Biology subjects

Drabik, D.

Publications and source records attributed to Drabik, D..

9 recordsLinked to original sources

bioRxiv2026

Bacterial-Mimetic Membranes Reveal Hopanoid-Associated Domain-Like Lateral Heterogeneity

Bacterial membranes are increasingly recognized as laterally heterogeneous assemblies whose local organization can regulate transport, stress adaptation, and interactions with membrane-active compounds. However, the physical principles by which bacterial lipid composition generates spatially distinct membrane environments remain poorly understood, partly because experimentally tractable models that reproducibly exhibit lateral segregation and permit quantitative characterization are limited. Here, we show that a multicomponent, hopanoid-containing bacterial-inspired membrane spontaneously self-organizes into laterally distinct physical environments that are consistently resolved in experiments and molecular simulations. Giant unilamellar vesicles prepared from a lipid mixture inspired by lipid classes found in hopanoid-producing bacteria, including Methylorubrum extorquens, exhibit stable micron-scale lateral segregation, which is independently reproduced in compositionally matched coarse-grained molecular dynamics simulations. The resulting membrane environments differ in composition, packing, order, mobility, and mechanical properties. Hopanoid-associated domain-like regions are more condensed, more ordered, and less mobile, whereas PE-rich non-domain regions remain more laterally expanded and exhibit faster lipid diffusion. At the global level, the bacterial-inspired membrane displays greater bending rigidity than a fluid phosphatidylcholine reference, while ATR-FTIR measurements independently support increased lipid-chain ordering and denser membrane packing. Together, these findings establish that hopanoid-containing bacterial-inspired membranes can spontaneously generate coexisting physical environments whose distinct local properties collectively determine global membrane behavior. The resulting experimental-computational framework provides a quantitative basis for investigating bacterial-like membrane heterogeneity and how local composition, dynamics, and mechanics govern responses to membrane-targeting perturbations.

biophysics↗

bioRxiv2026

Lateral Membrane Heterogeneity Shapes Antimicrobial Association and Convergent Mechanical Responses

Bacterial membranes are laterally heterogeneous, creating local physicochemical environments that can shape interactions with membrane-active antimicrobials. However, whether this spatial organization only affects local drug association or propagates into collective membrane responses remains unclear. Here we show that lateral membrane heterogeneity shapes antimicrobial association while distinct molecular responses converge on a common loss of membrane mechanical stability. Combining coarse-grained molecular dynamics, giant unilamellar vesicle fluctuation spectroscopy and microfluidic trapping, we follow octenidine, chlorhexidine and polymyxin B from molecular association to vesicle-scale behaviour. All three compounds preferentially associate with domain-associated membrane environments, but differ in how this preference changes with loading and in their effects on lipid mobility. Despite these differences, all three shift the membrane toward a mechanically softer state, while increasing exposure accelerates loss of vesicle stability under flow. These findings identify lateral membrane heterogeneity as an active determinant of antimicrobial response and provide a physical framework for understanding membrane-targeting activity beyond bulk composition and membrane-averaged charge.

biophysics↗

bioRxiv2026

Opposing Roles of Cholesterol and Cholesterol Sulfate in Proton Transfer and Diffusion at Membrane Interfaces

Sterols are fundamental components of biological membranes that modulate membrane fluidity and organisation, yet their role in governing interfacial proton dynamics remains underexplored. Here, we elucidate how cholesterol (Ch) and cholesterol sulfate (ChS) regulate excited-state proton transfer (PT) and long-range proton diffusion (PD) using a complementary dual-approach experimental framework combined with molecular dynamics (MD) simulations. Using a membrane-anchored photoacid in small unilamellar vesicles, we demonstrate that Ch accelerates local PT dynamics in gel-phase phosphatidylcholine membranes by inducing a fluid, liquid-ordered phase. Surprisingly, ChS inhibits local PT despite its negative headgroup. MD simulations reveal this inhibition stems from deeper probe embedding within ChS containing bilayers and the reduced basicity of sulfate relative to phosphate. Conversely, solid-state electrical measurements on supported lipid bilayers show a stark reversal for long range proton conduction (lateral PD): ChS increases lateral proton conductance by 400 fold under controlled relative humidity, whereas Ch decreases conductivity. This divergence arises mainly because ChS supplies titratable sulfate charge carriers, whereas Ch dilutes key phosphate proton mediators that promote a percolating interfacial hydrogen bonding network without providing charge carriers. Our findings demonstrate that sterols exert scale-dependent control over membrane PT/PD, revealing how headgroup chemistry, membrane fluidity, and hydration synergistically govern bioenergetic proton dynamics.

