Phospholipid Bilayer Nanodiscs Research Articles

Structure of the turnover-ready state of an ancestral respiratory complex I

Respiratory complex I is pivotal for cellular energy conversion, harnessing energy from NADH:ubiquinone oxidoreduction to drive protons across energy-transducing membranes for ATP synthesis. Despite detailed structural information on complex I, its mechanism of catalysis remains elusive due to lack of accompanying functional data for comprehensive structure-function analyses. Here, we present the 2.3-Å resolution structure of complex I from the α-proteobacterium Paracoccus denitrificans, a close relative of the mitochondrial progenitor, in phospholipid-bilayer nanodiscs. Three eukaryotic-type supernumerary subunits (NDUFS4, NDUFS6 and NDUFA12) plus a novel L-isoaspartyl-O-methyltransferase are bound to the core complex. Importantly, the enzyme is in a single, homogeneous resting state that matches the closed, turnover-ready (active) state of mammalian complex I. Our structure reveals the elements that stabilise the closed state and completes P. denitrificans complex I as a unified platform for combining structure, function and genetics in mechanistic studies.

The application of nanodiscs in membrane protein drug discovery & development and drug delivery.

The phospholipid bilayer nanodiscs (LNDs), as a rapidly-developing tool in recent years, provide a natural bio-memebrane environment to maintain the native conformation and functions of membrane proteins as well as a versatile delivery vehicle for a variety of hydrophobic and hydrophilic drugs. We have seen unprecedented advantages of phospholipid bilayer nanodiscs in membrane protein structure characterization, biochemical and physiological studies of membrane proteins, membrane environment studies, drug discovery & development, and drug delivery. Many previous reviews have been mainly focused on the advantages of nanodiscs in membrane protein researches, but few have touched upon the importance and potential application of nanodiscs in pharmaceutical industries. This review will provide general description of the structural characteristics, advantages, classification, and applications of phospholipid nanodiscs, with particular focus on nanodisc-enabled membrane protein drug discovery & development as well as drug delivery.

Global fitting of multiple data frames from SEC-SAXS to investigate the structure of next-generation nanodiscs.

The combination of online size-exclusion chromatography and small-angle X-ray scattering (SEC-SAXS) is rapidly becoming a key technique for structural investigations of elaborate biophysical samples in solution. Here, a novel model-refinement strategy centred around the technique is outlined and its utility is demonstrated by analysing data series from several SEC-SAXS experiments on phospholipid bilayer nanodiscs. Using this method, a single model was globally refined against many frames from the same data series, thereby capturing the frame-to-frame tendencies of the irradiated sample. These are compared with models refined in the traditional manner, in which refinement is based on the average profile of a set of consecutive frames from the same data series without an in-depth comparison of individual frames. This is considered to be an attractive model-refinement scheme as it considerably lowers the total number of parameters refined from the data series, produces tendencies that are automatically consistent between frames, and utilizes a considerably larger portion of the recorded data than is often performed in such experiments. Additionally, a method is outlined for correcting a measured UV absorption signal by accounting for potential peak broadening by the experimental setup.

Large Nanodiscs: A Potential Game Changer in Structural Biology of Membrane Protein Complexes and Virus Entry

Phospho-lipid bilayer nanodiscs have gathered much scientific interest as a stable and tunable membrane mimetic for the study of membrane proteins. Until recently the size of the nanodiscs that could be produced was limited to ~ 16 nm. Recent advances in nanodisc engineering such as covalently circularized nanodiscs (cND) and DNA corralled nanodiscs (DCND) have opened up the possibility of engineering nanodiscs of size up to 90 nm. This enables widening the application of nanodiscs from single membrane proteins to investigating large protein complexes and biological processes such as virus-membrane fusion and synaptic vesicle fusion. Another aspect of exploiting the large available surface area of these novel nanodiscs could be to engineer more realistic membrane mimetic systems with features such as membrane asymmetry and curvature. In this review, we discuss the recent technical developments in nanodisc technology leading to construction of large nanodiscs and examine some of the implicit applications.

