Docking of HIV protease to silver nanoparticles
Journal
Journal of the Taiwan Institute of Chemical Engineers
Journal Volume
60
Pages
83-91
Date Issued
2016
Author(s)
Abstract
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 Cys 95 , Trp 6 and Trp 42 . Circular dichroism spectra reveal disappearance of £\-helices and £]-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. ? 2015 Taiwan Institute of Chemical Engineers.
Subjects
Docking
HIV protease
Molecular dynamics simulation
Silver nanoparticles
Other Subjects
Chains; Circular dichroism spectroscopy; Dichroism; Diseases; Docking; Enzymes; High resolution transmission electron microscopy; Hydrophobicity; Light scattering; Light transmission; Metal nanoparticles; Molecular dynamics; Nanoparticles; Surface plasmon resonance; Transmission electron microscopy; Ultraviolet visible spectroscopy; Viruses; Circular dichroism spectra; Electrostatic potentials; HIV-protease; Hydrophobic amino acids; Hydrophobic interactions; Interactive simulations; Molecular dynamics simulations; Silver nanoparticles; Silver
Type
journal article