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Langmuir

American Chemical Society (ACS)

All preprints, ranked by how well they match Langmuir's content profile, based on 31 papers previously published here. The average preprint has a 0.02% match score for this journal, so anything above that is already an above-average fit. Older preprints may already have been published elsewhere.

1
Long chain lipids facilitate insertion of large nanoparticles into membranes of small unilamellar vesicles

Marzouq, A.; Morgenstein, L.; Yudovich, S.; Atkins, A.; Grupi, A.; Weiss, S.

2021-07-13 biophysics 10.1101/2021.07.12.452073 medRxiv
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Insertion of hydrophobic nanoparticles into phospholipid bilayers is limited to small particles that can incorporate into the hydrophobic membrane core in between the two lipid leaflets. Incorporation of nanoparticles above this size limit requires development of challenging surface engineering methodologies. In principle, increasing membrane thickness should facilitate incorporation of larger nanoparticles. Here, we explore the effect of incorporating very long phospholipids (C24:1) into small unilamellar vesicles on the membrane insertion efficiency of hydrophobic nanoparticles that are 5-13 nm in diameter. To this end, we improved an existing vesicle preparation protocol and utilized cryogenic electron microscopy imaging to examine the mode of interaction and to evaluate the insertion efficiency of membrane-inserted nanoparticles. We also perform classical, coarse-grained molecular dynamics simulations to identify changes in lipid membrane structural properties that may increase insertion efficiency. Our results indicate that long-chain lipids increase the insertion efficiency by preferentially accumulating near membrane-inserted nanoparticles to reduce the thermodynamically unfavorable disruption of the membrane.

2
Quantification of Cholesterol Incorporation in Giant Unilamellar Vesicles Produced by a Modified cDICE Method

Arribas Perez, M.; Koenderink, G. H.

2025-11-10 biophysics 10.1101/2025.11.10.687550 medRxiv
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AbstractCholesterol is an essential component of eukaryotic cell membranes, influencing membrane packing, fluidity, and domain formation. Replicating these properties in model membranes is critical for reconstitution studies, but common emulsion-based methods for producing giant unilamellar vesicles (GUVs) fail to incorporate cholesterol efficiently. Here, we use methyl-{beta}- cyclodextrin-cholesterol (M{beta}CD-CL) complexes to deliver cholesterol into GUVs produced by the emulsion droplet interface crossing encapsulation (eDICE) method and demonstrate a convenient way to quantify the degree of cholesterol incorporation using fluorescent membrane biosensors. Spectral imaging of NR12A as well as fluorescence lifetime imaging of Flipper-TR revealed dose- dependent increases in cholesterol content for DOPC GUVs upon M{beta}CD-CL addition, consistent with increased membrane order. By calibrating these effects against GUVs with defined cholesterol contents prepared via gel-assisted swelling, we found that the cholesterol content of eDICE vesicles can be increased to at least 40 mol%. Binary mixtures of DOPC with saturated lipids (DMPC and PC(18:0-14:0)) showed a similar trend as pure DOPC GUVs. Interestingly, we could trigger liquid-ordered domain formation by adding cholesterol to DOPC:DMPC vesicles. Our findings provide a quantitative and non-disruptive method to modulate and assess cholesterol content in emulsion-based GUVs, advancing their use in bottom-up synthetic biology and membrane biophysics.

3
Characterization of divalent cation interactions with AASTY nanodiscs

Timcenko, M.; Autzen, A. A. A.; Autzen, H. E.

2021-10-07 biochemistry 10.1101/2021.10.07.463511 medRxiv
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Amphiphilic copolymers show promise in extracting membrane proteins directly from lipid bilayers into native nanodiscs. However, many such copolymers are polyanionic and sensitive to divalent cations, limiting their applicability. We characterize the Ca2+ and Mg2+ sensitivity of poly(acrylic acid-co-styrene) (AASTY) copolymers with analytical UV and fluorescent size exclusion chromatography, enabling us to separate signals from nanodiscs, copolymers, and soluble aggregates. We find that divalent cations promote aggregation and precipitation of both free and lipid bound copolymers. We see that excess, free copolymer acts as a cation sink that protects nanodiscs from Ca2+ induced aggregation. Removal of the free copolymer through dialysis induces aggregation that can be mitigated by KCl. Finally, we find that the nanodisc size is dynamic and dependent on lipid concentration. Our results offer insight to nanodisc behaviour, and can help guide experimental design, aimed at mitigating the shortcomings inherent in negatively charged nanodisc forming copolymers.

