Aurore: new software for neutron reflectivity data analysis

Translocation of Antimicrobial Peptides across Model Membranes: The Role of Peptide Chain Length

Cushioned lipid bilayers are structures consisting of a lipid bilayer supported on a solid substrate with an intervening layer of soft material. They offer possibilities for studying the behavior and interactions of biological membranes more accurately under physiological conditions. In this work, we continue our studies of cushion formation induced by histatin 5 (24Hst5), focusing on the effect of the length of the peptide chain. 24Hst5 is a short, positively charged, intrinsically disordered saliva peptide, and here, both a shorter (14Hst5) and a longer (48Hst5) peptide variant were evaluated. Experimental surface active techniques were combined with coarse-grained Monte Carlo simulations to obtain information about these peptides. Results show that at 10 mM NaCl, both the shorter and the longer peptide variants behave like 24Hst5 and a cushion below the bilayer is formed. At 150 mM NaCl, however, no interaction is observed for 24Hst5. On the contrary, a cushion is formed both in the case of 14Hst5 and 48Hst5, and in the latter, an additional thick, diffuse, and highly hydrated layer of peptide and lipid molecules is formed, on top of the bilayer. Similar trends were observed from the simulations, which allowed us to hypothesize that positively charged patches of the amino acids lysine and arginine in all three peptides are essential for them to interact with and translocate over the bilayer. We therefore hypothesize that electrostatic interactions are important for the interaction between the solid-supported lipid bilayers and the peptide depending on the linear charge density through the primary sequence and the positively charged patches in the sequence. The understanding of how, why, and when the cushion is formed opens up the possibility for this system to be used in the research and development of new drugs and pharmaceuticals.

Softness matters: effects of compression on the behavior of adsorbed microgels at interfaces

Deformable colloids and macromolecules adsorb at interfaces as they decrease the interfacial energy between the two media. The deformability, or softness, of these particles plays a pivotal role in the properties of the interface. In this study, we employ a comprehensive in situ approach, combining neutron reflectometry with molecular dynamics simulations, to thoroughly examine the profound influence of softness on the structure of microgel Langmuir monolayers under compression. Lateral compression of both hard and soft microgel particle monolayers induces substantial structural alterations, leading to an amplified protrusion of the microgels into the aqueous phase. However, a critical distinction emerges: hard microgels are pushed away from the interface, in stark contrast to the soft ones, which remain firmly anchored to it. Concurrently, on the air-exposed side of the monolayer, lateral compression induces a flattening of the surface of the hard monolayer. This phenomenon is not observed for the soft particles as the monolayer is already extremely flat even in the absence of compression. These findings significantly advance our understanding of the key role of softness on both the equilibrium phase behavior of the monolayer and its effect when soft colloids are used as stabilizers of responsive interfaces and emulsions.

Investigation on the relationship between lipid composition and structure in model membranes composed of extracted natural phospholipids

HYPOTHESIS

Unravelling the structural diversity of cellular membranes is a paramount challenge in life sciences. In particular, lipid composition affects the membrane collective behaviour, and its interactions with other biological molecules.

EXPERIMENTS

Here, the relationship between membrane composition and resultant structural features was investigated by surface pressure-area isotherms, Brewster angle microscopy and neutron reflectometry on in vitro membrane models of the mammalian plasma and endoplasmic-reticulum-Golgi intermediate compartment membranes in the form of Langmuir monolayers. Natural extracted yeast lipids were used because, unlike synthetic lipids, the acyl chain saturation pattern of yeast and mammalian lipids are similar.

FINDINGS

The structure of the model membranes, orthogonal to the plane of the membrane, as well as their lateral packing, were found to depend strongly on their specific composition, with cholesterol having a major influence on the in-plane morphology, yielding a coexistence of liquid-order and liquid-disorder phases.

Neural network analysis of neutron and X-ray reflectivity data: automated analysis using mlreflect, experimental errors and feature engineering

A Python-based analysis pipeline for the fast analysis of X-ray and neutron reflectivity data using neural networks is presented.

