Exploration of Residue Binding Energy of Potential Ankyrin for Dengue Virus II from MD Simulations

Abstract

Computational approach was employed to evaluate the binding activity of potential ankyrin and domain III of the envelope protein of dengue virus II. Ankyrin serves as an alternative to antibody due to several advantages. Both the ankyrin and domain III were docked using Z-dock protocol in Discovery Studio suite of programme. The docked complex was simulated under GPU-accelerated workstation for long time scale and followed by binding free energy calculation using Molecular Mechanics-Poisson-Boltzmann Surface Area/Generalized Born Solvent Area (MM-PBSA/GBSA). Decomposed binding free energy located the possible hot spots on ankyrin and also domain III. Several amino residues on ankyrin were observed to be potent mutation points by comparing the energy from snapshots extracted during 3 ns and 6-10 ns.