4
Tween-20 induces the structural remodelling of single lipid vesicles

Dresser, L. G.; Graham, S. P.; Miller, L. M.; Schaefer, C.; Conteduca, D.; Johnson, S.; Leake, M. C.; Quinn, S. D.

2022-03-01 biophysics 10.1101/2022.03.01.482482 medRxiv
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The interaction of Tween-20 with lipid membranes is crucial for a number of biotechnological applications including viral inactivation and membrane protein extraction, but the underlying mechanistic details have remained elusive. Evidence from ensemble assays supports a global model of Tween-20 induced membrane disruption that broadly encompasses association of the surfactant with the membrane surface, membrane fragmentation and the release of mixed micelles to solution, but whether this process involves intermediate and dynamic transitions between regimes is an open question. In search of the mechanistic origins of membrane disruption, increasing focus is put on identifying Tween-20 interactions with highly controllable model membranes. In light of this, and to unveil quantitative mechanistic details, we employed highly interdisciplinary biophysical approaches, including quartz-crystal microbalance with dissipation monitoring, steady-state and time-resolved fluorescence and FRET spectroscopy, dynamic light scattering, fluorescence correlation spectroscopy, wide-field single-vesicle imaging and scanning electron microscopy, to interrogate the interactions between Tween-20 and both freely-diffusing and surface-immobilized model-membrane vesicles. Using ultrasensitive sensing approaches, we discovered that Tween-20 leads to a stepwise and phase-dependent structural remodelling of sub-micron sized vesicles that includes permeabilization and swelling, even at detergent concentrations below the critical micellar concentration. These insights into the structural perturbation of lipid vesicles upon Tween-20 interaction highlight the impact on vesicle conformation prior to complete solubilization, and the tools presented may have general relevance for probing the interaction between lipid vesicles and a wide variety of disruptive agents.

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The Influence of Multivalent Charge and PEGylation on Shape Transitions in Fluid Lipid Assemblies: From Vesicles to Discs, Rods, and Spheres

Steffes, V. M.; Zhang, Z.; Ewert, K. K.; Safinya, C. R.

2023-08-13 biophysics 10.1101/2023.08.09.552538 medRxiv
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Lipids, and cationic lipids in particular, are of interest as delivery vectors for hydrophobic drugs such as the cancer therapeutic paclitaxel, and the structures of lipid assemblies affect their efficacy. We investigated the effect of incorporating the multivalent cationic lipid MVL5 (+5e) and poly(ethylene glycol)-lipids (PEG-lipids), alone and in combination, on the structure of fluid-phase lipid assemblies of the charge-neutral lipid 1,2-dioleoyl-sn-glycero-phosphocholine (DOPC). This allowed us to elucidate lipid-liposome structure correlations in sonicated formulations with high charge density, which are not accessible with univalent lipids such as the well-studied DOTAP (+1e). Cryogenic TEM allowed us to determine the structure of the lipid assemblies, revealing diverse combinations of vesicles and disc-shaped, worm-like, and spherical micelles. Remarkably, MVL5 forms an essentially pure phase of disc micelles at 50 mol% MVL5. At higher (75 mol%) content of MVL5, short and intermediate-length worm-like micellar rods were observed and, in ternary mixtures with PEG-lipid, longer and highly flexible worm-like micelles formed. Independent of their length, the worm-like micelles coexisted with spherical micelles. In stark contrast, DOTAP forms mixtures of vesicles, disc micelles and spherical micelles at all studied compositions, even when combined with PEG-lipids. The observed similarities and differences in the effects of charge (multivalent versus univalent) and high curvature (multivalent charge versus PEG-lipid) on assembly structure provide insights into parameters that control the size of fluid lipid nanodiscs, relevant for future applications.

