Lipid tails modulate antimicrobial peptide membrane incorporation and activity

Interaction Dynamics of Liposomal Fatty Acids with Gram-Positive Bacterial Membranes

The increasing prevalence of antibiotic-resistant bacteria has driven the need for alternative therapeutic strategies, with liposomal fatty acids (LipoFAs) emerging as promising candidates due to their potent antibacterial properties. Despite growing interest, the detailed biophysical interactions between LipoFAs and bacterial membranes remain underexplored. In this study, we systematically investigate the mechanistic interactions of liposomal linolenic acid (LipoLNA), linoleic acid (LipoLLA), and oleic acid (LipoOA) with model Gram-positive bacterial membranes using quartz crystal microbalance with dissipation (QCM-D) and fluorescence microscopy. QCM-D analysis revealed that LipoOA displayed the highest rate of membrane fusion, followed by LipoLLA and LipoLNA. Fluorescence microscopy highlighted distinct morphological changes induced by each LipoFA: LipoLNA generated large membrane buds, LipoLLA formed smaller dense protrusions, and LipoOA caused rapid incorporation with uniform dense spots. Furthermore, fluorescence recovery after photobleaching (FRAP) demonstrated that LipoLNA significantly enhanced lipid mobility and membrane fluidity, as confirmed by Laurdan generalized polarization measurements. The extent of unsaturation in LipoFAs was found to play a critical role in their interaction mechanism, with higher degrees of unsaturation inducing greater local curvature stress, increased membrane permeability, and substantial ATP leakage, ultimately leading to improved bactericidal activity. Notably, liposomal formulations exhibited enhanced biocompatibility compared to free fatty acids. These findings provide valuable mechanistic insights into how LipoFAs perturb bacterial membranes, supporting their potential application as alternative antibacterial agents.

Designing a Novel Ultrashort Cyclic [R3W4V] Antimicrobial Peptide with Superior Antimicrobial Potential Based on the Transmembrane Structure to Facilitate Pore Formation

The clinical application of antimicrobial peptides (AMPs) is frequently hindered by the inherent limitations of linear peptides. Previous studies have primarily focused on the physicochemical properties of AMPs, and there is a scarcity of information regarding the transmembrane structure and interactions of AMPs with cell membranes and their antimicrobial activity. The present study is the first to propose that the backbone cyclization of linear R3W4V (l(R3W4V)) into the cyclic R3W4V (c[R3W4V]) form can enhance the stability of its transmembrane structure and consequently improve its antibacterial activity. The results of the bacterial inhibition assays performed herein demonstrated that the antibacterial activity of c[R3W4V] against Staphylococcus aureus and Bacillus subtilis was approximately 17-fold and 19-fold higher than that of l(R3W4V). The effect of c[R3W4V] on the structure of the bilayer membrane was further assessed via well-tempered bias-exchange metadynamics simulations and long-time conventional unbiased molecular dynamics simulations. This study demonstrated that the single c[R3W4V] peptide assumes a stable transmembrane configuration. Consequently, as the number of peptides accumulating in the membrane core increases at higher peptide-lipid ratios, a higher number of phospholipid headgroups embedded into the hydrophobic lipid core, leading to membrane fusion, permeabilization, and deformation of the upper and lower leaflets of the bilayer. The study provides a novel computational perspective on enhancing the antimicrobial efficacy of AMPs and highlights the importance of peptide-membrane structures, dynamics, and interactions in promoting the membrane-disruptive potential of peptides.

In-depth phospholipid profiling of plant-pathogenic bacteria after treatment with antimicrobial random peptide mixtures

BACKGROUND

The ability of plant-pathogenic bacteria to develop antimicrobial resistance against crop protection products represents a significant challenge. An alternative to conventional crop protecting products could be random peptide mixtures (RPMs), which potentially target the phospholipid-containing cell membrane. The randomized arrangement of the peptides minimizes the risk of bacterial resistance developing against the RPMs. However, not all plant-pathogenic bacteria exhibited growth inhibition after RPM treatment. Our prior studies revealed correlations between bacterial growth inhibition and changes in the fatty acid pattern following treatment. However, additional data on the intact phospholipid composition are essential to further understand and improve novel RPMs.

