Structural evaluation of phospholipid bicelles for solution-state studies of membrane-associated biomolecules

Morphological control and modern applications of bicelles

Bicellar systems have become popularized as their rich morphology can be applied in biochemistry, physical chemistry, and drug delivery technology. To the biochemical field, bicelles are powerful model membranes for the study of transmembrane protein behavior, membrane transport, and environmental interactions with the cell. Their morphological responses to environmental changes reveal a profound fundamental understanding of physical chemistry related to the principle of self-assembly. Recently, they have also drawn significant attention as theranostic nanocarriers in biopharmaceutical and diagnostic research due to their superior cellular uptake compared to liposomes. It is evident that applications are becoming broader, demanding to understand how the bicelle will form and behave in various environments. To consolidate current works on the bicelle's modern applications, this review will discuss various effects of composition and environmental conditions on the morphology, phase behavior, and stability. Furthermore, various applications such as payload entrapment and polymerization templating are presented to demonstrate their versatility and chemical nature.

Facade-Based Bicelles as a New Tool for Production of Active Membrane Proteins in a Cell-Free System

Integral membrane proteins are important components of a cell. Their structural and functional studies require production of milligram amounts of proteins, which nowadays is not a routine process. Cell-free protein synthesis is a prospective approach to resolve this task. However, there are few known membrane mimetics that can be used to synthesize active membrane proteins in high amounts. Here, we present the application of commercially available "Facade" detergents for the production of active rhodopsin. We show that the yield of active protein in lipid bicelles containing Facade-EM, Facade-TEM, and Facade-EPC is several times higher than in the case of conventional bicelles with CHAPS and DHPC and is comparable to the yield in the presence of lipid-protein nanodiscs. Moreover, the effects of the lipid-to-detergent ratio, concentration of detergent in the feeding mixture, and lipid composition of the bicelles on the total, soluble, and active protein yields are discussed. We show that Facade-based bicelles represent a prospective membrane mimetic, available for the production of membrane proteins in a cell-free system.

SARS-CoV-2 omicron variants harbor spike protein mutations responsible for their attenuated fusogenic phenotype

Since the emergence of the Omicron variants at the end of 2021, they quickly became the dominant variants globally. The Omicron variants may be more easily transmitted compared to the earlier Wuhan and the other variants. In this study, we aimed to elucidate mechanisms of the altered infectivity associated with the Omicron variants. We systemically evaluated mutations located in the S2 sequence of spike and identified mutations that are responsible for altered viral fusion. We demonstrated that mutations near the S1/S2 cleavage site decrease S1/S2 cleavage, resulting in reduced fusogenicity. Mutations in the HR1 and other S2 sequences also affect cell-cell fusion. Based on nuclear magnetic resonance (NMR) studies and in silico modeling, these mutations affect fusogenicity possibly at multiple steps of the viral fusion. Our findings reveal that the Omicron variants have accumulated mutations that contribute to reduced syncytial formation and hence an attenuated pathogenicity.

Investigation of lipid/protein interactions in trifluoroethanol-water mixtures proposes the strategy for the refolding of helical transmembrane domains

Membrane proteins are one of the keystone objects in molecular biology, but their structural studies often require an extensive search for an appropriate membrane-like environment and an efficient refolding protocol for a recombinant protein. Isotropic bicelles are a convenient membrane mimetic used in structural studies of membrane proteins. Helical membrane domains are often transferred into bicelles from trifluoroethanol-water mixtures. However, the protocols for such a refolding are empirical and the process itself is still not understood in detail. In search of the optimal refolding approaches for helical membrane proteins, we studied here how membrane proteins, lipids, and detergents interact with each other at various trifluoroethanol-water ratios. Using high-resolution NMR spectroscopy and dynamic light scattering, we determined the key states of the listed compounds in the trifluoroethanol/water mixture, found the factors that could be critical for the efficiency of refolding, and proposed several most optimal protocols. These protocols were developed on the transmembrane domain of neurotrophin receptor TrkA and tested on two model helical membrane domains-transmembrane of Toll-like receptor TLR9 and voltage-sensing domain of a potassium channel KvAP.

Interaction of the bacterial division regulator MinE with lipid bicelles studied by NMR spectroscopy

The bacterial MinE and MinD division regulatory proteins form a standing wave enabling MinC, which binds MinD, to inhibit FtsZ polymerization everywhere except at the midcell, thereby assuring correct positioning of the cytokinetic septum and even distribution of contents to daughter cells. The MinE dimer undergoes major structural rearrangements between a resting six-stranded state present in the cytoplasm, a membrane-bound state, and a four-stranded active state bound to MinD on the membrane, but it is unclear which MinE motifs interact with the membrane in these different states. Using NMR, we probe the structure and global dynamics of MinE bound to disc-shaped lipid bicelles. In the bicelle-bound state, helix α1 no longer sits on top of the six-stranded β-sheet, losing any contact with the protein core, but interacts directly with the bicelle surface; the structure of the protein core remains unperturbed and also interacts with the bicelle surface via helix α2. Binding may involve a previously identified excited state of free MinE in which helix α1 is disordered, thereby allowing it to target the membrane surface. Helix α1 and the protein core undergo nanosecond rigid body motions of differing amplitudes in the plane of the bicelle surface. Global dynamics on the sub-millisecond time scale between a ground state and a sparsely populated excited state are also observed and may represent a very early intermediate on the transition path between the resting six-stranded and active four-stranded conformations. In summary, our results provide insights into MinE structural rearrangements important during bacterial cell division.

Expanding the Toolbox for Bicelle-Forming Surfactant–Lipid Mixtures

Bicelles are disk-shaped models of cellular membranes used to study lipid–protein interactions, as well as for structural and functional studies on transmembrane proteins. One challenge for the incorporation of transmembrane proteins in bicelles is the limited range of detergent and lipid combinations available for the successful reconstitution of proteins in model membranes. This is important, as the function and stability of transmembrane proteins are very closely linked to the detergents used for their purification and to the lipids that the proteins are embedded in. Here, we expand the toolkit of lipid and detergent combinations that allow the formation of stable bicelles. We use a combination of dynamic light scattering, small-angle X-ray scattering and cryogenic electron microscopy to perform a systematic sample characterization, thus providing a set of conditions under which bicelles can be successfully formed.

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

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

Aligned peptoid-based macrodiscs for structural studies of membrane proteins by oriented-sample NMR

Development of a robust, uniform, and magnetically orientable lipid mimetic will undoubtedly advance solid-state NMR of macroscopically aligned membrane proteins. Here, we report on a novel lipid membrane mimetic based on peptoid belts. The peptoids, composed of 15 residues, were synthesized by alternating N-(2-phenethyl)glycine with N-(2-carboxyethyl)glycine residues at a 2:1 molar ratio. The chemically synthesized peptoids possess a much lower degree of polydispersity versus styrene-maleic acid polymers, thus yielding uniform discs. Moreover, the peptoid oligomers are more flexible and do not require a specific folding, unlike lipoproteins, in order to wrap around the hydrophobic membrane core. The NMR spectra measured for the membrane-bound form of Pf1 coat protein incorporated in this new lipid mimetics demonstrate a higher order parameter and uniform linewidths compared with the conventional bicelles and peptide-based macrodiscs. Importantly, unlike bicelles, the peptoid-based macrodiscs are detergent free.