6
Structural Characterisation of Nanoparticle-Supported Lipid Bilayers by Grazing Incidence X-ray and Neutron Scattering

Paracini, N.; Gutfreund, P.; Welbourn, R.; Gonzales, J. F.; Zhu, K.; Miao, Y.; Nageshwar, Y.; Darwish, T. A.; Garvey, C.; Waldie, S.; Larsson, J.; Wolff, M.; Cardenas, M.

2022-07-08 biophysics 10.1101/2022.07.07.499146 medRxiv
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The structure of supported lipid bilayers formed on a monolayer of nanoparticles was determined using a combination of grazing incidence X-ray and neutron scattering techniques. Ordered nanoparticle arrays assembled on a silicon crystal using a Langmuir-Schaefer deposition were shown to be suitable and stable substrates for the formation of curved and fluid lipid bilayers that retained lateral mobility, as shown by fluorescence recovery after photobleaching. A comparison between the structure of the curved bilayer assembled around the nanoparticles with the planar lipid membrane formed on the flat underlying silicon oxide surface revealed a [~]5 [A] thinner bilayer on the curved interface, resolving the effects of curvature on the lipid packing and overall bilayer structure. The combination of neutron scattering techniques, which grant access to sub-nanometre scale structural information at buried interfaces, and nanoparticle-supported lipid bilayers, offers a novel approach to investigate the effects of membrane curvature on lipid bilayers.

7
Increasing the compositional heterogeneity of single-chain amphiphile membranes supported by coacervate cores alters stability and properties of the hybrid protocells

Joshi, M. P.; Lee, J.; Chan, M.; Keating, C. D.

2026-02-05 biochemistry 10.64898/2026.02.02.703427 medRxiv
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Coacervate droplets and lipid vesicles are two classes of self-assembled compartments that have been proposed as protocell models. Hybrid protocells, in which a coacervate core is surrounded by a lipid membrane, can integrate the advantages of both protocell systems while overcoming their limitations. Although hybrid protocell membranes have been produced with a variety of diacyl phospholipids related to modern biology and some single-chain amphiphiles inspired by prebiotic scenarios, little is known about how mixtures of single-chain amphiphiles impact hybrid protocell membrane formation and properties. Given the plausible diversity of amphiphiles in the prebiotic milieu, the resulting membranes would have inherently incorporated multiple lipids of different types, potentially altering the properties and viability of hybrid protocells in their environment. Here, we systematically increased the compositional heterogeneity of hybrid protocell membranes by using different prebiotically relevant single-chain amphiphiles of varying head groups and alkyl chain lengths. These membranes were assembled around model coacervate droplets generated from polyallylamine hydrochloride and adenosine diphosphate, and the effect of heterogeneity on membrane properties and stability was evaluated. Compared to protocells with homogeneous membranes, those with heterogeneous amphiphile membranes exhibited higher yields, smaller sizes, and greater sub-compartment formation. Also, they showed increased membrane order, retained similar lateral lipid diffusion, and showed population-level variability in permeability to small anionic molecules. Notably, heterogeneous membranes showed enhanced structural stability under acidic conditions, retaining key properties like size and sub-compartment heterogeneity, thereby broadening the pH range over which hybrid protocells remain intact. These findings suggest that amphiphile diversity not only would have influenced the structural properties of hybrid protocells but also created diversity within the protocell population and enhanced their robustness, thereby playing a crucial role in protocell evolution on early Earth.

8
Phospholipid membrane formation templated by coacervatedroplets

Pir Cakmak, F.; Marianelli, A. M.; Keating, C. D.

2021-02-18 biophysics 10.1101/2021.02.17.431720 medRxiv
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We report formation of coacervate-supported phospholipid membranes by hydrating a dried lipid film in the presence of coacervate droplets. In contrast to traditional giant lipid vesicles formed by gentle hydration in the absence of coacervates, the coacervate-templated membrane vesicles are more uniform in size, shape, and apparent lamellarity. Due to their fully-coacervate model cytoplasm, these simple artificial cells are macromolecularly crowded and can be easily pre-loaded with high concentrations of proteins or nucleic acids. Coacervate-supported membranes were characterized by fluorescence imaging, polarization, fluorescence recovery after photobleaching of labeled lipids, lipid quenching experiments, and solute uptake experiments. Our findings are consistent with the presence of lipid membranes around the coacervates, with many droplets fully coated with what appear to be continuous lipid bilayers. Within the same population, other coacervate droplets are coated with membranes having defects or pores that permit solute entry, and still others are coated with multilayered membranes. These membranes surrounding protein-based coacervate droplets provided protection from a protease added to the external solution. The simplicity of producing artificial cells having a coacervate model cytoplasm surrounded by a model membrane is at the same time interesting as a potential mechanism for prebiotic protocell formation and appealing for biotechnology. We anticipate that such structures could serve as a new type of model system for understanding interactions between intracellular phases and cell- or organelle membranes, which are implicated in a growing number of processes ranging from neurotransmission to signaling.

