- Title
- Docking of HIV protease to silver nanoparticles
- Creator
- Whiteley, Chris G, Shing, C-Y, Kuo, C-C, Lee, Duu-Jong
- Date
- 2016
- Type
- text
- Type
- article
- Identifier
- http://hdl.handle.net/10962/67105
- Identifier
- vital:29032
- Identifier
- https://doi.org/10.1016/j.jtice.2015.10.029
- Description
- publisher version
- Description
- 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.
- Format
- 9 pages, pdf
- Publisher
- Elsevier
- Language
- English
- Relation
- Journal of the Taiwan Institute of Chemical Engineers, Whiteley, C.G., Shing, Y., Kuo, C-C. and Lee, D-J. (2016) Docking of HIV protease to silver nanoparticles. Journal of the Taiwan Institute of Chemical Engineers, 60, p 83-91. https://doi.org/10.1016/j.jtice.2015.10.029, Journal of the Taiwan Institute of Chemical Engineers volume 60 number 83 91 March 2016 1876-1070
- Rights
- Taiwan Institute of Chemical Engineers
- Rights
- Use of this resource is governed by the terms and conditions of the Journal of the Taiwan Institute of Chemical Engineers Open Access Statement (https://www.elsevier.com/journals/journal-of-the-taiwan-institute-of-chemical-engineers/1876-1070/guide-for-authors)
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Whiteley, Christopher (Emeritus Prof)
RU Department of Biochemistry, Microbiology and Bioinformatics
SDG 03. Good Health and Well-Being
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