X-ray structural investigations of fusion intermediates: Lipid model systems and beyond

Neural network analysis of neutron and X-ray reflectivity data incorporating prior knowledge

Due to the ambiguity related to the lack of phase information, determining the physical parameters of multilayer thin films from measured neutron and X-ray reflectivity curves is, on a fundamental level, an underdetermined inverse problem. This ambiguity poses limitations on standard neural networks, constraining the range and number of considered parameters in previous machine learning solutions. To overcome this challenge, a novel training procedure has been designed which incorporates dynamic prior boundaries for each physical parameter as additional inputs to the neural network. In this manner, the neural network can be trained simultaneously on all well-posed subintervals of a larger parameter space in which the inverse problem is underdetermined. During inference, users can flexibly input their own prior knowledge about the physical system to constrain the neural network prediction to distinct target subintervals in the parameter space. The effectiveness of the method is demonstrated in various scenarios, including multilayer structures with a box model parameterization and a physics-inspired special parameterization of the scattering length density profile for a multilayer structure. In contrast to previous methods, this approach scales favourably when increasing the complexity of the inverse problem, working properly even for a five-layer multilayer model and a periodic multilayer model with up to 17 open parameters.

Mechanisms of SNARE proteins in membrane fusion

Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are a family of small conserved eukaryotic proteins that mediate membrane fusion between organelles and with the plasma membrane. SNAREs are directly or indirectly anchored to membranes. Prior to fusion, complementary SNAREs assemble between membranes with the aid of accessory proteins that provide a scaffold to initiate SNARE zippering, pulling the membranes together and mediating fusion. Recent advances have enabled the construction of detailed models describing bilayer transitions and energy barriers along the fusion pathway and have elucidated the structures of SNAREs complexed in various states with regulatory proteins. In this Review, we discuss how these advances are yielding an increasingly detailed picture of the SNARE-mediated fusion pathway, leading from first contact between the membranes via metastable non-bilayer intermediates towards the opening and expansion of a fusion pore. We describe how SNARE proteins assemble into complexes, how this assembly is regulated by accessory proteins and how SNARE complexes overcome the free energy barriers that prevent spontaneous membrane fusion.

Stacks of monogalactolipid bilayers can transform into a lattice of water channels

The lipid matrix of thylakoid membranes is a lamellar bilayer, but under a certain condition it can convert locally into a nonlamellar structure. This is possible because one of the main membrane lipids, MGDG, promotes the formation of an inverse hexagonal phase. Here, the spontaneous transformation of aligned hydrated MGDG bilayers into nonlamellar structures is investigated using all-atom molecular dynamics simulation. Previous studies have demonstrated that MGDG polar head groups connect vertically across the interface. In this study, the evolution of the system's initial structure into a lattice of water channels and contacted surfaces created by numerous vertical MGDG connections depended on the width of the hydrating water layers. These widths controlled the bilayers' ability to bend, which was a prerequisite for channel formation. Locally, an intensive exchange of MGDG molecules between apposing bilayer leaflets occurred, although a stable semi-toroidal stalk did not develop.

Lipid/water interface of galactolipid bilayers in different lyotropic liquid-crystalline phases

In this study, carried out using computational methods, the organisation of the lipid/water interface of bilayers composed of galactolipids with both α-linolenoyl acyl chains is analysed and compared in three different lyotropic liquid-crystalline phases. These systems include the monogalactosyldiglyceride (MGDG) and digalactosyldiglyceride (DGDG) bilayers in the lamellar phase, the MGDG double bilayer during stalk phase formation and the inverse hexagonal MGDG phase. For each system, lipid-water and direct and water-mediated lipid-lipid interactions between the lipids of one bilayer leaflet and those of two apposing leaflets at the onset of new phase (stalk) formation, are identified. A network of interactions between DGDG molecules and its topological properties are derived and compared to those for the MGDG bilayer.

A stalk fluid forming above the transition from the lamellar to the rhombohedral phase of lipid membranes

In this work, we present evidence for the formation of transient stalks in aligned multilamellar stacks of lipid membranes. Just above the phase transition from the fluid ([Formula: see text]) lamellar phase to the rhombohedral phase (R), where lipid stalks crystallize on a super-lattice within the lipid bilayer stack, we observe a characteristic scattering pattern, which can be attributed to a correlated fluid of transient stalks. Excess (off-axis) diffuse scattering with a broad modulation around the position which later transforms to a sharp peak of the rhombohedral lattice, gives evidence for the stalk fluid forming as a pre-critical effect, reminiscent of critical phenomena in the vicinity of second-order phase transitions. Using high-resolution off-specular X-ray scattering and lineshape analysis we show that this pre-critical regime is accompanied by an anomalous elasticity behavior of the membrane stack, in particular an increase in inter-bilayer compressibility, i.e., a decrease in the compression modulus.