biophysics↗

bioRxiv2026

A Bottom-Up Approach to Fungal Plasma Membrane Model: Lipid Mixture Design and Biophysical-Mechanical Characterization

The rising incidence of invasive fungal diseases emphasizes the need for novel therapeutic strategies, including membrane-targeting antifungal agents, which require representative lipid models for detailed molecular-level studies. In this work, we propose a consensus quinary fungal plasma membrane model based on lipidomic literature data, specifically PC:PE:PI:PA:PS phospholipid model with ratio of 44:29:13:8:6. Using a bottom-up approach, we characterized the biophysical properties of this system - with particular emphasis on mechanical parameters such as bending rigidity and area compressibility - by combining molecular dynamics simulations with experimental flicker-noise and ATR-FTIR spectroscopies. Furthermore, we investigated the effect of two key non-phospholipid components: ergosterol and triacylglycerols. Biophysical analysis revealed that DPPI and its specific interactions with DSPS induced the most substantial deviations in baseline membrane parameters, particularly area per lipid, membrane thickness, and area compressibility, while DSPS influenced bending rigidity change and DLiPA primarily affected lipid packing defects. In addition, ergosterol and TGs were found to influence all of the investigated parameters to different degree. Notably, the overall biophysical profile of the proposed FPMM closely mimicked that of natural vesicles derived from yeast lipid extracts, establishing this model may provide a reliable platform for studying fungal membrane biophysics and lipid-targeting interactions.

biophysics↗

bioRxiv2025

Is efficiency of protein incorporations governed by membrane properties? An α-synuclein and ceramide-1-phosphate investigation.

In protein-membrane interactions membranes provide an environment that enables proteins to fulfill multiple functions. Yet our knowledge about specificity of protein-membrane interactions is not sufficient. It is our hipothesis that this specificity is governed to a large extend by the properties of membrane itself. This study investigates the protein-membrane interactions in the case of -synuclein (S) and ceramide-1-phosphate (C1P) enriched membranes. The interactions between S and lipids were reported to be governed by various factors, including lipid composition, membrane curvature, charge and fluidity. On the other hand, C1P is anionic lipid and the shape of its molecule is similar to that of PA, which was reported to strongly interact with S. There are three main aspect of this work. First of all interactions between S and C1P enriched membranes is investigated using microscale thermophoresis. Secondly, systematic characterization of membrane systems is performed using both in vitro and in silico techniques. Eventually, principal component analysis and multiple linear regression are used to determine phenomenological dependency of those interactions in function of membrane properties.

biophysics↗

bioRxiv2024

Proton migration on biological membranes: Lipid phase, temperature, and composition dependence of proton transfer processes and membrane proton barrier

Biological membranes play a major role in diffusing protons on their surfaces between transmembrane protein complexes. The retention of protons on the membranes surface is commonly described by a membrane-associated proton barrier that determines the efficiency of protons escaping from surface to bulk, which correlates with the proton diffusion (PD) dimensionality at the membranes surface. Here, we explore the role of the membranes biophysical properties and its ability to accept a proton from a light-triggered proton donor situated on the membranes surface and to support PD around the probe. By changing lipid composition and temperature, while going through the melting point of the membrane, we directly investigate the role of the membrane phase in PD. We show that the proton transfer process from the proton donor to the membrane is more efficient in the liquid phase of the membrane than in the gel phase, with very low calculated activation energies that are also dependent on the lipid composition of the membrane. We further show that the liquid phase of the membrane allows higher dimensionalities (close to 3) of PD around the probe, indicating lower membrane proton barriers. In the gel phase, we show that the dimensionality of PD is lower, in some cases reaching values closer to 1, thus implying specific pathways for PD, which results in a higher proton recombination rate with the membrane-tethered probe. Computational simulations indicate that the change in PD between the two phases can be correlated to the membranes stiffness and looseness at each phase. Significance statementProton diffusion on the surface of biological membranes serves a vital role in migrating protons into bioenergetic systems. Here, we explore how the biophysical properties of the membrane determine proton migration and proton retention on the surface of the membrane, i.e., the membrane proton barrier. We show that the membrane phase, which is also influenced by lipid composition, has a crucial role in the proton circuity of biological membranes. We found that the gel phase reduces the proton diffusion dimensionality and that the proton barrier is determined by lipid composition. Our results highlight the complexity of proton migration on the surface of biological membranes and the associated biophysical parameters that influence the proton diffusion process.

biophysics↗

bioRxiv2024

The interplay between proton diffusion across biological membranes and their biophysical properties highlights the role of defects in mixed lipid membranes