Dilute Bicelles for Glycosyltransferase Studies, Novel Bicelles with Phosphatidylinositol

Solution-state NMR can be used to study protein-lipid interactions, in particular, the effect that proteins have on lipids. One drawback is that only small assemblies can be studied, and therefore, fast-tumbling bicelles are commonly used. Bicelles contain a lipid bilayer that is solubilized by detergents. A complication is that they are only stable at high concentrations, exceeding the CMC of the detergent. This issue has previously been addressed by introducing a detergent (Cyclosfos-6) with a substantially lower CMC. Here, we developed a set of bicelles using this detergent for studies of membrane-associated mycobacterial proteins, for example, PimA, a key enzyme for bacterial growth. To mimic the lipid composition of mycobacterial membranes, PI, PG, and PC lipids were used. Diffusion NMR was used to characterize the bicelles, and spin relaxation was used to measure the dynamic properties of the lipids. The results suggest that bicelles are formed, although they are smaller than "conventional" bicelles. Moreover, we studied the effect of MTSL-labeled PimA on bicelles containing PI and PC. The paramagnetic label was shown to have a shallow location in the bicelle, affecting the glycerol backbone of the lipids. We foresee that these bicelles will be useful for detailed studies of protein-lipid interactions.

Mechanisms of membrane protein crystallization in 'bicelles'

Despite remarkable progress, mainly due to the development of LCP and ‘bicelle’ crystallization, lack of structural information remains a bottleneck in membrane protein (MP) research. A major reason is the absence of complete understanding of the mechanism of crystallization. Here we present small-angle scattering studies of the evolution of the “bicelle” crystallization matrix in the course of MP crystal growth. Initially, the matrix corresponds to liquid-like bicelle state. However, after adding the precipitant, the crystallization matrix transforms to jelly-like state. The data suggest that this final phase is composed of interconnected ribbon-like bilayers, where crystals grow. A small amount of multilamellar phase appears, and its volume increases concomitantly with the volume of growing crystals. We suggest that the lamellar phase surrounds the crystals and is critical for crystal growth, which is also common for LCP crystallization. The study discloses mechanisms of “bicelle” MP crystallization and will support rational design of crystallization.

Scrutinizing the Feasibility of Nonionic Surfactants to Form Isotropic Bicelles of Curcumin: a Potential Antiviral Candidate Against COVID-19

Investigating bicelles as an oral drug delivery system and exploiting their structural benefits can pave the way to formulate hydrophobic drugs and potentiate their activity. Herein, the ability of non-ionic surfactants (labrasol^®, tween 80, cremophore EL and pluronic F127) to form curcumin loaded bicelles with phosphatidylcholine, utilizing a simple method, was investigated. Molecular docking was used to understand the mechanism of bicelles formation. The % transmittance and TEM exhibited bicelles formation with labrasol^® and tween 80, while cremophor EL and pluronic F127 tended to form mixed micelles. The surfactant-based nanostructures significantly improved curcumin dissolution (99.2 ± 2.6% within 10 min in case of tween 80-based bicelles) compared to liposomes and curcumin suspension in non-sink conditions. The prepared formulations improved curcumin ex vivo permeation over liposomes and drug suspension. Further, the therapeutic antiviral activity of the formulated curcumin against SARS-CoV-2 was potentiated over drug suspension. Although both Labrasol^® and tween 80 bicelles could form bicelles and enhance the oral delivery of curcumin when compared to liposomes and drug suspension, the mixed micelles formulations depicted superiority than bicelles formulations. Our findings provide promising formulations that can be utilized for further preclinical and clinical studies of curcumin as an antiviral therapy for COVID-19 patients.

A Simple Method for Continuous Synthesis of Bicelles in Microfluidic Systems

Bicelle has great potential for drug delivery systems due to its small size and biocompatibility. The conventional method of bicelle preparation contains a long process and harsh conditions, which limit its feasibility and damage the biological substances. For these reasons, a continuous manufacturing method in mild conditions has been demanded. Here, we propose a novel method for DMPC/DHPC bicelle synthesis based on a microfluidic device without heating and freezing processes. Bicelles were successfully prepared using this continuous method, which was identified by the physicochemical properties and morphologies of the synthesized assemblies. Experimental and analytical studies confirm that there is critical lipid concentration and critical mixing time for bicelle synthesis in this microfluidic system. Furthermore, a linear relation between the actual composition of bicelle and initial lipid ratio is deduced, and this enables the size of bicelles to be controlled.

Transient lipid-bound states of spike protein heptad repeats provide insights into SARS-CoV-2 membrane fusion

Entry of SARS-CoV-2 into a host cell is mediated by spike, a class I viral fusion protein responsible for merging the viral and host cell membranes. Recent studies have revealed atomic-resolution models for both the postfusion 6-helix bundle (6HB) and the prefusion state of spike. However, a mechanistic understanding of the molecular basis for the intervening structural transition, important for the design of fusion inhibitors, has remained elusive. Using nuclear magnetic resonance spectroscopy and other biophysical methods, we demonstrate the presence of α-helical, membrane-bound, intermediate states of spike’s heptad repeat (HR1 and HR2) domains that are embedded at the lipid-water interface while in a slow dynamic equilibrium with the postfusion 6HB state. These results support a model where the HR domains lower the large energy barrier associated with membrane fusion by destabilizing the host and viral membranes, while 6HB formation actively drives their fusion by forcing physical proximity.

Lipid Membrane Mimetics in Functional and Structural Studies of Integral Membrane Proteins

Integral membrane proteins (IMPs) fulfill important physiological functions by providing cell-environment, cell-cell and virus-host communication; nutrients intake; export of toxic compounds out of cells; and more. However, some IMPs have obliterated functions due to polypeptide mutations, modifications in membrane properties and/or other environmental factors-resulting in damaged binding to ligands and the adoption of non-physiological conformations that prevent the protein from returning to its physiological state. Thus, elucidating IMPs' mechanisms of function and malfunction at the molecular level is important for enhancing our understanding of cell and organism physiology. This understanding also helps pharmaceutical developments for restoring or inhibiting protein activity. To this end, in vitro studies provide invaluable information about IMPs' structure and the relation between structural dynamics and function. Typically, these studies are conducted on transferred from native membranes to membrane-mimicking nano-platforms (membrane mimetics) purified IMPs. Here, we review the most widely used membrane mimetics in structural and functional studies of IMPs. These membrane mimetics are detergents, liposomes, bicelles, nanodiscs/Lipodisqs, amphipols, and lipidic cubic phases. We also discuss the protocols for IMPs reconstitution in membrane mimetics as well as the applicability of these membrane mimetic-IMP complexes in studies via a variety of biochemical, biophysical, and structural biology techniques.

