Dataset Information

Interlayer water regulates the bio-nano interface of a ?-sheet protein stacking on graphene.

ABSTRACT: Using molecular dynamics simulations, we investigated an integrated bio-nano interface consisting of a ?-sheet protein stacked onto graphene. We found that the stacking assembly of the model protein on graphene could be controlled by water molecules. The interlayer water filled within interstices of the bio-nano interface could suppress the molecular vibration of surface groups on protein, and could impair the CH···? interaction driving the attraction of the protein and graphene. The intermolecular coupling of interlayer water would be relaxed by the relative motion of protein upon graphene due to the interaction between water and protein surface. This effect reduced the hindrance of the interlayer water against the assembly of protein on graphene, resulting an appropriate adsorption status of protein on graphene with a deep free energy trap. Thereby, the confinement and the relative sliding between protein and graphene, the coupling of protein and water, and the interaction between graphene and water all have involved in the modulation of behaviors of water molecules within the bio-nano interface, governing the hindrance of interlayer water against the protein assembly on hydrophobic graphene. These results provide a deep insight into the fundamental mechanism of protein adsorption onto graphene surface in water.

SUBMITTER: Lv W

PROVIDER: S-EPMC4650828 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Interlayer water regulates the bio-nano interface of a β-sheet protein stacking on graphene.

Lv Wenping W Xu Guiju G Zhang Hongyan H Li Xin X Liu Shengju S Niu Huan H Xu Dongsheng D Wu Ren'an R

Scientific reports 20150105

Using molecular dynamics simulations, we investigated an integrated bio-nano interface consisting of a β-sheet protein stacked onto graphene. We found that the stacking assembly of the model protein on graphene could be controlled by water molecules. The interlayer water filled within interstices of the bio-nano interface could suppress the molecular vibration of surface groups on protein, and could impair the CH···π interaction driving the attraction of the protein and graphene. The intermolecu ...[more]

PMID: 25557857

Similar Datasets

Project description:Introduction:Biomedical applications of nanoparticles (NPs) as enzyme inhibitors have recently come to light. Oxides of metals native to the physiological environment (eg, Fe, Zn, Mg, etc.) are of particular interest-especially the functional consequences of their enzyme interaction. Materials and methods:Here, Fe2O3, zinc oxide (ZnO), magnesium oxide (MgO) and nickel oxide (NiO) NPs are compared to copper (Cu) and boron carbide (B4C) NPs. The functional impact of NP interaction to the model enzyme luciferase is determined by 2-dimensional fluorescence difference spectroscopy (2-D FDS) and 2-dimensional photoluminescence difference spectroscopy (2-D PLDS). By 2-D FDS analysis, the change in maximal intensity and in 2-D FDS area under the curve (AUC) is in the order Cu~B4C>ZnO>NiO>>Fe2O3>MgO. The induced changes in protein conformation are confirmed by tryptic digests and gel electrophoresis. Results:Analysis of possible trypsin cleavage sites suggest that cleavage mostly occurs in the range of residues 112-155 and 372-439, giving a major 45 kDa band. By 2-D PLDS, it is found that B4C NPs completely ablate bioluminescence, while Cu and Fe2O3 NPs yield a unique bimodal negative decay rate, -7.67×103 and -3.50×101 relative light units respectively. Cu NPs, in particular, give a remarkable 271% change in enzyme activity. Molecular dynamics simulations in water predicted that the surfaces of metal oxide NPs become capped with metal hydroxide groups under physiological conditions, while the surface of B4C becomes populated with boronic acid or borinic acid groups. These predictions are supported by the experimentally determined zeta potential. Thin layer chromatography patterns further support this conception of the NP surfaces, where stabilizing interactions were in the order ionic>polar>non-polar for the series tested. Conclusion:Overall the results suggest that B4C and Cu NP functional dynamics on enzyme biochemistry are unique and should be examined further for potential ramifications on other model, physiological or disease-relevant enzymes.

Project description:In the present work, nitrogen-doped reduced graphene oxide (NrGO) was synthesized via a hydrothermal treatment of graphene oxide (GO) in the presence of urea. Gold nanoparticles (Au(0) NPs) were immobilized over the surface of NrGO (Au(0)-NrGO). Characterization of the Au(0)-NrGO nanocomposite via FT-IR spectroscopy, Raman spectroscopy, elemental mapping and XPS revealed the doping of N atoms during the reduction of GO. XRD and XPS studies confirmed the presence of Au(0) NPs and EDS analysis showed a 4.51 wt% loading of Au NPs in the Au(0)-NrGO nanocomposite. The morphology of Au(0)-NrGO was explored by SEM and TEM, which showed the presence of spherical Au metal NPs uniformly immobilized on the surface of NrGO. Further, studies on lysozyme (Lys) in the presence of Au(0)-NrGO by UV-visible, fluorescence, and circular dichroism spectroscopy revealed a conformational change in Lys and electrostatic interaction between Lys and Au(0)-NrGO. The DLS result showed an enhancement in the size of the Au(0)-NrGO and Lys conjugates. The Au(0)-NrGO-induced conformational changes in the structure of Lys resulted in a significant decrease in its activity at a certain concentration of Au(0)-NrGO. Moreover, the results showed that Lys favorably binds with the surface of Au(0)-NrGO, resulting in the formation of 2-D scaffolds possibly due to electrostatic and hydrophobic interactions, H-bonding, and interactions between the AuNPs and sulfur-containing amino acid residues of Lys. SEM exhibited the formation of conjugates in the form of 2-D scaffolds due to the biomolecular interactions between Lys and Au(0)-NrGO. The TEM studies revealed that Lys agglomerated around the Au(0) NPs immobilized on the surface of NrGO, which suggests the formation of a protein corona (PC) around the AuNPs. Furthermore, the favorable Au(0) NP-sulphur (PC) interaction was confirmed by the disappearance of the S-S stretching band in the Raman spectra. Overall, the results obtained provide insight into the nano-bio interface and formation of Au(0) NP-PC, which can be used for bioinspired applications, such as biosensing and imaging and the development of advanced functional Au NPs.

Dataset Information

Interlayer water regulates the bio-nano interface of a ?-sheet protein stacking on graphene.

Publications

Interlayer water regulates the bio-nano interface of a β-sheet protein stacking on graphene.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets