Making a macro problem nano: bacterial lipid nanodiscs as potential vaccine candidates [Slides]
Abstract not provided.
59 BASIC BIOLOGICAL SCIENCES↗
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Characterization of bacterial lipid nanodiscs as potential vaccine candidates
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Pimentel, Olivia Raquel Chavez↗
High-throughput cell-free screening of eukaryotic membrane protein expression in lipidic mimetics
Membrane proteins play essential roles in cellular function and metabolism. Nonetheless, biophysical and structural studies of membrane proteins are impeded by the difficulty of their expression in and purification from heterologous cell-based systems. As an alternative to these cell-based systems, cell-free protein synthesis has proven to be an exquisite method for screening membrane protein targets in a variety of lipidic mimetics. Here we report a high-throughput screening workflow and applied it to screen 61eukaryotic membrane protein targets. For each target, we tested its expression in lipidic mimetics: two detergents, two liposomes, and two nanodiscs. We show that 35 membrane proteins (57%) can be expressed in a soluble fraction in at least one of the mimetics with the two detergents performing significantly better than nanodiscs and liposomes, in that order. Using the established cell-free workflow, we studied the production and biophysical assays for mitochondrial pyruvate carrier (MPC) complexes. Our studies show that the complexes produced in cell-free are functional competent in complex formation and substrate binding. Our results highlight the utility of using cell-free systems for screening and production of eukaryotic membrane proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Cryo-EM structures of Escherichia coli cytochrome bo 3 reveal bound phospholipids and ubiquinone-8 in a dynamic substrate binding site
Two independent structures of the proton-pumping, respiratory cytochrome bo3 ubiquinol oxidase (cyt bo 3 ) have been determined by cryogenic electron microscopy (cryo-EM) in styrene–maleic acid (SMA) copolymer nanodiscs and in membrane scaffold protein (MSP) nanodiscs to 2.55- and 2.19-Å resolution, respectively. The structures include the metal redox centers (heme b, heme o 3 , and Cu B ), the redox-active cross-linked histidine–tyrosine cofactor, and the internal water molecules in the proton-conducting D channel. Each structure also contains one equivalent of ubiquinone-8 (UQ8) in the substrate binding site as well as several phospholipid molecules. The isoprene side chain of UQ8 is clamped within a hydrophobic groove in subunit I by transmembrane helix TM0, which is only present in quinol oxidases and not in the closely related cytochrome c oxidases. Both structures show carbonyl O1 of the UQ8 headgroup hydrogen bonded to D75I and R71 I . In both structures, residue H98 I occupies two conformations. In conformation 1, H98 I forms a hydrogen bond with carbonyl O4 of the UQ8 headgroup, but in conformation 2, the imidazole side chain of H98 I has flipped to form a hydrogen bond with E14 I at the N-terminal end of TM0. We propose that H98 I dynamics facilitate proton transfer from ubiquinol to the periplasmic aqueous phase during oxidation of the substrate. Computational studies show that TM0 creates a channel, allowing access of water to the ubiquinol headgroup and to H98 I .
bioenergetics↗
Elucidating interprotein energy transfer dynamics within the antenna network from purple bacteria
In photosynthesis, absorbed light energy transfers through a network of antenna proteins with near-unity quantum efficiency to reach the reaction center, which initiates the downstream biochemical reactions. While the energy transfer dynamics within individual antenna proteins have been extensively studied over the past decades, the dynamics between the proteins are poorly understood due to the heterogeneous organization of the network. Previously reported timescales averaged over such heterogeneity, obscuring individual interprotein energy transfer steps. Here, we isolated and interrogated interprotein energy transfer by embedding two variants of the primary antenna protein from purple bacteria, light-harvesting complex 2 (LH2), together into a near-native membrane disc, known as a nanodisc. We integrated ultrafast transient absorption spectroscopy, quantum dynamics simulations, and cryogenic electron microscopy to determine interprotein energy transfer timescales. By varying the diameter of the nanodiscs, we replicated a range of distances between the proteins. The closest distance possible between neighboring LH2, which is the most common in native membranes, is 25 Å and resulted in a timescale of 5.7 ps. Larger distances of 28 to 31 Å resulted in timescales of 10 to 14 ps. Corresponding simulations showed that the fast energy transfer steps between closely spaced LH2 increase transport distances by ∼15%. Overall, our results introduce a framework for well-controlled studies of interprotein energy transfer dynamics and suggest that protein pairs serve as the primary pathway for the efficient transport of solar energy.
