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At least 235 records · Page 13
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Antivesiculation and Complete Unbinding of Tail-Tethered Lipids

Here, we report the effect of tail-tethering on vesiculation and complete unbinding of bilayered membranes. Amphiphilic molecules of a bolalipid, resembling the tail-tethered molecular structure of archaeal lipids, with two identical zwitterionic phosphatidylcholine headgroups self-assemble into a large flat lamellar membrane, in contrast to the multilamellar vesicles (MLVs) observed in its counterpart, monopolar nontethered zwitterionic lipids. The antivesiculation is confirmed by small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cyro-TEM). With the net charge of zero and higher bending rigidity of the membrane (confirmed by neutron spin echo (NSE) spectroscopy), the current membrane theory would predict that membranes should stack with each other (aka “bind”) due to dominant van der Waals attraction, while the outcome of the nonstacking (“unbinding”) membrane suggests that the theory needs to include entropic contribution for the nonvesicular structures. This report pioneers an understanding of how the tail-tethering of amphiphiles affects the structure, enabling better control over the final nanoscale morphology.

36 MATERIALS SCIENCE↗
DOE OSTI2022

A Unique Bacterial Pelletized Cultivation Platform in Rhodococcus opacus PD630 Enhanced Lipid Productivity and Simplified Harvest for Lignin Bioconversion

Pelletized liquid cultivation has been widely explored because of its advantages in biomanufacturing, such as easier biomass harvesting, higher product yield, and lower medium viscosity and energy consumption. In this study, we discovered that the nonfilamentous bacterium Rhodococcus opacus PD630 could form pellets during the fermentation of alkaline pretreatment liquor containing lignin as a carbon source. This discovery advanced our understanding of bacterium pelletization, as only filamentous fungi and filamentous bacteria were reported to form pellets without the addition of external agents such as flocculants or polymers in previous research. Several factors were investigated to understand how they affect the process of pelletization. Notably, the lipid content in the pellets was much higher than in the scattered bacteria at low nitrogen concentration (<0.5 g/L), under which condition (high carbon to nitrogen ratio) the industrial microbial production for lipids was carried out. Moreover, the highest pellet percentage (~60% of the total biomass) was observed at 30 g/L soluble solid content, an agitation rate of 180 rpm, 1.4 g/L NH 4 NO 3 , an initial optical density (OD 600 ) of 10, and a centrifugation speed of 6000 rpm. Further, the study also opens new avenues to decrease harvesting and cultivation cost as well as energy consumption for microbial fermentation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Resurfacing promotes antibacterial activity of a lipid A–binding nanobody

Nanobodies have been pursued as candidates for antimicrobial design due to their small size and versatile binding capacities, but direct antibacterial activity of a nanobody has yet to be described. Here, we employed a bacterial surface display platform to screen a synthetic library of nanobody variants for antimicrobial potential. We identified a candidate that binds the essential lipid A component of gram-negative lipopolysaccharide. Nonetheless, this nanobody required a weakened outer membrane to access its target and elicit its toxic activity. Borrowing from observations of innate immune proteins, we found that resurfacing nanobodies with positively charged residues enabled them to bind and perturb the gram-negative outer membrane, but this alone was not sufficient for toxic activity. However, when we resurface our lipid A-targeting nanobody, it gained the ability to disrupt the outer membrane and enact its antibacterial function against wild-type bacteria. This development of a dual-function nanobody that can reach and bind previously inaccessible gram-negative targets introduces a route for antimicrobial biologic advancement.

antibacterial↗
DOE OSTI2020

Geometry and dynamics of lipid membranes: The Scriven-Love number

The equations governing lipid membrane dynamics in planar, spherical, and cylindrical geometries are presented here. Unperturbed and first-order perturbed equations are determined and nondimensionalized. In membrane systems with a nonzero base flow, perturbed in-plane and out-of-plane quantities are found to vary over different length scales. Here, a new dimensionless number, named the Scriven-Love number, and the well-known Föppl–von Kármán number result from a scaling analysis. The Scriven-Love number compares out-of-plane forces arising from the in-plane, intramembrane viscous stresses to the familiar elastic bending forces, while the Föppl–von Kármán number compares tension to bending forces. Both numbers are calculated in past experimental works, and span a wide range of values in various biological processes across different geometries. In situations with large Scriven-Love and Föppl–von Kármán numbers, the dynamical response of a perturbed membrane is dominated by out-of-plane viscous and surface tension forces—with bending forces playing a negligible role. Calculations of non-negligible Scriven-Love numbers in various biological processes and in vitro experiments show in-plane intramembrane viscous flows cannot generally be ignored when analyzing lipid membrane behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Real Space and Time Imaging of Collective Headgroup Dipole Motions in Zwitterionic Lipid Bilayers

