Damage to the Peptidoglycan in the Cell Wall Caused by Reactive Oxygen Species: A Molecular Dynamics Simulation

Using molecular dynamics simulations with the ReaxFF force field, we investigate the oxidization mechanism of reactive oxygen species (ROS) on three different peptidoglycans (PGs) in an aqueous environment, which are A3α type, A1γ type, and B1α type, respectively. Our findings revealed ROS can dehydrogenate and break C-C and C-O bonds. We identified distinct mechanisms for C-O bond dissociation, which occurred in four contexts: on MurNAc, on GlcNAc, and between MurNAc and GlcNAc, as well as between the stem peptide and MurNAc. Additionally, we observed a C-C dissociation mechanism occurring on GlcNAc. However, no dissociation mechanism for C-N bonds was detected even when the temperature was increased. Moreover, we found that ROS had a significantly higher capacity to extract H atoms from O atoms than C atoms. Under the same concentration of ROS, we noted that the dehydrogenation ratio of A3α type PG was the most facile, even though the dissociation of C-C and C-O bonds was relatively weak. In contrast, the B1α type PG exhibited the lowest dehydrogenation ratio while showing the highest dissociation rates for C-C and C-O bonds, with A1γ type PG in between them. This study offers new insights into understanding the bactericidal effects of plasma at the atomic level.