RESULTS

Accordingly, we developed an analytical setup for in-depth bacterial lipid membrane characterization based on two complementary methods in conjunction with chemometric data evaluation to study the impact of RPM treatment on phospholipid class and species level. An efficient phospholipid class quantitation using hydrophilic interaction liquid chromatography (HILIC)-based lipid class separation with uniform charged aerosol detection (CAD) revealed distinct differences in the class composition of six plant-pathogenic bacteria. Moreover, branched-chain fatty acid (BCFA)-comprising phospholipid profiling via liquid chromatography-tandem mass spectrometry (LC-MS/MS) provided additional lipid species information to classify the investigated bacteria based on the number of bound BCFA. The combination of these techniques served for a comprehensive characterization of the bacterial membrane adaptation to the RPM treatment, which showed some correlations with the inhibitory effects of the RPMs.

SIGNIFICANCE

In this proof-of-concept study, HILIC-CAD phospholipid quantitation and BCFA-comprising phospholipid profiling were introduced as complementary techniques for in-depth characterization of bacterial cell membranes as well as membrane adaptations at both phospholipid class and species level. Our developed analytical setup may facilitate future studies targeting in-depth characterization of bacterial lipid membranes.

What's the defect? Using mass defects to study oligomerization of membrane proteins and peptides in nanodiscs with native mass spectrometry

Many membrane proteins form functional complexes that are either homo- or hetero-oligomeric. However, it is challenging to characterize membrane protein oligomerization in intact lipid bilayers, especially for polydisperse mixtures. Native mass spectrometry of membrane proteins and peptides inserted in lipid nanodiscs provides a unique method to study the oligomeric state distribution and lipid preferences of oligomeric assemblies. To interpret these complex spectra, we developed novel data analysis methods using macromolecular mass defect analysis. Here, we provide an overview of how mass defect analysis can be used to study oligomerization in nanodiscs, discuss potential limitations in interpretation, and explore strategies to resolve these ambiguities. Finally, we review recent work applying this technique to studying formation of antimicrobial peptide, amyloid protein, and viroporin complexes with lipid membranes.

Investigating Daptomycin-Membrane Interactions Using Native MS and Fast Photochemical Oxidation of Peptides in Nanodiscs

Daptomycin is a cyclic lipopeptide antibiotic that targets the lipid membrane of Gram-positive bacteria. Membrane fluidity and charge can affect daptomycin activity, but its mechanisms are poorly understood because it is challenging to study daptomycin interactions within lipid bilayers. Here, we combined native mass spectrometry (MS) and fast photochemical oxidation of peptides (FPOP) to study daptomycin-membrane interactions with different lipid bilayer nanodiscs. Native MS suggests that daptomycin incorporates randomly and does not prefer any specific oligomeric states when integrated into bilayers. FPOP reveals significant protection in most bilayer environments. Combining the native MS and FPOP results, we observed that stronger membrane interactions are formed with more rigid membranes, and pore formation may occur in more fluid membranes to expose daptomycin to FPOP oxidation. Electrophysiology measurements further supported the observation of polydisperse pore complexes from the MS data. Together, these results demonstrate the complementarity of native MS, FPOP, and membrane conductance experiments to shed light on how antibiotic peptides interact with and within lipid membranes.

Lipids and EGCG Affect α-Synuclein Association and Disruption of Nanodiscs

Lipid membranes have recently been implicated in protein misfolding and disease etiology, including for α-synuclein and Parkinson's disease. However, studying the intersection of protein complex formation, membrane interactions, and bilayer disruption simultaneously is challenging. In particular, the efficacies of small molecule inhibitors for toxic protein aggregation are not well understood. Here, we used native mass spectrometry in combination with lipid nanodiscs to study α-synuclein-membrane interactions. α-Synuclein did not interact with zwitterionic 1,2-dimyristoyl-sn-glycero-3-phosphocholine lipids but interacted strongly with anionic 1,2-dimyristoyl-sn-glycero-3-phospho(1'-rac-glycerol) lipids, eventually leading to membrane disruption. Unsaturated 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho(1'-rac-glycerol) (POPG) lipid nanodiscs were also prone to bilayer disruption, releasing α-synuclein:POPG complexes. Interestingly, the fibril inhibitor, (-)-epigallocatechin gallate (EGCG), prevented membrane disruption but did not prevent the incorporation of α-synuclein into nanodisc complexes. Thus, although EGCG inhibits fibrillization, it does not inhibit α-synuclein from associating with the membrane.