Fusion Peptide of SARS-CoV-2 Spike Rearranges into a Wedge Inserted in Bilayered Micelles

The receptor binding and proteolysis of Spike of SARS-CoV-2 release its S2 subunit to rearrange and catalyze viral-cell fusion. This deploys the fusion peptide for insertion into the cell membranes targeted. We show that this fusion peptide transforms from intrinsic disorder in solution into a wedge-shaped structure inserted in bilayered micelles, according to chemical shifts, 15N NMR relaxation, and NOEs. The globular fold of three helices contrasts the open, extended forms of this region observed in the electron density of compact prefusion states. In the hydrophobic, narrow end of the wedge, helices 1 and 2 contact the fatty acyl chains of phospholipids, according to NOEs and proximity to a nitroxide spin label deep in the membrane mimic. The polar end of the wedge may engage and displace lipid head groups and bind Ca2+ ions for membrane fusion. Polar helix 3 protrudes from the bilayer where it might be accessible to antibodies.

Investigating the Disordered and Membrane-Active Peptide A-Cage-C Using Conformational Ensembles

The driving forces and conformational pathways leading to amphitropic protein-membrane binding and in some cases also to protein misfolding and aggregation is the subject of intensive research. In this study, a chimeric polypeptide, A-Cage-C, derived from α-Lactalbumin is investigated with the aim of elucidating conformational changes promoting interaction with bilayers. From previous studies, it is known that A-Cage-C causes membrane leakages associated with the sporadic formation of amorphous aggregates on solid-supported bilayers. Here we express and purify double-labelled A-Cage-C and prepare partially deuterated bicelles as a membrane mimicking system. We investigate A-Cage-C in the presence and absence of these bicelles at non-binding (pH 7.0) and binding (pH 4.5) conditions. Using in silico analyses, NMR, conformational clustering, and Molecular Dynamics, we provide tentative insights into the conformations of bound and unbound A-Cage-C. The conformation of each state is dynamic and samples a large amount of overlapping conformational space. We identify one of the clusters as likely representing the binding conformation and conclude tentatively that the unfolding around the central W23 segment and its reorientation may be necessary for full intercalation at binding conditions (pH 4.5). We also see evidence for an overall elongation of A-Cage-C in the presence of model bilayers.

Structural basis for allosteric control of the SERCA-Phospholamban membrane complex by Ca2+ and phosphorylation

Phospholamban (PLN) is a mini-membrane protein that directly controls the cardiac Ca²⁺-transport response to β-adrenergic stimulation, thus modulating cardiac output during the fight-or-flight response. In the sarcoplasmic reticulum membrane, PLN binds to the sarco(endo)plasmic reticulum Ca²⁺-ATPase (SERCA), keeping this enzyme's function within a narrow physiological window. PLN phosphorylation by cAMP-dependent protein kinase A or increase in Ca²⁺ concentration reverses the inhibitory effects through an unknown mechanism. Using oriented-sample solid-state NMR spectroscopy and replica-averaged NMR-restrained structural refinement, we reveal that phosphorylation of PLN's cytoplasmic regulatory domain signals the disruption of several inhibitory contacts at the transmembrane binding interface of the SERCA-PLN complex that are propagated to the enzyme's active site, augmenting Ca²⁺ transport. Our findings address long-standing questions about SERCA regulation, epitomizing a signal transduction mechanism operated by posttranslationally modified bitopic membrane proteins.

Membrane Interactions of α-Synuclein Revealed by Multiscale Molecular Dynamics Simulations, Markov State Models, and NMR

α-Synuclein (αS) is a presynaptic protein that binds to cell membranes and is linked to Parkinson's disease (PD). Binding of αS to membranes is a likely first step in the molecular pathophysiology of PD. The αS molecule can adopt multiple conformations, being largely disordered in water, adopting a β-sheet conformation when present in amyloid fibrils, and forming a dynamic multiplicity of α-helical conformations when bound to lipid bilayers and related membrane-mimetic surfaces. Multiscale molecular dynamics simulations in conjunction with nuclear magnetic resonance (NMR) and cross-linking mass spectrometry (XLMS) measurements are used to explore the interactions of αS with an anionic lipid bilayer. The simulations and NMR measurements together reveal a break in the helical structure of the central non-amyloid-β component (NAC) region of αS in the vicinity of residues 65-70, which may facilitate subsequent oligomer formation. Coarse-grained simulations of αS starting from the structure of αS when bound to a detergent micelle reveal the overall pattern of protein contacts to anionic lipid bilayers, while subsequent all-atom simulations provide details of conformational changes upon membrane binding. In particular, simulations and NMR data for liposome-bound αS indicate incipient β-strand formation in the NAC region, which is supported by intramolecular contacts seen via XLMS and simulations. Markov state models based on the all-atom simulations suggest a mechanism of conformational change of membrane-bound αS via a dynamic helix break in the region of residue 65 in the NAC region. The emergent dynamic model of membrane-interacting αS advances our understanding of the mechanism of PD, potentially aiding the design of novel therapeutic approaches.

MPBuilder: A PyMOL Plugin for Building and Refinement of Solubilized Membrane Proteins Against Small Angle X-ray Scattering Data

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SAXS is a unique tool to study MP systems in the native-like environment.

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The lack of user-friendly software hinders SAXS data interpretation of MPs.

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We present a novel plugin for the widely used molecular visualization system PyMol.

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MPBuilder allows to build and refine models against SAXS data.

Membrane proteins (MPs) are the target of numerous structural and functional studies in biological and medical/pharmaceutical sciences. Strategies for the high-throughput structural analysis of MPs and of their perturbations driven by ligands having potential therapeutic applications are uncommon, often requiring scaled up crystallization, electron microscopy, and nuclear magnetic resonance (NMR) efforts. Small-angle X-ray scattering (SAXS) provides a rapid means to study low resolution structures and conformational changes of native MPs in solution without cumbersome sample preparations/treatment. The method requires the MPs solubilized in an appropriate medium (eg. detergents, mixed micelles and nanodiscs) and reliable and robust models are needed to describe the relevant complexes. Here we present MPBuilder, a simple and versatile tool for the generation and refinement of all-atom MP systems in the popular software PyMOL, an environment familiar to most biologists. MPBuilder provides building capability for protein-detergent, bicelle, and lipid-scaffold (saposin nanoparticles, nanodiscs) complexes and links this to the ATSAS software package modules for model refinement and validation against the SAXS data.

Aescin - a natural soap for the formation of lipid nanodiscs with tunable size

The saponin β-aescin from the seed extract of the horse chestnut tree Aesculus hippocastanum has demonstrated a beneficial role in clinical therapy which is in part related to its strong interaction with biological membranes. In this context the present work investigates the self-assembly of nm-sized discoidal lipid nanoparticles composed of β-aescin and the phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). The discoidal lipid nanoparticles reassemble from small discs into larger discs, ribbons and finally stacks of sheets upon heating from gel-phase to fluid phase DMPC. The morphological transition of the lipid nano-particles is mainly triggered by the phospholipid phase state change. The final morphology depends on the phospholipid-to-saponin ratio and the actual temperature. The study is conducted by small-angle X-ray scattering (SAXS) and transmission (TEM) and freeze fracture electron microscopy (FFEM) are used to cover larger length scales. Two different models, representing a disc and ribbon-like shape are applied to the SAXS data, evaluating possible geometries and molecular mixing of the nano-particles. The stacked sheets are analysed by the Caillé theory.