9
Introducing a fusogenicity metric for lipid nanoparticle formulation

Zheng, L.; Baliga, M.; Gallagher, S. F.; Gao, A. Z.; Rueben, J.; Go, Y. K.; Deserno, M.; Leal, C.

2026-03-04 biophysics 10.64898/2026.03.02.708638 medRxiv
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Lipid nanoparticles (LNPs) are the most successful drug delivery carrier to date, but optimizing lipid formulations to improve membrane fusion capabilities for effective drug release has been challenging due to lack of a quantitative measure for fusogenicity. Here we introduce a new framework based on small angle X-ray scattering to experimentally measure [Formula] for lipids used in LNP formulations such as glycerol monooleate (GMO) and ionizable lipids (SM-102 and ALC-0315). Q intrinsically captures spontaneous curvature (J0), which is traditionally used to assess fusogenicity. The change of cubic lattice parameters with temperature was measured for GMO-containing lipid mixtures, and the Q extracted quantitatively correlated with LNP fusogenicity power validated by fluorescence-based fusion assays and cryogenic electron microscopy. Fusogenicity of SM-102 and ALC-0315 was quantified by adding them to host membranes and assessing change in Q. This framework provides researchers with the ability to optimize the fusogenicity of LNP formulations for potent drug release and enhances understanding of parameters governing fusion in all biomembranes.

10
Molecular Dynamics Simulations Unveil the Aggregation Patterns and Salting out of Polyarginines at Zwitterionic POPC Bilayers in Solutions of Various Ionic Strengths

Hong, M. N. T.; Vazdar, M.

2024-04-24 biochemistry 10.1101/2024.04.24.590968 medRxiv
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This study employs molecular dynamics (MD) simulations to investigate the adsorption and aggregation behavior of simple polyarginine cell-penetrating peptides (CPPs), specifically modeled as R9 peptides, at zwitterionic phosphocholine POPC membranes under varying ionic strengths of two peptide concentrations and two concentrations of NaCl and CaCl2. The results reveal an intriguing phenomenon of R9 aggregation at the membrane, which is dependent on the ionic strength indicating a salting-out effect. As the peptide concentration and ionic strength increase, peptide aggregation also increases, with aggregate lifetimes and sizes showing a corresponding rise, accompanied by the total decrease of adsorbed peptides at the membrane surface. Notably, in high ionic strength environments, large R9 aggregates, such as octamers, are also observed occasionally. The salting-out, typically uncommon for short positively charged peptides, is attributed to the unique properties of arginine amino acid, specifically by its side chain containing amphiphilic guanidinium (Gdm+) ion which makes both intermolecular hydrophobic like-charge Gdm+ - Gdm+ and salt-bridge Gdm+ - C-terminus interactions, where the former are increased with the ionic strength, and the latter decreased due to electrostatic screening. The aggregation behavior of R9 peptides at membranes can also linked to their CPP translocation properties, suggesting that aggregation may aid in translocation across cellular membranes.

11
Effects of mixing technique and ethanol removal on lipidnanoparticle physicochemical properties

Mitra, H.; Bethiana, T.; Jia, D.; Majidi, M.; Mota-Santiago, P.; Milogrodzka, I.; Manni, L. S.; Ristroph, K. D.; Ardekani, A. M.

