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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 total adsorption probability of the twenty alpha amino acids onto the TiO2 NP surface.Here, adsorption is counted when any side chain heavy atom is within 5 Å of the TiO2 surface. The four groups of amino acids – Charged, Aromatic, Polar, and Nonpolar – are separated by a dash line.
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f3: The total adsorption probability of the twenty alpha amino acids onto the TiO2 NP surface.Here, adsorption is counted when any side chain heavy atom is within 5 Å of the TiO2 surface. The four groups of amino acids – Charged, Aromatic, Polar, and Nonpolar – are separated by a dash line.

Mentions: Figure 3 shows the total adsorption probability for each amino acid, which was calculated by integrating the probability distribution over a distance range of 0–5 Å (i.e., counted when any side chain heavy atom is within 5 Å of the TiO2 surface). Notably, we found that the adsorption probabilities for the charged residues – arginine (Arg), lysine (Lys), aspartate (Asp), and glutamate (Glu) – are significantly higher than the probabilities for the other amino acid groups (aromatic, polar, and nonpolar; see the “Model and Methods” sections for details). In the charged group, the basic residues, Arg and Lys, show the highest adsorption probabilities with values of 23.2% and 19.4%, respectively, followed by the two acidic residues, Asp (13.5%) and Glu (7.2%), which have relatively lower adsorption probabilities. At the other extreme, all the non-charged amino acids show very weak adsorption probability values to the TiO2 NP. Also we found that residues with a hydroxyl group in their side chains, e.g., the aromatic Tyr and the polar Ser and Thr, display slight preference for positioning in the first water layer, which is consistent with previous results20, where the methanol molecule was used as a surrogate for Ser (Fig. S2). Additionally, residues with the carboxamide group in their side chain, that is polar residues asparagine (Asn) and glutamine (Gln), can be adsorbed either in the first water layer or in the NP surface (Fig. S2). Consistent with our findings, a number of recent studies484950 has suggested the pivotal role of charged and polar residues to promote the adhesion of short oligopeptide onto the surface of titania. In any case, amino acids from the charged group dominate the adsorption events. Therefore, in the following sections we will focus on elucidating the detailed mechanisms involved in the adsorption of Arg, Lys, Asp, and Glu on the TiO2 NP surface.


An In Silico study of TiO 2 nanoparticles interaction with twenty standard amino acids in aqueous solution
The total adsorption probability of the twenty alpha amino acids onto the TiO2 NP surface.Here, adsorption is counted when any side chain heavy atom is within 5 Å of the TiO2 surface. The four groups of amino acids – Charged, Aromatic, Polar, and Nonpolar – are separated by a dash line.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

f3: The total adsorption probability of the twenty alpha amino acids onto the TiO2 NP surface.Here, adsorption is counted when any side chain heavy atom is within 5 Å of the TiO2 surface. The four groups of amino acids – Charged, Aromatic, Polar, and Nonpolar – are separated by a dash line.
Mentions: Figure 3 shows the total adsorption probability for each amino acid, which was calculated by integrating the probability distribution over a distance range of 0–5 Å (i.e., counted when any side chain heavy atom is within 5 Å of the TiO2 surface). Notably, we found that the adsorption probabilities for the charged residues – arginine (Arg), lysine (Lys), aspartate (Asp), and glutamate (Glu) – are significantly higher than the probabilities for the other amino acid groups (aromatic, polar, and nonpolar; see the “Model and Methods” sections for details). In the charged group, the basic residues, Arg and Lys, show the highest adsorption probabilities with values of 23.2% and 19.4%, respectively, followed by the two acidic residues, Asp (13.5%) and Glu (7.2%), which have relatively lower adsorption probabilities. At the other extreme, all the non-charged amino acids show very weak adsorption probability values to the TiO2 NP. Also we found that residues with a hydroxyl group in their side chains, e.g., the aromatic Tyr and the polar Ser and Thr, display slight preference for positioning in the first water layer, which is consistent with previous results20, where the methanol molecule was used as a surrogate for Ser (Fig. S2). Additionally, residues with the carboxamide group in their side chain, that is polar residues asparagine (Asn) and glutamine (Gln), can be adsorbed either in the first water layer or in the NP surface (Fig. S2). Consistent with our findings, a number of recent studies484950 has suggested the pivotal role of charged and polar residues to promote the adhesion of short oligopeptide onto the surface of titania. In any case, amino acids from the charged group dominate the adsorption events. Therefore, in the following sections we will focus on elucidating the detailed mechanisms involved in the adsorption of Arg, Lys, Asp, and Glu on the TiO2 NP surface.

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.