1H/13C/15N triple-resonance experiments for structure determinaton of membrane proteins by oriented-sample NMR

The benefits of triple-resonance experiments for structure determination of macroscopically oriented membrane proteins by solid-state NMR are discussed. While double-resonance ¹H/¹⁵N experiments are effective for structure elucidation of alpha-helical domains, extension of the method of oriented samples to more complex topologies and assessing side-chain conformations necessitates further development of triple-resonance (¹H/¹³C/¹⁵N) NMR pulse sequences. Incorporating additional spectroscopic dimensions involving ¹³C spin-bearing nuclei, however, introduces essential complications arising from the wide frequency range of the ¹H-¹³C dipolar couplings and ¹³C CSA (>20 ​kHz), and the presence of the ¹³C-¹³C homonuclear dipole-dipole interactions. The recently reported ROULETTE-CAHA pulse sequence, in combination with the selective z-filtering, can be used to evolve the structurally informative ¹H-¹³C dipolar coupling arising from the aliphatic carbons while suppressing the signals from the carbonyl and methyl regions. Proton-mediated magnetization transfer under mismatched Hartman-Hahn conditions (MMHH) can be used to correlate ¹³C and ¹⁵N nuclei in such triple-resonance experiments for the subsequent ¹⁵N detection. The recently developed pulse sequences are illustrated for n-acetyl Leucine (NAL) single crystal and doubly labeled Pf1 coat protein reconstituted in magnetically aligned bicelles. An interesting observation is that in the case of ¹⁵N-labeled NAL measured at ¹³C natural abundance, the triple (¹H/¹³C/¹⁵N) MMHH scheme predominantly gives rise to long-range intermolecular magnetization transfers from ¹³C to ¹⁵N spins; whereas direct Hartmann-Hahn ¹³C/¹⁵N transfer is entirely intramolecular. The presented developments advance NMR of oriented samples for structure determination of membrane proteins and liquid crystals.

Proteostasis of Islet Amyloid Polypeptide: A Molecular Perspective of Risk Factors and Protective Strategies for Type II Diabetes

The possible link between hIAPP accumulation and β-cell death in diabetic patients has inspired numerous studies focusing on amyloid structures and aggregation pathways of this hormone. Recent studies have reported on the importance of early oligomeric intermediates, the many roles of their interactions with lipid membrane, pH, insulin, and zinc on the mechanism of aggregation of hIAPP. The challenges posed by the transient nature of amyloid oligomers, their structural heterogeneity, and the complex nature of their interaction with lipid membranes have resulted in the development of a wide range of biophysical and chemical approaches to characterize the aggregation process. While the cellular processes and factors activating hIAPP-mediated cytotoxicity are still not clear, it has recently been suggested that its impaired turnover and cellular processing by proteasome and autophagy may contribute significantly toward toxic hIAPP accumulation and, eventually, β-cell death. Therefore, studies focusing on the restoration of hIAPP proteostasis may represent a promising arena for the design of effective therapies. In this review we discuss the current knowledge of the structures and pathology associated with hIAPP self-assembly and point out the opportunities for therapy that a detailed biochemical, biophysical, and cellular understanding of its aggregation may unveil.

Structure and Dynamics of GPCRs in Lipid Membranes: Physical Principles and Experimental Approaches

Over the past decade, the vast amount of information generated through structural and biophysical studies of GPCRs has provided unprecedented mechanistic insight into the complex signalling behaviour of these receptors. With this recent information surge, it has also become increasingly apparent that in order to reproduce the various effects that lipids and membranes exert on the biological function for these allosteric receptors, in vitro studies of GPCRs need to be conducted under conditions that adequately approximate the native lipid bilayer environment. In the first part of this review, we assess some of the more general effects that a membrane environment exerts on lipid bilayer-embedded proteins such as GPCRs. This is then followed by the consideration of more specific effects, including stoichiometric interactions with specific lipid subtypes. In the final section, we survey a range of different membrane mimetics that are currently used for in vitro studies, with a focus on NMR applications.

The Diversity and Similarity of Transmembrane Trimerization of TNF Receptors

Receptors in the tumor necrosis factor receptor superfamily (TNFRSF) regulate proliferation of immune cells or induce programmed cell death, and many of them are candidates for antibody-based immunotherapy. Previous studies on several death receptors in the TNFRSF including Fas, p75NTR, and DR5 showed that the transmembrane helix (TMH) of these receptors can specifically oligomerize and their oligomeric states have direct consequences on receptor activation, suggesting a much more active role of TMH in receptor signaling than previously appreciated. Here, we report the structure of the TMH of TNFR1, another well studied member of the TNFRSF, in neutral bicelles that mimic a lipid bilayer. We find that TNFR1 TMH forms a defined trimeric complex in bicelles, and no evidences of higher-order clustering of trimers have been detected. Unexpectedly, a conserved proline, which is critical for Fas TMH trimerization, does not appear to play an important role in TNFR1 TMH trimerization, which is instead mediated by a glycine near the middle of the TMH. Further, TNFR1 TMH trimer shows a larger hydrophobic core than that of Fas or DR5, with four layers of hydrophobic interaction along the threefold axis. Comparison of the TNFR1 TMH structure with that of Fas and DR5 reveals reassuring similarities that have functional implications but also significant structural diversity that warrants systematic investigation of TMH oligomerization property for other members of the TNFRSF.

Effects of fluidity and charge density on the morphology of a bicellar mixture - A SANS study

The spontaneously formed structures of physiologically relevant lipid model membranes made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1'-rac-glycerol) and 1,2-hexanoyl-sn-glycero-3-phosphocholine have been evaluated in depth using small angle neutron scattering. Although a common molar ratio of long- to short- chain phospholipids (~4) as reported in many bicellar mixtures was used, discoidal bicelles were not found as the major phase throughout the range of lipid concentration and temperature studied, indicating that the required condition for the formation of bicelle is the immiscibility between the long- and short- chain lipids, which were in the gel and L_α phases, respectively, in previous reports. In this study, all lipids are in the L_α phase. The characterization outcome suggests that the spontaneous structures tie strongly with the physical parameters of the system such as melting transition temperature of the long-chain lipid, total lipid concentration and charge density of the system. Multilamellar vesicles, unilamellar vesicles, ribbons and perforated lamellae can be obtained based on the analysis of the small angle neutron scattering results, leading to the construction of structural diagrams. This report provides the important map to choose suitable lipid systems for the structural study of membrane-associated proteins, design of theranostic nanocarriers or other related research fields.