2025-11-08 biophysics 10.1101/2025.11.07.686408 medRxiv
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Optimizing the production of lipid nanoparticle (LNP) therapeutics is necessary for drug delivery efficiency, stability, and scalability. A small but growing body of literature has begun to recognize that LNP properties (e.g., size, shape, and internal structure) depend on the flow conditions during mixing for antisolvent precipitation, in which LNPs are formulated. Here, we use different mixers, varying flow patterns (e.g., laminar or turbulent mixing) and flow rate ratios (FRR), i.e., 3:1 and 1:1, to prepare a standard LNP formulation. We then characterize the resulting formulations using small angle x-ray scattering (SAXS) to provide insights into particle shape/morphology, internal organization (L and HII phases) of yeast RNA (yRNA), and structural differences/similarities that arise from the different mixing methods. The effect of ethanol removal on the LNPs structure, formulated from each mixing technique, is also discussed. We observed the 3:1 FRR mixers outperform the 1:1 configurations in certain desired LNP physiochemical properties. The differences observed in the LNPs produced across the two configurations are discussed. Furthermore, we use computational fluid dynamics to explain the turbulent mixing schemes among the 3:1 and 1:1 mixers.

12
In Silico Engineering of Stable siRNA Lipid Nanoparticles: Exploring the Impact of Ionizable Lipid Concentrations for Enhanced Formulation Stability

Biswal, M. R.; Roy, S.; Singh, J. K.

2024-09-27 biophysics 10.1101/2024.09.25.614899 medRxiv
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Lipid nanoparticles (LNPs) are crucial in advancing the delivery of RNA-based therapeutics within the domain of gene therapy. A comprehensive understanding of their formation and stability is critical for optimizing the clinical efficacy of LNPs. This study systematically investigates the influence of concentration variations of positive and neutral ionizable lipids - specifically, 2-[2,2-bis[(9Z,12Z)-octadeca-9,12-dienyl]-1,3-dioxolan-4-yl]-N,N-dimethylethanamine (DLinKC2-DMA) and 1,2-Dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE) - along with cholesterol and polyethylene glycol, on the formation of LNPs and encapsulation of small interfering RNA (siRNA). Utilizing coarse-grained classical molecular dynamics (MD) simulations with a system size matching experimental range (approximately 0.6 million beads), we conduct a comparative analysis and offer mechanistic insights into siRNA formulation within LNPs containing positive and neutral DLinKC2-DMA. We found that the LNPs with positive ionizable lipids encapsulate more than twice the siRNA compared to the LNPs with neutral ionizable lipids. In addition to the formation of LNPs, our study extends to the forces governing siRNA escape from LNPs, employing steered molecular dynamics simulations. The force experienced by siRNA to cross the LNP lipid layer containing positive ionizable lipids was 400kJ/mol/nm more than that of neutral ionizable lipids, suggesting the encapsulation is more favorable with positive ionisable lipids.

13
A Multiscale Framework for Uncovering Surfactant Mediated Viral Capsid Disruption

Masirevic, S.; Marzinek, J. K.; Kong, M. L. Y.; Lin, G.; Chen, H.; Liu, J.; Chua, C.; Maupin, C. M.; Verma, C. S.; Fox, S. J.; Bond, P. J.

2025-06-17 biophysics 10.1101/2025.06.16.659739 medRxiv
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Disinfection remains a critical strategy for controlling the transmission of infectious diseases. However, small non-enveloped viruses exhibit exceptional resistance to many disinfectants, often requiring harsh protein-disrupting chemicals for effective inactivation, thereby limiting their applicability in personal care products due to associated side effects. Sodium dodecyl sulphate (SDS) is a widely used anionic surfactant known for its virucidal efficacy; however, the molecular details of its action against robust non-enveloped viruses remain poorly understood, limiting efforts to design safer and more targeted antiviral formulations. In this study, a multiscale simulation approach combining a novel atomic-resolution icosahedral "scaffold framework" and coarse-grained modelling was developed to elucidate the mechanism of SDS-driven disruption of MS2 bacteriophage capsid, a surrogate for non-enveloped viruses. Experimental analyses including dynamic light scattering and transmission electron microscopy revealed that SDS inactivates MS2 in a strongly pH-dependent manner, triggering capsid disassembly at acidic pH while leaving particles largely intact at neutral pH. Molecular dynamics simulations demonstrated that SDS micelles preferentially associate with hexameric pores and inter-dimer clefts under acidic conditions, where protonation of acidic residues weakens the electrostatic network of the capsid surface. Together, these findings provide a detailed molecular framework for SDS virucidal action and highlight the importance of environmental pH in modulating surfactant-virus interactions. These insights offer a foundation for designing next-generation antiviral surfactants with improved efficacy and biocompatibility.

