Antibacterial mechanism of peptide Asp-Tyr-Asp-Asp based on multiomics and molecular dynamics [E. coli]

In this study, the mechanism of action of the small molecular peptide (DYDD) exhibiting antibacterial properties the application of the peptide in the field of food preservation have been presented. Metabolomics and transcriptomic techniques were used to analyze the metabolic effects of DYDD on E. coli. The differential metabolite screening and cluster analysis techniques were used for analyzing the data. It was found that DYDD could up-regulate 44 metabolites, down-regulate 105 metabolites and DYDD primarily affected 35 metabolic pathways in E. coli. Combined with transcriptome analysis, DYDD primarily influenced the metabolic pathways of E. coli by regulating the genes participating in the amino acid metabolic pathways and sulfur metabolic pathways. Then, the effects of DYDD on POPC-, POPE-, and POPG-based membranes were analyzed using the molecular dynamics simulation. The results showed that DYDD had the strongest binding with Pope membrane, and the insertion of DYDD not only led to the disorder of phospholipid head groups, but also increased the surface area and permeability of the membrane. Finally, DYDD was applied to chestnut kernel infected by E. coli. The results showed that DYDD had good antibacterial effect, could delay the decay and browning of chestnut kernel, and had fresh-keeping effect. Overall design: Escherichia coli was incubated in TSB at 37 C for 8 h. During the logarithmic phase, 200 µL of bacterial solution was added to 200 mL of liquid medium, 200 µL of sterile water (control group; E_CK), or 50 mg/mL of DYDD solution (treatment group; P_DDDY). The bacteria were then cultured on a shaking table at 150 R/min and 37 C for 24 h, centrifuged at 6000 R/min and 4 C for 10 min, washed with PBS three times, and then collected and stored at -80 C.