Versatile formation of supported lipid bilayers from bicellar mixtures of phospholipids and capric acid

Originally developed for the structural biology field, lipid bicelle nanostructures composed of long- and short-chain phospholipid molecules have emerged as a useful interfacial science tool to fabricate two-dimensional supported lipid bilayers (SLBs) on hydrophilic surfaces due to ease of sample preparation, scalability, and versatility. To improve SLB fabrication prospects, there has been recent interest in replacing the synthetic, short-chain phospholipid component of bicellar mixtures with naturally abundant fatty acids and monoglycerides, i.e., lauric acid and monocaprin. Such options have proven successful under specific conditions, however, there is room for devising more versatile fabrication options, especially in terms of overcoming lipid concentration-dependent SLB formation limitations. Herein, we investigated SLB fabrication by using bicellar mixtures consisting of long-chain phospholipid and capric acid, the latter of which has similar headgroup and chain length properties to lauric acid and monocaprin, respectively. Quartz crystal microbalance-dissipation, epifluorescence microscopy, and fluorescence recovery after photobleaching experiments were conducted to characterize lipid concentration-dependent bicelle adsorption onto silicon dioxide surfaces. We identified that uniform-phase SLB formation occurred independently of total lipid concentration when the ratio of long-chain phospholipid to capric acid molecules ("q-ratio") was 0.25 or 2.5, which is superior to past results with lauric acid- and monocaprin-containing bicelles in which cases lipid concentration-dependent behavior was observed. Together, these findings demonstrate that capric acid-containing bicelles are versatile tools for SLB fabrication and highlight how the molecular structure of bicelle components can be rationally finetuned to modulate self-assembly processes at solid-liquid interfaces.

Biologically interfaced nanoplasmonic sensors

Understanding biointerfacial processes is crucial in various fields across fundamental and applied biology, but performing quantitative studies via conventional characterization techniques remains challenging due to instrumentation as well as analytical complexities and limitations. In order to accelerate translational research and address current challenges in healthcare and medicine, there is an outstanding need to develop surface-sensitive technologies with advanced measurement capabilities. Along this line, nanoplasmonic sensing has emerged as a powerful tool to quantitatively study biointerfacial processes owing to its high spatial resolution at the nanoscale. Consequently, the development of robust biological interfacing strategies becomes imperative to maximize its characterization potential. This review will highlight and discuss the critical role of biological interfacing within the context of constructing nanoplasmonic sensing platforms for biointerfacial science applications. Apart from paving the way for the development of highly surface-sensitive characterization tools that will spur fundamental biological interaction studies and improve the overall understanding of biological processes, the basic principles behind biointerfacing strategies presented in this review are also applicable to other fields that involve an interface between an inorganic material and a biological system.

Formulation of Bicelles Based on Lecithin-Nonionic Surfactant Mixtures

Bicelles have been intensively studied for use as drug delivery carriers and in biological studies, but their preparation with low-cost materials and via a simple process would allow their use for other purposes as well. Herein, bicelles were prepared through a semi-spontaneous method using a mixture of hydrogenated soybean lecithin (SL) and a nonionic surfactant, polyoxyethylene cholesteryl ether (ChEO₁₀), and then we investigated the effect of composition and temperature on the structure of bicelles, which is important to design tailored systems. As the fraction of ChEO₁₀ (X_C) was increased, a bimodal particle size distribution with a small particle size of several tens of nanometers and a large particle size of several hundred nanometers was obtained, and only small particles were observed when X_C ≥ 0.6, suggesting the formation of significant structure transition (liposomes to bicelles). The small-angle neutron scattering (SANS) spectrum for these particles fitted a core-shell bicelle model, providing further evidence of bicelle formation. A transition from a monomodal to a bimodal size distribution occurred as the temperature was increased, with this transition taking place at lower temperatures when higher SL-ChEO₁₀ concentrations were used. SANS showed that this temperature-dependent size change was reversible, suggesting the SL-ChEO₁₀ bicelles were stable against temperature, hence making them suitable for several applications.

Supported Lipid Bilayer Formation from Phospholipid-Fatty Acid Bicellar Mixtures

Supported lipid bilayers (SLBs) are versatile cell membrane-mimicking biointerfaces for various applications such as biosensors and drug delivery systems, and there is broad interest in developing simple, cost-effective methods to achieve SLB fabrication. One promising approach involves the deposition of quasi-two-dimensional bicelle nanostructures that are composed of long-chain phospholipids and either short-chain phospholipids or detergent molecules. While a variety of long-chain phospholipids have been used to prepare bicelles for SLB fabrication applications, only two short-chain phospholipids, 1,2-dihexanoyl-sn-glycero-3-phosphocholine and 1,2-diheptanoyl-sn-glycero-3-phosphocholine (collectively referred to as DHPC), have been investigated. There remains an outstanding need to identify natural alternatives to DHPC, especially ones that are more affordable, to improve fabrication prospects and application opportunities. Herein, we explored the potential to fabricate SLBs from bicellar mixtures composed of long-chain phospholipids and lauric acid (LA), which is a low-cost, naturally abundant fatty acid that is widely used in soapmaking and various industrial applications. Quartz crystal microbalance-dissipation (QCM-D) experiments were conducted to track bicelle adsorption onto silica surfaces as a function of bicelle composition and lipid concentration, along with time-lapse fluorescence microscopy imaging and fluorescence recovery after photobleaching (FRAP) experiments to further characterize lipid adlayer properties. The results identified optimal conditions where it is possible to efficiently form SLBs from LA-containing bicelles at low lipid concentrations while also unraveling mechanistic insights into the bicelle-mediated SLB formation process and verifying that LA-containing bicelles are biocompatible with human cells for surface coating applications.

Targeted Delivery of Adamantylated Peptidoglycan Immunomodulators in Lipid Nanocarriers: NMR Shows That Cargo Fragments Are Available on the Surface

We present an in-depth investigation of the membrane interactions of peptidoglycan (PGN)-based immune adjuvants designed for lipid-based delivery systems using NMR spectroscopy. The derivatives contain a cargo peptidoglycan (PGN) dipeptide fragment and an adamantyl group, which serves as an anchor to the lipid bilayer. Furthermore, derivatives with a mannose group that can actively target cell surface receptors on immune cells are also studied. We showed that the targeting mannose group and the cargo PGN fragment are both available on the lipid bilayer surface, thereby enabling interactions with cognate receptors. We found that the nonmannosylated compounds are incorporated stronger into the lipid assemblies than the mannosylated ones, but the latter compounds penetrate deeper in the bilayer. This might be explained by stronger electrostatic interactions available for zwitterionic nonmannosylated derivatives as opposed to the compounds in which the charged N-terminus is capped by mannose groups. The higher incorporation efficiency of the nonmannosylated compounds correlated with a larger relative enhancement in immune stimulation activities upon lipid incorporation compared to that of the derivatives with the mannose group. The chirality of the adamantyl group also influenced the incorporation efficiency, which in turn correlated with membrane-associated conformations that affect possible intermolecular interactions with lipid molecules. These findings will help in improving the development of PGN-based immune adjuvants suitable for delivery in lipid nanoparticles.

