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bioRxiv · 10.1101/2025.10.02.679978

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

Niknam Hamidabad, M.·Mansbach, R.
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Abstract

Membrane-active antimicrobial peptides (AMPs) are a promising potential solution to combat rising antimicrobial resistance (AMR) due to their selective interaction with negatively charged bacterial membranes, but their behavior is controlled by their charge states, which in turn depend on the local pH in which they find themselves. In this study, we employ constant pH molecular dynamics (CpHMD) simulations to investigate the pH-dependent behavior of a 13-residue-long positively charge AMP, GL13K, focusing on the deprotonation states of lysine residues in a single GL13K AMP and their impact on its structural dynamics. We determine pKa values of the critical lysine residues and show that the last lysine located near the C-terminus (LYS11) has a significant deprotonation difference with other lysine residues. We observe that increasing the pH results in changes in the metastable conformational states including collapse of the peptide and highlight the stabilization of a potentially therapeutically-relevant {beta} hairpin configuration in pH levels leading to partial protonation of the lysines. Overall, our study shows the pH-dependent conformational dynamics and pKa variations of lysine residues in the GL13K antimicrobial peptide, providing critical insights into its structural behavior in solution. These findings establish a necessary rigorous foundation for further exploration of GL13K in more complex systems, advancing its potential development as an antimicrobial agent.

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Niknam Hamidabad, M., Mansbach, R.. 2025-10-03. Revealing pH-dependent antimicrobial peptide, GL13K, characteristics: A constant pH molecular dynamics study. https://doi.org/10.1101/2025.10.02.679978

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