The Python package mlreflect is demonstrated, which implements an optimized pipeline for the automated analysis of reflectometry data using machine learning. The package combines several training and data treatment techniques discussed in previous publications. The predictions made by the neural network are accurate and robust enough to serve as good starting parameters for an optional subsequent least-mean-squares (LMS) fit of the data. For a large data set of 242 reflectivity curves of various thin films on silicon substrates, the pipeline reliably finds an LMS minimum very close to a fit produced by a human researcher with the application of physical knowledge and carefully chosen boundary conditions. The differences between simulated and experimental data and their implications for the training and performance of neural networks are discussed. The experimental test set is used to determine the optimal noise level during training. The extremely fast prediction times of the neural network are leveraged to compensate for systematic errors by sampling slight variations in the data.

New Design of a Sample Cell for Neutron Reflectometry in Liquid–Liquid Systems and Its Application for Studying Structures at Air–Liquid and Liquid–Liquid Interfaces

Knowledge of interfacial structures in liquid–liquid systems is imperative, especially for improving two-phase biological and chemical reactions. Therefore, we developed a new sample cell for neutron reflectometry (NR), which enables us to observe the layer structure around the interface, and investigated the adsorption behavior of a typical surfactant, sodium dodecyl sulfate (SDS), on the toluene-d8-D2O interface under the new experimental conditions. The new cell was characterized by placing the PTFE frame at the bottom to produce a smooth interface and downsized compared to the conventional cell. The obtained NR profiles were readily analyzable and we determined a slight difference in the SDS adsorption layer structure at the interface between the toluene-d8-D2O and air-D2O systems. This could be owing to the difference in the adsorption behavior of the SDS molecules depending on the interfacial conditions.

Using refnx to Model Neutron Reflectometry Data from Phospholipid Bilayers

Neutron reflectometry has emerged as a powerful method for studying the structure of thin films in contact with solution at sub-molecular spatial resolution (Penfold and Thomas, J Phys Condens Matter 2:1369-1412, 1990). This type of experiment is undertaken at large international central facilities and experience in data analysis and interpretation is not always available "locally". Here, we describe the application of the refnx software suite (Nelson and Prescott, J Appl Crystallogr 52:193-200, 2019) to the analysis of a single phospholipid bilayer deposited at a silicon/buffer interface. The data is modeled such that the fitted parameters are readily interpretable by researchers working with lipid bilayers.

Neural network analysis of neutron and x-ray reflectivity data: pathological cases, performance and perspectives

Neutron and x-ray reflectometry (NR and XRR) are powerful techniques to investigate the structural, morphological and even magnetic properties of solid and liquid thin films. While neutrons and x-rays behave similarly in many ways and can be described by the same general theory, they fundamentally differ in certain specific aspects. These aspects can be exploited to investigate different properties of a system, depending on which particular questions need to be answered. Having demonstrated the general applicability of neural networks to analyze XRR and NR data before (Greco et al 2019 J. Appl. Cryst. 52 1342), this study discusses challenges arising from certain pathological cases as well as performance issues and perspectives. These cases include a low signal-to-noise ratio, a high background signal (e.g. from incoherent scattering), as well as a potential lack of a total reflection edge (TRE). By dynamically modifying the training data after every mini batch, a fully-connected neural network was trained to determine thin film parameters from reflectivity curves. We show that noise and background intensity pose no significant problem as long as they do not affect the TRE. However, for curves without strong features the prediction accuracy is diminished. Furthermore, we compare the prediction accuracy for different scattering length density combinations. The results are demonstrated using simulated data of a single-layer system while also discussing challenges for multi-component systems.

anaklasis: a compact software package for model-based analysis of specular neutron and X-ray reflectometry data sets

A new software package (anaklasis) for model-based analysis of specular neutron and X-ray reflectivity is introduced. Key features include a user-friendly compact interfacial model definition scheme and a complete set of methods for co-refining data and estimating parameter uncertainty.

anaklasis constitutes a set of open-source Python scripts that facilitate a range of specular neutron and X-ray reflectivity calculations, involving the generation of theoretical curves and the comparison/fitting of interfacial model reflectivity against experimental data sets. The primary focus of the software is twofold: on one hand to offer a more natural framework for model definition, requiring minimum coding literacy, and on the other hand to include advanced analysis methods that have been proposed in recent work. Particular attention is given to the ability to co-refine reflectivity data and to the estimation of model-parameter uncertainty and covariance using bootstrap analysis and Markov chain Monte Carlo sampling. The compactness and simplicity of model definition together with the streamlined analysis do not present a steep learning curve for the user, an aspect that may accelerate the generation of reproducible, easily readable and statistically accurate reports in future neutron and X-ray reflectivity related literature.