Biomimetic Models to Investigate Membrane Biophysics Affecting Lipid-Protein Interaction

Biological membranes are highly dynamic in their ability to orchestrate vital mechanisms including cellular protection, organelle compartmentalization, cellular biomechanics, nutrient transport, molecular/enzymatic recognition, and membrane fusion. Controlling lipid composition of different membranes allows cells to regulate their membrane characteristics, thus modifying their physical properties to permit specific protein interactions and drive structural function (membrane deformation facilitates vesicle budding and fusion) and signal transduction. Yet, how lipids control protein structure and function is still poorly understood and needs systematic investigation. In this review, we explore different in vitro membrane models and summarize our current understanding of the interplay between membrane biophysical properties and lipid-protein interaction, taken as example few proteins involved in muscular activity (dystrophin), digestion and Legionella pneumophila effector protein DrrA. The monolayer model with its movable barriers aims to mimic any membrane deformation while surface pressure modulation imitates lipid packing and membrane curvature changes. It is frequently used to investigate peripheral protein binding to the lipid headgroups. Examples of how lipid lateral pressure modifies protein interaction and organization within the membrane are presented using various biophysical techniques. Interestingly, the shear elasticity and surface viscosity of the monolayer will increase upon specific protein(s) binding, supporting the importance of such mechanical link for membrane stability. The lipid bilayer models such as vesicles are not only used to investigate direct protein binding based on the lipid nature, but more importantly to assess how local membrane curvature (vesicles with different size) influence the binding properties of a protein. Also, supported lipid bilayer model has been used widely to characterize diffusion law of lipids within the bilayer and/or protein/biomolecule binding and diffusion on the membrane. These membrane models continue to elucidate important advances regarding the dynamic properties harmonizing lipid-protein interaction.

Anisotropic active ligandations in siRNA-Loaded hybrid nanodiscs lead to distinct carcinostatic outcomes by regulating nano-bio interactions

Active targeting modification is one of the foremost nanomedicine strategies for the efficacy improvement. Compared to the homogeneous ligandation on spherical nanocarriers, non-spherical nanomedicines usually make the ligand modification more complicated. The modified ligands always exhibit anisotropy and heterogeneity. However, there is very little systematic study on these diversified anisotropic modifications. The efficacy difference and underlying mechanism were still unclear. Here, we separately fabricated hybrid nanodiscs (NDs) conjugated with cRGD on the edge and plane surfaces to engineer two anisotropic targeting nanocarriers (E-cRGD-NDs and P-cRGD-NDs, respectively) for gene delivery. The ligand anisotropy endowed NDs with diversified cellular interactions, and caused different efficacies between E-cRGD-NDs and P-cRGD-NDs. Of note, E-cRGD-NDs showed significant superiority in siRNA loading, cellular uptake, silence efficiency, protein expression and even in vivo efficacy. The mechanism investigation revealed the functional anisotropy specifically for E-cRGD-NDs. The edge modification of cRGD efficiently separated the targeting and siRNA loading domains, maximizing their respective functions. These findings reflected the unique effect of ligand anisotropy, also provided a new strategy for the targeting screening of extensive nanomedicines.

Reconstitution of full-length human caveolin-1 into phospholipid bicelles: Validation by analytical ultracentrifugation

A significant hurdle in obtaining biophysical information on membrane proteins is developing a successful strategy for their reconstitution into a suitable membrane mimic. In particular, utilization of the more 'native-like' membrane mimics such as bicelles is generally more challenging than simple micellar solubilization. Caveolin-1, an integral membrane protein involved in membrane curvature, endocytosis, mechano-protection, and signal transduction, has been shown to be particularly recalcitrant to standard reconstitution protocols due to its highly hydrophobic characteristics. Herein we describe a robust method to incorporate recombinantly produced full-length caveolin-1 into bicelles at levels needed for biophysical experimentation. The benchmark of successful reconstitution is the obtainment of protein in a homogeneous state; therefore, we developed a validation procedure to monitor the success of the reconstitution using analytical ultracentrifugation of density-matched bicelles. Our findings indicated that our protocol produces a very homogeneous preparation of caveolin-1 associated with bicelles, and that caveolin-1 is highly α-helical (by circular dichroism spectroscopy). We believe that this methodology will serve as a general strategy to facilitate biophysical studies on membrane proteins.

Evaluation of Molecular Ordering in Bicelle Bilayer Membranes Based on Induced Circular Dichroism Spectra

Bicelles are submicrometer-sized disc-shaped molecular self-assemblies that can be obtained in aqueous solution by dispersing mixtures of certain amphiphiles. Although phospholipid bicelle and phospholipid vesicle assemblies adopt similar lipid bilayer structures, the differences in bilayer characteristics, especially physicochemical properties such as bilayer fluidity, are not clearly understood. Herein, we report the lipid ordering properties of bicelle bilayer membranes based on induced circular dichroism (ICD) and fluorescence polarization analyses using 1,6-diphenyl-1,3,5-hexatriene (DPH) as a probe. Bicelles were prepared by using 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC), while pure DMPC vesicles and pure DHPC micelles were used as references. At temperatures below the phase transition temperature of DMPC, the bicelles showed lower membrane fluidities, whereas DHPC micelles showed higher membrane fluidity, suggesting no significant differences in bilayer fluidity between the bicelle and vesicle assemblies. The ICD signals of DPH were induced only when the membrane was in ordered (solid-ordered or ripple-gel) phases. In the bicelle systems, the ICD of DPH was more significant than that of the DMPC vesicle. The induced chirality of DPH was dependent on the chirality of the bilayer lipid. Compared to that of the DMPC/DHPC bicelle, the ICD of the 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/DHPC bicelle was higher, while that of the bovine sphingomyelin/DHPC bicelle was lower. Because the lipids are tightly packed in the ordered phase, the ICD intensity reflects the molecular ordering state of the lipids in the bicelle bilayer.

Self-Assembly of Phosphocholine Derivatives Using the ELBA Coarse-Grained Model: Micelles, Bicelles, and Reverse Micelles

The ELBA coarse-grained force field was originally developed for lipids, and its water model is described as a single-site Lennard-Jones particle with electrostatics modeled by an embedded point-dipole, while other molecules in this force field have a three (or four)-to-one mapping scheme. Here, ELBA was applied to investigate the self-assembly processes of dodecyl-phosphocholine (DPC) micelle, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/1,2-dihexaoyl-sn-glycero-3-phosphocholine (DPPC/DHPC) bicelles, and DPPC/cyclohexane/water reverse micelles through coarse-grained molecular dynamics (MD) simulations. New parameters were obtained using a simplex algorithm-based calibration procedure to determine the Lennard-Jones parameters for cyclohexane, dodecane, and cyclohexane-dodecane cross-interactions. Density, self-diffusion coefficient, surface tension, and mixture excess volume were found to be in fair agreement with experimental data. These new parameters were used in the simulations, and the obtained structures were analyzed for shape, size, volume, and surface area. Except for the shape of DPC micelles, all other properties match well with available experimental data and all-atom simulations. Remarkably, in agreement with experiments the rodlike shape of the DPPC reverse micelle is well described by ELBA, while all-atom data in the literature predicts a disclike shape. To further check the consistency of the force field in reproducing the correct shapes of reverse micelles, additional simulations were performed doubling the system size. Two distinct reverse micelles were obtained both presenting the rodlike shape and correct aggregation number.