Lipid bilayers are supramolecular structures responsible for a range of processes, such as transmembrane transport of ions and solutes, and sorting and replication of genetic materials, to name just a few. Some of these processes are transient and currently, cannot be visualized in real space and time. Here, we developed an approach using 1D, 2D, and 3D Van Hove correlation functions to image collective headgroup dipole motions in zwitterionic phospholipid bilayers. We show that both 2D and 3D spatiotemporal images of headgroup dipoles are consistent with commonly understood dynamic features of fluids. However, analysis of the 1D Van Hove function reveals lateral transient and re-emergent collective dynamics of the headgroup dipoles—occurring at picosecond time scales—that transmit and dissipate heat at longer times, due to relaxation processes. At the same time, the headgroup dipoles also generate membrane surface undulations due a collective tilting of the headgroup dipoles. A continuous intensity band of headgroup dipole spatiotemporal correlations—at nanometer length and nanosecond time scales—indicates that dipoles undergo stretching and squeezing elastic deformations. Importantly, the above mentioned intrinsic headgroup dipole motions can be externally stimulated at GHz-frequency scale, enhancing their flexoelectric and piezoelectric capabilities (i.e., increased conversion efficiency of mechanical energy into electric energy). In conclusion, we discuss how lipid membranes can provide molecular-level insights about biological learning and memory, and as platforms for the development of the next generation of neuromorphic computers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Growth, total lipid, and omega-3 fatty acid production by Nannochloropsis spp. cultivated with raw plant substrate

Improving productivity and lipid concentration in microalgae is important for the economic success of both biofuel and microalgae coproducts production. Nannochloropsis spp. are marine microalgae currently being grown at large-scale for the production of biofuel and lipid coproducts. In this work, we demonstrate improvements of growth and omega-3 production in Nannochloropsis gaditana CCMP526 and Nannochloropsis oceanica CCAP849/10 with plant substrate addition, a potentially economical option for increasing microalgal productivity. Furthermore, we examine growth in the presence of corn stover, switchgrass, sugarcane bagasse, and yard waste. By examining the microbial ecology of N. gaditana cultures with and without plant substrate and with and without antibiotics, we discovered a potential bacterial interaction in these cultures, but its presence is not necessary for algal growth improvements in the presence of plant substrate. Analysis of plant substrate morphology by scanning electron microscopy (SEM) after cultivation in media with and without N. gaditana shows a degradation of specific plant structural features and a colonization of the plant phloem by N. gaditana. An examination of N. gaditana in a Congo red plate assay indicates potential cellulolytic activity, but a preliminary examination of the potential cellulase transcripts does not reveal differential expression of a candidate in the presence of plant. This evidence demonstrates potential raw plant utilization by a marine microalga for increased productivity and provides a potentially economical option for increasing coproduct concentration at industrial scale without genetic engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Macromolecular Crowding Affects Voltage-Dependent Alamethicin Pore Formation in Lipid Bilayer Membranes

Macromolecular crowding is known to modulate chemical equilibria, reaction rates, and molecular binding events, both in aqueous solutions and at lipid bilayer membranes, natural barriers that enclose the crowded environments of cells and their subcellular compartments. Previous studies on the effects of macromolecular crowding in aqueous compartments on conduction through membranes have focused on single-channel ionic conduction through previously formed pores at thermodynamic equilibrium. Furthermore, the effects of macromolecular crowding on the mechanism of pore formation itself were studied using the droplet interface bilayer (DIB) technique with the voltage-dependent pore-forming peptide alamethicin (alm). Macromolecular crowding was varied using 8 kDa molecular weight polyethylene glycol (PEG8k) or 500 kDa dextran (DEX500k) in two aqueous droplets on both sides of the bilayer membrane. In general, voltage thresholds for pore formation in the presence of crowders in the droplets decreased compared to their values in the absence of crowders, due to excluded volume effects, water binding by PEG, and changes in the ordering of water molecules and hydrogen-bonding interactions involving the polar lipid headgroups. In addition, asymmetric crowder loading (e.g., PEG8k–DEX500k on either side of the membrane) resulted in transmembrane osmotic pressure gradients that either enhanced or degraded the ionic conduction through the pores.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Relaxor Ferroelectric-Like Spatiotemporal Memory in Field-Driven Lipid Bilayers

