The in vivo structure of biological membranes and evidence for lipid domains

Nonstereotypical Distribution and Effect of Ergosterol in Lipid Membranes

Ergosterol, found in fungi and some protist membranes, is understudied compared with cholesterol from animal membranes. Generally, ergosterol is assumed to modulate membranes in the same manner as cholesterol, based on their similar chemical structures. Here we reveal some fundamental structural and dynamical differences between them. Neutron diffraction shows that ergosterol is embedded in the lipid bilayer much shallower than cholesterol. Ergosterol does not change the membrane thickness as much as cholesterol does, indicating little condensation effect. Neutron spin echo shows that ergosterol can rigidify and soften membranes at different concentrations. The lateral lipid diffusion measured by quasielastic neutron scattering indicates that ergosterol promotes a jump diffusion of the lipid, whereas cholesterol keeps the same continuous lateral diffusion as the pure lipid membrane. Our results point to quite distinct interactions of ergosterol with membranes compared with cholesterol. These insights provide a basic understanding of membranes containing ergosterol with implications for phenomena such as lipid rafts and drug interactions.

Nanoscopic lipid domains determined by microscopy and neutron scattering

Biological membranes are highly complex supramolecular assemblies, which play central roles in biology. However, their complexity makes them challenging to study their nanoscale structures. To overcome this challenge, model membranes assembled using reduced sets of membrane-associated biomolecules have been found to be both excellent and tractable proxies for biological membranes. Due to their relative simplicity, they have been studied using a range of biophysical characterization techniques. In this review article, we will briefly detail the use of fluorescence and electron microscopies, and X-ray and neutron scattering techniques used over the past few decades to study the nanostructure of biological membranes.

Macromolecular Crowding, Phase Separation, and Homeostasis in the Orchestration of Bacterial Cellular Functions

Macromolecular crowding affects the activity of proteins and functional macromolecular complexes in all cells, including bacteria. Crowding, together with physicochemical parameters such as pH, ionic strength, and the energy status, influences the structure of the cytoplasm and thereby indirectly macromolecular function. Notably, crowding also promotes the formation of biomolecular condensates by phase separation, initially identified in eukaryotic cells but more recently discovered to play key functions in bacteria. Bacterial cells require a variety of mechanisms to maintain physicochemical homeostasis, in particular in environments with fluctuating conditions, and the formation of biomolecular condensates is emerging as one such mechanism. In this work, we connect physicochemical homeostasis and macromolecular crowding with the formation and function of biomolecular condensates in the bacterial cell and compare the supramolecular structures found in bacteria with those of eukaryotic cells. We focus on the effects of crowding and phase separation on the control of bacterial chromosome replication, segregation, and cell division, and we discuss the contribution of biomolecular condensates to bacterial cell fitness and adaptation to environmental stress.

Bacterial membrane dynamics: Compartmentalization and repair

In every bacterial cell, the plasma membrane plays a key role in viability as it forms a selective barrier between the inside of the cell and its environment. This barrier function depends on the physical state of the lipid bilayer and the proteins embedded or associated with the bilayer. Over the past decade or so, it has become apparent that many membrane-organizing proteins and principles, which were described in eukaryote systems, are ubiquitous and play important roles in bacterial cells. In this minireview, we focus on the enigmatic roles of bacterial flotillins in membrane compartmentalization and bacterial dynamins and ESCRT-like systems in membrane repair and remodeling.

The Membrane-Mediated Interaction of Liquid-Ordered Lipid Domains in the Presence of Amphipathic Peptides

The lipid membranes of living cells are composed of a large number of lipid types and can undergo phase separation with the formation of nanometer-scale liquid-ordered lipid domains, also called rafts. Raft coalescence, i.e., the fusion of lipid domains, is involved in important cell processes, such as signaling and trafficking. In this work, within the framework of the theory of elasticity of lipid membranes, we explore how amphipathic peptides adsorbed on lipid membranes may affect the domain-domain fusion processes. We show that the elastic deformations of lipid membranes drive amphipathic peptides to the boundary of lipid domains, which leads to an increase in the average energy barrier of the domain-domain fusion, even if the surface concentration of amphipathic peptides is low and the domain boundaries are only partially occupied by the peptides. This inhibition of the fusion of lipid domains may lead to negative side effects of using amphipathic peptides as antimicrobial agents.

Micro-Executor of Natural Products in Metabolic Diseases

Obesity, diabetes, and cardiovascular diseases are the major chronic metabolic diseases that threaten human health. In order to combat these epidemics, there remains a desperate need for effective, safe, and easily available therapeutic strategies. Recently, the development of natural product research has provided new methods and options for these diseases. Numerous studies have demonstrated that microRNAs (miRNAs) are key regulators of metabolic diseases, and natural products can improve lipid and glucose metabolism disorders and cardiovascular diseases by regulating the expression of miRNAs. In this review, we present the recent advances involving the associations between miRNAs and natural products and the current evidence showing the positive effects of miRNAs for natural product treatment in metabolic diseases. We also encourage further research to address the relationship between miRNAs and natural products under physiological and pathological conditions, thus leading to stronger support for drug development from natural products in the future.

Biophysical studies of lipid nanodomains using different physical characterization techniques

For the past 50 years, evidence for the existence of functional lipid domains has been steadily accumulating. Although the notion of functional lipid domains, also known as "lipid rafts," is now widely accepted, this was not always the case. This ambiguity surrounding lipid domains could be partly attributed to the fact that they are highly dynamic, nanoscopic structures. Since most commonly used techniques are sensitive to microscale structural features, it is therefore, not surprising that it took some time to reach a consensus regarding their existence. In this review article, we will discuss studies that have used techniques that are inherently sensitive to nanoscopic structural features (i.e., neutron scatting, nuclear magnetic resonance, and Förster resonance energy transfer). We will also mention techniques that may be of use in the future (i.e., cryoelectron microscopy, droplet interface bilayers, inelastic x-ray scattering, and neutron reflectometry), which can further our understanding of the different and unique physicochemical properties of nanoscopic lipid domains.

Detergent-Resistant Membranes in Chloroplasts and Mitochondria of the Halophyte Salicornia perennans under Salt Stress

Halophytes represent important models for studying the key mechanisms of salt tolerance. One approach to the development of new knowledge of salt tolerance is to study the properties of detergent-resistant membranes (DRMs). In this work, the lipid profiles of DRMs of chloroplasts and mitochondria of euhalophyte Salicornia perennans Willd, before and after their exposure to shock concentrations of NaCl, have been investigated. We found that DRMs of chloroplasts are enriched in cerebrosides (CERs) and that sterols (STs) dominate the mass of mitochondrial DRMs. Also, it has been proven that (i) the impact of salinity provokes obvious growth in the content of CERs in DRMs of chloroplasts; (ii) the content of STs in DRMs of chloroplasts does not change under the influence of NaCl; (iii) salinity also causes some elevation in the content of monounsaturated and saturated fatty acids (FAs). Considering the fact that DRMs represent integral parts of both chloroplast and mitochondrial membranes, the authors have come to the conclusion that the cells of euhalophyte S. perennans, under the impact of salinity, presumes the choice (by the cell) of some specific composition of lipids and FAs in the membrane. This may be considered as a specific protection reaction of the plant cell against salinity.