Elucidation of molecular functions of human tumor suppressor protein 101F6 by reconstitution into phospholipid bilayer nanodiscs

A candidate human tumor suppressor gene 101F6 product was expressed successfully in Pichia pastoris yeast cells. The purified 101F6 protein was successfully incorporated into phospholipid bilayer nanodiscs with different sizes by employing two reconstitution methods; self-assembly and reconstitution into the preformed empty nanodisc. The reconstituted 101F6 protein could be reduced with ascorbate quickly and was very stable even at ambient temperatures.

Reconstitution and NMR Characterization of the Ion-Channel Accessory Subunit Barttin in Detergents and Lipid-Bilayer Nanodiscs.

Barttin is an accessory subunit of ClC-K chloride channels expressed in the kidney and the inner ear. Main functions of ClC-K/barttin channels are the generation of the cortico-medullary osmotic gradients in the kidney and the endocochlear potential in the inner ear. Mutations in the gene encoding barttin, BSND, result in impaired urinary concentration and sensory deafness. Barttin is predicted to be a two helical integral membrane protein that directly interacts with its ion channel in the membrane bilayer where it stabilizes the channel complex, promotes its incorporation into the surface membrane and leads to channel activation. It therefore is an attractive target to address fundamental questions of intermolecular communication within the membrane. However, so far inherent challenges in protein expression and stabilization prevented comprehensive in vitro studies and structural characterization. Here we demonstrate that cell-free expression enables production of sufficient quantities of an isotope-labeled barttin variant (I72X Barttin, capable to promote surface membrane insertion and channel activation) for NMR-based structural studies. Additionally, we established purification protocols as well as reconstitution strategies in detergent micelles and phospholipid bilayer nanodiscs. Stability, folding, and NMR data quality are reported as well as a suitable assignment strategy, paving the way to its structural characterization.

Structural insights from lipid-bilayer nanodiscs link \u03b1-Synuclein membrane-binding modes to amyloid fibril formation

The protein α-Synuclein (αS) is linked to Parkinson’s disease through its abnormal aggregation, which is thought to involve cytosolic and membrane-bound forms of αS. Following previous studies using micelles and vesicles, we present a comprehensive study of αS interaction with phospholipid bilayer nanodiscs. Using a combination of NMR-spectroscopic, biophysical, and computational methods, we structurally and kinetically characterize αS interaction with different membrane discs in a quantitative and site-resolved way. We obtain global and residue-specific αS membrane affinities, and determine modulations of αS membrane binding due to αS acetylation, membrane plasticity, lipid charge density, and accessible membrane surface area, as well as the consequences of the different binding modes for αS amyloid fibril formation. Our results establish a structural and kinetic link between the observed dissimilar binding modes and either aggregation-inhibiting properties, largely unperturbed aggregation, or accelerated aggregation due to membrane-assisted fibril nucleation.

Reconstitution of Voltage-Activated Potassium Channel into Phospholipid Bilayer

Voltage-activated ion channels are expressed in the membranes of excitable cells, and open and close in response to changes in membrane voltage. Physiologically, they play diverse roles, from the generation of action potentials to triggering the release of neurotransmitters at synapses. To study the biochemical properties, these ion channels are usually purified and studied under detergent-solubilized condition, but many ion channels behave differently in detergent when compared to their native membrane environment. One recently introduced technique to overcome this issue is using lipid bilayer nanodiscs. Nanodiscs are a few nanometer-sized hockey-puck-shaped lipid bilayers solubilized by engineered apolipoprotein, membrane scaffold protein (MSP). MSP is comprised of short repeats of amphipathic alpha helies that surround the hydrophobic acyl chains of phospholipids. To investigate the structure and biochemical properties of voltage-activated potassium (Kv) channels in a membrane environment, we reconstituted a Kv channel into phospholipid bilayer nanodiscs using phospholipid and MSP. We first attempted to assemble empty nandiscs (nanodisc without Kv) to determine the optimal ratio between lipid and MSP that provides the best yields. Using these conditions, we reconstituted Kv channels into nanodiscs, and show that they elute as a single peak in gel-filtration chromatography. SDS-PAGE result indicates that the preparation contains each subunit corresponding to the Kv and MSP, confirming successful reconstitution of the Kv into nanodiscs. We also show that a voltage-sensor toxin can bind to the Kv channel in nanodiscs, confirming that the architecture of the Kv channel is well maintained in nanodiscs.