Supported Lipid Bilayer Formation: Beyond Vesicle Fusion

Supported lipid bilayers (SLBs) are cell-membrane-mimicking platforms that can be formed on solid surfaces and integrated with a wide range of surface-sensitive measurement techniques. SLBs are useful for unravelling details of fundamental membrane biology and biophysics as well as for various medical, biotechnology, and environmental science applications. Thus, there is high interest in developing simple and robust methods to fabricate SLBs. Currently, vesicle fusion is a popular method to form SLBs and involves the adsorption and spontaneous rupture of lipid vesicles on a solid surface. However, successful vesicle fusion depends on high-quality vesicle preparation, and it typically works with a narrow range of material supports and lipid compositions. In this Feature Article, we summarize current progress in developing two new SLB fabrication techniques termed the solvent-assisted lipid bilayer (SALB) and bicelle methods, which have compelling advantages such as simple sample preparation and compatibility with a wide range of material supports and lipid compositions. The molecular self-assembly principles underpinning the two strategies and important experimental parameters are critically discussed, and recent application examples are presented. Looking forward, we envision that these emerging SLB fabrication strategies can be widely adopted by specialists and nonspecialists alike, paving the way to enriching our understanding of lipid membrane properties and realizing new application possibilities.

Measuring Lipid Transfer Protein Activity Using Bicelle-Dilution Model Membranes

In vitro assessment of lipid intermembrane transfer activity by cellular proteins typically involves measurement of either radiolabeled or fluorescently labeled lipid trafficking between vesicle model membranes. Use of bilayer vesicles in lipid transfer assays usually comes with inherent challenges because of complexities associated with the preparation of vesicles and their rather short "shelf life". Such issues necessitate the laborious task of fresh vesicle preparation to achieve lipid transfer assays of high quality, precision, and reproducibility. To overcome these limitations, we have assessed model membrane generation by bicelle dilution for monitoring the transfer rates and specificity of various BODIPY-labeled sphingolipids by different glycolipid transfer protein (GLTP) superfamily members using a sensitive fluorescence resonance energy transfer approach. Robust, protein-selective sphingolipid transfer is observed using donor and acceptor model membranes generated by dilution of 0.5 q-value mixtures. The sphingolipid transfer rates are comparable to those observed between small bilayer vesicles produced by sonication or ethanol injection. Among the notable advantages of using bicelle-generated model membranes are (i) easy and straightforward preparation by means that avoid lipid fluorophore degradation and (ii) long "shelf life" after production (≥6 days) and resilience to freeze-thaw storage. The bicelle-dilution-based assay is sufficiently robust, sensitive, and stable for application, not only to purified LTPs but also for LTP activity detection in crude cytosolic fractions of cell homogenates.

Peptide-bicelle interaction: Following variations in size and morphology by a combined NMR-SAXS approach

Changes in membrane properties occurring upon protein interaction are key questions in understanding membrane protein function. To report on the occurring size and shape variation we present here a combined NMR-SAXS method performed under physiological conditions using the same samples, enabling determination of a global parameter, the hydration radius (r_H) and estimating the bicelle shape. We use zwitterionic (DMPC/DHPC) and negatively charged (DMPC/DHPC/DMPG) bicelles and investigate the interaction with model transmembrane and surface active peptides (KALP23 and melittin). ¹H NMR measurements based mostly on the translational diffusion coefficient D determination are used to characterize cmc values of DHPC micelles under the investigated conditions, to describe DHPC distribution with exact determination of the q (long chain/short chain) lipid ratio, to estimate aggregation numbers and effective r_H values. The scattering curve is used to fit a lenticular core-shell model enabling us to describe the bicelle shape in terms of ellipsoidal axis length parameters. For all studied systems formation of oblate ellipsoids is found. Even though the r_G/r_H ratio would be an elegant way to characterize shape variations, we show that changes occurring upon peptide-bicelle interaction in the "effective" size and in the measure on the anisometry - morphology - of the objects can be described by using r_H and the simplistic ellipsoidal core-shell model. While the influence of the transmembrane KALP peptide is significant, effects upon addition of surface active melittin peptide seem negligible. This synergy of techniques under controlled conditions can provide information about bicellar shape modulation occurring during peptide-bicelle interactions.

Sequential and Environmental Dependence of Conformation in a Small Opioid Peptide

We report the structural characterization of the μ-selective endogenous opioid endomorphin-1 (EM-1) via an array of nuclear magnetic resonance experiments in both aqueous conditions and, for the first time, in isotropic lipid bicelles, which mimic its endogenous environment. Consistent with computationally derived hypotheses, EM-1 is found to significantly populate a compact, turn-like structure in aqueous solution. This structure is only present as a minor species when the peptide is subjected to a lipid environment, in which the presented NMR data suggests that the major conformer of EM-1 lacks internal hydrogen bonds. The interaction of EM-1 with lipid bilayers is characterized by both tryptophan fluorescence and two-dimensional diffusion ordered NMR spectroscopy; these experiments suggest that the interaction with the surface of phospholipid bilayers, operating as a change in bulk solvation, is responsible for the observed conformational rearrangement in EM-1.

Solution NMR: A powerful tool for structural and functional studies of membrane proteins in reconstituted environments

A third of the genes in prokaryotic and eukaryotic genomes encode membrane proteins that are either essential for signal transduction and solute transport or function as scaffold structures. Unlike many of their soluble counterparts, the overall structural and functional organization of membrane proteins is sparingly understood. Recent advances in X-ray crystallography, cryo-EM, and nuclear magnetic resonance (NMR) are closing this gap by enabling an in-depth view of these ever-elusive proteins at atomic resolution. Despite substantial technological advancements, however, the overall proportion of membrane protein entries in the Protein Data Bank (PDB) remains <4%. This paucity is mainly attributed to difficulties associated with their expression and purification, propensity to form large multisubunit complexes, and challenges pertinent to identification of an ideal detergent, lipid, or detergent/lipid mixture that closely mimic their native environment. NMR is a powerful technique to obtain atomic-resolution and dynamic details of a protein in solution. This is accomplished through an assortment of isotopic labeling schemes designed to acquire multiple spectra that facilitate deduction of the final protein structure. In this review, we discuss current approaches and technological developments in the determination of membrane protein structures by solution NMR and highlight recent structural and mechanistic insights gained with this technique. We also discuss strategies for overcoming size limitations in NMR applications, and we explore a plethora of membrane mimetics available for the structural and mechanistic understanding of these essential cellular proteins.

Small-Angle X-ray Scattering Studies on the Structure of Disc-Shaped Bicelles Incorporated with Neutral PEGylated Lipids

In this study, small-angle X-ray scattering (SAXS) is successfully employed to investigate the structure of the DPPC/diC7PC disc-shaped bicelles incorporated with different amounts of C16-PEG2000-Ceramide lipids. The incorporation of the C16-PEG2000-Ceramide lipids could provide an antifouling capability to the bicelle for biomedical applications. However, traditionally it is believed that most of the incorporated PEGlylated lipids should lie in the rim of the disc-shaped bicelle. In this study, high sensitivity SAXS reveals the distribution of the added C16-PEG2000-Ceramide lipids in both the planar region and in the rim of the bicelle. The PEG brushes of C16-PEG2000-Ceramide lipids form a second shell outside the lipid headgroup shell of the bicelle. A double shell disc bicelle model is used in analyzing the SAXS data. The lipid density of C16-PEG2000-Ceramide in the rim is found to be about 1.7 times the C16-PEG2000-Ceramide lipid density in the planar region for all three C16-PEG2000-Ceramide concentrations, 1, 2, and 3 mM. Moreover, the bicelle core radius can be predicted well using the actual molecular ratio of lipids in the planar region to the lipids in the rim of the bicelles in the model calculation.

