Dataset Information

Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide.

ABSTRACT: Recent experiments have reported that the fragment of viral protein R (Vpr), Vpr13-33, can assemble and change its conformation after adsorbed on graphene oxide (GO) and then reduce its cytotoxicity. This discovery is of great importance, since the mutation of Vpr13-33 can decrease the viral replication, viral load and delay the disease progression. However, the interactions between Vpr13-33 and GO at atomic level are still unclear. In this study, we performed molecular dynamics simulation to investigate the dynamic process of the adsorption of Vpr13-33 onto GO and the conformation change after aggregating on GO surface. We found that Vpr13-33 was adsorbed on GO surface very quickly and lost its secondary structure. The conformation of peptides-GO complex was highly stable because of π-π stacking and electrostatic interactions. When two peptides aggregated on GO, they did not dimerize, since the interactions between the two peptides were much weaker than those between each peptide and GO.

SUBMITTER: Zeng S

PROVIDER: S-EPMC4838942 | biostudies-literature | 2016 Apr

REPOSITORIES: biostudies-literature

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Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide.

Zeng Songwei S Zhou Guoquan G Guo Jianzhong J Zhou Feng F Chen Junlang J

Scientific reports 20160421

Recent experiments have reported that the fragment of viral protein R (Vpr), Vpr13-33, can assemble and change its conformation after adsorbed on graphene oxide (GO) and then reduce its cytotoxicity. This discovery is of great importance, since the mutation of Vpr13-33 can decrease the viral replication, viral load and delay the disease progression. However, the interactions between Vpr13-33 and GO at atomic level are still unclear. In this study, we performed molecular dynamics simulation to in ...[more]

PMID: 27097898

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Project description:Controlling the structure of graphene oxide (GO) phases and their smaller analogues, graphene (oxide) quantum dots (GOQDs), is vitally important for any of their widespread intended applications: highly ordered arrangements of nanoparticles for thin-film or membrane applications of GO, dispersed nanoparticles for composite materials and three-dimensional porous arrangements for hydrogels. In aqueous environments, it is not only the chemical composition of the GO flakes that determines their morphologies; external factors such as pH and the coexisting cations also influence the structures formed. By using accurate models of GO that capture the heterogeneity of surface oxidation and very large-scale coarse-grained molecular dynamics that can simulate the behaviour of GO at realistic sizes of GOQDs, the driving forces that lead to the various morphologies in aqueous solution are resolved. We find the morphologies are determined by a complex interplay between electrostatic, [Formula: see text]-[Formula: see text] and hydrogen bonding interactions. Assembled morphologies can be controlled by changing the degree of oxidation and the pH. In acidic aqueous solution, the GO flakes vary from fully aggregated over graphitic domains to partial aggregation via hydrogen bonding between hydroxylated domains, leading to the formation of planar extended flakes at high oxidation ratios and stacks at low oxidation ratios. At high pH, where the edge carboxylic acid groups are deprotonated, electrostatic repulsion leads to more dispersion, but a variety of aggregation behaviour is surprisingly still observed: over graphitic regions, via hydrogen bonding and "face-edge" interactions. Calcium ions cause additional aggregation, with a greater number of "face-face" and "edge-edge" aggregation mechanisms, leading to irregular aggregated structures. "Face-face" aggregation mechanisms are enhanced by the GO flakes possessing distinct domains of hydroxylated and graphitic regions, with [Formula: see text]-[Formula: see text] and hydrogen bonding interactions prevalent between these regions on aggregated flakes respectively. These findings furnish explanations for the aggregation characteristics of GO and GOQDs, and provide computational methods to design directed synthesis routes for self-assembled and associated applications.

Dataset Information

Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide.

Publications

Molecular simulations of conformation change and aggregation of HIV-1 Vpr13-33 on graphene oxide.

Similar Datasets

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