Liver microsomal lipid enhances the activity and redox coupling of colocalized cytochrome P450 reductase-cytochrome P450 3A4 in nanodiscs.

The haem‐containing mono‐oxygenase cytochrome P450 3A4 (CYP3A4) and its redox partner NADPH‐dependent cytochrome P450 oxidoreductase (CPR) are among the most important enzymes in human liver for metabolizing drugs and xenobiotic compounds. They are membrane‐bound in the endoplasmic reticulum (ER). How ER colocalization and the complex ER phospholipid composition influence enzyme activity are not well understood. CPR and CYP3A4 were incorporated into phospholipid bilayer nanodiscs, both singly, and together in a 1 : 1 ratio, to investigate the significance of membrane insertion and the influence of varying membrane composition on steady‐state reaction kinetics. Reaction kinetics were analysed using a fluorimetric assay with 7‐benzyloxyquinoline as substrate for CYP3A4. Full activity of the mono‐oxygenase system, with electron transfer from NADPH via CPR, could only be reconstituted when CPR and CYP3A4 were colocalized within the same nanodiscs. No activity was observed when CPR and CYP3A4 were each incorporated separately into nanodiscs then mixed together, or when soluble forms of CPR were mixed with preassembled CYP3A4‐nanodiscs. Membrane integration and colocalization are therefore essential for electron transfer. Liver microsomal lipid had an enhancing effect compared with phosphatidylcholine on the activity of CPR alone in nanodiscs, and a greater enhancing effect on the activity of CPR‐CYP3A4 nanodisc complexes, which was not matched by a phospholipid mixture designed to mimic the ER composition. Furthermore, liver lipid enhanced redox coupling within the system. Thus, natural ER lipids possess properties or include components important for enhanced catalysis by CPR‐CYP3A4 nanodisc complexes. Our findings demonstrate the importance of using natural lipid preparations for the detailed analysis of membrane protein activity.

Phospholipid bilayer affinities and solvation characteristics by electrokinetic chromatography with a nanodisc pseudostationary phase.

Phospholipid bilayer nanodiscs composed of 1,2-dimyristoyl-sn-glycero-3-phosphocholine and synthetic maleic acid-styrene copolymer belts have been introduced as a pseudostationary phase (PSP) in electrokinetic chromatography and demonstrated good performance. The nanodiscs provide a suitable migration range and high theoretical plate counts. Using this nanodisc pseudostationary phase, the affinity of the bilayer structure for probe solutes was determined and characterized. Good correlation is observed between retention factors and octanol water partition coefficients for particular categories of solutes, but the general correlation is weak primarily because the nanodiscs show stronger affinity than octanol for hydrogen bond donors. This suggests that a more appropriate application of this technology is to measure and characterize interactions between solutes and lipid bilayers directly. Linear solvation energy relationship analysis of the nanodisc-solute interactions in this study demonstrates that the nanodiscs provide a solvation environment with low cohesivity and weak hydrogen bond donating ability, and provide relatively strong hydrogen bond acceptor strength.

Preparation and Characterization of Stable α-Synuclein Lipoprotein Particles

Multiple neurodegenerative diseases are caused by the aggregation of the human α-Synuclein (α-Syn) protein. α-Syn possesses high structural plasticity and the capability of interacting with membranes. Both features are not only essential for its physiological function but also play a role in the aggregation process. Recently it has been proposed that α-Syn is able to form lipid-protein particles reminiscent of high-density lipoproteins. Here, we present a method to obtain a stable and homogeneous population of nanometer-sized particles composed of α-Syn and anionic phospholipids. These particles are called α-Syn lipoprotein (nano)particles to indicate their relationship to high-density lipoproteins formed by human apolipoproteins in vivo and of in vitro self-assembling phospholipid bilayer nanodiscs. Structural investigations of the α-Syn lipoprotein particles by circular dichroism (CD) and magic angle solid-state nuclear magnetic resonance (MAS SS-NMR) spectroscopy establish that α-Syn adopts a helical secondary structure within these particles. Based on cryo-electron microscopy (cryo-EM) and dynamic light scattering (DLS) α-Syn lipoprotein particles have a defined size with a diameter of ∼23 nm. Chemical cross-linking in combination with solution-state NMR and multiangle static light scattering (MALS) of α-Syn particles reveal a high-order protein-lipid entity composed of ∼8-10 α-Syn molecules. The close resemblance in size between cross-linked in vitro-derived α-Syn lipoprotein particles and a cross-linked species of endogenous α-Syn from SH-SY5Y human neuroblastoma cells indicates a potential functional relevance of α-Syn lipoprotein nanoparticles.

