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.

Modeling Study of OH Radical-Dominated H-Abstraction Reaction for Understanding Nucleotides Oxidation Induced by Cold Atmospheric Plasmas

“…When RONS particles exceed physiological levels within organisms, oxidative stress ensues, potentially leading to severe outcomes. ROS have been shown to interact with various macromolecules, exerting profound effects on cells, including the oxidation of cell membranes, proteins, and DNA during the sterilization process of CAP [15][16][17]. Furthermore, ROS function as pivotal intracellular signal regulators, modulating numerous cellular signaling pathways through diverse mechanisms instrumental in cell transformation, inflammatory responses, tumor proliferation, and metastasis [18,19].…”

“…Reactive MD simulation is the most commonly used method in plasma medicine and has the advantage of describing the breaking and formation of chemical bonds, and recently, the machine learning technology is also introduced to the reactive MD simulation for efficiently understanding the bond reactions [29]. Compared to QM calculations, it can handle much larger systems and much longer time scales [17,[30][31][32][33].…”