A Small-Angle Neutron Scattering, Calorimetry and Densitometry Study to Detect Phase Boundaries and Nanoscale Domain Structure in a Binary Lipid Mixture

Techniques that can probe nanometer length scales, such as small-angle neutron scattering (SANS), have become increasingly popular to detect phase separation in membranes. But to extract the phase composition and domain structure from the SANS traces, complementary information is needed. Here, we present a SANS, calorimetry and densitometry study of a mixture of two saturated lipids that exhibits solidus-liquidus phase coexistence: 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine (dDPPC, tail-deuterated DPPC) and 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC). With calorimetry, we investigated the phase diagram for this system and found that the boundary traces for both multilamellar vesicles (MLVs) as well as 50 nm unilamellar vesicles overlap. Because the solidus boundary was mostly inaccessible by calorimetry, we investigated it by both SANS and molecular volume measurements for a 1:1 dDPPC:DLPC lipid mixture. From the temperature behavior of the molecular volume for the 1:1 dDPPC:DLPC mixture, as well as the individual molecular volume of each lipid species, we inferred that the liquidus phase consists of only fluid-state lipids while the solidus phase consists of lipids that are in gel-like states. Using this solidus-liquidus phase model, the SANS data were analyzed with an unrestricted shape model analysis software: MONSA. The resulting fits show irregular domains with dendrite-like features as those previously observed on giant unilamellar vesicles (GUVs). The surface pair correlation function describes a characteristic domain size for the minority phase that decreases with temperature, a behavior found to be consistent with a concomitant decrease in membrane mismatch between the liquidus and solidus phases.

DENSS-multiple: A structure reconstruction method using contrast variation of small-angle neutron scattering based on the DENSS algorithm

The 3D structure of biomacromolecules, such as protein and DNA/RNA, provide keys to understanding their biological functions. Among many structural biology techniques, small-angle scattering techniques with ab initio methods have been widely used to reveal biomolecular structures in relevant solution conditions. Recently, a method called DENsity from Solution Scattering (DENSS) was developed to reconstruct the scattering density directly from biological small-angle X-ray and neutron scattering data instead of using a dummy atom modeling approach. Here, a method named DENSS-Multiple was developed to work simultaneously on multiple datasets from small-angle neutron scattering (SANS) contrast variation data. The easily manipulable neutron contrast has been widely exploited to study the structure and function of biological macromolecules and their complexes in solution. This new method provides a single structural result that includes all the information represented by different contrasts from SANS. The results from DENSS-Multiple generally have better resolution than those from DENSS, and more subtle features are represented by density variations from different phases of a structure. DENSS-Multiple was tested on various examples, including simulated and experimental data. These results, along with DENSS-Multiple's applications and limitations, are discussed herein.

Small-Angle Neutron Scattering for Studying Lipid Bilayer Membranes

Small-angle neutron scattering (SANS) is a powerful tool for studying biological membranes and model lipid bilayer membranes. The length scales probed by SANS, being from 1 nm to over 100 nm, are well-matched to the relevant length scales of the bilayer, particularly when it is in the form of a vesicle. However, it is the ability of SANS to differentiate between isotopes of hydrogen as well as the availability of deuterium labeled lipids that truly enable SANS to reveal details of membranes that are not accessible with the use of other techniques, such as small-angle X-ray scattering. In this work, an overview of the use of SANS for studying unilamellar lipid bilayer vesicles is presented. The technique is briefly presented, and the power of selective deuteration and contrast variation methods is discussed. Approaches to modeling SANS data from unilamellar lipid bilayer vesicles are presented. Finally, recent examples are discussed. While the emphasis is on studies of unilamellar vesicles, examples of the use of SANS to study intact cells are also presented.

Improved chemical and isotopic labeling of biomembranes in Bacillus subtilis by leveraging CRISPRi inhibition of beta-ketoacyl-ACP synthase (fabF)

Assessing the structure of living microbial cell membranes is a challenging analytical goal. The cell membrane is defined by its transverse structure, an approximately 5 nm-thick selectively permeable bilayer that serves many important cellular functions. Compositionally complex, dynamic, and organized in both the transverse and lateral dimensions, understanding the cell membrane structure—and the role that structure plays in cellular function, communication, and environmental sensing is an active scientific effort. Previously, we have devised a novel isotopic labeling approach for membrane lipids to enable direct in vivo structural studies of the cell membrane in the Gram-positive bacterium, Bacillus subtilis, using small-angle neutron scattering. This was accomplished through a genetic inhibition of fatty acid (FA) degradation (ΔfadN) and a chemical inhibition of FA biosynthesis using cerulenin, an irreversible inhibitor of type II fatty acid synthases. Here, we improve upon the previous system by introducing a dCas9/sgRNA-fabF complex that blocks transcription of the essential fabF gene when under xylose induction. This leads to greater sensitivity to cerulenin in the mutant strain (JEBS102) and more robust cell growth when supplementary FAs are introduced to the culture medium. A subtle change in FA uptake is noted when compared to the prior labeling strategy. This is seen in the gas chromatography/mass spectrometry (GC/MS) data as a higher ratio of n16:0 to a15:0, and manifests in an apparent increase in the membrane thickness determined via neutron scattering. This represents an improved method of isotopic labeling for the cell membrane of Bacillus subtilis; enabling improved investigations of cellular uptake and utilization of FAs, cell membrane structure and organization as a phenotypic response to metabolic and environmental changes.

