Molecular Dynamic Study on the Structure and Thermal Stability of Mutant Pediocin Pa-1 Designed to Contain Extra Cystein Residues

Abstract

Abstract Pediocin and pediocin-like bacteriocins are antimicrobial compounds used in the food industry owing to their remarkable thermal stability and resistance to heat. Enhancing their stability at elevated temperatures and harnessing a bacteriocin derivative molecule produced through such improvements holds promise not only in the food industry but also within the pharmaceutical sector due to their broad-spectrum potential. Although previous studies have examined the two disulfide bonds present in Pediocin PA-1, there has been no inclination to increase the number of disulfide bonds. This study aimed to design mutant peptides by introducing a third disulfide bond, in addition to the two naturally occurring ones in pediocin PA-1, and assess the thermal stability of these mutant peptides. In this study, five mutant peptides (Mut 1, Mut 2, Mut 3, Mut 4, Mut 5) with dual Cys mutations were designed. Initially, the thermal stability of these peptides across a range of temperatures (298–394 K) was evaluated through 100 nanoseconds of molecular dynamics simulations. Subsequently, the most stable mutant peptides (Mut 1, Mut 4, and Mut 5) were selected for further investigation. Molecular dynamics simulations lasting 300 nanoseconds were conducted and analyzed to observe the thermal stability of these structures. The analysis encompassed parameters such as RMSD, RMSF, DSSP, and SASA. The stabilization of these structures was compared with Pediocin PA-1, chosen as the reference molecule. In silico analysis revealed that the free Cys residues did not form a third disulfide bond. Furthermore, most mutants (Mut 1, Mut 5), including the reference structure, exhibited a loss of their helical structure, which is known to be crucial for antimicrobial activity, and the disruption of one of the naturally occurring disulfide bonds at high temperatures. Conversely, Mut 4 retained two disulfide bonds even at elevated temperatures, preserved its helical structure, and demonstrated a thermal stability profile similar to that of Pediocin PA-1. The findings of this study suggest that Mut 4, a highly stable peptide, may represent an exceptionally heat-resistant antimicrobial alternative, contingent upon further analysis to confirm its activity.