Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2023.05.02.539057

Molecular Mechanisms Underlying Medium-Chain Length Free Fatty Acid-regulated Activity of the Phospholipase PlaF from P. aeruginosa

Gentile, R.·Modric, M.·Thiele, B.·Jaeger, K.-E.·Kovacic, F.·Gohlke, H.
View original source ↗Export metadata ↓

Abstract

PlaF is a membrane-bound phospholipase A1 from P. aeruginosa that is involved in remodeling membrane glycerophospholipids (GPLs) and modulation of virulence-associated signaling and metabolic pathways. Previously, we identified the role of medium-chain free fatty acids (FFA) in inhibiting PlaF activity and promoting homodimerization, yet the underlying molecular mechanism remained elusive. Here, we used unbiased and biased molecular dynamics simulations and free energy computations to assess how PlaF interacts with FFAs localized in the water milieu surrounding the bilayer or within the bilayer, and how these interactions regulate PlaF activity. Medium-chain FFAs localized in the upper bilayer leaflet can stabilize inactive dimeric PlaF, likely through interactions with charged surface residues as experimentally validated. Potential of mean force (PMF) computations indicate that membrane-bound FFAs may facilitate the activation of monomeric PlaF by lowering the activation barrier of changing into a tilted, active configuration. We estimated that the coupled equilibria of PlaF monomerization-dimerization and tilting at the physiological concentration of PlaF lead to the majority of PlaF forming inactive dimers when in a cell membrane loaded with decanoic acid (C10). This is in agreement with a suggested in vivo product feedback loop and GC-MS profiling results indicating that PlaF catalyzes the release of C10 from P. aeruginosa membranes. Additionally, we found that C10 in the water milieu can access the catalytic site of active monomeric PlaF, contributing to the competitive component of C10-mediated PlaF inhibition. Our study provides mechanistic insights into how medium-chain FFA may regulate the activity of PlaF, a potential bacterial drug target.

Explore related subjects

biophysicsPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Gentile, R., Modric, M., Thiele, B., Jaeger, K.-E., Kovacic, F., Gohlke, H.. 2023-05-03. Molecular Mechanisms Underlying Medium-Chain Length Free Fatty Acid-regulated Activity of the Phospholipase PlaF from P. aeruginosa. https://doi.org/10.1101/2023.05.02.539057

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Lipid Scrambling Amplifies Plasma Membrane Undulations via Anti-Registered Domains Stabilized by Long-Chain Sphingomyelin

Lipid scrambling, which dissipates the transbilayer lipid asymmetry of plasma membranes (PMs), plays an essential role in various large-scale membrane remodeling processes. Although lipid domains have been implicated in these processes, the underlying mechanisms remain poorly understood, owing to the lack of a molecular-level picture of how lipid scrambling reorganizes these domains. Here, using coarse-grained molecular dynamics simulations of asymmetric and fully scrambled PM models, we show that lipid scrambling markedly enhances membrane undulations. We identify two key features of the domain organization underlying this enhancement in the scrambled PM: domain anti-registration, which couples to membrane curvature through a mismatch in preferred curvature between the two leaflets, and scrambling-induced domain enlargement, which permits this curvature to extend over large length scales. Simulations with different sphingomyelin (SM) compositions demonstrate that long-chain SMs stabilize anti-registered domains and the associated membrane curvature. Together, these results suggest a physical mechanism by which lipid scrambling primes the PM for remodeling through the reorganization of lipid domains, with long-chain SMs playing a key role. We also find that the interleaflet domain organization of the scrambled PM model depends strongly on system size, shifting from anti-registration to registration as the simulation box is reduced, and we discuss the origin of this finite-size effect.

biophysics↗
bioRxiv2026

Evaluating speech-like distortion product otoacoustic emissions: a comparison of time- and frequency-domain metrics across three datasets

Speech-like distortion-product otoacoustic emissions (DPOAEs) allow cochlear activity to be measured during the perception of natural, continuous speech and have been used to study attentional effects in the cochlea. The technique is still young, however, and existing studies differ in stimulus design and in the metric used to quantify the emissions, which makes their results difficult to compare. Here, we reanalysed three existing datasets (106 participants, 14 stimulus types) with a common pipeline. We compared six metrics: the band power of the recording, the magnitude-squared coherence (MSC) between the recording and a DPOAE template, and four metrics derived from their complex cross-correlation, namely peak magnitude, signal-to-noise ratio (SNR), peak area and peak width. A separability index quantified how well each metric separated in-ear recordings from out-of-ear control recordings without emissions. Band power, MSC and SNR separated best, with mean separability indices of about 0.9, whereas the peak magnitude performed worst and was inverted for half of the stimulus types. Since band power does not require a DPOAE template, it serves as a sanity check of the setup rather than as evidence for an emission. The MSC was insensitive to the latency of the emission but well suited for comparisons across stimuli, whereas the cross-correlation additionally provided the latency. The emissions differed significantly between the stimulus types of the three datasets, and those below about 700 Hz were measured least reliably. We derive practical recommendations for the analysis and stimulus design of future experiments.

biophysics↗
bioRxiv2026

Overlap of competing voices may mask attentional effects on speech-like distortion product otoacoustic emissions

Whether selective auditory attention modulates the cochlear amplifier through the medial olivocochlear system remains debated. Using speech-like distortion-product otoacoustic emissions (DPOAEs), elicited by waveforms that follow the harmonics of natural speech, we previously found that selectively attending one of two competing talkers reduced the emissions related to the resolved harmonics of the female voice. Here, we attempted to reproduce this effect in a design that separated different frequency regimes and harmonic resolvability. Forty-four participants attended one of two competing talkers, a female and a male voice, presented to one ear, while speech-like DPOAEs related to both voices were recorded from the other ear. Stimuli were derived from resolved and unresolved harmonics in a low-frequency (up to 1.5 kHz) and a transitional (1.5 to 4 kHz) regime, which required pitch-shifting both voices so that their fundamental frequencies were much closer to each other than in the original study. Speech-like DPOAEs emerged for most stimulus types, although they were weak for some and absent for one. Their amplitude, however, did not depend on attention for any stimulus type. Further time-domain metrics showed only isolated attentional effects of opposite direction for two stimulus types, and a frequency-domain metric showed none. A cochlear excitation model suggests that, due to the closely spaced fundamental frequencies of the two voices, the emissions most comparable to the original study presumably arose at cochlear locations shared by both voices, where attention would modulate both voices alike.

biophysics↗