Restoring structural parameters of lipid mixtures from small-angle X-ray scattering data

Modulating a model membrane of sphingomyelin by a tricyclic antidepressant drug

Tricyclic medicine such as amitriptyline (AMT) hydrochloride, initially developed to treat depression, is also used to treat neuropathic pain, anxiety disorder, and migraines. The mechanism of functioning of this type of drugs is ambiguous. Understanding the mechanism is important for designing new drug molecules with higher pharmacological efficiency. Hence, in the present study, biophysical approaches have been taken to shed light on their interactions with a model cellular membrane of brain sphingomyelin in the form of monolayer and multi-lamellar vesicles. The surface pressure-area isotherm infers the partitioning of a drug molecule into the lipid monolayer at the air water interface, providing a higher surface area per molecule and reducing the in-plane elasticity. Further, the surface electrostatic potential of the lipid monolayer is found to increase due to the insertion of drug molecule. The interfacial rheology revealed a reduction of the in-plane viscoelasticity of the lipid film, which, depends on the adsorption of the drug molecule onto the film. Small-angle X-ray scattering (SAXS) measurements on multilamellar vesicles (MLVs) have revealed that the AMT molecules partition into the hydrophobic core of the lipid membrane, modifying the organization of lipids in the membrane. The modified physical state of less rigid membrane and the transformed electrostatics of the membrane could influence its interaction with synaptic vesicles and neurotransmitters making higher availability of the neurotransmitters in the synaptic cleft.

Small-angle X-ray and neutron scattering applied to lipid-based nanoparticles: Recent advancements across different length scales

Lipid-based nanoparticles (LNPs), ranging from nanovesicles to non-lamellar assemblies, have gained significant attention in recent years, as versatile carriers for delivering drugs, vaccines, and nutrients. Small-angle scattering methods, employing X-rays (SAXS) or neutrons (SANS), represent unique tools to unveil structure, dynamics, and interactions of such particles on different length scales, spanning from the nano to the molecular scale. This review explores the state-of-the-art on scattering methods applied to unveil the structure of lipid-based nanoparticles and their interactions with drugs and bioactive molecules, to inform their rational design and formulation for medical applications. We will focus on complementary information accessible with X-rays or neutrons, ranging from insights on the structure and colloidal processes at a nanoscale level (SAXS) to details on the lipid organization and molecular interactions of LNPs (SANS). In addition, we will review new opportunities offered by Time-resolved (TR)-SAXS and -SANS for the investigation of dynamic processes involving LNPs. These span from real-time monitoring of LNPs structural evolution in response to endogenous or external stimuli (TR-SANS), to the investigation of the kinetics of lipid diffusion and exchange upon interaction with biomolecules (TR-SANS). Finally, we will spotlight novel combinations of SAXS and SANS with complementary on-line techniques, recently enabled at Large Scale Facilities for X-rays and neutrons. This emerging technology enables synchronized multi-method investigation, offering exciting opportunities for the simultaneous characterization of the structure and chemical or mechanical properties of LNPs.

Mechanics of biomimetic free-standing lipid membranes: insights into the elasticity of complex lipid compositions

The creation of free-standing lipid membranes has been so far of remarkable interest to investigate processes occurring in the cell membrane since its unsupported part enables studies in which it is important to maintain cell-like physicochemical properties of the lipid bilayer, that nonetheless depend on its molecular composition. In this study, we prepare pore-spanning membranes that mimic the composition of plasma membranes and perform force spectroscopy indentation measurements to unravel mechanistic insights depending on lipid composition. We show that this approach is highly effective for studying the mechanical properties of such membranes. Furthermore, we identify a direct influence of cholesterol and sphingomyelin on the elasticity of the bilayer and adhesion between the two leaflets. Eventually, we explore the possibilities of imaging in the unsupported membrane regions. For this purpose, we investigate the adsorption and movement of a peripheral protein, the fibroblast growth factor 2, on the complex membrane.

A review on the measurement of the bending rigidity of lipid membranes

This review provides an overview of the latest developments in both experimental and simulation techniques used to assess the bending rigidity of lipid membranes. It places special emphasis on experimental methods that utilize model vesicles to manipulate lipid compositions and other experimental parameters to determine the bending rigidity of the membrane. It also describes two commonly used simulation methods for estimating bending rigidity. The impact of various factors on membrane bending rigidity is summarized, including cholesterol, lipids, salt concentration, surface charge, membrane phase state, peptides, proteins, and polyethylene glycol. These factors are shown to influence the bending rigidity, contributing to a better understanding of the biophysical properties of membranes and their role in biological processes. Furthermore, the review discusses future directions and potential advancements in this research field, highlighting areas where further investigation is required.