Proton circuits within biological membranes are at the heart of natural bioenergetic systems, whereas different biological membranes are characterized by different lipid compositions. In this study, we investigate how the composition of mixed lipid membranes influences the proton transfer (PT) properties of the membrane by following the excited-state PT (ESPT) process from a tethered probe to the membrane with time-scales and length-scales of PT that are relevant to bioenergetic systems. Two processes can happen during ESPT: the initial PT from the probe to the membrane at short timescales, followed by diffusion of dissociated protons around the probe on the membrane, and the possible geminate recombination with the probe at longer timescales. Here, we use membranes that are composed of mixtures of phosphatidylcholine (PC) and phosphatidic acid (PA). We show that the changes in the ESPT properties are not monotonous with the concentration of the lipid mixture; at low concentration of PA in PC, we find that the membrane is a poor proton acceptor. Molecular dynamics simulations indicate that at this certain lipid mixture, the membrane has the least defects (more structured and unflawed). Accordingly, we suggest that defects can be an important factor in facilitating PT. We further show that the composition of the membrane affects the geminate proton diffusion around the probe, whereas, on a time-scale of tens of nanoseconds, the dissociated proton is mostly lateral restricted to the membrane plane in PA membranes, while in PC, the diffusion is less restricted by the membrane.

biophysics↗

bioRxiv2022

Effect of leaflet asymmetry on mechanical properties of lipid bilayers with phosphatidic acid

The asymmetry of membranes has a significant impact on their biophysical characteristics and behavior. This study investigates the composition and mechanical properties of symmetric and asymmetric membranes in giant unilamellar vesicles (GUVs) made of phosphatidylcholine (POPC) and phosphatidic acid (POPA). A combination of fluorescence quantification, zeta potential measurements, micropipette aspiration and bilayer molecular dynamics simulations are used to characterize these membranes. The outer leaflet composition in vesicles is found consistent across the two preparation methods we employed, namely electroformation and inverted emulsion transfer. However, characterizing the inner leaflet poses challenges. Micropipette aspiration of GUVs show that oil residues do not substantially alter membrane elasticity, but simulations reveal increased membrane thickness and decreased interleaflet coupling in the presence of oil. Asymmetric membranes with a POPC:POPA mixture in the outer leaflet and POPC in the inner leaflet display similar stretching elasticity values to symmetric POPC:POPA membranes, suggesting potential POPA insertion into the inner leaflet during vesicle formation and suppressed asymmetry. The inverse compositional asymmetry, with POPC in the outer leaflet and POPC:POPA in the inner yield less stretchable membranes with higher compressibility modulus compared to their symmetric counterparts. Challenges in achieving and predicting compositional correspondence highlight the limitations of phase-transfer-based methods. Additionally, caution is advised when using fluorescently labeled lipids (even at low fractions of 0.5 mol%), as unexpected gel-like domains in symmetric POPC:POPA membranes were observed only with a specific type of labeled DOPE (dioleoylphosphatidylethanolamine) and the same fraction of unlabeled DOPE. The latter suggest that such phase separation may result from interactions between lipids and membrane fluorescent probes. Overall, this study underscores the complexity of factors influencing GUV membrane asymmetry, emphasizing the need for further research and improvement of characterization techniques. SIGNIFICANCEAsymmetrically charged lipid bilayer models are superior to commonly used symmetrical ones, exhibiting naturally present asymmetry, thereby exhibiting a more adequate range of biophysical membrane characteristics better reflecting biological membranes. This study focuses on the mechanical properties of phosphatidic acid (PA)-enriched membranes, a crucial lipid for cellular lipid metabolism, e.g. glycerophospholipid synthesis, and for signal transduction. Micropipette aspiration, fluorescent PA-sensor, and zeta potential studies demonstrate that asymmetric membranes are less stretchable than symmetric ones. Accompanying in silico studies on the symmetric membranes confirm that oil impurities do not influence the membrane stretching elasticity but increase its thickness and decrease the coupling of the two leaflets, which sheds light on the elastic behavior of experimental models of asymmetric lipid bilayers.

biophysics↗

bioRxiv2022

Investigation of nano- and micro-domains formed by ceramide-1-phosphate in freestanding lipid bilayers

Biological membranes are known for their complex nature and formation of domains is crucial for proper execution of multiple cellular processes. Such domains, mostly due to their nanoscale character, are rarely studied since implementation of techniques for their quantitative investigation is difficult. In this article we introduce spot-variation z-scan FCS implemented for the first time for artificial lipid vesicles of defined lipid composition. We used this approach to investigate behaviour of different species of ceramide-1-phosphate within membranes. We were able to provide quantitative description of lipid domains generated by ceramide-1-phosphate in nano and microscale. Aligning these results with in silico studies helped us to validate the approach and draw conclusions on complex behaviour of signalling lipids within biological membranes.

biophysics↗