59 BASIC BIOLOGICAL SCIENCES↗
Recovery of particulate methane monooxygenase structure and activity in a lipid bilayer
Bacterial methane oxidation using the enzyme particulate methane monooxygenase (pMMO) contributes to the removal of environmental methane, a potent greenhouse gas. Crystal structures determined using inactive, detergent-solubilized pMMO lack several conserved regions neighboring the proposed active site. We show that reconstituting pMMO in nanodiscs with lipids extracted from the native organism restores methane oxidation activity. Multiple nanodisc-embedded pMMO structures determined by cryo–electron microscopy to 2.14- to 2.46-angstrom resolution reveal the structure of pMMO in a lipid environment. The resulting model includes stabilizing lipids, regions of the PmoA and PmoC subunits not observed in prior structures, and a previously undetected copper-binding site in the PmoC subunit with an adjacent hydrophobic cavity. These structures provide a revised framework for understanding and engineering pMMO function.
Science & Technology - Other Topics↗
Rapid T cell engineering to counter emerging threats (Full Technical Report)
Instead of genetic engineering, we sought to determine if a rapid method of membrane protein delivery could generate functional CAR-T cells in a rapid, safer, cost-effective manner. Using cell free protein synthesis, we generated CAR proteins embedded in a nanodisc, and thus effectively solubilized the protein. We demonstrated the first functional CAR proteins outside of a cellular context. We next tested uptake into immune cells and found extremely high uptake into T cells and multiple other populations of immune cells. We found some evidence of cytotoxicity in vitro conferred by the nanodisc delivered protein.
59 BASIC BIOLOGICAL SCIENCES↗
Structure of Diisobutylene Maleic Acid Copolymer (DIBMA) and Its Lipid Particle as a “Stealth” Membrane-Mimetic for Membrane Protein Research
The study of membrane proteins remains challenging, especially in a native membrane environment. Recently, major progress has been made using maleic acid copolymers, such as styrene maleic acid, to purify membrane proteins and study them directly with native lipids associated with the membrane. Additional maleic acid copolymers, such as diisobutylene maleic acid (DIBMA) membrane-mimetic systems, are being developed and found to have improved spectroscopic properties and pH stability. We studied DIBMA and its lipid particles in solution to better understand its assembly, without and with the lipids, to provide an insight regarding how to use it in solution for better membrane extraction. Using small-angle neutron and X-ray scattering (SANS/SAXS), we show that DIBMA organizes into structures of different size scales at various concentrations and ionic strengths. The polymer performed reasonably well under most solvent conditions except in very low concentrations and high-salt conditions that could result in limited interaction with lipids. To explore DIBMA lipid particles as a suitable membrane-mimetic system for neutron scattering studies of membrane proteins, we measured and determined the contrast-matching point of DIBMA to be ~12% (v/v) D 2 O — similar to that of most protiated lipid molecules but distinct from that of regular protiated proteins — providing a natural contrast for separating their neutron scattering signals. Using SANS contrast variation, we demonstrated that the scattering from the whole lipid particle can be annihilated. Further, we determined that a well-defined lipid nanodisc structure with DIBMA was contrast-matched. These results demonstrate that the DIBMA lipid particle is an outstanding “stealth” membrane-mimetic for membrane proteins. The results provide a structural framework for understanding the organization and assembly process of the polymer itself and the lipid molecules. Such an understanding is imperative for structural techniques such as cryo-electron microscopy, nuclear magnetic resonance, small-angle scattering, and other biophysical techniques.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
High Mass Analysis with a Fourier Transform Ion Cyclotron Resonance Mass Spectrometer: From Inorganic Salt Clusters to Antibody Conjugates and Beyond
