Size characterization of extracellular vesicles (EVs) and drug delivery liposomes is of great importance in their applications in diagnosis and therapy of diseases. There are many different size characterization techniques used in the field, which often report different size values. Besides technological biases, these differences originate from the fact that various methods measure different physical quantities to determine particle size. In this study, the size of synthetic liposomes with nominal diameters of 50nm and 100nm, and red blood cell-derived EVs (REVs) were measured with established optical methods, such as dynamic light scattering (DLS) and nanoparticle tracking analysis (NTA), and with emerging non-optical methods such as microfluidic resistive pulse sensing (MRPS) and very small-angle neutron scattering (VSANS). The comparison of the hydrodynamic sizes obtained by DLS and NTA with the sizes corresponding to the excluded volume of the particles by MRPS enabled the estimation of the thickness of the hydration shell of the particles. The comparison of diameter values corresponding to the boundary of the phospholipid bilayer obtained from VSANS measurements with MRPS size values revealed the thickness of the polyethylene glycol-layer in case of synthetic liposomes, and the thickness of the protein corona in case of REVs.

CHARMM is one of the most widely used biomolecular force fields. Although developed in close connection with a dedicated molecular simulation engine of the same name, it is also usable with other codes. GROMACS is a well-established, highly optimized, and multipurpose software for molecular dynamics, versatile enough to accommodate many different force field potential functions and the associated algorithms. Due to conceptional differences related to software design and the large amount of numeric data inherent to residue topologies and parameter sets, conversion from one software format to another is not straightforward. Here, we present an automated and validated means to port the CHARMM force field to a format read by the GROMACS engine, harmonizing the different capabilities of the two codes in a self-documenting and reproducible way with a bare minimum of user interaction required. Being based entirely on the upstream data files, the presented approach does not involve any hard-coded data, in contrast with previous attempts to solve the same problem. The heuristic approach used for perceiving the local internal geometry is directly applicable for analogous transformations of other force fields.

Silica nanoparticles (SNPs) belong to the most widely produced nanomaterials nowadays. Particle size distribution (PSD) is a key property of SNPs that needs to be accurately determined for a successful application. Many single particle and ensemble characterization methods are available for the determination of the PSD of SNPs, each having different advantages and limitations. Since most preparation protocols for SNPs can yield bimodal or heterogeneous PSDs, the capability of a given method to resolve bimodal PSD is of great importance. In this work, four different methods, namely transmission electron microscopy (TEM), dynamic light scattering (DLS), microfluidic resistive pulse sensing (MRPS) and small-angle X-ray scattering (SAXS) were used to characterize three different, inherently bimodal SNP samples. We found that DLS is unsuitable to resolve bimodal PSDs, while MRPS has proven to be an accurate single-particle size and concentration characterization method, although it is limited to sizes above 50 nm. SAXS was found to be the only method which provided statistically significant description of the bimodal PSDs. However, the analysis of SAXS curves becomes an ill-posed inverse mathematical problem for broad size distributions, therefore the use of orthogonal techniques is required for the reliable description of the PSD of SNPs.

We report on the structural evaluation of high fat fish oil-in-water emulsions emulsified with sodium caseinate (CAS) and phosphatidylcholine (PC). The microemulsions contained 70% (w/w) fish oil with 1.05-1.4% (w/w) CAS and 0.4-1.75% (w/w) PC and were studied by the combination of light scattering together with small-angle X-ray and neutron scattering (SAXS/SANS). Aqueous CAS forms aggregates having a denser core of about 100 kDa and less dense shell about 400 kDa with the hard sphere diameter of 20.4 nm. PC appears as multilayers whose coherence length spans from 40 to 100 nm. PC monolayer separates oil and water phases. Moreover, 80% CAS particles are loosely bound to the interface but are not forming continuous coverage. The distance between aggregated CAS particles in microemulsion is increased compared to CAS aggregates in pure CAS-in-water system. PC multilayers become larger in the presence of oil-water interface compared to the pure PC mixtures. Bilayers become larger with increasing PC concentration. This study forms a structural base for the combination of CAS and PC emulsifiers forming a well-defined thin and dense PC layer together with thick but less dense CAS layer, which is assumed to explain its better oxidative stability compared to single emulsifiers.

Developing unique mechanisms of action are essential to combat the growing issue of antimicrobial resistance. Supramolecular assemblies combining the improved biostability of non-natural compounds with the complex membrane-attacking mechanisms of natural peptides are promising alternatives to conventional antibiotics. However, for such compounds the direct visual insight on antibacterial action is still lacking. Here we employ a design strategy focusing on an inducible assembly mechanism and utilized electron microscopy (EM) to follow the formation of supramolecular structures of lysine-rich heterochiral β³-peptides, termed lamellin-2K and lamellin-3K, triggered by bacterial cell surface lipopolysaccharides. Combined molecular dynamics simulations, EM and bacterial assays confirmed that the phosphate-induced conformational change on these lamellins led to the formation of striped lamellae capable of incising the cell envelope of Gram-negative bacteria thereby exerting antibacterial activity. Our findings also provide a mechanistic link for membrane-targeting agents depicting the antibiotic mechanism derived from the in-situ formation of active supramolecules.