Mycobacterial resistance to zinc poisoning requires assembly of P-ATPase-containing membrane metal efflux platforms

The human pathogen Mycobacterium tuberculosis requires a P_1B-ATPase metal exporter, CtpC (Rv3270), for resistance to zinc poisoning. Here, we show that zinc resistance also depends on a chaperone-like protein, PacL1 (Rv3269). PacL1 contains a transmembrane domain, a cytoplasmic region with glutamine/alanine repeats and a C-terminal metal-binding motif (MBM). PacL1 binds Zn²⁺, but the MBM is required only at high zinc concentrations. PacL1 co-localizes with CtpC in dynamic foci in the mycobacterial plasma membrane, and the two proteins form high molecular weight complexes. Foci formation does not require flotillin nor the PacL1 MBM. However, deletion of the PacL1 Glu/Ala repeats leads to loss of CtpC and sensitivity to zinc. Genes pacL1 and ctpC appear to be in the same operon, and homologous gene pairs are found in the genomes of other bacteria. Furthermore, PacL1 colocalizes and functions redundantly with other PacL orthologs in M. tuberculosis. Overall, our results indicate that PacL proteins may act as scaffolds that assemble P-ATPase-containing metal efflux platforms mediating bacterial resistance to metal poisoning.

The human pathogen Mycobacterium tuberculosis requires a metal exporter, CtpC, for resistance to zinc poisoning. Here, the authors show that zinc resistance also depends on a chaperone-like protein that binds zinc ions, forms high-molecular-weight complexes with CtpC in the cytoplasmic membrane, and is required for CtpC function.

Membranes under the Magnetic Lens: A Dive into the Diverse World of Membrane Protein Structures Using Cryo-EM

Membrane proteins are highly diverse in both structure and function and can, therefore, present different challenges for structure determination. They are biologically important for cells and organisms as gatekeepers for information and molecule transfer across membranes, but each class of membrane proteins can present unique obstacles to structure determination. Historically, many membrane protein structures have been investigated using highly engineered constructs or using larger fusion proteins to improve solubility and/or increase particle size. Other strategies included the deconstruction of the full-length protein to target smaller soluble domains. These manipulations were often required for crystal formation to support X-ray crystallography or to circumvent lower resolution due to high noise and dynamic motions of protein subdomains. However, recent revolutions in membrane protein biochemistry and cryo-electron microscopy now provide an opportunity to solve high resolution structures of both large, >1 megadalton (MDa), and small, <100 kDa (kDa), drug targets in near-native conditions, routinely reaching resolutions around or below 3 Å. This review provides insights into how the recent advances in membrane biology and biochemistry, as well as technical advances in cryo-electron microscopy, help us to solve structures of a large variety of membrane protein groups, from small receptors to large transporters and more complex machineries.

Multiscale lipid membrane dynamics as revealed by neutron spectroscopy

The plasma membrane is one of the principal structural components of the cell and, therefore, one of the key components of the cellular life. Because the membrane's dynamics links the membrane's structure and function, the complexity and the broad range of the membrane's motions are essential for the enormously diverse functionality of the cell membrane. Even for the main membrane component, the lipid bilayer, considered alone, the range and complexity of the lipid motions are remarkable. Spanning the time scale from sub-picosecond to minutes and hours, the lipid motion in a bilayer is challenging to study even when a broad array of dynamic measurement techniques is employed. Neutron scattering plays a special role among such dynamic measurement techniques, particularly, because it involves the energy transfers commensurate with the typical intra- and inter- molecular dynamics and the momentum transfers commensurate with intra- and inter-molecular distances. Thus, using neutron scattering-based techniques, the spatial and temporal information on the lipid motion can be obtained and analysed simultaneously. Protium vs. deuterium sensitivity and non-destructive character of the neutron probe add to the remarkable prowess of neutron scattering for elucidating the lipid dynamics. Herein we present an overview of the neutron scattering-based studies of lipid dynamics in model membranes, with a discussion of the direct relevance and implications to the real-life cell membranes. The latter are much more complex systems than simple model membranes, consisting of heterogeneous non-stationary domains composed of lipids, proteins, and other small molecules, such as carbohydrates. Yet many fundamental aspects of the membrane behavior and membrane interactions with other molecules can be understood from neutron scattering measurements of the model membranes. For example, such studies can provide a great deal of information on the interactions of antimicrobial compounds with the lipid matrix of a pathogen membrane, or the interactions of drug molecules with the plasma membrane. Finally, we briefly discuss the recently emerging field of neutron scattering membrane studies with a reach far beyond the model membrane systems.

Physicochemical characteristics of droplet interface bilayers

Droplet interface bilayer (DIB) is a lipid bilayer formed when two lipid monolayer-coated aqueous droplets are brought in contact within an oil phase. DIBs, especially post functionalization, are a facile model system to study the biophysics of the cell membrane. Continued advances in enhancing and functionalizing DIBs to be a faithful cell membrane mimetic requires a deep understanding of the physicochemical characteristics of droplet interface bilayers. In this review, we provide a comprehensive overview of the current scientific understanding of DIB characteristics starting with the key experimental frameworks for DIB generation, visualization and functionalization. Subsequently we report experimentally measured physical, electrical and transport characteristics of DIBs across physiologically relevant lipids. Advances in simulations and mathematical modelling of DIBs are also discussed, with an emphasis on revealing principles governing the key physicochemical characteristics. Finally, we conclude the review with important outstanding questions in the field.

CHESS: The future direct geometry spectrometer at the second target station

CHESS, chopper spectrometer examining small samples, is a planned direct geometry neutron chopper spectrometer designed to detect and analyze weak signals intrinsic to small cross sections (e.g., small mass, small magnetic moments, or neutron absorbing materials) in powders, liquids, and crystals. CHESS is optimized to enable transformative investigations of quantum materials, spin liquids, thermoelectrics, battery materials, and liquids. The broad dynamic range of the instrument is also well suited to study relaxation processes and excitations in soft and biological matter. The 15 Hz repetition rate of the Second Target Station at the Spallation Neutron Source enables the use of multiple incident energies within a single source pulse, greatly expanding the information gained in a single measurement. Furthermore, the high flux grants an enhanced capability for polarization analysis. This enables the separation of nuclear from magnetic scattering or coherent from incoherent scattering in hydrogenous materials over a large range of energy and momentum transfer. This paper presents optimizations and technical solutions to address the key requirements envisioned in the science case and the anticipated uses of this instrument.

Small-angle neutron scattering contrast variation studies of biological complexes: Challenges and triumphs

Small-angle neutron scattering (SANS) has been a beneficial tool for studying the structure of biological macromolecules in solution for several decades. Continued improvements in sample preparation techniques, including deuterium labeling, neutron instrumentation and complementary techniques such as small-angle x-ray scattering (SAXS), cryo-EM, NMR and x-ray crystallography, along with the availability of more powerful structure prediction algorithms and computational resources has made SANS more important than ever as a means to obtain unique information on the structure of biological complexes in solution. In particular, the contrast variation (CV) technique, which requires a large commitment in both sample preparation and measurement time, has become more practical with the advent of these improved resources. Here, challenges and recent triumphs as well as future prospects are discussed.