Interaction of Caffeine with Model Lipid Membranes

Caffeine is not only a widely consumed active stimulant, but it is also a model molecule commonly used in pharmaceutical sciences. In this work, by performing quartz-crystal microbalance and neutron reflectometry experiments we investigate the interaction of caffeine molecules with a model lipid membrane. We determined that caffeine molecules are not able to spontaneously partition from an aqueous environment, enriched in caffeine, into a bilayer. Caffeine could be however included in solid-supported lipid bilayers if present with lipids during self-assembly. In this case, thanks to surface-sensitive techniques, we determined that caffeine molecules are preferentially located in the hydrophobic region of the membrane. These results are highly relevant for the development of new drug delivery vectors, as well as for a deeper understanding of the membrane permeation role of purine molecules.

Insertion and activation of functional Bacteriorhodopsin in a floating bilayer

The proton pump transmembrane protein bacteriorhodopsin was successfully incorporated into planar floating lipid bilayers in gel and fluid phases, by applying a detergent-mediated incorporation method. The method was optimized on single supported bilayers by using quartz crystal microbalance, atomic force and fluorescence microscopy techniques. Neutron and X-ray reflectometry were used on both single and floating bilayers with the aim of determining the structure and composition of this membrane-protein system before and after protein reconstitution at sub-nanometer resolution. Lipid bilayer integrity and protein activity were preserved upon the reconstitution process. Reversible structural modifications of the membrane, induced by the bacteriorhodopsin functional activity triggered by visible light, were observed and characterized at the nanoscale.

Solid-supported lipid bilayers - A versatile tool for the structural and functional characterization of membrane proteins

The cellular membrane is central to the development of single-and multicellular life, as it separates the delicate cellular interior from the hostile environment. It exerts tight control over entry and exit of substances, is responsible for signaling with other cells in multicellular organisms and prevents pathogens from entering the cell. In the case of bacteria and viruses, the cellular membrane also hosts the proteins enabling invasion of the host organism. In a very real sense therefore, the cellular membrane is central to all life. The study of the cell membrane and membrane proteins in particular has therefore attracted significant attention. Due to the enormous variety of tasks performed by the membrane, it is a highly complex and challenging structure to study. Ideally, membrane components would be studied in isolation from this environment, but unlike water soluble proteins, the amphiphilic environment provided by the cellular membrane is key to the structure and function of the cell membrane. Therefore, model membranes have been developed to provide an environment in which a membrane protein can be studied. This review presents a set of tools that enable the comprehensive characterization of membrane proteins: electrochemical tools, surface plasmon resonance, neutron scattering, the surface forces apparatus and atomic force microscopy are discussed, with a particular focus on experimental technique and data evaluation.

A general approach to maximise information density in neutron reflectometry analysis

Neutron and x-ray reflectometry are powerful techniques facilitating the study of the structure of interfacial materials. The analysis of these techniques is ill-posed in nature requiring the application of model-dependent methods. This can lead to the over- and under- analysis of experimental data when too many or too few parameters are allowed to vary in the model. In this work, we outline a robust and generic framework for the determination of the set of free parameters that are capable of maximising the information density of the model. This framework involves the determination of the Bayesian evidence for each permutation of free parameters; and is applied to a simple phospholipid monolayer. We believe this framework should become an important component in reflectometry data analysis and hope others more regularly consider the relative evidence for their analytical models.

On the lipid flip-flop and phase transition coupling

We measured the passive lipid flip-flop of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in solid supported lipid bilayers across their main gel to fluid (Lβ → Lα) phase transition. By performing time and temperature resolved neutron reflectometry experiments, we demonstrated that asymmetric systems prepared in the gel phase are stable for at least 24 hours. Lipid flip-flop was found to be intrinsically linked to the amount of lipid molecules in the fluid phase. Moreover, the  increase of this amount during the broad phase transition was found to be the main key factor for the timing of the flip-flop process. By measuring different temperature scan rate, we could demonstrate that, in the case of supported bilayers and for the temperature investigated, the lipid flip flop is characterised by an activation energy of 50 kJ mol-1 and a timescale on the order of few hours. Our results demonstrate the origin on the discrepancies between passive flip-flop in bulk systems and at interfaces.

