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

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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.


Free energy profile of the adsorption Lys on the TiO2 NP surface and representative configurations (B–D). The H-Bonds in the triad water-amino acid-TiO2 NP, are indicated by green dash lines.
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f5: Free energy profile of the adsorption Lys on the TiO2 NP surface and representative configurations (B–D). The H-Bonds in the triad water-amino acid-TiO2 NP, are indicated by green dash lines.

Mentions: In the case of Lys, the adsorption free energy contains two minima, K1 and K3, at 1.89 nm and 2.14 nm, with an associated energy of −12.73 kJ/mol and 0.08 kJ/mol, respectively. There is a free energy barrier between the K1 and K3 minima (moving from the bulk toward the surface) of 5.65 kJ/mol (~2 kT at room temperature) at a distance separation from the surface of 2.01 nm (K2), as indicated in Fig. 5A. The difference between the energy profiles for both basic residues can be ascribed to the distinct properties of the guanidinium and amino side chain groups. Unlike the terminal group in the Arg side chain, which displays a relatively large, rigid, and planar geometry, the terminal group in Lys is smaller in size and less capable of establishing a large number of electrostatic interactions (smaller hydrogen-binding capability). Thus, and in contrast to Arg, during the Lys absorption onto the NP surface, only a maximum of three hydrogen bonds can be formed with O atoms from the TiO2 NP, which would not be enough to offset the reduction in entropy related with the organization of water molecules in the first water layer, resulting in the presence of an energy barrier in the Lys free energy profile (Fig. 5A and B). The second minima, K3, (Fig. 5D) in the Lys adsorption profile is located at a distance from the surface (2.14 nm) that corresponds to the second water layer region (SL). The small value for this energy well (0.08 kJ/mol) indicates an almost free movement from the SL toward the bulk water region. Similarly to the case of Arg, the water molecules from the first water layer can establish favorable hydrogen bond interactions with the amino side chain group of Lys to stabilize its absorption onto the NP surface. In sharp contrast, K2 is in transition point and water molecules from the second water layer favor the desorption of Lys on the NP surface, as shown in Fig. 5C.


An In Silico study of TiO 2 nanoparticles interaction with twenty standard amino acids in aqueous solution
Free energy profile of the adsorption Lys on the TiO2 NP surface and representative configurations (B–D). The H-Bonds in the triad water-amino acid-TiO2 NP, are indicated by green dash lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f5: Free energy profile of the adsorption Lys on the TiO2 NP surface and representative configurations (B–D). The H-Bonds in the triad water-amino acid-TiO2 NP, are indicated by green dash lines.
Mentions: In the case of Lys, the adsorption free energy contains two minima, K1 and K3, at 1.89 nm and 2.14 nm, with an associated energy of −12.73 kJ/mol and 0.08 kJ/mol, respectively. There is a free energy barrier between the K1 and K3 minima (moving from the bulk toward the surface) of 5.65 kJ/mol (~2 kT at room temperature) at a distance separation from the surface of 2.01 nm (K2), as indicated in Fig. 5A. The difference between the energy profiles for both basic residues can be ascribed to the distinct properties of the guanidinium and amino side chain groups. Unlike the terminal group in the Arg side chain, which displays a relatively large, rigid, and planar geometry, the terminal group in Lys is smaller in size and less capable of establishing a large number of electrostatic interactions (smaller hydrogen-binding capability). Thus, and in contrast to Arg, during the Lys absorption onto the NP surface, only a maximum of three hydrogen bonds can be formed with O atoms from the TiO2 NP, which would not be enough to offset the reduction in entropy related with the organization of water molecules in the first water layer, resulting in the presence of an energy barrier in the Lys free energy profile (Fig. 5A and B). The second minima, K3, (Fig. 5D) in the Lys adsorption profile is located at a distance from the surface (2.14 nm) that corresponds to the second water layer region (SL). The small value for this energy well (0.08 kJ/mol) indicates an almost free movement from the SL toward the bulk water region. Similarly to the case of Arg, the water molecules from the first water layer can establish favorable hydrogen bond interactions with the amino side chain group of Lys to stabilize its absorption onto the NP surface. In sharp contrast, K2 is in transition point and water molecules from the second water layer favor the desorption of Lys on the NP surface, as shown in Fig. 5C.

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.