Mechanism of Graphene Oxide as an Enzyme Inhibitor from Molecular Dynamics Simulations

Graphene and its water-soluble derivative, graphene oxide (GO), have attracted huge attention because of their interesting physical and chemical properties, and they have shown wide applications in various fields including biotechnology and biomedicine. Recently, GO has been shown to be the most efficient inhibitor for α-chymotrypsin (ChT) compared with all other artificial inhibitors. However, how GO interacts with bioactive proteins and its potential in enzyme engineering have been rarely explored. In this study, we investigate the interactions between ChT and graphene/GO by using molecular dynamics (MD) simulation. We find that ChT is adsorbed onto the surface of GO or graphene during 100 ns MD simulations. The α-helix of ChT plays as an important anchor to interact with GO. The cationic and hydrophobic residues of ChT form strong interactions with GO, which leads to the deformation of the active site of ChT and the inhibition of ChT. In comparison, the active site of ChT is only slightly affected after ChT adsorbed onto the graphene surface. In addition, the secondary structure of ChT is not affected after it is adsorbed onto GO or graphene surface. Our results illustrate the mechanism of the interaction between GO/graphene and enzyme and provide guidelines for designing efficient artificial inhibitors

The Selective Interaction between Silica Nanoparticles and Enzymes from Molecular Dynamics Simulations

<div><p>Nanoscale particles have become promising materials in many fields, such as cancer therapeutics, diagnosis, imaging, drug delivery, catalysis, as well as biosensors. In order to stimulate and facilitate these applications, there is an urgent need for the understanding of the interaction mode between the nano-particles and proteins. In this study, we investigate the orientation and adsorption between several enzymes (cytochrome c, RNase A, lysozyme) and 4 nm/11 nm silica nanoparticles (SNPs) by using molecular dynamics (MD) simulation. Our results show that three enzymes are adsorbed onto the surfaces of both 4 nm and 11 nm SNPs during our MD simulations and the small SNPs induce greater structural stabilization. The active site of cytochrome c is far away from the surface of 4 nm SNPs, while it is adsorbed onto the surface of 11 nm SNPs. We also explore the influences of different groups (-OH, -COOH, -NH₂ and CH₃) coated onto silica nanoparticles, which show significantly different impacts. Our molecular dynamics results indicate the selective interaction between silicon nanoparticles and enzymes, which is consistent with experimental results. Our study provides useful guides for designing/modifying nanomaterials to interact with proteins for their bio-applications.</p></div

Comparison of the structure of lysozyme adsorbed onto different diameter of SNPs.

<p>(a) align the crystal structure (gray) with the structure adsorbed onto 4 nm SNP (blue), (b) align the crystal structure (gray) with the structure adsorbed onto 11 nm SNP (red). The structures are the conformations after 100 ns MD simulation.</p

Cytochrome c adsorbed onto 2 nm SNPs coated with (a)-CH₃, (b)-COOH, (c)-NH₂ and (d)-OH.

<p>The structures are the conformations after 100 ns MD simulation.</p

The binding mode of TBU (tertiary-butyl alcohol, highlighted in the stick model) in (a) the crystal structure of RNase A, (b) the structure of RNase A adsorbed onto 4 nm SNP (after 100 ns MD simulation), (c) the structure of RNase A adsorbed onto 11 nm SNP (after 100 ns MD simulation).

<p>The binding mode of TBU (tertiary-butyl alcohol, highlighted in the stick model) in (a) the crystal structure of RNase A, (b) the structure of RNase A adsorbed onto 4 nm SNP (after 100 ns MD simulation), (c) the structure of RNase A adsorbed onto 11 nm SNP (after 100 ns MD simulation).</p

Calculated RMSF of Cα atoms vs protein residue number for (a) cytochrome c (103 residues), (b) RNase A (124 residues), and (c) lysozyme (130 residues) during the MD simulation.

<p>A comparison between the RMSF plot for natural structures of proteins, proteins adsorbed onto the surface of 4 nm SNPs, and the proteins adsorbed onto the surface of 11 ns SNPs.</p

Side view of the energy-minimized molecular structure of the (a) part of 4 nm SNPs, (b) part of 11 nm SNPs and (c) different chemical groups (-CH3, -COOH, -NH2, -OH) coated onto 2 nm SNPs.

<p>Side view of the energy-minimized molecular structure of the (a) part of 4 nm SNPs, (b) part of 11 nm SNPs and (c) different chemical groups (-CH3, -COOH, -NH2, -OH) coated onto 2 nm SNPs.</p

Comparison of the structure of cytochrome c adsorbed onto different diameter of SNPs.

<p>(a) align the crystal structure (gray) with the structure adsorbed onto 4 nm SNP (blue), (b) align the crystal structure (gray) with the structure adsorbed onto 11 nm SNP (red). The structures are the conformations after 100 ns MD simulation.</p

Time evolutions for (a) cytochrome c, (b) RNase A, and (c) lysozyme during 100 ns MD simulations.

<p>The values are the average value from two independent MD simulations.</p

Time evolutions for cytochrome c adsorbed onto different chemical groups coated onto silica nano-particles during 100 ns MD simulations.

<p>(a) RMSD of cytochrome c adsorbed onto SNPs coated with -CH₃ and with -COOH, (b) RMSD of cytochrome c adsorbed onto SNPs coated with -NH₂ and with -OH.</p