Absorption of the [bmim][Cl] Ionic Liquid in DMPC Lipid Bilayers across Their Gel, Ripple, and Fluid Phases

Lipid bilayers are a key component of cell membranes and play a crucial role in life and in bio-nanotechnology. As a result, controlling their physicochemical properties holds the promise of effective therapeutic strategies. Ionic liquids (ILs)—a vast class of complex organic electrolytes—have shown a high degree of affinity with lipid bilayers and can be exploited in this context. However, the chemical physics of IL absorption and partitioning into lipid bilayers is yet to be fully understood. This work focuses on the absorption of the model IL [bmim][Cl] into 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayers across their gel, ripple, and fluid phases. Here, by small-angle neutron scattering, we show that (i) the IL cations are absorbed in the lipid bilayer in all its thermodynamic phases and (ii) the amount of IL inserted into the lipid phase increased with increasing temperature, changing from three to four IL cations per 10 lipids with increasing temperature from 10 °C in the gel phase to 40 °C in the liquid phase, respectively. An explicative hypothesis, based on the entropy gain coming from the IL hydration water, is presented to explain the observed temperature trend. The ability to control IL absorption with temperature can be used as a handle to tune the effect of ILs on biomembranes and can be exploited in bio-nanotechnological applications.

Fluidity is the way to life: lipid phase separation in bacterial membranes

A hallmark of biological membranes is the dynamic localization of lipids and proteins. Lipids respond to temperature reduction below a critical point with phase separation, and poikilothermic animals and also bacteria adapt their lipid content to prevent gel phase formation in membranes. In a new study, Gohrbandt et al (2022) show that reduced membrane fluidity in bacterial cells causes reversible phase separation without membrane rupture in vivo, highlighting the physical robustness of biological membranes.

Interaction of a Short Antimicrobial Peptide on Charged Lipid Bilayer: A Case Study on Aurein 1.2 Peptide

Aurein 1.2 (aurein) is a short but active α-helical antimicrobial peptide discovered in Australian tree frogs (Litoria aurea). It shows inhibition on a broad spectrum of bacteria and cancer cells. With well-defined helicity, amphipathicity, and cationic charges, it readily binds to membranes and causes membrane change and disruption. This study provides details on how aurein interacts with charged lipid membranes by using neutron membrane diffraction (NMD) and neutron spin echo (NSE) spectroscopy on complex peptide-membrane systems. NMD provides higher resolution lipid bilayer structures than solution scattering. NMD revealed the peptide is mostly associated in the lipid headgroup region. Even at moderately high concentrations (e.g., peptide:lipid ratio of 1:30), aurein is located at the acyl chain-headgroup region without deep penetration into the hydrophobic acyl chain. However, it does reduce the elasticity of the membrane at that concentration, which was corroborated by the NSE results. Furthermore, NSE shows that aurein first softens the membrane, like many other α-helical peptides at low concentration, but then makes the membrane much more rigid, even without membrane pore formation. Combining our previous studies, the evidence shows that aurein at relatively low concentrations still modifies lipid distribution significantly and can cause membrane thinning and lateral segregation of charged lipids. At the same time, the membrane's mechanical properties are modified with much slower lipid diffusion. This suggests that aurein can attack the microbial membrane without the need to form membrane pores or disintegrate membranes; instead, it promotes the formation of domains at low concentration.

Recent advances in small-angle scattering and its expanding impact in structural biology

Applications of small-angle scattering (SAS) in structural biology have benefited from continuing developments in instrumentation, tools for data analysis, modeling capabilities, standards for data and model presentation, and data archiving. The interplay of these capabilities has enabled SAS to contribute to advances in structural biology as the field pushes the boundaries in studies of biomolecular complexes and assemblies as large as whole cells, membrane proteins in lipid environments, and dynamic systems on time scales ranging from femtoseconds to hours. This review covers some of the important advances in biomolecular SAS capabilities for structural biology focused on over the last 5 years and presents highlights of recent applications that demonstrate how the technique is exploring new territories.

Membrane Domain Localization and Interaction of the Prion-Family Proteins, Prion and Shadoo with Calnexin

The cellular prion protein (PrP^C) is renowned for its infectious conformational isoform PrP^Sc, capable of templating subsequent conversions of healthy PrP^Cs and thus triggering the group of incurable diseases known as transmissible spongiform encephalopathies. Besides this mechanism not being fully uncovered, the protein’s physiological role is also elusive. PrP^C and its newest, less understood paralog Shadoo are glycosylphosphatidylinositol-anchored proteins highly expressed in the central nervous system. While they share some attributes and neuroprotective actions, opposing roles have also been reported for the two; however, the amount of data about their exact functions is lacking. Protein–protein interactions and membrane microdomain localizations are key determinants of protein function. Accurate identification of these functions for a membrane protein, however, can become biased due to interactions occurring during sample processing. To avoid such artifacts, we apply a non-detergent-based membrane-fractionation approach to study the prion protein and Shadoo. We show that the two proteins occupy similarly raft and non-raft membrane fractions when expressed in N2a cells and that both proteins pull down the chaperone calnexin in both rafts and non-rafts. These indicate their possible binding to calnexin in both types of membrane domains, which might be a necessary requisite to aid the inherently unstable native conformation during their lifetime.

Molecular Organization of a Raft-like Domain in a Polyunsaturated Phospholipid Bilayer: A Supervised Machine Learning Analysis of Molecular Dynamics Simulations

Numerous health benefits are associated with omega-3 polyunsaturated fatty acids (n-3 PUFA) consumed in fish oils. An understanding of the mechanism remains elusive. The plasma membrane as a site of action is the focus in this study. With large-scale all-atom MD simulations run on a model membrane (1050 lipid molecules), we observed the evolution over time (6 μs) of a circular (raft-like) domain composed of N-palmitoylsphingomyelin (PSM) and cholesterol embedded into a surrounding (non-raft) patch composed of polyunsaturated 1-palmitoyl-2-docosahexaenoylphosphatylcholine (PDPC) (1:1:1 mol). A supervised machine learning algorithm was developed to characterize the migration of each lipid based on molecular conformation and the local environment. PDPC molecules were seen to infiltrate the ordered raft-like domain in a small amount, while a small concentration of PSM and cholesterol molecules was seen to migrate into the disordered non-raft region. Enclosing the raft-like domain, a narrow (∼2 nm in width) interfacial zone composed of PDPC, PSM, and cholesterol that buffers the substantial difference in order (ΔS_CD ≈ 0.12) between raft-like and non-raft environments was seen to form. Our results suggest that n-3 PUFA regulate the architecture of lipid rafts enriched in sphingolipids and cholesterol with a minimal effect on order within their interior in membranes.

