Reactive molecular dynamics simulations on interaction mechanisms of cold atmospheric plasmas and peptides

Abstract

Plasma medicine is a rapidly growing multidisciplinary field, which mainly focuses on the application of Cold Atmospheric Plasma (CAP) in bioengineering. Several experiments have suggested that amino acids in proteins are excellent targets for plasma-derived chemical species. To gain a deep insight into the oxidative modification of proteins induced by CAP, a ReaxFF-based reactive Molecular Dynamics simulations are performed to investigate the reaction mechanism of Reactive Oxygen Species produced in CAP and the model peptides. The simulation results show that sulfur-containing amino acids with high reactivity could be oxidized to sulfuric acid moiety through sulfonation, and only H-abstraction reaction can take place for aromatic amino acids. The oxidation of five-membered ring amino acids could be observed by yielding the ring-open products in the simulations. Additionally, the dehydrogenation and hydroxylation of carbon-chain amino acids were also found from the simulations, with the formation of the hydroxyl group. The polar amino acids with the electron-rich structure were oxidized to a variety of products, such as di-hydroxylated lysine and hydroxylated asparagine. This study provides a crucial step to understand the processes of oxidative modifications and inactivation of proteins induced by CAP, showing a deep insight on the mechanism of plasma medicine.