Assembly and characterization of gp160-nanodiscs: A new platform for biochemical characterization of HIV envelope spikes

The human immunodeficiency virus (HIV) is the causative agent of acquired immune deficiency syndrome (AIDS) and is thus responsible for significant morbidity and mortality worldwide. Despite considerable effort, preparation of an effective vaccine for AIDS has been elusive and it has become clear that a fundamental understanding of the relevant antigenic targets on HIV is essential. The Env trimer spike is the only viral antigen present on the surface of the viral particle and it is the target of all broadly neutralizing antibodies isolated to date. Thus, a soluble, homogeneous, and well-defined preparation of Env trimers is an important first step toward biochemical and structural characterization of the antigenic spike. Phospholipid bilayer nanodiscs represent a relatively new technology that can serve as a platform for the assembly of membrane proteins into a native membrane-like environment. Here we describe the preparation and characterization of unprocessed full-length, natively glycoslyated gp160 Env proteins incorporated into nanodiscs (gp160-ND). The particles are soluble and well defined in the absence of detergent, and possess a morphology anticipated of Env incorporated into a lipid ND. Importantly, the gp160-NDs retain CD4 and Env antibody binding characteristics expected of a functional trimer spike and their incorporation into a lipid membrane allows interrogation of epitopes associated with the membrane-proximal ectodomain region of gp41. These studies provide the groundwork for the use of gp160-ND in more detailed biochemical and structural studies that may set the stage for their use in vaccine development.

Kinetic and Thermodynamic Analysis of Cholesterol Transfer between Phospholipid Vesicles and Nanodiscs.

We investigated interparticle transfer of cholesterol (Chol) between large unilamellar vesicles (LUVs) and phospholipid bilayer nanodiscs. The Chol transfer rate from LUVs to nanodiscs was decreased by an increase in the Chol content or incorporation of sphingomyelin in donor phosphatidylcholine/Chol LUVs but was not influenced by the lipid composition of acceptor particles. These results suggest that Chol dissociation from the lipid bilayer into aqueous phase is the rate-limiting step of the transfer and that the process depends on the fluidity of the donor membranes. The Chol dissociation rate from nanodiscs was faster than that from LUVs with similar lipid composition. Chol preferably partitioned to LUVs rather than nanodiscs, which is consistent with the faster dissociation rate from nanodiscs. The activation energy of Chol dissociation from nanodiscs was 1.7 kJ/mol lower than that from LUV, which was brought by increased (less negative) activation entropy and enthalpy. In addition, fluorescence lifetime and anisotropy data revealed that the lipid bilayer of nanodiscs is more tightly packed than that of LUVs. These results suggest that the tighter lipid packing in nanodiscs destabilizes the Chol-containing bilayer by reducing the entropy, which facilitates Chol dissociation.

ATP-dependent Conformational Changes Trigger Substrate Capture and Release by an ECF-type Biotin Transporter