Deciphering lipid transfer between and within membranes with time-resolved small-angle neutron scattering

This review focuses on time-resolved neutron scattering, particularly time-resolved small angle neutron scattering (TR-SANS), as a powerful in situ noninvasive technique to investigate intra- and intermembrane transport and distribution of lipids and sterols in lipid membranes. In contrast to using molecular analogues with potentially large chemical tags that can significantly alter transport properties, small angle neutron scattering relies on the relative amounts of the two most abundant isotope forms of hydrogen: protium and deuterium to detect complex membrane architectures and transport processes unambiguously. This review discusses advances in our understanding of the mechanisms that sustain lipid asymmetry in membranes-a key feature of the plasma membrane of cells-as well as the transport of lipids between membranes, which is an essential metabolic process.

Fed-batch production of deuterated protein in Escherichia coli for neutron scattering experimentation

Neutron scattering is a powerful technique for determining the structure and dynamics of biological materials in a variety of environmental conditions. A distinguishing property of the neutron is its sensitivity to detecting hydrogen and distinguishing it from its isotope deuterium. This enables unique types of experiments that take advantage of this differential sensitivity called isotopic contrast variation. Using this approach, the chemistry of the system is not changed, but the visibility of individual sample components can be tuned by varying the deuterium content of the system under investigation. Deuterated proteins are commonly produced in bacterial systems that are adapted to growth in D₂O minimal media. To maximize the yield of deuterium-labeled protein and efficiently utilize D₂O and occasionally the deuterated substrate, fed-batch processes are routinely used to maximize biomass production without compromising cell viability. A step-by-step procedure will be described along with a case study of the production of deuterated green fluorescent protein. Limitations of the process will also be discussed.

An Stomatin, Prohibitin, Flotillin, and HflK/C-Domain Protein Required to Link the Phage-Shock Protein to the Membrane in Bacillus subtilis

Membrane surveillance and repair is of utmost importance to maintain cellular integrity and allow cellular life. Several systems detect cell envelope stress caused by antimicrobial compounds and abiotic stresses such as solvents, pH-changes and temperature in bacteria. Proteins containing an Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH)-domain, including bacterial flotillins have been shown to be involved in membrane protection and membrane fluidity regulation. Here, we characterize a bacterial SPFH-domain protein, YdjI that is part of a stress induced complex in Bacillus subtilis. We show that YdjI is required to localize the ESCRT-III homolog PspA to the membrane with the help of two membrane integral proteins, YdjG/H. In contrast to classical flotillins, YdjI resides in fluid membrane regions and does not enrich in detergent resistant membrane fractions. However, similarly to FloA and FloT from B. subtilis, deletion of YdjI decreases membrane fluidity. Our data reveal a hardwired connection between phage shock response and SPFH proteins.

Amphipathic Peptides Impede Lipid Domain Fusion in Phase-Separated Membranes

Cell membranes are heterogeneous in lipid composition which leads to the phase separation with the formation of nanoscopic liquid-ordered domains, also called rafts. There are multiple cell processes whereby the clustering of these domains into a larger one might be involved, which is responsible for such important processes as signal transduction, polarized sorting, or immune response. Currently, antimicrobial amphipathic peptides are considered promising antimicrobial, antiviral, and anticancer therapeutic agents. Here, within the framework of the classical theory of elasticity adapted for lipid membranes, we investigate how the presence of the peptides in a phase-separated membrane influences the fusion of the domains. We show that the peptides tend to occupy the boundaries of liquid-ordered domains and significantly increase the energy barrier of the domain-domain fusion, which might lead to misregulation of raft clustering and adverse consequences for normal cell processes.

Studying the surfaces of bacteria using neutron scattering: finding new openings for antibiotics

The use of neutrons as a scattering probe to investigate biological membranes has steadily grown in the past three decades, shedding light on the structure and behaviour of this ubiquitous and fundamental biological barrier. Meanwhile, the rise of antibiotic resistance has catalysed a renewed interest in understanding the mechanisms underlying the dynamics of antibiotics interaction with the bacterial cell envelope. It is widely recognised that the key reason behind the remarkable success of Gram-negative pathogens in developing antibiotic resistance lies in the effectiveness of their outer membrane (OM) in defending the cell from antibacterial compounds. Critical to its function, the highly asymmetric lipid distribution between the inner and outer bilayer leaflets of the OM, adds an extra level of complexity to the study of this crucial defence barrier. Here we review the opportunities offered by neutron scattering techniques, in particular reflectometry, to provide structural information on the interactions of antimicrobials with in vitro models of the OM. The differential sensitivity of neutrons towards hydrogen and deuterium makes them a unique probe to study the structure and behaviour of asymmetric membranes. Molecular-level understanding of the interactions between antimicrobials and the Gram-negative OM provides valuable insights that can aid drug development and broaden our knowledge of this critically important biological barrier.

The dynamic face of lipid membranes

Cell membranes - primarily composed of lipids, sterols, and proteins - form a dynamic interface between living cells and their environment. They act as a mechanical barrier around the cell while selectively facilitating material transport, signal transduction, and various other functions necessary for the cell viability. The complex functionality of cell membranes and the hierarchical motions and responses they exhibit demand a thorough understanding of the origin of different membrane dynamics and how they are influenced by molecular additives and environmental cues. These dynamic modes include single-molecule diffusion, thermal fluctuations, and large-scale membrane deformations, to name a few. This review highlights advances in investigating structure-driven dynamics associated with model cell membranes, with a particular focus on insights gained from neutron scattering and spectroscopy experiments. We discuss the uniqueness of neutron contrast variation and its remarkable potential in probing selective membrane structure and dynamics on spatial and temporal scales over which key biological functions occur. We also present a summary of current and future opportunities in synergistic combinations of neutron scattering with molecular dynamics (MD) simulations to gain further understanding of the molecular mechanisms underlying complex membrane functions.

Lipids, membranes, colloids and cells: A long view

This paper revisits long-standing ideas about biological membranes in the context of an equally long-standing, but hitherto largely unappreciated, perspective of the cell based on concepts derived from the physics and chemistry of colloids. Specifically, we discuss important biophysical aspects of lipid supramolecular structure to understand how the intracellular milieu may constrain lipid self-assembly. To this end we will develop four lines of thought: first, we will look at the historical development of the current view of cellular structure and physiology, considering also the plurality of approaches that influenced its formative period. Second, we will review recent basic research on the structural and dynamical properties of lipid aggregates as well as the role of phase transitions in biophysical chemistry and cell biology. Third, we will present a general overview of contemporary studies into cellular compartmentalization in the context of a very rich and mostly forgotten general theory of cell physiology called the Association-Induction Hypothesis, which was developed around the time that the current view of cells congealed into its present form. Fourth, we will examine some recent developments in cellular studies, mostly from our laboratory, that raise interesting issues about the dynamical aspects of cell structure and compartmentalization. We will conclude by suggesting what we consider are relevant questions about the nature of cellular processes as emergent phenomena.

