Potential functional changes in native lysozyme induced by carbon nanotubes studied by molecular dynamics simulations

Abstract

A carbon nanotube (CNT) can affect biological systems, ranging from toxicity to changes in functionality. Here, a series of long-scale (1–2 µs) molecular dynamics simulations were conducted to investigate the adsorption and interaction of lysozyme with the CNT, a possible mechanism for altering protein flexibility and function. Four systems were examined: native lysozyme/CNT, denatured lysozyme/CNT, and both systems post-docking. Our results indicate that native lysozyme does not undergo conformational changes when initially captured by a CNT. However, after docking, the native lysozyme/CNT complex exhibits conformational changes. In contrast, the denatured lysozyme binds more effectively to the CNT in both pre- and post-docking scenarios. Key amino acid residues, arginine and tryptophan, have been identified as crucial for lysozyme/CNT interactions. The surface of the CNT adsorbs lysozyme through π-π stacking and van der Waals interactions, with these multimodal interactions serving as the main driving force for protein anchoring to the nanotube. These results also underscore the significance of docking in the simulation of protein/nanoparticle interactions, which can lead to entirely different conclusions regarding, for example, the toxicity or functionality of a given nanoparticle life.