Developments in small-angle X-ray scattering (SAXS) for characterizing the structure of surfactant-macromolecule interactions and their complex

The surfactant-macromolecule interactions (SMI) are one of the most critical topics for scientific research and industrial application. Small-angle X-ray scattering (SAXS) is a powerful tool for comprehensively studying the structural and conformational features of macromolecules at a size ranging from Angstroms to hundreds of nanometers with a time-resolve in milliseconds scale. The SAXS integrative techniques have emerged for comprehensively analyzing the SMI and the structure of their complex in solution. Here, the various types of emerging interactions of surfactant with macromolecules, such as protein, lipid, nuclear acid, polysaccharide and virus, etc. have been systematically reviewed. Additionally, the principle of SAXS and theoretical models of SAXS for describing the structure of SMI as well as their complex has been summarized. Moreover, the recent developments in the applications of SAXS for charactering the structure of SMI have been also highlighted. Prospectively, the capacity to complement artificial intelligence (AI) in the structure prediction of biological macromolecules and the high-throughput bioinformatics sequencing data make SAXS integrative structural techniques expected to be the primary methodology for illuminating the self-assembling dynamics and nanoscale structure of SMI. As advances in the field continue, we look forward to proliferating uses of SAXS based upon its abilities to robustly produce mechanistic insights for biology and medicine.

Multilamellar ceramide core-structured microvehicles with substantial skin barrier function recovery

This study introduces a multilamellar ceramide core-structured microvehicle platform for substantial skin barrier function recovery. Our approach essentially focused on fabricating bacterial cellulose nanofiber (BCNF)-enveloped ceramide-rich lipid microparticles (CerMPs) by solidifying BCNF-armored oil-in-water Pickering emulsions. The oil drops consisted of Ceramide NP (a phytosphingosine backbone N-acylated with a saturated stearic acid) and fatty alcohols (FAs) with a designated stoichiometry. The thin BCNF shell layer completely blocked the growth of ceramide molecular crystals from the CerMPs for a long time. The CerMP cores displayed a multilamellar structure wherein the interlayer distance and lateral packing could be manipulated using FAs with different alkyl chain lengths. The CerMPs remarkably lowered the trans-epidermal water loss while restoring the structural integrity of the epidermis in damaged skin. The results obtained herein highlight that the CerMP system provides a practical methodology for developing various types of skin-friendly formulations that can strengthen the skin barrier function.

Cholesterol stabilization of phospholipid vesicles against bile-induced solubilization

Sphingomyelin (SM) and cholesterol complex to form functional liquid-ordered (L_o) domains. It has been suggested that the detergent resistance of these domains plays a key role during gastrointestinal digestion of the milk fat globule membrane (MFGM), which is rich in both SM and cholesterol. Small-angle X-ray scattering was employed to determine the structural alterations that occur when milk sphingomyelin (MSM)/cholesterol, egg sphingomyelin (ESM)/cholesterol, soy phosphatidylcholine (SPC)/cholesterol, and milk fat globule membrane (MFGM) phospholipid/cholesterol model bilayer systems were incubated with bovine bile under physiological conditions. The persistence of diffraction peaks was indicative of multilamellar vesicles of MSM with cholesterol concentrations > 20 % mol, and also for ESM with or without cholesterol. The complexation of ESM with cholesterol is therefore capable of inhibiting the resulting vesicles from disruption by bile at lower cholesterol concentrations than MSM/cholesterol. After subtraction of background scattering by large aggregates in the bile, a Guinier fitting was used to determine changes in the radii of gyration (R_gs) over time for the biliary mixed micelles after mixing the vesicle dispersions with bile. Swelling of the micelles by phospholipid solubilization from vesicles was a function of cholesterol concentration, with less swelling of the micelles occurring as the cholesterol concentration was increased. With 40% mol cholesterol, the R_gs of the bile micelles mixed with MSM/cholesterol, ESM/cholesterol, and MFGM phospholipid/cholesterol were equal to the control (PIPES buffer + bovine bile), indicating negligible swelling of the biliary mixed micelles.