Morphologies and Structure of Brain Lipid Membrane Dispersions

This study aims to explore the variety of previously unknown morphologies that brain lipids form in aqueous solutions. We study how these structures are dependent on cholesterol content, salt solution composition, and temperature. For this purpose, dispersions of porcine sphingomyelin with varying amounts of cholesterol as well as dispersions of porcine brain lipid extracts were investigated. We used cryo-TEM to investigate the dispersions at high-salt solution content together with small-angle (SAXD) and wide-angle X-ray diffraction (WAXD) and differential scanning calorimetry (DSC) for dispersions in the corresponding salt solution at high lipid content. Sphingomyelin forms multilamellar vesicles in large excess of aqueous salt solution. These vesicles appear as double rippled bilayers in the images and as split Bragg peaks in SAXD together with a very distinct lamellar phase pattern. These features disappear with increasing temperature, and addition of cholesterol as the WAXD data shows that the peak corresponding to the chain crystallinity disappears. The dispersions of sphingomyelin at high cholesterol content form large vesicular type of structures with smooth bilayers. The repeat distance of the lamellar phase depends on temperature, salt solution composition, and slightly with cholesterol content. The brain lipid extracts form large multilamellar vesicles often attached to assemblies of higher electron density. We think that this is probably an example of supra self-assembly with a multiple-layered vesicle surrounding an interior cubic microphase. This is challenging to resolve. DSC shows the presence of different kinds of water bound to the lipid aggregates as a function of the lipid content. Comparison with the effect of lithium, sodium, and calcium salts on the structural parameters of the sphingomyelin and the morphologies of brain lipid extract morphologies demonstrate that lithium has remarkable effects also at low content.

Dynamic "Molecular Portraits" of Biomembranes Drawn by Their Lateral Nanoscale Inhomogeneities

To date, it has been reliably shown that the lipid bilayer/water interface can be thoroughly characterized by a sophisticated so-called "dynamic molecular portrait". The latter reflects a combination of time-dependent surface distributions of various physicochemical properties, inherent in both model lipid bilayers and natural multi-component cell membranes. One of the most important features of biomembranes is their mosaicity, which is expressed in the constant presence of lateral inhomogeneities, the sizes and lifetimes of which vary in a wide range-from 1 to 10³ nm and from 0.1 ns to milliseconds. In addition to the relatively well-studied macroscopic domains (so-called "rafts"), the analysis of micro- and nanoclusters (or domains) that form an instantaneous picture of the distribution of structural, dynamic, hydrophobic, electrical, etc., properties at the membrane-water interface is attracting increasing interest. This is because such nanodomains (NDs) have been proven to be crucial for the proper membrane functioning in cells. Therefore, an understanding with atomistic details the phenomena associated with NDs is required. The present mini-review describes the recent results of experimental and in silico studies of spontaneously formed NDs in lipid membranes. The main attention is paid to the methods of ND detection, characterization of their spatiotemporal parameters, the elucidation of the molecular mechanisms of their formation. Biological role of NDs in cell membranes is briefly discussed. Understanding such effects creates the basis for rational design of new prospective drugs, therapeutic approaches, and artificial membrane materials with specified properties.

Computer simulations of a heterogeneous membrane with enhanced sampling techniques

Computational determination of the equilibrium state of heterogeneous phospholipid membranes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in membranes are long compared to typical time scales of computer simulations. Here, we evaluate the combination of the enhanced sampling techniques molecular dynamics with alchemical steps and Monte Carlo with molecular dynamics with a coarse-grained model of membranes (Martini) to reduce the number of steps and force evaluations that are needed to reach equilibrium. We illustrate a significant gain compared to straightforward molecular dynamics of the Martini model by factors between 3 and 10. The combination is a useful tool to enhance the study of phase separation and the formation of domains in biological membranes.

Biomembrane Structure and Material Properties Studied With Neutron Scattering

Cell membranes and their associated structures are dynamical supramolecular structures where different physiological processes take place. Detailed knowledge of their static and dynamic structures is therefore needed, to better understand membrane biology. The structure–function relationship is a basic tenet in biology and has been pursued using a range of different experimental approaches. In this review, we will discuss one approach, namely the use of neutron scattering techniques as applied, primarily, to model membrane systems composed of lipid bilayers. An advantage of neutron scattering, compared to other scattering techniques, is the differential sensitivity of neutrons to isotopes of hydrogen and, as a result, the relative ease of altering sample contrast by substituting protium for deuterium. This property makes neutrons an ideal probe for the study of hydrogen-rich materials, such as biomembranes. In this review article, we describe isotopic labeling studies of model and viable membranes, and discuss novel applications of neutron contrast variation in order to gain unique insights into the structure, dynamics, and molecular interactions of biological membranes. We specifically focus on how small-angle neutron scattering data is modeled using different contrast data and molecular dynamics simulations. We also briefly discuss neutron reflectometry and present a few recent advances that have taken place in neutron spin echo spectroscopy studies and the unique membrane mechanical data that can be derived from them, primarily due to new models used to fit the data.

Evolution of the analytical scattering model of live Escherichia coli

A previously reported multi-scale model for (ultra-)small-angle X-ray (USAXS/SAXS) and (very) small-angle neutron scattering (VSANS/SANS) of live Escherichia coli was revised on the basis of compositional/metabolomic and ultrastructural constraints. The cellular body is modeled, as previously described, by an ellipsoid with multiple shells. However, scattering originating from flagella was replaced by a term accounting for the oligosaccharide cores of the lipopolysaccharide leaflet of the outer membrane including its cross-term with the cellular body. This was mainly motivated by (U)SAXS experiments showing indistinguishable scattering for bacteria in the presence and absence of flagella or fimbrae. The revised model succeeded in fitting USAXS/SAXS and differently contrasted VSANS/SANS data of E. coli ATCC 25922 over four orders of magnitude in length scale. Specifically, this approach provides detailed insight into structural features of the cellular envelope, including the distance of the inner and outer membranes, as well as the scattering length densities of all bacterial compartments. The model was also successfully applied to E. coli K12, used for the authors' original modeling, as well as for two other E. coli strains. Significant differences were detected between the different strains in terms of bacterial size, intermembrane distance and its positional fluctuations. These findings corroborate the general applicability of the approach outlined here to quantitatively study the effect of bactericidal compounds on ultrastructural features of Gram-negative bacteria without the need to resort to any invasive staining or labeling agents.