14
Characterizing the Interactions of Cell Membrane-Disrupting Peptides with Lipid-Functionalized Single-Walled Carbon Nanotube Systems for Antimicrobial Screening

Yadav, A.; Kelich, P.; Kallmyer, N. E.; Reuel, N. F.; Vukovic, L.

2023-01-25 bioengineering 10.1101/2023.01.25.525557 medRxiv
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Lipid-functionalized single-walled carbon nanotubes (SWNTs) have garnered significant interest for their potential use in a wide range of biomedical applications. In this work, we used molecular dynamics simulations to study the equilibrium properties of SWNTs surrounded by the phosphatidylcholine (POPC) corona phase, and their interactions with three cell membrane disruptor peptides: colistin, TAT peptide, and crotamine-derived peptide. Our results show that SWNTs favor asymmetrical positioning within the POPC corona, so that one side of the SWNT, covered by the thinnest part of the corona, comes in contact with charged and polar functional groups of POPC and water. We also observed that colistin and TAT insert deeply into POPC corona, while crotamine-derived peptide only adsorbs to the corona surface. Compared to crotamine-derived peptide, colistin and TAT also induce larger perturbations in the thinnest region of the corona, by allowing more water molecules to directly contact the SWNT surface. In separate simulations, we show that three examined peptides exhibit similar insertion and adsorption behaviors when interacting with POPC bilayers, confirming that peptide-induced perturbations to POPC in conjugates and bilayers are similar in nature and magnitude. Furthermore, we observed correlations between the peptide-induced structural perturbations and the near-infrared emission of the lipid-functionalized SWNTs, which suggest that the optical signal of the conjugates transduces the morphological changes in the lipid corona. Overall, our findings indicate that lipid-functionalized SWNTs could serve as simplified cell membrane model systems for pre-screening of new antimicrobial compounds that disrupt cell membranes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/525557v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@4c5645org.highwire.dtl.DTLVardef@1b3cd30org.highwire.dtl.DTLVardef@1643c6corg.highwire.dtl.DTLVardef@1bb096e_HPS_FORMAT_FIGEXP M_FIG C_FIG

15
Molecular mechanisms of liposome interactions with bacterial envelopes

Scheeder, A.; Brockhoff, M.; Ward, E.; Kaminski Schierle, G. S.; Mela, I.; Kaminski, C. F.

2023-10-10 biophysics 10.1101/2023.10.07.561336 medRxiv
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Although fusogenic liposomes offer a promising approach for the delivery of antibiotic payloads across the cell envelope of Gram-negative bacteria, there is still limited understanding of the individual nanocarrier interactions with the bacterial target. Using super-resolution microscopy, we characterize the interaction dynamics of positively charged fusogenic liposomes with Gram-negative (Escherichia coli) and Gram-positive (Bacillus subtilis) bacteria. The liposomes merge with the outer membrane (OM) of Gram-negative bacteria, while attachment or lipid internalization is observed in Gram-positive cells. Employing total internal reflection fluorescence microscopy, we demonstrated liposome fusion with model supported lipid bilayers. For whole E. coli cells, however, we observed heterogeneous membrane integrations, primarily involving liposome attachment and hemifusion events. With increasing lipopolysaccharide length the likelihood of full-fusion events was reduced. The integration of artificial lipids into the OM of Gram-negative cells led to membrane destabilization, resulting in decreased bacterial vitality, membrane detachment, and improved co-delivery of Vancomycin--an effective antibiotic against Gram-positive cells. These findings provide significant insights into the interactions of individual nanocarriers with bacterial envelopes at the single-cell level, uncovering effects that would be missed in bulk measurements. This highlights the importance of conducting single-particle and single-cell investigations to assess the performance of next-generation drug delivery platforms.

16
Vibrio cholerae adhesin-derived peptide mediates strong pull-off forces in aqueous high ionic strength environments

Ahmed, S. T.; Zhai, S.; Huang, X.; Saluja, S.; Adewole, A.; Ioffe, A.; Merg, A.; Yan, J.; Andresen Eguiluz, R. C.