Interaction with Human Serum Proteins Reveals Biocompatibility of Phosphocholine-Functionalized SPIONs and Formation of Albumin-Decorated Nanoparticles

Nanoparticles (NPs) are increasingly exploited as diagnostic and therapeutic devices in medicine. Among them, superparamagnetic nanoparticles (SPIONs) represent very promising tools for magnetic resonance imaging, local heaters for hyperthermia, and nanoplatforms for multimodal imaging and theranostics. However, the use of NPs, including SPIONs, in medicine presents several issues: first, the encounter with the biological world and proteins in particular. Indeed, nanoparticles can suffer from protein adsorption, which can affect NP functionality and biocompatibility. In this respect, we have investigated the interaction of small SPIONs covered by an amphiphilic double layer of oleic acid/oleylamine and 1-octadecanoyl-sn-glycero-3-phosphocholine with two abundant human plasma proteins, human serum albumin (HSA) and human transferrin. By means of spectroscopic and scattering techniques, we analyzed the effect of SPIONs on protein structure and the binding affinities, and only found strong binding in the case of HSA. In no case did SPIONs alter the protein structure significantly. We structurally characterized HSA/SPIONs complexes by means of light and neutron scattering, highlighting the formation of a monolayer of protein molecules on the NP surface. Their interaction with lipid bilayers mimicking biological membranes was investigated by means of neutron reflectivity. We show that HSA/SPIONs do not affect lipid bilayer features and could be further exploited as a nanoplatform for future applications. Overall, our findings point toward a high biocompatibility of phosphocholine-decorated SPIONs and support their use in nanomedicine.

Applications of neutron reflectometry in biology

Over the last 10 years, neutron reflectometry (NR) has emerged as a powerful technique for the investigation of biologically relevant thin films. The great advantage of NR with respect to many other surface-sensitive techniques is its sub-nanometer resolution that enables structural characterizations at the molecular level. In the case of bio-relevant samples, NR is non-destructive and can be used to probe thin films at buried interfaces or enclosed in bulky sample environment equipment. Moreover, recent advances in biomolecular deutera-tion enabled new labeling strategies to highlight certain structural features and to resolve with better accuracy the location of chemically similar molecules within a thin film.

In this chapter I will describe some applications of NR to bio-relevant samples and discuss some of the data analysis approaches available for biological thin films. In particular, examples on the structural characterization of biomembranes, protein films and protein-lipid interactions will be described.

Structure of DPPC Monolayers at the Air/Buffer Interface: A Neutron Reflectometry and Ellipsometry Study

Langmuir monolayers of 1,2-dipalmitoyl-sn-glycerol-3-phosphocholine, known as DPPC, at the air/water interface are extensively used as model systems of biomembranes and pulmonary surfactant. The properties of these monolayers have been mainly investigated by surface pressure–area isotherms coupled with different complementary techniques such as Brewster angle microscopy, for example. Several attempts using neutron reflectometry (NR) or ellipsometry have also appeared in the literature. Here, we report structural information obtained by using NR and ellipsometry on DPPC monolayers in the liquid condensed phase. On one side, NR can resolve the thickness of the aliphatic tails and the degree of hydration of the polar headgroups. On the other side, ellipsometry gives information on the refractive index and, therefore, on the physical state of the monolayer. The thickness and surface excess obtained by multiple-angle-of-incidence ellipsometry (MAIE) is compared with the results from NR measurements yielding a good agreement. Besides, a novel approach is reported to calculate the optical anisotropy of the DPPC monolayer that depends on the orientation of the aliphatic chains. The results from both NR and ellipsometry are also discussed in the context of the existing results for DPPC monolayers at the air/water interface. The differences observed are rationalized by the presence of buffer molecules interacting with phospholipids.

Spontaneous Formation of Cushioned Model Membranes Promoted by an Intrinsically Disordered Protein

In this article, it is shown that by exposing commonly used lipids for biomembrane mimicking studies, to a solution containing the histidine-rich intrinsically disordered protein histatin 5, a protein cushion spontaneously forms underneath the bilayer. The underlying mechanism is attributed to have an electrostatic origin, and it is hypothesized that the observed behavior is due to proton charge fluctuations promoting attractive electrostatic interactions between the positively charged proteins and the anionic surfaces, with concomitant counterion release. Hence, we anticipate that this novel "green" approach of forming cushioned bilayers can be an important tool to mimic the cell membrane without the disturbance of the solid substrate, thereby achieving a further understanding of protein-cell interactions.