Energy-coupling factor (ECF) transporters for vitamins and metal ions in prokaryotes consist of two ATP-binding cassette-type ATPases, a substrate-specific transmembrane protein (S component) and a transmembrane protein (T component) that physically interacts with the ATPases and the S component. The mechanism of ECF transporters was analyzed upon reconstitution of a bacterial biotin transporter into phospholipid bilayer nanodiscs. ATPase activity was not stimulated by biotin and was only moderately reduced by vanadate. A non-hydrolyzable ATP analog was a competitive inhibitor. As evidenced by cross-linking of monocysteine variants and by site-specific spin labeling of the Q-helix followed by EPR-based interspin distance analyses, closure and reopening of the ATPase dimer (BioM2) was a consequence of ATP binding and hydrolysis, respectively. A previously suggested role of a stretch of small hydrophobic amino acid residues within the first transmembrane segment of the S units for S unit/T unit interactions was structurally and functionally confirmed for the biotin transporter. Cross-linking of this segment in BioY (S) using homobifunctional thiol-reactive reagents to a coupling helix of BioN (T) indicated a reorientation rather than a disruption of the BioY/BioN interface during catalysis. Fluorescence emission of BioY labeled with an environmentally sensitive fluorophore was compatible with an ATP-induced reorientation and consistent with a hypothesized toppling mechanism. As demonstrated by [(3)H]biotin capture assays, ATP binding stimulated substrate capture by the transporter, and subsequent ATP hydrolysis led to substrate release. Our study represents the first experimental insight into the individual steps during the catalytic cycle of an ECF transporter in a lipid environment.

Smaller Nanodiscs are Suitable for Studying Protein Lipid Interactions by Solution NMR.

Phospholipid bilayer nanodiscs, a newly developed model membrane system, provides "native-like" membrane environment for membrane protein studies. Nanodiscs assembled by membrane scaffold protein and phospholipid bilayer, with defined sizes that can be accurately regulated by changing the amino acid residues of the MSP construct. Herein we described the expression and purification of ΔMSP, a deletion mutant of the membrane scaffold protein. Smaller nanodiscs with mixed lipids were assembled, and the observed (31)P NMR spectra showed identical chemical shifts to those of nanodiscs with pure POPC and POPE lipids, indicating they share similar chemical environments. The success of incorporation STIM1-TM into nanodiscs indicated the application of this smaller nanodisc system can be used to membrane protein studies by solution NMR.

Phospholipid bilayer nanodiscs: a powerful tool to study the structural organization and biochemical reactivity of proteins in membrane-like environments.

Nanodiscs are disc-like structures formed by two copies of a membrane scaffold protein, engineered from apolipoprotein A-I, surrounding a phospholipid mixture that can incorporate membrane proteins preserving their natural properties. They behave as soluble entities allowing the use of high-resolution structural techniques to determine the structural organization of the embedded membrane protein, and the use of solution biochemical-biophysical tools to measure its activity, assembly and interactions with other proteins in membranelike environments. In addition, nanodiscs are biocompatible which makes them an attractive technology to be used in therapy, drug discovery, and other biotechnological applications.

Influence of the lipid membrane environment on structure and activity of the outer membrane protein Ail from Yersinia pestis

The surrounding environment has significant consequences for the structural and functional properties of membrane proteins. While native structure and function can be reconstituted in lipid bilayer membranes, the detergents used for protein solubilization are not always compatible with biological activity and, hence, not always appropriate for direct detection of ligand binding by NMR spectroscopy. Here we describe how the sample environment affects the activity of the outer membrane protein Ail (attachment invasion locus) from Yersinia pestis. Although Ail adopts the correct β-barrel fold in micelles, the high detergent concentrations required for NMR structural studies are not compatible with the ligand binding functionality of the protein. We also describe preparations of Ail embedded in phospholipid bilayer nanodiscs, optimized for NMR studies and ligand binding activity assays. Ail in nanodiscs is capable of binding its human ligand fibronectin and also yields high quality NMR spectra that reflect the proper fold. Binding activity assays, developed to be performed directly with the NMR samples, show that ligand binding involves the extracellular loops of Ail. The data show that even when detergent micelles support the protein fold, detergents can interfere with activity in subtle ways.

Radioligand Binding to Nanodisc-Reconstituted Membrane Transporters Assessed by the Scintillation Proximity Assay

The scintillation proximity assay is a powerful technique for measuring radioligand binding to membrane transporters and has become an integral part of high-throughput drug discovery screening efforts. Here we adapt the method for use with purified LeuT, a prokaryotic secondary transporter, reconstituted into phospholipid bilayer nanodiscs. This application surmounts potential challenges with background interference from endogenously expressed proteins, aggregation and loss of binding activity often accompanying detergent solubilization from native cell membranes, and heterogeneity in size and transporter orientation, where at least some ligand binding sites are inaccessible, associated with reconstitution into lipid vesicles.

