Revealing pH-dependent antimicrobial peptide, GL13K, characteristics: A constant pH molecular dynamics study ^†

Antimicrobial peptides (AMPs) are a promising potential solution to combat antimicrobial resistance (AMR) due to their positive charges, which induce selective interaction with negatively charged bacterial membranes. Certain AMPs exhibit a low hemolytic index and non-forming fibrils at physiological pH (7.4), enhancing their therapeutic potential. In this study, we employ constant pH molecular dynamics (CpHMD) simulations to investigate the pH-dependent behavior of a 13-residue-long positively charged AMP, GL13K, focusing on the deprotonation states of lysine residues in a single GL13K AMP and their impact on its structural dynamics. We show that the last lysine located near the C-terminus (LYS11) has a significant deprotonation ratio difference with other lysine residues at the reported average experimental side chain pKa value. We observe that increasing the pH results in eventual decrease of the radius of gyration and end-to-end radius and dominance of random coil structure in metastable states. Overall, our study shows the pH-dependent conformational dynamics and pK _a variations of lysine residues in the GL13K antimicrobial peptide, providing critical insights into its structural behavior in solution. These findings establish a foundation for further exploration of GL13K in multi-peptide systems, advancing its potential development as an antimicrobial agent.