National Taiwan University Science & Technology, Taiwan
Title: Docking of HIV aspartic protease to gold nanoparticles: Molecular dynamics simulations
Biography: Chris Whiteley
Statement of the Problem: There is an increasing need for the development of new drug protocols against human immunedeficiency
virus (HIV) and HIV protease (HIVPR) is identified as a promising biomedical target in this regard.
Methodology: The interaction of gold nanoparticles (AuNP) with HIVPR is modelled using a molecular dynamics simulation
computer programme (Colores) from the Situs suite package.
Findings: The simulation of the ‘docking’, first as a rigid-body docked complex, and eventually through flexible-fit analysis,
creates 36 different complexes from four initial orientations of the nanoparticle strategically positioned around the surface of
the enzyme [Fig A]. The rigid-body docked complex is conformationally flexible to accommodate the AuNP that orientates
itself within the ‘docking’ site until a more stable structure is formed at convergence. Normalization of the data, for these
AuNP-HIVPR complexes, is obtained from changes to interactive binding energy profiles, RMSD, B-factors, dihedral angles
[phi, Δφ; psi, Δψ; chi, Δχ], size, volume occupied by Cα [ΔVcα], secondary structural elements (α-helix, β-strands, random
coil), number of contact residues, their hydrophobicities and surface electrostatic potentials.
Conclusion & Significance: From a molecular dynamic simulation perspective it is possible to provide insights into the ‘best’
most probable AuNP-HIVPR complex formed no matter which biophysical technique is monitored.