Kelvin-Helmholtz-like instability of phospholipid bilayers under shear flow: System-size dependence

We performed a series of molecular dynamics (MD) simulations of phospholipid bilayers under shear flow to estimate the effect of the system size on Kelvin-Helmholtz (KH)-like instability of the bilayer at the molecular scale. To extend the estimation by the MD simulations to the microscale, we introduced linear stability analysis for the fluid-fluid interface consisting of a thin membrane. For both the MD simulations and theoretical model, the critical velocity difference across the bilayer, where instability occurs, decreased with increasing wavelength of the bilayer undulation λ, which corresponds to the system size. When λ was more than about ten times larger than the bilayer thickness, the critical velocity difference in the MD simulations was in quantitative agreement with that obtained by the theoretical model. This means that the theoretical model is applicable for the shear-induced KH-like instability of the bilayer for large λ. The theoretical model showed that the critical velocity difference for the KH-like instability was proportional to λ^{-3/2}. Based on these results, we discuss the implications of the shear-induced bilayer instability in the shear-induced cell damage observed in experiments.

Graphene-based sensing of oxygen transport through pulmonary membranes

Lipid-protein complexes are the basis of pulmonary surfactants covering the respiratory surface and mediating gas exchange in lungs. Cardiolipin is a mitochondrial lipid overexpressed in mammalian lungs infected by bacterial pneumonia. In addition, increased oxygen supply (hyperoxia) is a pathological factor also critical in bacterial pneumonia. In this paper we fabricate a micrometer-size graphene-based sensor to measure oxygen permeation through pulmonary membranes. Combining oxygen sensing, X-ray scattering, and Atomic Force Microscopy, we show that mammalian pulmonary membranes suffer a structural transformation induced by cardiolipin. We observe that cardiolipin promotes the formation of periodic protein-free inter-membrane contacts with rhombohedral symmetry. Membrane contacts, or stalks, promote a significant increase in oxygen gas permeation which may bear significance for alveoli gas exchange imbalance in pneumonia.

Grazing-incidence X-ray scattering of lamellar thin films

Recently, surface and thin-film studies using area detectors have become prevalent. An important class of such systems are lamellar thin films formed by small molecules, liquid crystals or semicrystalline polymers. Frequently, the lamellae align more or less parallel to the substrate. Such structures can be easily discerned by their characteristic X-ray scattering close to the incident plane. This paper describes how such patterns can be simulated, in order to extract morphological information about the thin film.

Flexible sample cell for real-time GISAXS, GIWAXS and XRR: design and construction

Since the properties of functional materials are highly dependent on their specific structure, and since the structural changes, for example during crystallization, induced by coating and annealing processes are significant, the study of structure and its formation is of interest for fundamental and applied science. However, structure analysis is often limited to ex situ determination of final states due to the lack of specialized sample cells that enable real-time investigations. The lack of such cells is mainly due to their fairly complex design and geometrical restrictions defined by the beamline setups. To overcome this obstacle, an advanced sample cell has been designed and constructed; it combines automated doctor blading, solvent vapor annealing and sample hydration with real-time grazing-incidence wide- and small-angle scattering (GIWAXS/GISAXS) and X-ray reflectivity (XRR). The sample cell has limited spatial requirements and is therefore widely usable at beamlines and laboratory-scale instruments. The cell is fully automatized and remains portable, including the necessary electronics. In addition, the cell can be used by interested scientists in cooperation with the Institute for Crystallography and Structural Physics and is expandable with regard to optical secondary probes. Exemplary research studies are presented, in the form of coating of P3HT:PC₆₁PM thin films, solvent vapor annealing of DRCN5T:PC₇₁BM thin films, and hydration of supported phospholipid multilayers, to demonstrate the capabilities of the in situ cell.