Analysis of proteins and complexes under native mass spectrometric (MS) and solution conditions was typically performed using time-of-flight (ToF) analyzers, due to their routine high m/z transmission and detection capabilities. However, over recent years, the ability of Orbitrap-based mass spectrometers to transmit and detect a range of high molecular weight species is well documented. Herein, we describe how a 15 Tesla Fourier transform ion cyclotron resonance mass spectrometer (15 T FT-ICR MS) is more than capable of analyzing a wide range of ions in the high m/z scale (>5000), in both positive and negative instrument polarities, ranging from the inorganic cesium iodide salt clusters; a humanized IgG1k monoclonal antibody (mAb; 148.2 kDa); an IgG1-mertansine drug conjugate (148.5 kDa, drug-to-antibody ratio; DAR 2.26); an IgG1-siRNA conjugate (159.1 kDa; ribonucleic acid to antibody ratio; RAR 1); the membrane protein aquaporin-Z (97.2 kDa) liberated from a C8E4 detergent micelle; the empty MSP1D1-nanodisc (142.5 kDa) and the tetradecameric chaperone protein complex GroEL (806.2 kDa; GroEL dimer at 1.6 MDa). We also investigate different regions of the FT-ICR MS that impact ion transmission and desolvation. Finally, we demonstrate how the transmission of these species and resultant spectra are highly consistent with those previously generated on both quadrupole-ToF (Q-ToF) and Orbitrap instrumentation. This article serves as an impactful example of how FT-ICR mass analyzers are competitive to Q-ToFs and Orbitraps for high mass detection at high m/z.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies
Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via high-density lipoprotein (HDL) and low-density lipoprotein (LDL) maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics, and to develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Codelivery of Paclitaxel and Parthenolide in Discoidal Bicelles for a Synergistic Anticancer Effect: Structure Matters
Nanotechnology has long been used to improve the tumor targeting of chemotherapeutics. The structure of these nanocarriers greatly affects their efficacy and toxicity. Herein, structurally stable nanodiscoidal phospholipid bicelles, which are capable of encapsulating anticancer drugs, paclitaxel (PTX) and parthenolide (PTL), are designed. This nanodiscoidal bicelle structure is shown previously to exhibit longer blood circulation, deeper tumor penetration, and increased tumor cell uptake compared with spherical particles of similar compositions. Structural characterization and loading capacity of the PTX‐ and PTL‐ loaded nanodiscs are conducted along with an investigation into the cytotoxicity of the bicelles based on the drug‐to‐lipid ratios of both drugs loaded separately and in combination. A significant synergistic effect between both loaded drugs is also observed in A549 lung cancer and drug‐resistant MDA‐MB‐231 cell lines. An in vivo study using mice bearing subcutaneous A549 tumors shows a long circulation time of the intravenously injected DiR‐loaded bicelles and significant antitumor efficacy of the PTX‐ and PTL‐loaded bicelles. This efficacious self‐assembled nanoparticle system displays great potential as a nanoplatform to codeliver multiple therapeutics or diagnostics for improving cancer therapy.
Rad, Armin Tahmasbi↗
Small angle neutron scattering and lipidomic analysis of a native, trimeric PSI-SMALP from a thermophilic cyanobacteria
The use of styrene-maleic acid copolymers (SMAs) to produce membrane protein-containing nanodiscs without the initial detergent isolation has gained significant interest over the last decade. We have previously shown that a Photosystem I SMALP from the thermophilic cyanobacterium, Thermosynechococcus elongatus (PSI-SMALP), has much more rapid energy transfer and charge separation in vitro than detergent isolated PSI complexes. In this study, we have utilized small-angle neutron scattering (SANS) to better understand the geometry of these SMALPs. These techniques allow us to investigate the size and shape of these particles in their fully solvated state. Further, the particle's proteolipid core and detergent shell or copolymer belt can be interrogated separately using contrast variation, a capability unique to SANS. Here we report the dimensions of the Thermosynechococcus elongatus PSI-SMALP containing a PSI trimer. At ~1.5 MDa, PSI-SMALP is the largest SMALP to be isolated; our lipidomic analysis indicates it contains ~1300 lipids/per trimeric particle, >40-fold more than the PSI-DDM particle and > 100 fold more than identified in the 1JB0 crystal structure. Interestingly, the lipid composition to the PSI trimer in the PSI-SMALP differs significantly from bulk thylakoid composition, being enriched ~50 % in the anionic sulfolipid, SQDG. Finally, utilizing the contrast match point for the SMA 1440 copolymer, we also can observe the ~1 nm SMA copolymer belt surrounding this SMALP for the first time, consistent with most models of SMA organization.