Lipid membranes are often regarded as passive barriers, yet their nonlinear dielectric response remains poorly understood. Using all-atom molecular dynamics, we show that fully hydrated dipalmitoylphosphatidylcholine bilayers exhibit relaxor ferroelectric-like behavior under time-dependent electric fields. Unlike crystalline relaxors, which are bipolar and display little remanent polarization, lipid bilayers exhibit a unipolar polarization response: even an alternating current field produces persistent, asymmetric polarization. Furthermore, the underlying free-energy landscape contains two distinct minima, a nonpolarized state and a unipolarly polarized state, between which stochastic thermally activated transitions occur. Directionally resolved Van Hove analysis reveals pronounced anisotropy arising from out-of-plane electric dipole alignment, interleaflet coupling, and lateral polarization domains. Each field cycle nucleates polarization at distinct sites and monitors their relaxation, marking a crossover from thermal fluctuations to field-sustained polarization. Remarkably, these polarized domains persist after field removal, generating long-lived, spatially coherent dipolar patterns that encode nanoscale polarization memory. Potassium chloride amplifies these effects via dielectric screening and a modified hydration structure, enhancing electric dipole flexibility and cooperativity. Together, these results establish protein-free bilayers as nonlinear, history-dependent dielectrics capable of sustaining field-tunable electromechanical coupling, providing an emergent physical foundation for nanoscale information storage and memory phenomena reminiscent of short- and long-term plasticity in soft neuromorphic systems.

Insulators↗
DOE OSTI2020

Mechanisms of activation and desensitization of full-length glycine receptor in lipid nanodiscs

Glycinergic synapses play a central role in motor control and pain processing in the central nervous system. Glycine receptors (GlyRs) are key players in mediating fast inhibitory neurotransmission at these synapses. While previous high-resolution structures have provided insights into the molecular architecture of GlyR, several mechanistic questions pertaining to channel function are still unanswered. Here, we present Cryo-EM structures of the full-length GlyR protein complex reconstituted into lipid nanodiscs that are captured in the unliganded (closed), glycine-bound (open and desensitized), and allosteric modulator-bound conformations. A comparison of these states reveals global conformational changes underlying GlyR channel gating and modulation. The functional state assignments were validated by molecular dynamics simulations, and the observed permeation events are in agreement with the anion selectivity and conductance of GlyR. These studies provide the structural basis for gating, ion selectivity, and single-channel conductance properties of GlyR in a lipid environment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Structure of the Sec14 domain of Kalirin reveals a distinct class of lipid-binding module in RhoGEFs

Gated entry of lipophilic ligands into the enclosed hydrophobic pocket in stand-alone Sec14 domain proteins often links lipid metabolism to membrane trafficking. Similar domains occur in multidomain mammalian proteins that activate small GTPases and regulate actin dynamics. The neuronal RhoGEF Kalirin, a central regulator of cytoskeletal dynamics, contains a Sec14 domain (Kal bSec14 ) followed by multiple spectrin-like repeats and catalytic domains. Previous studies demonstrated that Kalirin lacking its Sec14 domain fails to maintain cell morphology or dendritic spine length, yet whether and how Kal bSec14 interacts with lipids remain unknown. Here, we report the structural and biochemical characterization of Kal bSec14 . Kal bSec14 adopts a closed conformation, sealing off the canonical ligand entry site, and instead employs a surface groove to bind a limited set of lysophospholipids. The low-affinity interactions of Kal bSec14 with lysolipids are expected to serve as a general model for the regulation of Rho signaling by other Sec14-containing Rho activators.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Graphene-extracted membrane lipids facilitate the activation of integrin α v β 8

Despite the remarkable electrochemical properties of graphene, strong van der Waals attraction between graphene and biomolecules often causes cytotoxicity, which hinders its applications in the biomedical field. Unfortunately, surface passivation of graphene might stimulate undesired immune response as the nanomaterial triggers cytokine production through membrane receptor activation. In this work, we use all-atom Molecular Dynamics (MD) simulations to unravel the underlying mechanism of graphene-induced inside-out activation of integrin αvβ8, a prominent membrane receptor expressed in immune cells. We model the transmembrane (TM) domains of integrin αvβ8 in a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid bilayer and observe the structural changes in the integrin–membrane complex when interacting with a graphene nanosheet across the membrane. We find that the β8 TM domain interacts with the graphene nanosheet directly or indirectly through extracted lipids, facilitating the pulling of a β8 subunit away from an αv subunit and thus leading to the disruption of the TM domain association by breaking the hydrophobic cluster in the cytoplasmic domains of the αv and β8 subunits. Alanine substitution of two conserved phenylalanine residues on the αv subunit at this hydrophobic cluster further reveals the importance of a stable T-shaped structure in retaining integrin in its inactive state. Our results agree with previous studies on the interactions between other integrin subtypes and their endogenous activators, suggesting an intriguing role that the graphene nanosheet may play in the integrin-related signal transduction during its interaction with the membrane.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Assembly of small silica nanoparticles using lipid-tethered DNA ‘bonds’