BornAgain: software for simulating and fitting grazing-incidence small-angle scattering

BornAgain is a free and open-source multi-platform software framework for simulating and fitting X-ray and neutron reflectometry, off-specular scattering, and grazing-incidence small-angle scattering (GISAS). This paper concentrates on GISAS. Support for reflectometry and off-specular scattering has been added more recently, is still under intense development and will be described in a later publication. BornAgain supports neutron polarization and magnetic scattering. Users can define sample and instrument models through Python scripting. A large subset of the functionality is also available through a graphical user interface. This paper describes the software in terms of the realized non-functional and functional requirements. The web site https://www.bornagainproject.org/ provides further documentation.

β-Lactoglobulin Adsorption Layers at the Water/Air Surface: 3. Neutron Reflectometry Study on the Effect of pH

Several characteristics of β-lactoglobulin (BLG) layers adsorbed at the air/water interface exhibit a strong pH dependence, but our knowledge on the underlying structure-property relations is still fragmental. Here, we therefore extend our recent studies by neutron reflectometry (NR) and provide a comprehensive overview through direct measurements of the surface excess Γ and the layers' molecular structure. This enables comparison with available literature data to draw general conclusions. The NR experiments were performed at various pH values and within a wide range of protein concentrations, C_BLG. Adsorption kinetics measurements in air-contrast-matched-water and over a narrow Q_z range enabled direct quantification of the dynamic surface excess Γ(t) and are found to be consistent with ellipsometry data. Near the isoelectric point, pI, the rates of adsorption and Γ are maximal but only at sufficiently high C_BLG. NR data collected over a wider Q_z range and in two aqueous isotopic contrasts revealed the structure of adsorbed BLG layers at a steady state close to equilibrium. Independent of the pH, BLG was found to form dense monolayers with average thicknesses of 1.1 nm, suggesting flattening of the BLG globules upon adsorption as compared with their bulk dimensions (≈3.5 nm). Near pI and at sufficiently high C_BLG, a thick (≈5.5 nm) but looser secondary sublayer is additionally formed adjacent to the dense primary monolayer. The thickness of this sublayer can be interpreted in terms of disordered BLG dimers. The results obtained and notably the specific interfacial structuring of BLG near pI complement previous observations relating the impact of solution pH and C_BLG on other interfacial characteristics such as surface pressure and surface dilational viscoelasticity modulus.

Attractive Interaction between Fully Charged Lipid Bilayers in a Strongly Confined Geometry

We investigate the interaction between highly charged lipid bilayers in the presence of monovalent counterions. Neutron and X-ray reflectivity experiments show that the water layer between like-charged bilayers is thinner than for zwitterionic lipids, demonstrating the existence of counterintuitive electrostatic attractive interaction between them. Such attraction can be explained by taking into account the correlations between counterions within the Strong Coupling limit, which falls beyond the classical Poisson-Boltzmann theory of electrostatics. Our results show the limit of the Strong Coupling continuous theory in a highly confined geometry and are in agreement with a decrease in the water dielectric constant due to a surface charge-induced orientation of water molecules.

Molecular insights into the behaviour of bile salts at interfaces: a key to their role in lipid digestion

HYPOTHESES

Understanding the mechanisms underlying lipolysis is crucial to address the ongoing obesity crisis and associated cardiometabolic disorders. Bile salts (BS), biosurfactants present in the small intestine, play key roles in lipid digestion and absorption. It is hypothesised that their contrasting functionalities - adsorption at oil/water interfaces and shuttling of lipolysis products away from these interfaces - are linked to their structural diversity. We investigate the interfacial films formed by two BS, sodium taurocholate (NaTC) and sodium taurodeoxycholate (NaTDC), differing by the presence or absence of a hydroxyl group on their steroid skeleton.

EXPERIMENTS

Their adsorption behaviour at the air/water interface and interaction with a phospholipid monolayer - used to mimic a fat droplet interface - were assessed by surface pressure measurements and ellipsometry, while interfacial morphologies were characterised in the lateral and perpendicular directions by Brewster angle microscopy, X-ray and neutron reflectometry, and molecular dynamics simulations.

FINDINGS

Our results provide a comprehensive molecular-level understanding of the mechanisms governing BS interfacial behaviour. NaTC shows a higher affinity for the air/water and lipid/water interfaces, and may therefore favour enzyme adsorption, whereas NaTDC exhibits a higher propensity for desorption from these interfaces, and may thus more effectively displace hydrolysis products from the interface, through dynamic exchange.