2025-08-29 biophysics 10.1101/2025.08.25.672170 medRxiv
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In this letter, the pull-off forces of adsorbed films of four Bap1-inspired peptides in various solvents were investigated on negatively charged mica substrates using the surface forces apparatus (SFA), complemented with dynamic light scattering (DLS) for characterizing the aggregation behavior of peptides in solution. Bap1-inspired peptides consisted of the 57 amino acid wild-type sequence (WT); a scrambled version of the WT used to investigate the impact of the primary amino acid sequence in pull-off forces (Scr); a ten amino acid sequence rich in hydrophobic content (CP) of the WT sequence, and an eight amino acid sequence (Sh1) that corresponds to the pseudo-repeating sequence in the 57 AA. SFA results showed remarkable pull-off forces for CP, particularly in the presence of salts: measured pull-off forces were 26.0 {+/-} 7.0 mN/m for no dwell-time and up to 42.0 {+/-} 8.8 mN/m when surfaces were left in contact for 30 minutes. DLS observations indicate that salts favor large peptide aggregation for all constructs (Hz > 1 {micro}m), as compared to milliQ (Hz {approx} 100-500 nm) water and DMSO (Hz {approx} 100 nm), resulting in heterogeneous peptide film thicknesses. This letter concludes with a comparison to the pull-off forces of mussel foot protein-inspired peptides reported in the literature.

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S-Alkyl-Phosphorothioate Modifications Reduce Thermal and Structural Stability of DNA Duplexes

Chandrasekhar, S.; Bricker, R.; Fadaei, F.; Schmidt, T. L.

2025-09-30 biochemistry 10.1101/2025.09.30.679560 medRxiv
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While phosphorothioate (PS) oligonucleotides are usually used in therapeutic applications, they also offer the cheapest and synthetically most straightforward route to introduce hydrophobic modifications for applications in structural DNA nanotechnology and biophysics. For this, the sulfur atom is S-alkylated with alkyl iodides, enabling a hydrophobically tunable interface of DNA nanostructures with lipid bilayers. While longer and more alkyls per helical turn should lead to stronger interactions with lipid membranes, we found that excessive S-alkylations strongly inhibit hybridization of oligonucleotides to their complementary strands and decrease their melting temperature, despite a reduction in electrostatic repulsion between the two strands. Moreover, both the type and placement of alkyl modifications influence the melting temperature. Atomistic molecular dynamics simulations reveal two complementary mechanisms that explain the experimental findings. First, S-alkylated oligonucleotides are more compact and less dynamic than unmodified ones, likely inhibiting their ability to hybridize to their complementary strands. Second, S-alkyls in double-stranded DNA promote defect formation due to alkyl modifications having hydrophobic interactions with other alkyl groups and nucleobases, therefore reducing the thermal and structural stability of alkylated DNA duplexes. This study serves as a practical guide for tuning hydrophobicity while maintaining structural stability in membrane-interfacing DNA nanostructures.

18
Application of D4 Fluorescent Probes for Quantitative and Spatial Analysis of Cholesterol in Cells

de La Chappelle, A.; Boiko, E.; Karakus, C.; Trahin, A.; Aulas, A.; Di Scala, C.

2026-04-04 biochemistry 10.64898/2026.04.01.715848 medRxiv
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Cholesterol is a key component of cellular membranes, regulating membrane organization, fluidity, and signaling. However, cholesterol analysis remains technically challenging, as no single method currently allows both accurate quantification and spatially resolved visualization. Biochemical assays provide accurate quantification but lack spatial resolution, whereas imaging strategies can perturb membrane organization or cholesterol accessibility. Here, we describe optimized protocols using fluorescent D4 probes derived from the cholesterol-binding domain of perfringolysin O (D4-mCherry and D4-GFP) to detect, visualize, and quantify cholesterol in biological samples. We detail procedures for probe production, purification, and application, and establish conditions that ensure robust and reproducible labeling of membrane-accessible cholesterol. By combining fluorescence-based imaging with quantitative analysis, this approach enables the assessment of cholesterol distribution while preserving its native membrane environment. The proposed methodology provides a versatile and reliable framework for studying cholesterol in a wide range of experimental systems.