Structure determination protocol for transmembrane domain oligomers

The transmembrane (TM) anchors of cell surface proteins have been one of the 'blind spots' in structural biology because they are generally very hydrophobic, sometimes dynamic, and thus difficult targets for structural characterization. A plethora of examples show these membrane anchors are not merely anchors but can multimerize specifically to activate signaling receptors on the cell surface or to stabilize envelope proteins in viruses. Through a series of studies of the TM domains (TMDs) of immune receptors and viral membrane proteins, we have established a robust protocol for determining atomic-resolution structures of TM oligomers by NMR in bicelles that closely mimic a lipid bilayer. Our protocol overcomes hurdles typically encountered by structural biology techniques such as X-ray crystallography and cryo-electron microscopy (cryo-EM) when studying small TMDs. Here, we provide the details of the protocol, covering five major technical aspects: (i) a general method for producing isotopically labeled TM or membrane-proximal (MP) protein fragments that involves expression of the protein (which is fused to TrpLE) into inclusion bodies and releasing the target protein by cyanogen bromide (CNBr) cleavage; (ii) determination of the oligomeric state of TMDs in bicelles; (iii) detection of intermolecular contacts using nuclear Overhauser effect (NOE) experiments; (iv) structure determination; and (v) paramagnetic probe titration (PPT) to characterize the membrane partition of the TM oligomers. This protocol is broadly applicable for filling structural gaps of many type I/II membrane proteins. The procedures may take 3-6 months to complete, depending on the complexity and stability of the protein sample.

Understanding How Membrane Surface Charge Influences Lipid Bicelle Adsorption onto Oxide Surfaces

The adsorption of two-dimensional bicellar disks onto solid supports is an emerging fabrication technique to form supported lipid bilayers (SLBs) that is efficient and requires minimal sample preparation. To date, nearly all relevant studies have focused on zwitterionic lipid compositions and silica-based surfaces, and extending the scope of investigation to other lipid compositions and surfaces would improve our understanding of application possibilities and underpinning formation processes. Herein, using the quartz crystal microbalance-dissipation technique, we systematically investigated the adsorption of charged lipid bicelles onto silicon dioxide, titanium oxide, and aluminum oxide surfaces. Depending on the lipid composition and substrate, we observed different adsorption pathways, including (i) SLB formation via one- or two-step adsorption kinetics, (ii) monotonic adsorption without SLB formation, and (iii) negligible adsorption. On each substrate, SLB formation could be achieved with particular lipid compositions, whereas the trend in adsorption pathways varied according to the substrate and could be controlled by adjusting the bicelle?substrate interaction strength. To rationalize these findings, we discuss how electrostatic and hydration forces affect bicelle?substrate interactions on different oxide surfaces. Collectively, our findings demonstrate the broad utility of lipid bicelles for SLB formation while revealing physicochemical insights into the role of interfacial forces in controlling bicelle adsorption pathways.

Higher-Order Clustering of the Transmembrane Anchor of DR5 Drives Signaling

Receptor clustering on the cell membrane is critical in the signaling of many immunoreceptors, and this mechanism has previously been attributed to the extracellular and/or the intracellular interactions. Here, we report an unexpected finding that for death receptor 5 (DR5), a receptor in the tumor necrosis factor receptor superfamily, the transmembrane helix (TMH) alone in the receptor directly assembles a higher-order structure to drive signaling and that this structure is inhibited by the unliganded ectodomain. Nuclear magnetic resonance structure of the TMH in bicelles shows distinct trimerization and dimerization faces, allowing formation of dimer-trimer interaction networks. Single-TMH mutations that disrupt either trimerization or dimerization abolish ligand-induced receptor activation. Surprisingly, proteolytic removal of the DR5 ectodomain can fully activate downstream signaling in the absence of ligand. Our data suggest a receptor activation mechanism in which binding of ligand or antibodies to overcome the pre-ligand autoinhibition allows TMH clustering and thus signaling.

Temperature dependent self-organization of DMPC membranes promoted by intermediate amounts of the saponin aescin

The plant-derived biosurfactant aescin is naturally present in many plants and is used for treatment of disorders such as varicose veins and inflammation of veins. The hemolytic activity of this saponin is attributed to its interaction with cholesterol in the red blood cell membrane. This work investigates the phase and aggregation behavior of saponin-containing model membranes consisting of the phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC). The aescin concentrations studied range from 1 mol% to 7 mol% with respect to the total lipid content. The methods of choice to elucidate the structural picture are small-angle scattering of X-rays (SAXS) and neutrons (SANS) and cryogenic transmission electron microscopy (cryo-TEM). SANS and SAXS revealed that at lower aescin contents vesicular structures are conserved and vesicles tend to aggregate already at aescin contents of around 1 mol%. Aggregation and vesicle deformation effects are found to be stronger when the phospholipids are in the L [Formula: see text] phase. With increasing aescin content, mixed structures, i.e. aggregated and deformed vesicles and solubilized bilayer fragments, are present. This was proven for a sample with 4 mol% aescin by cryo-TEM. An increasing aescin amount leads to membrane decomposition and free standing bilayers which tend to build stacks at high temperature. These stacks are characterized by SAXS using the modified Caillé theory. Analyses and model dependent fitting reveal formation of well-defined structures beginning at 7 mol% aescin.

Structure of Phospholipid Mixed Micelles (Bicelles) Studied by Small-Angle X-ray Scattering

Mixed phospholipid micelles (bicelles) are widely applied in nuclear magnetic resonance (NMR) studies of membrane proteins in solution, as they can solubilize these proteins and provide a membrane-like environment. In this work, the structure of bicelles of dihexanoyl phosphatidyl choline (DHPC) and dimyristoyl phosphatidyl choline (DMPC) at different ratios was determined by small-angle X-ray scattering (SAXS) at 37 °C. Samples with concentrations as applied for NMR measurements with 28 wt % lipids were diluted to avoid concentration effects in the SAXS data. The DMPC/DHPC ratio within the bicelles was kept constant by diluting with solutions of finite DHPC concentrations, where the concentration of free DHPC is the same as in the original solution. Absolute-scale modeling of the SAXS data using molecular and concentration constraints reveals a relatively complex set of morphologies of the lipid aggregates as a function of the molar ratio Q of DMPC to DHPC. At Q = 0 (pure DHPC lipids), oblate core-shell micelles are present. At Q = 0.5, the bicelles have a tablet-shaped core-shell cylindrical form with an ellipsoidal cross section. For Q = 1, 2, 3.2, and 4, the bicelles have a rectangular cuboidal structure with a core and a shell, for which the overall length and width increase with Q. At Q = ∞ (pure DMPC), there is coexistence between multilamellar structures and free bilayers. For Q = 1-4, the hydrocarbon core is relatively narrow and the headgroup thickness on the flat areas is larger than that of, respectively, pure DHPC and DMPC, suggesting some mixing of DHPC into these areas and staggering of the molecules. This is further supported by comparisons of the ratio of the areas of rim and flat parts and estimates of the composition of the flat areas.