Dehydration does not affect lipid-based hydration lubrication

Phosphatidylcholine (PC) lipid bilayers at surfaces massively reduce sliding friction, via the hydration lubrication mechanism acting at their highly-hydrated phosphocholine headgroups, a central paradigm of biological lubrication, particularly at articular cartilage surfaces where low friction is crucial for joint well-being. Nanotribological measurements probed the effect on such lubrication of dehydration by dimethyl sulfoxide (DMSO), known to strongly dehydrate the phosphocholine headgroups of such PC bilayers, i.e. reduce the thickness of the inter-bilayer water layer, and thus expected to substantially degrade the hydration lubrication. Remarkably, and unexpectedly, we found that the dehydration has little effect on the friction. We used several approaches, including atomic force microscopy, small- and wide-angle X-ray scattering and all-atom molecular dynamics simulations to elucidate this. Our results show that while DMSO clearly removes hydration water from the lipid head-groups, this is offset by both higher areal head-group density and by rigidity-enhancement of the lipid bilayers, both of which act to reduce frictional dissipation. This sheds strong light on the robustness of lipid-based hydration lubrication in biological systems, despite the ubiquitous presence of bio-osmolytes which compete for hydration water.

Recent advances in structural characterization of biomacromolecules in foods via small-angle X-ray scattering

Small-angle X-ray scattering (SAXS) is a method for examining the solution structure, oligomeric state, conformational changes, and flexibility of biomacromolecules at a scale ranging from a few Angstroms to hundreds of nanometers. Wide time scales ranging from real time (milliseconds) to minutes can be also covered by SAXS. With many advantages, SAXS has been extensively used, it is widely used in the structural characterization of biomacromolecules in food science and technology. However, the application of SAXS in charactering the structure of food biomacromolecules has not been reviewed so far. In the current review, the principle, theoretical calculations and modeling programs are summarized, technical advances in the experimental setups and corresponding applications of in situ capabilities: combination of chromatography, time-resolved, temperature, pressure, flow-through are elaborated. Recent applications of SAXS for monitoring structural properties of biomacromolecules in food including protein, carbohydrate and lipid are also highlighted, and limitations and prospects for developing SAXS based on facility upgraded and artificial intelligence to study the structural properties of biomacromolecules are finally discussed. Future research should focus on extending machine time, simplifying SAXS data treatment, optimizing modeling methods in order to achieve an integrated structural biology based on SAXS as a practical tool for investigating the structure-function relationship of biomacromolecules in food industry.

Computational methods for the analysis of solution small-angle X-ray scattering of biomolecules: ATSAS

The ATSAS software suite provides a comprehensive set of programs for the processing, analysis and modeling of small-angle scattering data, tailored for but not limited to data acquired on biological macromolecules. In this review the major components and developments in the ATSAS package are described, with a focus on user driven application. Data reduction, analysis and modeling approaches and strategies will be introduced and discussed. At the time of writing the latest package, ATSAS 3.1, is freely available for academic users at: https://www.embl-hamburg.de/biosaxs/software.html.

Multiscale Dynamics of Lipid Vesicles in Polymeric Microenvironment

Understanding dynamic and complex interaction of biological membranes with extracellular matrices plays a crucial role in controlling a variety of cell behavior and functions, from cell adhesion and growth to signaling and differentiation. Tremendous interest in tissue engineering has made it possible to design polymeric scaffolds mimicking the topology and mechanical properties of the native extracellular microenvironment; however, a fundamental question remains unanswered: that is, how the viscoelastic extracellular environment modifies the hierarchical dynamics of lipid membranes. In this work, we used aqueous solutions of poly(ethylene glycol) (PEG) with different molecular weights to mimic the viscous medium of cells and nearly monodisperse unilamellar DMPC/DMPG liposomes as a membrane model. Using small-angle X-ray scattering (SAXS), dynamic light scattering, temperature-modulated differential scanning calorimetry, bulk rheology, and fluorescence lifetime spectroscopy, we investigated the structural phase map and multiscale dynamics of the liposome–polymer mixtures. The results suggest an unprecedented dynamic coupling between polymer chains and phospholipid bilayers at different length/time scales. The microviscosity of the lipid bilayers is directly influenced by the relaxation of the whole chain, resulting in accelerated dynamics of lipids within the bilayers in the case of short chains compared to the polymer-free liposome case. At the macroscopic level, the gel-to-fluid transition of the bilayers results in a remarkable thermal-stiffening behavior of polymer–liposome solutions that can be modified by the concentration of the liposomes and the polymer chain length.