Phase Transitions in a Single Supported Phospholipid Bilayer: Real-Time Determination by Neutron Reflectometry

Time- and temperature-resolved neutron reflectometry allowed us to perform the real-time characterization of the structural changes taking place across phase transitions in solid supported-lipid bilayers (SLBs). We identified the presence of an isothermal phase transition, characterized by a symmetrical rearrangement of lipid molecules in both bilayer leaflets, followed by the main thermotropic phase transition, and characterized by an independent melting of the two leaflets. We demonstrated that the presence of a substrate increases the enthalpy of melting by the same amount for both SLB leaflets with respect to the values reported for freestanding bilayers. These results are highly relevant for the further understanding of cooperative structural dynamics in SLBs and for the investigation of thermally activated processes such as the transmembrane lipid translocation (flip flop).

The Role of Temperature and Lipid Charge on Intake/Uptake of Cationic Gold Nanoparticles into Lipid Bilayers

Understanding the molecular mechanisms governing nanoparticle-membrane interactions is of prime importance for drug delivery and biomedical applications. Neutron reflectometry (NR) experiments are combined with atomistic and coarse-grained molecular dynamics (MD) simulations to study the interaction between cationic gold nanoparticles (AuNPs) and model lipid membranes composed of a mixture of zwitterionic di-stearoyl-phosphatidylcholine (DSPC) and anionic di-stearoyl-phosphatidylglycerol (DSPG). MD simulations show that the interaction between AuNPs and a pure DSPC lipid bilayer is modulated by a free energy barrier. This can be overcome by increasing temperature, which promotes an irreversible AuNP incorporation into the lipid bilayer. NR experiments confirm the encapsulation of the AuNPs within the lipid bilayer at temperatures around 55 °C. In contrast, the AuNP adsorption is weak and impaired by heating for a DSPC-DSPG (3:1) lipid bilayer. These results demonstrate that both the lipid charge and the temperature play pivotal roles in AuNP-membrane interactions. Furthermore, NR experiments indicate that the (negative) DSPG lipids are associated with lipid extraction upon AuNP adsorption, which is confirmed by coarse-grained MD simulations as a lipid-crawling effect driving further AuNP aggregation. Overall, the obtained detailed molecular view of the interaction mechanisms sheds light on AuNP incorporation and membrane destabilization.

Model-independent recovery of interfacial structure from multi-contrast neutron reflectivity data

An indirect Fourier transform/simulated annealing method exploits the information content of multiple solvent contrast neutron reflectivity data and permits the model-independent recovery of interfacial structure at the air/liquid and solid/liquid interface.

Neutron specular reflectivity at soft interfaces provides sub-nanometre information concerning the molecular distribution of thin films, while the application of contrast variation can highlight the scattering from different parts of the system and lead to an overall reduction in fitting ambiguity. Traditional modelling approaches involve the construction of a trial scattering length density profile based on initial speculation and the subsequent refinement of its parameters through minimization of the discrepancy between the calculated and measured reflectivity. In practice this might produce an artificial bias towards specific sets of solutions. On the other hand, direct inversion of reflectivity data, despite its ability to provide a unique solution, is subject to limitations and experimental complications. Presented here is an integrated indirect Fourier transform/simulated annealing method that, when applied to multiple solvent contrast reflectivity data and within the limits of finite spatial resolution, leads to reliable reconstructions of the interfacial structure without the need for any a priori assumptions. The generality of the method permits its straightforward application in common experimental contrast-variation investigations at the solid/liquid and air/liquid interface.

refnx: neutron and X-ray reflectometry analysis in Python

refnx is a model-based neutron and X-ray reflectometry data analysis package written in Python. It is cross platform and has been tested on Linux, macOS and Windows. Its graphical user interface is browser based, through a Jupyter notebook. Model construction is modular, being composed from a series of components that each describe a subset of the interface, parameterized in terms of physically relevant parameters (volume fraction of a polymer, lipid area per molecule etc.). The model and data are used to create an objective, which is used to calculate the residuals, log-likelihood and log-prior probabilities of the system. Objectives are combined to perform co-refinement of multiple data sets and mixed-area models. Prior knowledge of parameter values is encoded as probability distribution functions or bounds on all parameters in the system. Additional prior probability terms can be defined for sets of components, over and above those available from the parameters alone. Algebraic parameter constraints are available. The software offers a choice of fitting approaches, including least-squares (global and gradient-based optimizers) and a Bayesian approach using a Markov-chain Monte Carlo algorithm to investigate the posterior distribution of the model parameters. The Bayesian approach is useful for examining parameter covariances, model selection and variability in the resulting scattering length density profiles. The package is designed to facilitate reproducible research; its use in Jupyter notebooks, and subsequent distribution of those notebooks as supporting information, permits straightforward reproduction of analyses.

