Aromaphilicity Index of Amino Acids: Molecular Dynamics Simulations of the Protein Binding Affinity for Carbon Nanomaterials

Abstract

Aromatic carbon nanomaterials, such as carbon nanotubes and graphene, undergo protein adsorption in the early stages of their uptake into biological systems, which determines their bioavailability and cytotoxicity. Although a mechanistic understanding of protein-nanomaterial interactions is essential for realizing safe and controlled in vivo applications of nanomaterials, it remains challenging to predict arbitrary protein-nanomaterial interactions. This study introduces an index, "aromaphilicity (aromatic-loving nature) index", for 20 proteinogenic amino acids. This index reflects the affinity of the amino acid side chains for the aromatic carbon surfaces, which was quantified by molecular dynamics simulations. This index is significantly correlated with the experimental data (R2 = 0.789) and successfully utilized as a versatile tool for predicting the affinity hot spots of the proteins for the aromatic carbon nanomaterials. This approach advances the understanding of the mechanism of protein-nanomaterial interactions and improves prediction of the biological impacts of nanomaterials.