The Cytoplasmic Tail of Influenza A Virus Hemagglutinin and Membrane Lipid Composition Change the Mode of M1 Protein Association with the Lipid Bilayer

Influenza A virus envelope contains lipid molecules of the host cell and three integral viral proteins: major hemagglutinin, neuraminidase, and minor M2 protein. Membrane-associated M1 matrix protein is thought to interact with the lipid bilayer and cytoplasmic domains of integral viral proteins to form infectious virus progeny. We used small-angle X-ray scattering (SAXS) and complementary techniques to analyze the interactions of different components of the viral envelope with M1 matrix protein. Small unilamellar liposomes composed of various mixtures of synthetic or "native" lipids extracted from Influenza A/Puerto Rico/8/34 (H1N1) virions as well as proteoliposomes built from the viral lipids and anchored peptides of integral viral proteins (mainly, hemagglutinin) were incubated with isolated M1 and measured using SAXS. The results imply that M1 interaction with phosphatidylserine leads to condensation of the lipid in the protein-contacting monolayer, thus resulting in formation of lipid tubules. This effect vanishes in the presence of the liquid-ordered (raft-forming) constituents (sphingomyelin and cholesterol) regardless of their proportion in the lipid bilayer. We also detected a specific role of the hemagglutinin anchoring peptides in ordering of viral lipid membrane into the raft-like one. These peptides stimulate the oligomerization of M1 on the membrane to form a viral scaffold for subsequent budding of the virion from the plasma membrane of the infected cell.

On the Tactics of Ab Initio Search for the Shape of Protein Particles from Small-Angle X-Ray Scattering Data

Abstract

The determination of 3D particle shapes from the one-dimensional data on small-angle scattering from macromolecule solutions is ambiguous. In addition, due to the poor conditionality of the inverse problem, the determination is unstable and depends on the search algorithm parameters. Consequently, in practice, it is necessary not only to estimate the degree of stability of the solution of the problem but also to select the parameters of both the search method and the model itself. A search tactic is considered which consists in sequential determination of a set of models of particle shape represented in the form of a structure consisting of small close-packed spherical beads. The set of solutions is obtained by varying the relative contributions of objective function terms: the criterion for the deviation of the model scattering curve from the experimental one and the penalties for the looseness and discontinuity of the body structure, and the deviation of the average number of bead contacts from a specified value. Examples of the solution of model problems and the determination of molecular shape from the measurements available in the SASBDB bank of structures are presented.

Structure and Interdigitation of Chain-Asymmetric Phosphatidylcholines and Milk Sphingomyelin in the Fluid Phase

We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center, we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, previously reported for gel phase structures, also extend to the more relevant physiological fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementarily performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. The extent of this back-bending was similar to that in chain symmetric bilayers. For both cases of adaptation to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.

ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis

The ATSAS software suite encompasses a number of programs for the processing, visualization, analysis and modelling of small-angle scattering data, with a focus on the data measured from biological macromolecules. Here, new developments in the ATSAS 3.0 package are described. They include IMSIM, for simulating isotropic 2D scattering patterns; IMOP, to perform operations on 2D images and masks; DATRESAMPLE, a method for variance estimation of structural invariants through parametric resampling; DATFT, which computes the pair distance distribution function by a direct Fourier transform of the scattering data; PDDFFIT, to compute the scattering data from a pair distance distribution function, allowing comparison with the experimental data; a new module in DATMW for Bayesian consensus-based concentration-independent molecular weight estimation; DATMIF, an ab initio shape analysis method that optimizes the search model directly against the scattering data; DAMEMB, an application to set up the initial search volume for multiphase modelling of membrane proteins; ELLLIP, to perform quasi-atomistic modelling of liposomes with elliptical shapes; NMATOR, which models conformational changes in nucleic acid structures through normal mode analysis in torsion angle space; DAMMIX, which reconstructs the shape of an unknown intermediate in an evolving system; and LIPMIX and BILMIX, for modelling multilamellar and asymmetric lipid vesicles, respectively. In addition, technical updates were deployed to facilitate maintainability of the package, which include porting the PRIMUS graphical interface to Qt5, updating SASpy - a PyMOL plugin to run a subset of ATSAS tools - to be both Python 2 and 3 compatible, and adding utilities to facilitate mmCIF compatibility in future ATSAS releases. All these features are implemented in ATSAS 3.0, freely available for academic users at https://www.embl-hamburg.de/biosaxs/software.html.