Research and application of hydrostatic high pressure in tumor vaccines (Review)

It is well known that hydrostatic pressure (HP) is a physical parameter that is now regarded as an important variable for life. High hydrostatic pressure (HHP) technology has influenced biological systems for more than 100 years. Food and bioscience researchers have shown great interest in HHP technology over the past few decades. The development of knowledge related to this area can better facilitate the application of HHP in the life sciences. Furthermore, new applications for HHP may come from these current studies, particularly in tumor vaccines. Currently, cancer recurrence and metastasis continue to pose a serious threat to human health. The limited efficacy of conventional treatments has led to the need for breakthroughs in immunotherapy and other related areas. Research into tumor vaccines is providing new insights for cancer treatment. The purpose of this review is to present the main findings reported thus far in the relevant scientific literature, focusing on knowledge related to HHP technology and tumor vaccines, and to demonstrate the potential of applying HHP technology to tumor vaccine development.

Increasing complexity in small-angle X-ray and neutron scattering experiments: from biological membrane mimics to live cells

Small-angle X-ray and neutron scattering are well-established, non-invasive experimental techniques to interrogate global structural properties of biological membrane mimicking systems under physiologically relevant conditions. Recent developments, both in bottom-up sample preparation techniques for increasingly complex model systems, and in data analysis techniques have opened the path toward addressing long standing issues of biological membrane remodelling processes. These efforts also include emerging quantitative scattering studies on live cells, thus enabling a bridging of molecular to cellular length scales. Here, we review recent progress in devising compositional models for joint small-angle X-ray and neutron scattering studies on diverse membrane mimics - with a specific focus on membrane structural coupling to amphiphatic peptides and integral proteins - and live Escherichia coli. In particular, we outline the present state-of-the-art in small-angle scattering methods applied to complex membrane systems, highlighting how increasing system complexity must be followed by an advance in compositional modelling and data-analysis tools.

Impact of antimicrobial peptides on E. coli-mimicking lipid model membranes: correlating structural and dynamic effects using scattering methods

Using X-rays and neutrons we address the effect of AMPs on structure and dynamics of lipids in bacterial model membranes.

Implementation of a self-consistent slab model of bilayer structure in the SasView suite

Slab models are simple and useful structural descriptions which have long been used to describe lyotropic lamellar phases, such as lipid bilayers. Typically, slab models assume a midline symmetry and break a bilayer structure into three pieces, a central solvent-free core and two symmetric outer layers composed of the soluble portion of the amphiphile and associated solvent. This breakdown matches reasonably well to the distribution of neutron scattering length density and therefore is a convenient and common approach for the treatment of small-angle scattering data. Here, an implementation of this model within the SasView software suite is reported. The implementation is intended to provide physical consistency through the area per amphiphile molecule and number of solvent molecules included within the solvent-exposed outer layer. The proper use of this model requires knowledge of (or good estimates for) the amphiphile and solvent molecule volume and atomic composition, ultimately providing a self-consistent data treatment with only two free parameters: the lateral area per amphiphile molecule and the number of solvent molecules included in the outer region per amphiphile molecule. The use of this code is demonstrated in the fitting of standard lipid bilayer data sets, obtaining structural parameters consistent with prior literature and illustrating the typical and ideal cases of fitting for neutron scattering data obtained using single or multiple contrast conditions. While demonstrated here for lipid bilayers, this model is intended for general application to block copolymers, surfactants, and other lyotropic lamellar phase structures for which a slab model is able to reasonably estimate the neutron scattering length density/electron-density profile of inner and outer layers of the lamellae.

Understanding the Structure and Dynamics of Complex Biomembrane Interactions by Neutron Scattering Techniques

The membrane is one of the key structural materials of biology at the cellular level. Composed predominantly of a bilayer of lipids with embedded and bound proteins, it defines the boundaries of the cell and many organelles essential to life and therefore is involved in almost all biological processes. Membrane-specific interactions, such as drug binding to a membrane receptor or the interactions of an antimicrobial compound with the lipid matrix of a pathogen membrane, are of interest across the scientific disciplines. Herein we present a review, aimed at nonexperts, of the major neutron scattering techniques used in membrane studies: small-angle neutron scattering, neutron membrane diffraction, neutron reflectometry, quasielastic neutron scattering, and neutron spin echo. Neutron scattering techniques are well suited to studying biological membranes. The nondestructive nature of cold neutrons means that samples can be measured for long periods without fear of beam damage from ultraviolet, electron, or X-ray radiation, and neutron beams are highly penetrating, thus offering flexibility in samples and sample environments. Most important is the strong difference in neutron scattering lengths between the two most abundant forms of hydrogen, protium and deuterium. Changing the relative amounts of protium/deuterium in a sample allows the production of a series of neutron scattering data sets, enabling the observation of differing components within complex membrane architectures. This approach can be as simple as using the naturally occurring neutron contrast between different biomolecules to study components in a complex by changing the solution H₂O/D₂O ratio or as complex as selectively labeling individual components with hydrogen isotopes. This review presents an overview of each experimental technique with the neutron instrument configuration, related sample preparation and sample environment, and data analysis, highlighted by a special emphasis on using prominent neutron contrast to understand structure and dynamics. This review gives researchers a practical introduction to the often enigmatic suite of neutron beamlines, thereby lowering the barrier to taking advantage of these large-facility techniques to achieve new understandings of membranes and their interactions with other molecules.

Dioxin impacts on lipid metabolism of soil microbes: towards effective detection and bioassessment strategies

Dioxins are the most toxic known environmental pollutants and are mainly formed by human activities. Due to their structural stability, dioxins persist for extended periods and can be transported over long distances from their emission sources. Thus, dioxins can be accumulated to considerable levels in both human and animal food chains. Along with sediments, soils are considered the most important reservoirs of dioxins. Soil microorganisms are therefore highly exposed to dioxins, leading to a range of biological responses that can impact the diversity, genetics and functional of such microbial communities. Dioxins are very hydrophobic with a high affinity to lipidic macromolecules in exposed organisms, including microbes. This review summarizes the genetic, molecular and biochemical impacts of dioxins on the lipid metabolism of soil microbial communities and especially examines modifications in the composition and architecture of cell membranes. This will provide a useful scientific benchmark for future attempts at soil ecological risk assessment, as well as in identifying potential dioxin-specific-responsive lipid biomarkers. Finally, potential uses of lipid-sequestering microorganisms as a part of biotechnological approaches to the bio-management of environmental contamination with dioxins are discussed.

