https://scholars.lib.ntu.edu.tw/handle/123456789/407713
標題: | Computer simulations of the interaction of human immunodeficiency virus (HIV) aspartic protease with spherical gold nanoparticles: Implications in acquired immunodeficiency syndrome (AIDS) | 作者: | Whiteley C.G. Lee D.-J. |
關鍵字: | docking;gold nanoparticles;HIV aspartic protease;molecular dynamics simulation | 公開日期: | 2016 | 卷: | 27 | 期: | 36 | 來源出版物: | Nanotechnology | 摘要: | 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£\, 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. ? 2016 IOP Publishing Ltd. |
URI: | https://scholars.lib.ntu.edu.tw/handle/123456789/407713 | ISSN: | 09574484 | DOI: | 10.1088/0957-4484/27/36/365101 | SDG/關鍵字: | Crystal structure; Dichroism; Dihedral angle; Docking; Enzymes; Fiber optic sensors; Gold; Human computer interaction; Metal nanoparticles; Molecular dynamics; Nanoparticles; Phase equilibria; Silver; Viruses; Acquired Immunodeficiency Syndrome; Aspartic protease; Gold Nanoparticles; Human immunodeficiency virus; Molecular dynamics simulations; Root mean square deviations; Secondary structural elements; X ray crystal structures; Diseases; gold; metal nanoparticle; peptide hydrolase; silver; acquired immune deficiency syndrome; computer simulation; human; Human immunodeficiency virus; molecular model; Acquired Immunodeficiency Syndrome; Computer Simulation; Gold; HIV; Humans; Metal Nanoparticles; Models, Molecular; Peptide Hydrolases; Silver |
顯示於: | 化學工程學系 |
在 IR 系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。