The interaction of antimicrobial peptides with lipid membranes is governed by a delicate balance of electrostatic, hydrophobic, and conformational forces. In this study, we employed molecular dynamics (MD) simulations to dissect the atomistic mechanisms underlying the pH-dependent behavior of Polybia-MP1 (MP1) and its histidine-containing analog (H-MP1) in anionic 7POPC:3POPG bilayers at pH 5.5 and pH 7.4. The simulations were designed to capture the dynamic evolution of peptide adsorption, insertion, structural reorganization, and lipid perturbation under physiologically relevant conditions.
All MD simulations began with the peptides positioned approximately 10 Å above the bilayer surface in aqueous solution. The protonation states of titratable residues—N-terminal amine, lysines (or histidines), and aspartic acids—were assigned based on their pKa values and the simulation pH. At pH 5.5, MP1 features fully protonated N-terminus and lysines, while aspartic acids remain deprotonated. For H-MP1 at pH 5.5, both the N-terminus and histidines are protonated; at pH 7.4, histidines are largely deprotonated, resulting in a significant reduction in net positive charge. These differences enabled direct comparison of how charge modulation affects membrane engagement.
Initial contact occurs via the N-terminus, which rapidly approaches the bilayer surface due to strong electrostatic attraction to anionic phospholipid headgroups. This step is followed by a rotational transition: the peptide reorients from a perpendicular to a parallel orientation relative to the bilayer plane. This reorientation is critical for full insertion and is observed consistently across all protonated systems. Notably, no stable adsorption was detected in H-MP1 simulations at pH 7.4, where the loss of charge from histidines prevents effective anchoring to the membrane interface.
Once adsorbed, both peptides adopt a parallel configuration, with their hydrophobic faces penetrating the acyl chain region. The C-terminus, amidated and enriched in nonpolar residues, embeds deeply into the hydrophobic core. The tryptophan residue (Trp3), positioned near the interfacial zone, remains stably embedded, consistent with fluorescence quenching data.Gastrin Antibody Technical Information Analysis of the Trp3 center-of-mass distance to the bilayer reveals that MP1 resides slightly deeper (11.3–14.7 Å) than H-MP1 (12.9–16.5 Å), indicating more efficient burial in the hydrophobic environment when histidines are protonated.
Secondary structure analysis shows that upon membrane binding, MP1 transitions from a disordered state to a stable α-helix, forming three additional i–i+4 hydrogen bonds compared to its aqueous form. In contrast, H-MP1 exhibits a transient, less stable helical conformation during the early stages of adsorption (perpendicular orientation), but achieves a fully helical structure only after reorientation. The number of persistent backbone hydrogen bonds increases from 3 to 8 in H-MP1 when aligned parallel to the bilayer, demonstrating that the amphipathic helix is stabilized by the interfacial environment.
Lipid packing disruption was quantified through order parameter calculations (SCH) of acyl chains. Both peptides reduce lipid order, but MP1 induces greater disorder over a longer range—up to 15 Å—while H-MP1’s effect diminishes beyond 10 Å. This spatial difference correlates with experimental observations of lytic efficiency and suggests MP1 induces larger-scale membrane destabilization.TMEM43 Antibody Purity
Energy decomposition revealed that electrostatic interactions contribute most significantly to initial binding, especially between cationic residues and phosphate groups.PMID:34985740 The N-terminus contributes disproportionately to this energy. Van der Waals forces, though weaker, play a supporting role, particularly around the Trp3 side chain, which experiences favorable hydrophobic interactions. Salt bridges—such as Lys4–Asp8 in MP1 and His4–Asp8 in H-MP1—stabilize the helical structure and enhance membrane affinity under acidic conditions.
In conclusion, MD simulations reveal that the pH sensitivity of H-MP1 arises not from a change in overall charge magnitude but from the precise protonation-dependent tuning of specific residues. Histidine protonation at low pH enables strong electrostatic steering, stable helix formation, deep insertion, and extensive lipid disorder—key factors driving enhanced lytic activity. In contrast, MP1 maintains robust performance across pH ranges due to its stable lysine charge and intrinsic structural adaptability. These findings underscore the importance of residue-specific ionization in designing smart AMPs capable of responding to microenvironmental cues. By leveraging such pH-responsive motifs, future therapeutic peptides can be engineered for selective targeting of acidic pathological sites, including tumors and infected tissues, minimizing off-target effects and improving clinical safety.MedChemExpress (MCE) offers a wide range of high-quality research chemicals and biochemicals (novel life-science reagents, reference compounds and natural compounds) for scientific use. We have professionally experienced and friendly staff to meet your needs. We are a competent and trustworthy partner for your research and scientific projects.Related websites: https://www.medchemexpress.com