59 BASIC BIOLOGICAL SCIENCES↗
Excipient screening by lyophilization provides insights into spray drying formulations for nanoparticle vaccines
Nanoparticles have shown great promise as delivery platforms in the development of tunable and safe vaccines. Nanolipoprotein particles (NLPs), also known as nanodiscs, are discoidal nanoparticles composed of a lipid bilayer stabilized at their periphery by apolipoproteins. Under the right conditions, the NLP self-assembly process is highly customizable in terms of lipids and apolipoprotein constituents, allowing for tunable physical and chemical characteristics. This flexibility allows a wide range of vaccine antigens and adjuvants to be incorporated onto the NLP platform for tailored vaccine design. The stability of NLPs during long term storage is a very important factor in developing a vaccine delivery platform suitable for widespread global use. When stored in a solution for extended periods of time, NLPs dissociate into their corresponding lipids and protein constituents, leading to particle degradation. Proper stabilization of NLPs can often be achieved by lyophilization (i.e. freeze-drying), a method widely used for various applications including pharmaceuticals. This process, however, can be damaging to particles without the presence of lyoprotectants or excipients that help maintain particle stability during lyophilization. Another method used to stabilize vaccines and pharmaceuticals is spray drying, a process that converts liquid formulations into dry powders through controlled heating and airflow. While spray drying is rapid, scalable, and cost-effective, lyophilization is typically a gentler process that better retains biomolecule structure and function. Both processes use excipients for particle stabilization, so lyophilization can be used as a surrogate to test stability of NLPs, to down-select formulations that may withstand the harsher conditions of spray drying. To screen different formulations, NLPs were synthesized and purified to homogeneity by size exclusion chromatography (SEC) and samples were prepared with a wide range of lyoprotectants and/or excipients. To assess the protective effects of excipients on NLPs upon spray drying, both pre- and post-lyophilized samples were analyzed by SEC. To assess the protective effects upon heating (encountered during the spray drying process), NLP samples were incubated at elevated temperatures prior to SEC analysis. The lyoprotectants and excipients evaluated in this study had different efficiencies in protecting NLPs during lyophilization and heating tests. Trehalose, for example, exhibits stabilization on NLPs both upon lyophilization and heating whereas leucine accelerated NLP dissociation. Although some lyoprotectants are effective by themselves, different combinations can decrease the stabilization of NLPs. Shelf-stable vaccines that do not require cold-chain storage are essential for global accessibility and our findings provide fundamental insight into how to advance NLP-based vaccines for these applications.
Serrano, Litzay J [Lawrence Livermore National Lab↗
CHARMM-GUI Bicelle Builder : An Extension of Membrane Builder for Modeling and Simulation of Bicelle Systems
Membrane mimetics, such as detergent micelles, nanodiscs, and amphipol complexes, which can provide membrane-like environments while retaining small and soluble features, have been utilized to study membrane proteins. A bicelle, composed of varying lipids and detergents, is a useful membrane mimetic because the lipid-to-detergent ratio, the q-value, can be adjusted to alter the properties of the aggregate, including the thickness and size of the bicelle. However, building a bicelle model for modeling and simulation studies requires nontrivial efforts, even for experts. We introduce CHARMM-GUI Bicelle Builder, a web-based platform that can generate various all-atom bicelle systems via a graphical user interface with all available lipids and detergents in Membrane Builder. To illustrate and validate Bicelle Builder with practical systems, we have modeled and simulated pure bicelles consisting of 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipids with 1,2-dihexanoyl-sn-glycero-3-phosphocholine (C6DHPC) detergents and protein–bicelle complexes, composed of DMPC with C6DHPC, foscholine-10 (FOS10), and lysophosphatidylcholine-12 (LPC12) detergents. Our simulation results indicate that Bicelle Builder can generate reliable and robust bicelle models with and without proteins that retain DMPC bilayer characteristics. Bicelle Builder is expected to help researchers better understand not only bicelles themselves but also atomistic-level structures of protein–bicelle complexes that are often difficult to access through experimental approaches.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
LHCSR1 Functions as a Dimmer Switch for Light Harvesting
In oxygenic photosynthesis, high light leads to a set of photoprotective processes, known as nonphotochemical quenching, that are required for fitness. In moss and algae, the pigment−protein complex, light-harvesting stress-related (LHCSR), is crucial for photoprotection. Acidification of the thylakoid lumen under high light triggers the activation of LHCSR and the conversion of the xanthophyll violaxanthin into zeaxanthin, which is found within LHCSR. These interrelated molecular components combine to turn on a safety valve that dissipates excess energy as heat. Previous studies of detergent-solubilized LHCSR1 found that pH and zeaxanthin regulate distinct quenching sites via the protein conformation. However, protein function in the native membrane environment can be significantly different. In this work, we applied single-molecule fluorescence spectroscopy to LHCSR1 in membrane nanodiscs. The membrane environment enhanced total quenching, regardless of pH or zeaxanthin-binding. pH-dependent quenching was still observed whereas zeaxanthin-dependent quenching was suppressed. Conformational changes also increased in the membrane, establishing that the local environment can change the nature of the equilibrium between light harvesting and photoprotection.
