In Silico Screening of Aptamers Configuration against Hepatitis B Surface Antigen

Figure 6

Molecular dynamics trajectories of (a) RMSD of HBsAg in complexes, (b) RMSD of aptamers in complexes, (c) number of intermolecular hydrogen bonds, and (d) minimum distance between HBsAg and aptamers for the 20 ns duration. Each aptamer-HBsAg complex reached equilibrium after 7-8 ns of simulation except H03a, which is after 12 ns of MD. The aptamers vibrate heavily even after binding to HBsAg (b); however the intermolecular H-bond formed between aptamer and HBsAg increases the complex stability (c) and maintains their distance to be in between 1.5 and 2.0 Å (d).

(a)

(b)

(c)

(d)