Melatonin Alters Fluid Phase Coexistence in POPC/DPPC/Cholesterol Membranes

The structure and biophysical properties of lipid membranes are important for cellular functions in health and disease. In Alzheimer's disease, the neuronal membrane is a target for toxic amyloid-β (Aβ). Melatonin is an important pineal gland hormone that has been shown to protect against Aβ toxicity in cellular and animal studies, but the molecular mechanism of this protection is not fully understood. Melatonin is a small membrane-active molecule that has been shown to interact with model lipid membranes and alter the membrane biophysical properties, such as membrane molecular order and dynamics. This effect of melatonin has been previously studied in simple model bilayers with one or two lipid components. To make it more relevant to neuronal membranes, we used a more complex ternary lipid mixture as our membrane model. In this study, we used ²H-NMR to investigate the effect of melatonin on the phase behavior of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and cholesterol lipid membranes. We used deuterium-labeled POPC-d₃₁ and DPPC-d₆₂,separately to probe the changes in hydrocarbon chain order as a function of temperature and melatonin concentration. We find that POPC/DPPC/cholesterol at molar proportions of 3:3:2 is close to liquid-disordered/liquid-ordered phase separation and that melatonin can induce phase separation in these ternary mixtures by preferentially incorporating into the disordered phase and increasing its level of disorder. At 5 mol% melatonin, we observed phase separation in samples with POPC-d₃₁, but not with DPPC-d₆₂, whereas at 10 mol% melatonin, phase separation was observed in both samples with either POPC-d₃₁ or DPPC-d₆₂. These results indicate that melatonin can have a strong effect on membrane structure and physical properties, which may provide some clues to understanding how melatonin protects against Aβ, and that choice of chain perdeuteration is an important consideration from a technical point of view.

A combined molecular/continuum-modeling approach to predict the small-angle neutron scattering of curved membranes

This paper develops a framework to compute the small-angle neutron scattering (SANS) from highly curved, dynamically fluctuating, and potentially inhomogeneous membranes. This method is needed to compute the scattering from nanometer-scale membrane domains that couple to curvature, as predicted by molecular modeling. The detailed neutron scattering length density of a small planar bilayer patch is readily available via molecular dynamics simulation. A mathematical, mechanical transformation of the planar scattering length density is developed to predict the scattering from curved bilayers. By simulating a fluctuating, curved, surface-continuum model, long time- and length-scales can be reached while, with the aid of the planar-to-curved transformation, the molecular features of the scattering length density can be retained. A test case for the method is developed by constructing a coarse-grained lipid vesicle following a protocol designed to relieve both the osmotic stress inside the vesicle and the lipid-number stress between the leaflets. A question was whether the hybrid model would be able to replicate the scattering from the highly deformed inner and outer leaflets of the small vesicle. Matching the scattering of the full (molecular vesicle) and hybrid (continuum vesicle) models indicated that the inner and outer leaflets of the full vesicle were expanded laterally, consistent with previous simulations of the Martini forcefield that showed thinning in small vesicles. The vesicle structure is inconsistent with a zero-tension leaflet deformed by a single set of elastic parameters, and the results show that this is evident in the scattering. The method can be applied to translate observations of any molecular model's neutron scattering length densities from small patches to large length and timescales.

Double membrane formation in heterogeneous vesicles

Lipids are capable of forming a variety of structures, including multi-lamellar vesicles. Layered lipid membranes are found in cell organelles, such as autophagosomes and mitochondria. Here, we present a mechanism for the formation of a double-walled vesicle (i.e., two lipid bilayers) from a unilamellar vesicle through the partitioning and phase separation of a small molecule. Using molecular dynamics simulations, we show that double membrane formation proceeds via a nucleation and growth process - i.e., after a critical concentration of the small molecules, a patch of double membrane nucleates and grows to cover the entire vesicle. We discuss the implications of this mechanism and theoretical approaches for understanding the evolution and formation of double membranes.

Lateral heterogeneity and domain formation in cellular membranes

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Review article describing recent experimental and theoretical membrane lateral heterogeneity research.

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Describes the static and dynamic physical concepts behind domain formation in model membranes.

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Describes coarse-grained, phenomenological approaches that result in phases associated with lipid lateral heterogeneity.

As early as the development of the fluid mosaic model for cellular membranes, researchers began observing the telltale signs of lateral heterogeneity. Over the decades this has led to the development of the lipid raft hypothesis and the ensuing controversy that has unfolded, as a result. Here, we review the physical concepts behind domain formation in lipid membranes, both of their structural and dynamic origins. This, then leads into a discussion of coarse-grained, phenomenological approaches that describe the wide range of phases associated with lipid lateral heterogeneity. We use these physical concepts to describe the interaction between raft-lipid species, such as long-chain saturated lipids, sphingomyelin, and cholesterol, and non-raft forming lipids, such as those with short acyl chains or unsaturated fatty acids. While debate has persisted on the biological relevance of lipid domains, recent research, described here, continues to identify biological roles for rafts and new experimental approaches have revealed the existence of lipid domains in living systems. Given the recent progress on both the biological and structural aspects of raft formation, the research area of membrane lateral heterogeneity will not only expand, but will continue to produce exciting results.

Asymmetric bilayers mimicking membrane rafts prepared by lipid exchange: Nanoscale characterization using AFM-Force spectroscopy

Sphingolipids-enriched rafts domains are proposed to occur in plasma membranes and to mediate important cellular functions. Notwithstanding, the asymmetric transbilayer distribution of phospholipids that exists in the membrane confers the two leaflets different potentials to form lateral domains as next to no sphingolipids are present in the inner leaflet. How the physical properties of one leaflet can influence the properties of the other and its importance on signal transduction across the membrane are questions still unresolved. In this work, we combined AFM imaging and Force spectroscopy measurements to assess domain formation and to study the nanomechanical properties of asymmetric supported lipid bilayers (SLBs) mimicking membrane rafts. Asymmetric SLBs were formed by incorporating N-palmitoyl-sphingomyelin (16:0SM) into the outer leaflet of preformed 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC)/Cholesterol SLBs through methyl-β-cyclodextrin-mediated lipid exchange. Lipid domains were detected after incorporation of 16:0SM though their phase state varied from gel to liquid ordered (Lo) phase if the procedure was performed at 24 or 37 °C, respectively. When comparing symmetric and asymmetric Lo domains, differences in size and morphology were observed, with asymmetric domains being smaller and more interconnected. Both types of Lo domains showed similar mechanical stability in terms of rupture forces and Young's moduli. Notably, force curves in asymmetric domains presented two rupture events that could be attributed to the sequential rupture of a liquid disordered (Ld) and a Lo phase. Interleaflet coupling in asymmetric Lo domains could also be inferred from those measurements. The experimental approach outlined here would significantly enhance the applicability of membrane 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.