Docking of HIV protease to silver nanoparticles

This interaction of silver nanoparticles (AgNP) with human immune-deficiency virus aspartic protease (HIVPR) is examined by molecular dynamics simulation using the Colores (Situs) package and biophysical techniques using UV-vis spectroscopy, dynamic light scattering, transmission electron microscopy and circular dichroism. The 'docking' of AgNP with HIVPR creates a complex [AgNP-HIVPR] to initiate a hypochromic time-dependent red-shift for the surface plasmon resonance maximum. MD simulations reflect large perturbations to enzyme conformations by fluctuations of both rmsd and B-factors. Increase in changes to electrostatic potentials within the enzyme, especially, with chain B, suggest hydrophobic interactions for the binding of the AgNP. This is supported by changes to mainchain and sidechain dihedrals for many hydrophobic amino acid including Cys⁹⁵, Trp⁶ and Trp⁴². Circular dichroism spectra reveal disappearance of α-helices and β-sheets and increase in random coil first from chain B then chain A. During initial stages of the interactive simulation the enzyme is conformational flexible to accommodate the AgNP, that docks with the enzyme under a cooperative mechanism, until a more stable structure is formed at convergence. There is a decrease in size of the HIVPR-AgNP complex measured by changes to the gyration radius supporting evidence that the AgNP associates, initially, with chain B.