Membrane curvature allosterically regulates the phosphatidylinositol cycle, controlling its rate and acyl-chain composition of its lipid intermediates

Signaling events at membranes are often mediated by membrane lipid composition or membrane physical properties. These membrane properties could act either by favoring the membrane binding of downstream effectors or by modulating their activity. Several proteins can sense/generate membrane physical curvature (i.e. shape). However, the modulation of the activity of enzymes by a membrane's shape has not yet been reported. Here, using a cell-free assay with purified diacylglycerol kinase ϵ (DGKϵ) and liposomes, we studied the activity and acyl-chain specificity of an enzyme of the phosphatidylinositol (PI) cycle, DGKϵ. By systematically varying the model membrane lipid composition and physical properties, we found that DGKϵ has low activity and lacks acyl-chain specificity in locally flat membranes, regardless of the lipid composition. On the other hand, these enzyme properties were greatly enhanced in membrane structures with a negative Gaussian curvature. We also found that this is not a consequence of preferential binding of the enzyme to those structures, but rather is due to a curvature-mediated allosteric regulation of DGKϵ activity and acyl-chain specificity. Moreover, in a fine-tuned interplay between the enzyme and the membrane, DGKϵ favored the formation of structures with greater Gaussian curvature. DGKϵ does not bear a regulatory domain, and these findings reveal the importance of membrane curvature in regulating DGKϵ activity and acyl-chain specificity. Hence, this study highlights that a hierarchic coupling of membrane physical property and lipid composition synergistically regulates membrane signaling events. We propose that this regulatory mechanism of membrane-associated enzyme activity is likely more common than is currently appreciated.

Structure of Lung-Mimetic Multilamellar Bodies with Lipid Compositions Relevant in Pneumonia

The hierarchical assembly of lipids, as modulated by composition and environment, plays a significant role in the function of biological membranes and a myriad of diseases. Elevated concentrations of calcium ions and cardiolipin (CL), an anionic tetra-alkyl lipid found in mitochondria and some bacterial cell membranes, have been implicated in pneumonia recently. However, their impact on the physicochemical properties of lipid assemblies in lungs and how it impairs alveoli function is still unknown. We use small- and wide-angle X-ray scattering (S/WAXS) and solid-state nuclear magnetic resonance (ssNMR) to probe the structure and dynamics of lung-mimetic multilamellar bodies (MLBs) in the presence of Ca²⁺ and CL. We conjecture that CL overexpressed in the hypophase of alveoli strongly affects the structure of lung-lipid bilayers and their stacking in the MLBs. Specifically, S/WAXS data revealed that CL induces significant shrinkage of the water-layer separating the concentric bilayers in multilamellar aggregates. ssNMR measurements indicate that this interbilayer tightening is due to undulation repulsion damping as CL renders the glycerol backbone of the membranes significantly more static. In addition to MLB dehydration, CL promotes intrabilayer phase separation into saturated-rich and unsaturated-rich lipid domains that couple across multiple layers. Expectedly, addition of Ca²⁺ screens the electrostatic repulsion between negatively charged lung membranes. However, when CL is present, addition of Ca²⁺ results in an apparent interbilayer expansion likely due to local structural defects. Combining S/WAXS and ssNMR on systems with compositions pertinent to healthy and unhealthy lung membranes, we propose how alteration of the physiochemical properties of MLBs can critically impact the breathing cycle.

Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective

Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion. Furthermore, we highlight the role of novel single-particle experiments and computational approaches in understanding the fusion process and their complementarity with other biophysical approaches.

Fusion pore in exocytosis: More than an exit gate? A β-cell perspective

Secretory vesicle exocytosis is a fundamental biological event and the process by which hormones (like insulin) are released into the blood. Considerable progress has been made in understanding this precisely orchestrated sequence of events from secretory vesicle docked at the cell membrane, hemifusion, to the opening of a membrane fusion pore. The exact biophysical and physiological regulation of these events implies a close interaction between membrane proteins and lipids in a confined space and constrained geometry to ensure appropriate delivery of cargo. We consider some of the still open questions such as the nature of the initiation of the fusion pore, the structure and the role of the Soluble N-ethylmaleimide-sensitive-factor Attachment protein REceptor (SNARE) transmembrane domains and their influence on the dynamics and regulation of exocytosis. We discuss how the membrane composition and protein-lipid interactions influence the likelihood of the nascent fusion pore forming. We relate these factors to the hypothesis that fusion pore expansion could be affected in type-2 diabetes via changes in disease-related gene transcription and alterations in the circulating lipid profile. Detailed characterisation of the dynamics of the fusion pore in vitro will contribute to understanding the larger issue of insulin secretory defects in diabetes.