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

This study uses long-scale molecular dynamics simulations (1–2 microseconds) to investigate how carbon nanotubes (CNTs) interact with lysozyme — an antimicrobial protein — and whether that interaction alters the protein's structure and function. Four scenarios were compared: native and denatured lysozyme, each with and without a docking step to optimize the initial protein-CNT configuration. The CNT surface adsorbs lysozyme primarily through π–π stacking and van der Waals interactions, with arginine and tryptophan residues identified as the key amino acids driving the binding. The results reveal a striking dependence on both protein state and simulation setup. Native lysozyme does not undergo significant conformational changes when simply placed near a CNT, but after docking, the complex exhibits notable structural reorganization. Denatured lysozyme, by contrast, binds more effectively in both scenarios, coating the nanotube surface with roughly three times as many residues as the native form. These findings highlight the importance of the docking step in protein–nanoparticle simulations, as its inclusion or omission can lead to entirely different conclusions about a nanoparticle's toxicity or functional impact. The paper was published in Scientific Reports in April 2025 by Vaez Allaei, Amininasab, Ishkhanyan, and Poghosyan.