19
Single-nanoparticle electrophoretic mobility and trapping using active-feedback 3D tracking

Johnson, A.; Welsher, K.

2024-07-11 biophysics 10.1101/2024.07.08.602591 medRxiv
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Nanoparticles (NP) are versatile materials with widespread applications across medicine and engineering. Despite rapid incorporation into drug delivery, therapeutics, and many more areas of research and development, there is a lack of robust characterization methods. Light scattering techniques such as dynamic light scattering (DLS) and electrophoretic light scattering (ELS) use an ensemble-averaged approach to the characterization of nanoparticle size and electrophoretic mobility (EPM), leading to inaccuracies when applied to polydisperse or heterogeneous populations. To address this lack of single-nanoparticle characterization, this work applies 3D Single-Molecule Active Real-time Tracking (3D-SMART) to simultaneously determine NP size and EPM on a per-particle basis. Single-nanoparticle EPM is determined by using active feedback to "lock on" to a single particle and apply an oscillating electric field along one axis. A maximum likelihood approach is applied to extract the single-particle EPM from the oscillating nanoparticle position along the field-actuated axis, while mean squared displacement is used along the non-actuated axes to determine size. Unfunctionalized and carboxyl-functionalized polystyrene NPs are found to have unique EPM based on their individual size and surface characteristics, and it is demonstrated that single-nanoparticle EPM is a more precise tool for distinguishing unique NP preparations than diffusion alone, able to determine the charge number of individual NPs to an uncertainty of less than 30. This method also explored individual nanoparticle EPM in various ionic strengths (0.25-5 mM) and found decreased EPM as a function of increasing ionic strength, in agreement with results determined via bulk characterization methods. Finally, it is demonstrated that the electric field can be manipulated in real time in response to particle position, resulting in one-dimensional electrokinetic trapping. Critically, this new single-nanoparticle EPM determination and trapping method does not require microfluidics, opening the possibility for the exploration of single-nanoparticle EPM in live tissue and more comprehensive characterization of nanoparticles in biologically relevant environments.

20
Molecular Insights into Cholesterol Concentration Effects on Planar and Curved Lipid Bilayers for Liposomal Drug Delivery

Khodadadi, E.; Khodadadi, E.; Chaturvedi, P.; Moradi, M.

2025-04-10 biophysics 10.1101/2025.04.06.647491 medRxiv
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Liposomal carriers provide a flexible and effective strategy for delivering therapeutics across a broad spectrum of diseases. Cholesterol is frequently included in these systems to improve membrane rigidity and limit permeability. Despite its widespread use, the optimal cholesterol-to-lipid proportion for achieving stable and efficient liposome performance remains to be fully determined. In this work, we apply all-atom molecular dynamics simulations to explore how different cholesterol concentrations influence the structural and dynamic characteristics of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) bilayers, considering both planar and curved membrane geometries. Bilayers with cholesterol molar ratios of 0%, 10%, 20%, 30%, 40%, and 50% were simulated, and key biophysical parameters including area per lipid (APL), membrane thickness, leaflet interdigitation, and deuterium order parameters (SCD) were analyzed. In planar bilayers, increasing cholesterol concentration led to a progressive decrease in APL from approximately 60 {degrees}A2 to 40 {degrees}A2, accompanied by increased membrane thickness and lipid ordering, consistent with cholesterols classical condensing effect. In contrast, curved bilayers exhibited a cholesterol-induced expansion effect, particularly in the inner leaflet, where APL increased from approximately 60 {degrees}A2 to 90 {degrees}A2 with rising cholesterol levels. SCD profiles showed that cholesterol enhanced tail ordering up to 40% concentration, beyond which the effect plateaued or slightly declined, suggesting structural saturation or packing frustration. Membrane thickness displayed a monotonic increase in planar bilayers but followed a nonlinear trend in curved systems due to curvature-induced stress. These findings highlight that cholesterols influence on membrane properties is highly dependent on bilayer geometry and asymmetry. While planar bilayers exhibit predictable responses, curved systems reveal nonclassical behaviors that challenge traditional models of cholesterol-lipid interactions. This work provides molecular-level insights and establishes a computational framework for the rational design of liposomal systems, emphasizing the need to account for curvature and asymmetry in membrane engineering.