Bayesian determination of the effect of a deep eutectic solvent on the structure of lipid monolayers

A novel reflectometry analysis method reveals the structure of lipid monolayers at the air-DES interface.

Structure and Composition of Native Membrane Derived Polymer-Supported Lipid Bilayers

Over the last two decades, supported lipid bilayers (SLBs) have been extensively used as model systems to study cell membrane structure and function. While SLBs have been traditionally produced from simple lipid mixtures, there has been a recent surge in compositional complexity to better mimic cellular membranes and thereby bridge the gap between classic biophysical approaches and cell experiments. To this end, native cellular membrane derived SLBs (nSLBs) have emerged as a new category of SLBs. As a new type of biomimetic material, an analytical workflow must be designed to characterize its molecular composition and structure. Herein, we demonstrate how a combination of fluorescence microscopy, neutron reflectometry, and secondary ion mass spectrometry offers new insights on structure, composition, and quality of nSLB systems formed using so-called hybrid vesicles, which are a mixture of native membrane material and synthetic lipids. With this approach, we demonstrate that the nSLB formed a continuous structure with complete mixing of the synthetic and native membrane components and a molecular stoichiometry that essentially mirrors that of the hybrid vesicles. Furthermore, structural investigation of the nSLB revealed that PEGylated lipids do not significantly thicken the hydration layer between the bilayer and substrate when on silicon substrates; however, nSLBs do have more topology than their simpler, purely synthetic counterparts. Beyond new insights regarding the structure and composition of nSLB systems, this work also serves to guide future researchers in producing and characterizing nSLBs from their cellular membrane of choice.

Towards biomimics of cell membranes: Structural effect of phosphatidylinositol triphosphate (PIP3) on a lipid bilayer

Phosphoinositide (PIP) lipids are anionic phospholipids playing a fundamental role for the activity of several transmembrane and soluble proteins. Among all, phosphoinositol-3',4',5'-trisphosphate (PIP₃) is a secondary signaling messenger that regulates the function of proteins involved in cell growth and gene transcription. The present study aims to reveal the structure of PIP-containing lipid membranes, which so far has been little explored. For this purpose, supported lipid bilayers (SLBs) containing 1,2-dioleoyl-sn-glycero-3-phospho-(1'-myo-inositol-3',4',5'-trisphosphate (DOPIP₃) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) were used as mimics of biomembranes. Surface sensitive techniques, i.e. Quartz Crystal Microbalance with Dissipation monitoring (QCM-D), Atomic Force Microscopy (AFM) and Neutron Reflectometry (NR), provided detailed information on the formation of the SLB and the location of DOPIP₃ in the lipid membrane. Specifically, QCM-D and AFM were used to identify the best condition for lipid deposition and to estimate the total bilayer thickness. On the other hand, NR was used to collect experimental structural data on the DOPIP₃ location and orientation within the lipid membrane. The two bilayer leaflets showed the same DOPIP₃ concentration, thus suggesting the formation of a symmetric bilayer. The headgroup layer thicknesses of the pure POPC and the mixed POPC/DOPIP₃ bilayer suggest that the DOPIP₃-headgroups have a preferred orientation, which is not perpendicular to the membrane surface, but instead it is close to the surrounding lipid headgroups. These results support the proposed PIP₃ tendency to interact with the other lipid headgroups as PC, so far exclusively suggested by MD simulations.

