Structures of the Antimicrobial Peptides MDP-1 and MDP-2:Molecular Dynamics Simulations
The artificial antimicrobial peptides mytilin-derived-peptide-1(MDP-1)and mytilin-derived-peptide-2(MDP-2)contain the same amino acid residues in opposite sequences,but the bacteriostatic activity of MDP-2 is greater than that of MDP-1.Previous liquid nuclear magnetic resonance spectroscopy experiments showed that both peptides showed β-turn structures in aqueous solution,and the differences in their hydropho-bic patch areas and the topological structures of the basic amino acids on the molecular surfaces were the main reasons for the differences in their activities.In order to deeply investigate the dynamic process of peptide hy-drophobic patch area and structural stability in aqueous solution,molecular dynamics was used to simulate the structural stability of MDP-1 and MDP-2 in aqueous solution and the process of changing the polarizable sur-face area of the solution.The results showed that the primary secondary structures of the antimicrobial peptides MDP-1 and MDP-2 were both β-hairpin in aqueous solution,but MDP-2 has a smaller RMSD value and RMSF value in aqueous solution,and its structure is more stable.The solution-accessible surface area is larg-er,which can have a larger contact area with the bacterial cell membrane,and therefore has a better bacterial inhibition effect.This study analyses the relationship between the hydrophobicity and structure of the antimi-crobial peptide and its antibacterial activity,provides a theoretical basis for the design and optimization of an-timicrobial peptides.
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