Enhancement Of Endothelial Cell Barrier Function By Antibody-Driven Affinity Modulation Of PECAM-1

Endothelial integrity is a critical parameter of hemostasis, and loss of barrier function contributes to the etiology and pathogenesis of both autoimmune and infectious disease. PECAM-1 is a cellular adhesion and signaling receptor comprised of six extracellular immunoglobulin (Ig) – like homology domains, a short transmembrane domain, and a 118 amino acid cytoplasmic domain that becomes serine and tyrosine phosphorylated upon activation. PECAM-1 is a major constituent of the endothelial cell intercellular junction, where up to 2 x 106 molecules concentrate upon cell-cell contact. Previous studies have shown that PECAM-1–PECAM-1 homophilic interactions mediated by N-terminal Ig domain 1 (IgD1) are required for border localization, and contribute importantly to steady-state endothelial cell barrier stability as well as the ability of the vascular endothelium to recover, both in vitro and in vivo, following inflammatory or hemostatic challenge. To examine whether the homophilic adhesive properties of PECAM-1 might be subject to regulation, we prepared phospholipid bilayer nanodiscs containing purified, full-length PECAM-1 and examined their ability to bind intact PECAM-1-expressing cells. Preliminary transmission electron microscopy studies indicated that PECAM-1-containing nanodiscs harbored a single, high-density refraction shadow, suggesting the presence of a single inserted PECAM-1 protein per nanodisc. Binding of these nanodiscs to either human umbilical vein endothelial cells or to PECAM-1-transfected HEK 293 cells required IgD1, as Fab fragments of the IgD1-specific monoclonal antibody (mAb), PECAM-1.3, completely blocked their binding. Interestingly, Fab fragments of mAbs PECAM-1.2 or 4G6, which bind closely-spaced epitopes within membrane-proximal IgD6, were found to enhance PECAM-1 nanodisc binding by 200-300%, suggesting that they induced a conformational change leading to a high-affinity form of PECAM-1. In support of this notion, rotary-shadowed electron micrographs of the purified PECAM-1 ectodomain revealed an ensemble of straight and bent molecular isoforms, reminiscent of conformational isomorphs that exist among members of the integrin family of adhesion receptors. Finally, to determine whether regulatable affinity modulation of this Ig superfamily member might be exploited to enhance or reinforce endothelial cell-cell borders, endothelial cell monolayer resistance was quantitatively measured using Electric Cell-substrate Impedance Sensing (ECIS), a real-time reporter of barrier function. As predicted, IgD1-specific mAb PECAM-1.3 delayed barrier recovery following thrombin-induced disruption of the endothelial cell monolayer, while IgD6-specific mAb PECAM-1.2 markedly enhanced the rate of barrier restoration. Both antibodies were without effect on endothelial cell monolayers in which PECAM-1 had been knocked down using a lentivirally-introduced PECAM-1 siRNA. Taken together, these data demonstrate that the homophilic binding affinity of PECAM-1 can be enhanced by IgD6-specific antibodies, and suggest a novel therapeutic modality for treating vascular endothelial injury-related disorders. Disclosures:No relevant conflicts of interest to declare.

Active Plasma Membrane P-type H+-ATPase Reconstituted into Nanodiscs Is a Monomer

Plasma membrane H(+)-ATPases form a subfamily of P-type ATPases responsible for pumping protons out of cells and are essential for establishing and maintaining the crucial transmembrane proton gradient in plants and fungi. Here, we report the reconstitution of the Arabidopsis thaliana plasma membrane H(+)-ATPase isoform 2 into soluble nanoscale lipid bilayers, also termed nanodiscs. Based on native gel analysis and cross-linking studies, the pump inserts into nanodiscs as a functional monomer. Insertion of the H(+)-ATPase into nanodiscs has the potential to enable structural and functional characterization using techniques normally applicable only for soluble proteins.