Computer simulations of the interaction of human immunodeficiency virus (HIV) aspartic protease with spherical gold nanoparticles: implications in acquired immunodeficiency syndrome (AIDS)
- Whiteley, Chris G, Lee, Duu-Jong
- Authors: Whiteley, Chris G , Lee, Duu-Jong
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67083 , vital:29030 , https://doi.org/10.1088/0957-4484/27/36/365101
- Description: publisher version , The interaction of gold nanoparticles (AuNP) with human immune-deficiency virus aspartic protease (HIVPR) is modelled using a regime of molecular dynamics simulations. The simulations of the 'docking', first as a rigid-body 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. The structural deviations of the enzymes from the initial x-ray crystal structure during each docking simulation are assessed by comparative analysis of secondary structural elements, root mean square deviations, B-factors, interactive bonding energies, dihedral angles, radius of gyration (R g), circular dichroism (CD), volume occupied by C α , electrostatic potentials, solvation energies and hydrophobicities. Normalisation of the data narrows the selection from the initial 36 to one 'final' probable structure. It is concluded that, after computer simulations on each of the 36 initial complexes incorporating the 12 different biophysical techniques, the top five complexes are the same no matter which technique is explored. The significance of the present work is an expansion of an earlier study on the molecular dynamic simulation for the interaction of HIVPR with silver nanoparticles. This work is supported by experimental evidence since the initial 'orientation' of the AgNP with the enzyme is the same as the 'final' AuNP-HIVPR complex generated in the present study. The findings will provide insight into the forces of the binding of the HIVPR to AuNP. It is anticipated that the protocol developed in this study will act as a standard process for the interaction of any nanoparticle with any biomedical target.
- Full Text: false
- Date Issued: 2016
- Authors: Whiteley, Chris G , Lee, Duu-Jong
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67083 , vital:29030 , https://doi.org/10.1088/0957-4484/27/36/365101
- Description: publisher version , The interaction of gold nanoparticles (AuNP) with human immune-deficiency virus aspartic protease (HIVPR) is modelled using a regime of molecular dynamics simulations. The simulations of the 'docking', first as a rigid-body 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. The structural deviations of the enzymes from the initial x-ray crystal structure during each docking simulation are assessed by comparative analysis of secondary structural elements, root mean square deviations, B-factors, interactive bonding energies, dihedral angles, radius of gyration (R g), circular dichroism (CD), volume occupied by C α , electrostatic potentials, solvation energies and hydrophobicities. Normalisation of the data narrows the selection from the initial 36 to one 'final' probable structure. It is concluded that, after computer simulations on each of the 36 initial complexes incorporating the 12 different biophysical techniques, the top five complexes are the same no matter which technique is explored. The significance of the present work is an expansion of an earlier study on the molecular dynamic simulation for the interaction of HIVPR with silver nanoparticles. This work is supported by experimental evidence since the initial 'orientation' of the AgNP with the enzyme is the same as the 'final' AuNP-HIVPR complex generated in the present study. The findings will provide insight into the forces of the binding of the HIVPR to AuNP. It is anticipated that the protocol developed in this study will act as a standard process for the interaction of any nanoparticle with any biomedical target.
- Full Text: false
- Date Issued: 2016
Docking of HIV protease to silver nanoparticles
- Whiteley, Chris G, Shing, C-Y, Kuo, C-C, Lee, Duu-Jong
- Authors: Whiteley, Chris G , Shing, C-Y , Kuo, C-C , Lee, Duu-Jong
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67105 , vital:29032 , https://doi.org/10.1016/j.jtice.2015.10.029
- Description: publisher version , 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.
- Full Text: false
- Date Issued: 2016
- Authors: Whiteley, Chris G , Shing, C-Y , Kuo, C-C , Lee, Duu-Jong
- Date: 2016
- Language: English
- Type: text , article
- Identifier: http://hdl.handle.net/10962/67105 , vital:29032 , https://doi.org/10.1016/j.jtice.2015.10.029
- Description: publisher version , 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.
- Full Text: false
- Date Issued: 2016
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