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An In Silico study of TiO 2 nanoparticles interaction with twenty standard amino acids in aqueous solution

View Article: PubMed Central - PubMed

ABSTRACT

Titanium dioxide (TiO2) is probably one of the most widely used nanomaterials, and its extensive exposure may result in potentially adverse biological effects. Yet, the underlying mechanisms of interaction involving TiO2 NPs and macromolecules, e.g., proteins, are still not well understood. Here, we perform all-atom molecular dynamics simulations to investigate the interactions between TiO2 NPs and the twenty standard amino acids in aqueous solution exploiting a newly developed TiO2 force field. We found that charged amino acids play a dominant role during the process of binding to the TiO2 surface, with both basic and acidic residues overwhelmingly preferred over the non-charged counterparts. By calculating the Potential Mean Force, we showed that Arg is prone to direct binding onto the NP surface, while Lys needs to overcome a ~2 kT free energy barrier. On the other hand, acidic residues tend to form “water bridges” between their sidechains and TiO2 surface, thus displaying an indirect binding. Moreover, the overall preferred positions and configurations of different residues are highly dependent on properties of the first and second solvation water. These molecular insights learned from this work might help with a better understanding of the interactions between biomolecules and nanomaterials.

No MeSH data available.


The initial configuration of the simulated system consisting of twenty alpha-amino acids and a single TiO2 NP in water solvated system.The dimensions of the water box are roughly 8 nm × 8 nm × 8 nm and it is rendered here as a blue surface. The positions of the twenty amino acids are randomly placed around the NP and are represented as vdW spheres. The titanium (Ti) and oxygen (O) atoms in the TiO2 NP are shown as pink and red van der Waals spheres, respectively.
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f1: The initial configuration of the simulated system consisting of twenty alpha-amino acids and a single TiO2 NP in water solvated system.The dimensions of the water box are roughly 8 nm × 8 nm × 8 nm and it is rendered here as a blue surface. The positions of the twenty amino acids are randomly placed around the NP and are represented as vdW spheres. The titanium (Ti) and oxygen (O) atoms in the TiO2 NP are shown as pink and red van der Waals spheres, respectively.

Mentions: To introduce a chemical environment into the individual amino acids that resembles that present in residues that are part of a protein, the N- and C-termini were capped with the acetyl (ACE) and N-methyl (CT3) groups, respectively. All the simulation systems were built and visualized using the VMD25 program (1.9.2 version). Each system consists of one spherical TiO2 NP and twenty capped amino acids embedded in a cubic water box of 8 nm in length (Fig. 1). The simulations were performed using the GROMACS (version 4.6.7) package26 program with the CHARMM22 force field2728. The TIP3P water model29 was applied for water molecules. Prior to production runs, all systems were minimized and equilibrated with the protocol used in our previous studies3031323334353637. During the equilibration and production runs, the temperature and pressure were maintained at 300 K and at 1 atm using a Langevin thermostat and barostat, respectively. The long-range Coulomb interactions were treated with the PME method38, while the van de Waals (vdW) interactions were handled with a smooth cutoff with a distance value of 1 nm. All the ten production runs were carried out for 100 ns each, resulting with a total aggregate simulation time of 1 μs, under the NPT ensemble. The equation of motion was integrated with a time step of 2 fs and coordinates were collected every 2 ps.


An In Silico study of TiO 2 nanoparticles interaction with twenty standard amino acids in aqueous solution
The initial configuration of the simulated system consisting of twenty alpha-amino acids and a single TiO2 NP in water solvated system.The dimensions of the water box are roughly 8 nm × 8 nm × 8 nm and it is rendered here as a blue surface. The positions of the twenty amino acids are randomly placed around the NP and are represented as vdW spheres. The titanium (Ti) and oxygen (O) atoms in the TiO2 NP are shown as pink and red van der Waals spheres, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC5121885&req=5

f1: The initial configuration of the simulated system consisting of twenty alpha-amino acids and a single TiO2 NP in water solvated system.The dimensions of the water box are roughly 8 nm × 8 nm × 8 nm and it is rendered here as a blue surface. The positions of the twenty amino acids are randomly placed around the NP and are represented as vdW spheres. The titanium (Ti) and oxygen (O) atoms in the TiO2 NP are shown as pink and red van der Waals spheres, respectively.
Mentions: To introduce a chemical environment into the individual amino acids that resembles that present in residues that are part of a protein, the N- and C-termini were capped with the acetyl (ACE) and N-methyl (CT3) groups, respectively. All the simulation systems were built and visualized using the VMD25 program (1.9.2 version). Each system consists of one spherical TiO2 NP and twenty capped amino acids embedded in a cubic water box of 8 nm in length (Fig. 1). The simulations were performed using the GROMACS (version 4.6.7) package26 program with the CHARMM22 force field2728. The TIP3P water model29 was applied for water molecules. Prior to production runs, all systems were minimized and equilibrated with the protocol used in our previous studies3031323334353637. During the equilibration and production runs, the temperature and pressure were maintained at 300 K and at 1 atm using a Langevin thermostat and barostat, respectively. The long-range Coulomb interactions were treated with the PME method38, while the van de Waals (vdW) interactions were handled with a smooth cutoff with a distance value of 1 nm. All the ten production runs were carried out for 100 ns each, resulting with a total aggregate simulation time of 1 μs, under the NPT ensemble. The equation of motion was integrated with a time step of 2 fs and coordinates were collected every 2 ps.

View Article: PubMed Central - PubMed

ABSTRACT

Titanium dioxide (TiO2) is probably one of the most widely used nanomaterials, and its extensive exposure may result in potentially adverse biological effects. Yet, the underlying mechanisms of interaction involving TiO2 NPs and macromolecules, e.g., proteins, are still not well understood. Here, we perform all-atom molecular dynamics simulations to investigate the interactions between TiO2 NPs and the twenty standard amino acids in aqueous solution exploiting a newly developed TiO2 force field. We found that charged amino acids play a dominant role during the process of binding to the TiO2 surface, with both basic and acidic residues overwhelmingly preferred over the non-charged counterparts. By calculating the Potential Mean Force, we showed that Arg is prone to direct binding onto the NP surface, while Lys needs to overcome a ~2 kT free energy barrier. On the other hand, acidic residues tend to form “water bridges” between their sidechains and TiO2 surface, thus displaying an indirect binding. Moreover, the overall preferred positions and configurations of different residues are highly dependent on properties of the first and second solvation water. These molecular insights learned from this work might help with a better understanding of the interactions between biomolecules and nanomaterials.

No MeSH data available.