Disruption of Asymmetric Lipid Bilayer Models Mimicking the Outer Membrane of Gram-Negative Bacteria by an Active Plasticin

The outer membrane (OM) of Gram-negative bacteria is a complex and asymmetric bilayer that antimicrobial peptides must disrupt in order to provoke the cell lysis. The inner and external leaflets of the OM are mainly composed of phospholipids (PL), and lipopolysaccharide (LPS), respectively. Supported lipid bilayers are interesting model systems to mimic the lipid asymmetric scaffold of the OM and determine the quantitative and mechanistic effect of antimicrobial agents, using complementary physicochemical techniques. We report the formation of asymmetric PL/LPS bilayers using the Langmuir-Blodgett/Langmuir-Schaefer technique on two different surfaces (sapphire and mica) with synthetic phospholipids constituting the inner leaflet and bacteria-extracted mutant LPS making up the outer one. The combination of neutron reflectometry and atomic force microscopy techniques allowed the examination of the asymmetric scaffold structure along the normal to the interface and its surface morphology in buffer conditions. Our results allow discrimination of two structurally related peptides, one neutral and inactive, and the other cationic and active. The active cationic plasticin PTCDA1-KF disrupts the asymmetric OM at relevant concentrations through a carpeting scenario characterized by a dramatic removal of lipid molecules from the surface.

Nanoroughness Strongly Impacts Lipid Mobility in Supported Membranes

In vivo lipid membranes interact with rough supramolecular structures such as protein clusters and fibrils. How these features whose size ranges from a few nanometers to a few tens of nanometers impact lipid and protein mobility is still being investigated. Here, we study supported phospholipid bilayers, a unique biomimetic model, deposited on etched surfaces bearing nanometric corrugations. The surface roughness and mean curvature are carefully characterized by AFM imaging using ultrasharp tips. Neutron specular reflectivity supplements this surface characterization and indicates that the bilayers follow the large-scale corrugations of the substrate. We measure the lateral mobility of lipids in both the fluid and gel phases by fluorescence recovery after patterned photobleaching. Although the mobility is independent of the roughness in the gel phase, it exhibits a 5-fold decrease in the fluid phase when the roughness increases from 0.2 to 10 nm. These results are interpreted with a two-phase model allowing for a strong decrease in the lipid mobility in highly curved or defect-induced gel-like nanoscale regions. This suggests a strong link between membrane curvature and fluidity, which is a key property for various cell functions such as signaling and adhesion.

Membrane Permeation versus Amyloidogenicity: A Multitechnique Study of Islet Amyloid Polypeptide Interaction with Model Membranes

Islet amyloid polypeptide (IAPP) is responsible for cell depletion in the pancreatic islets of Langherans, and for multiple pathological consequences encountered by patients suffering from type 2 Diabetes Mellitus. We have examined the amyloidogenicity and cytotoxic mechanisms of this peptide by investigating model-membrane permeation and structural effects of fragments of the human IAPP and several rat IAPP mutants. In vitro experiments and molecular dynamics simulations reveal distinct physical segregation, membrane permeation, and amyloid aggregation processes that are mediated by two separate regions of the peptide. These observations suggest a "detergent-like" mechanism, where lipids are extracted from the bilayer by the N-terminus of IAPP, and integrated into amyloid aggregates. The amyloidogenic aggregation would kinetically compete with the process of membrane permeation and, therefore, inhibit it. This hypothesis represents a new perspective on the mechanism underlying the membrane disruption by amyloid peptides, and could influence the development of new therapeutic strategies.

Neutron Reflectometry reveals the interaction between functionalized SPIONs and the surface of lipid bilayers

The safe application of nanotechnology devices in biomedicine requires fundamental understanding on how they interact with and affect the different components of biological systems. In this respect, the cellular membrane, the cell envelope, certainly represents an important target or barrier for nanosystems. Here we report on the interaction between functionalized SuperParamagnetic Iron Oxide Nanoparticles (SPIONs), promising contrast agents for Magnetic Resonance Imaging (MRI), and lipid bilayers that mimic the plasma membrane. Neutron Reflectometry, supported by Quartz Crystal Microbalance with Dissipation monitoring (QCM-D) experiments, was used to characterize this interaction by varying both SPION coating and lipid bilayer composition. In particular, the interaction of two different SPIONs, functionalized with a cationic surfactant and a zwitterionic phospholipid, and lipid bilayers, containing different amount of cholesterol, were compared. The obtained results were further validated by Dynamic Light Scattering (DLS) measurements and Cryogenic Transmission Electron Microscopy (Cryo-TEM) images. None of the investigated functionalized SPIONs were found to disrupt the lipid membrane. However, in all case we observed the attachment of the functionalized SPIONs onto the surface of the bilayers, which was affected by the bilayer rigidity, i.e. the cholesterol concentration.

Aurore: new software for neutron reflectivity data analysis. Corrigendum

An incorrect statement in the paper by Gerelli [J. Appl. Cryst. (2016), 49, 330–339] is corrected.