Hoffmann, Madeline P. [Massachusetts Inst. of Tech↗
Anionic Lipids Regulate the Light-Harvesting Complex 1-Reaction Center Photocycle in Purple Bacteria
Photosynthetic purple bacteria can capture and convert sunlight with a remarkable, nearly 100% quantum efficiency. The light-harvesting complex 1-reaction center (LH1-RC) core complex is the membrane complex fundamentally responsible for solar energy conversion. LH1-RC has a highly conserved surrounding lipid composition known to favor anionic lipids for an unknown function. Here, in this work, we compared experimentally the rate of LH1-to-RC energy transfer in detergent, membrane nanodiscs with varying lipid compositions, purified membrane fragments, and live cells. The energy transfer rate indicated that RC turnover decreased in neutral lipids, yet was partially restored in anionic lipids, revealing an unexpected lipid dependence. In complementary molecular dynamics simulations, the anionic lipid cardiolipin showed electrostatic interactions with LH1-RC that may mediate quinone exchange, providing a mechanism for the observed lipid dependence. Overall, these results revealed that anionic lipids facilitate LH1-RC redox cycling, identifying a functional role for membrane composition in photosynthetic solar energy conversion.
bacteria↗
Ligand-induced transmembrane conformational coupling in monomeric $\mathrm{EGFR}$
Single pass cell surface receptors regulate cellular processes by transmitting ligand-encoded signals across the plasma membrane via changes to their extracellular and intracellular conformations. This transmembrane signaling is generally initiated by ligand binding to the receptors in their monomeric form. While subsequent receptor-receptor interactions are established as key aspects of transmembrane signaling, the contribution of monomeric receptors has been challenging to isolate due to the complexity and ligand-dependence of these interactions. By combining membrane nanodiscs produced with cell-free expression, single-molecule Förster Resonance Energy Transfer measurements, and molecular dynamics simulations, we report that ligand binding induces intracellular conformational changes within monomeric, full-length epidermal growth factor receptor (EGFR). Our observations establish the existence of extracellular/intracellular conformational coupling within a single receptor molecule. We implicate a series of electrostatic interactions in the conformational coupling and find the coupling is inhibited by targeted therapeutics and mutations that also inhibit phosphorylation in cells. Collectively, these results introduce a facile mechanism to link the extracellular and intracellular regions through the single transmembrane helix of monomeric EGFR, and raise the possibility that intramolecular transmembrane conformational changes upon ligand binding are common to single-pass membrane proteins.
59 BASIC BIOLOGICAL SCIENCES↗
Conformational motions and ligand-binding underlying gating and regulation in IP 3 R channel
Inositol-1,4,5-trisphosphate receptors (IP3Rs) are activated by IP 3 and Ca 2+ and their gating is regulated by various intracellular messengers that finely tune the channel activity. Here, using single particle cryo-EM analysis we determined 3D structures of the nanodisc-reconstituted IP 3 R1 channel in two ligand-bound states. These structures provide unprecedented details governing binding of IP 3 , Ca 2+ and ATP, revealing conformational changes that couple ligand-binding to channel opening. Using a deep-learning approach and 3D variability analysis we extracted molecular motions of the key protein domains from cryo-EM density data. We find that IP 3 binding relies upon intrinsic flexibility of the ARM2 domain in the tetrameric channel. Our results highlight a key role of dynamic side chains in regulating gating behavior of IP 3 R channels. This work represents a stepping-stone to developing mechanistic understanding of conformational pathways underlying ligand-binding, activation and regulation of the channel.
59 BASIC BIOLOGICAL SCIENCES↗