. The three dimensional structures of miRNA-mRNA duplexes were prepared using RNA COMPOSER web server (Fig. 3). The first round of docking was performed between the miRNAs and AGO (PDB ID: 3F73, chain A) protein to inspect the binding affinity between the complexes. Out of 10 different poses resulted for docking complexes in Patch Dock server, the pose with highest geometrical shape complementary score [64] is considered as the best docked complex. The resulted geometrical shape complementary score and atomic contact energy scores are reported (Table 5), implicated a strong binding affinity between the miRNAs and AGO protein. The binding affinity between the AGO protein and miRNAs (miR-106a, miR-21, and miR-29b-2) is established through the observation of amino acids (miR-106a: LEU 132, ALA 133, VAL 152, LEU 153, ALA 170, ILE 173, LEU 267, LEU 279, ALA 479,VAL 620, VAL 663, VAL 666, and ILE 671; miR-21: ILE 173, VAL 264, LEU 267, LEU 279, ALA 354, ALA 414, ILE 434, ALA 644, ALA 648, and VAL 685; miR-29b-2: VAL 152, LEU 153, ALA 170, LEU 279, ALA 414, ALA 479, LEU 596, VAL 620, ALA 648, LEU 652, ALA 659, LEU 662, and VAL 663) which are strongly hydrophobic in nature and also amino acids with aromatic rings (miR-106a: TYR 135, TYR 171, TRP415, and PHE 487; miR-21: TYR 135, TYR 171, TRP 415, TYR 642, PHE 647, and PHE 649; miR-29b-2: TRP 156, TRP 415, TYR 642, PHE 647, and PHE649) within a distance of 3.5Å (Table 6, Fig. 4). The presence of hydrogen bonding pattern during interaction (Table 7, Fig. 5) also supported the fact of AGO protein driven miRNA based gene regulation.