Single-stranded DNA molecules modified with cholesterol functional groups are physically tethered to silica nanoparticles (diameter 25 nm) that are encapsulated in a lipid bilayer. Such tethering increases the azimuthal mobility of the DNA molecules across the nanoparticle surface and enables nonspecific bonding, eliminating the need for specialized surface chemistries (such as silane or thiol ligands). To induce assembly, double-stranded DNA ‘bridge’ molecules are then added with complementary nucleotides to the DNA ‘anchor’ molecules that are physically tethered to the lipids on the surface of the particles. Assembly is observed to occur at room temperature and without the need for temperature annealing. Using automated liquid handling tools, assemblies are created in high throughput and rapidly characterized using SAXS. It is determined that the relative concentration of DNA-to-silica and the ionic strength of the solution are important parameters that affect the resulting assembly. Analysis of SAXS data is performed using coarse-grained particle dynamics simulations. The results support the spontaneous formation of semi-crystalline particle assemblies by particle condensation, where the interparticle distance is tuned by the sequence of the DNA ‘bridge’ used to link the particles. Crystallinity analysis performed on the resulting simulations, optimized to match SAXS observations, suggest that particle clusters display increased crystallinity in the center of the clusters, but their maximum size remains relatively small (sub-micron) before settling occurs, which limits the extent of crystallization.

Chiang, Huat Thart [Univ. of Washington, Seattle, ↗
DOE OSTI2020

Calcium-triggered fusion of lipid membranes is enabled by amphiphilic nanoparticles

Significance Lipid membrane fusion is a critical component of biological transport, communication, and developmental processes. The fusion reaction is kinetically constrained since it contains multiple large energy barriers, so proteins and ions are used by natural systems to intervene and catalyze the reaction toward biologically relevant timescales. Here, we demonstrate how amphiphilic nanoparticles can prime lipid membranes for fusion so that complete fusion proceeds only upon exposure to an excess of calcium or other stimulus that would stress the outer leaflet. This is a major advance in the nascent field of controlled fusion and may unlock new avenues of research on how nanomaterials can be designed from first principles to perform targeted functional roles in biological systems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

FatPlants: a comprehensive information system for lipid-related genes and metabolic pathways in plants

Abstract FatPlants, an open-access, web-based database, consolidates data, annotations, analysis results, and visualizations of lipid-related genes, proteins, and metabolic pathways in plants. Serving as a minable resource, FatPlants offers a user-friendly interface for facilitating studies into the regulation of plant lipid metabolism and supporting breeding efforts aimed at increasing crop oil content. This web resource, developed using data derived from our own research, curated from public resources, and gleaned from academic literature, comprises information on known fatty-acid-related proteins, genes, and pathways in multiple plants, with an emphasis on Glycine max, Arabidopsis thaliana, and Camelina sativa. Furthermore, the platform includes machine-learning based methods and navigation tools designed to aid in characterizing metabolic pathways and protein interactions. Comprehensive gene and protein information cards, a Basic Local Alignment Search Tool search function, similar structure search capacities from AphaFold, and ChatGPT-based query for protein information are additional features. Database URL: https://www.fatplants.net/

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

LDIP cooperates with SEIPIN and LDAP to facilitate lipid droplet biogenesis in Arabidopsis

Cytoplasmic lipid droplets (LDs) are evolutionarily conserved organelles that store neutral lipids and play critical roles in plant growth, development, and stress responses. However, the molecular mechanisms underlying their biogenesis at the endoplasmic reticulum (ER) remain obscure. Here we show that a recently identified protein termed LD-associated protein [LDAP]-interacting protein (LDIP) works together with both endoplasmic reticulum-localized SEIPIN and the LD-coat protein LDAP to facilitate LD formation in Arabidopsis thaliana. Heterologous expression in insect cells demonstrated that LDAP is required for the targeting of LDIP to the LD surface, and both proteins are required for the production of normal numbers and sizes of LDs in plant cells. LDIP also interacts with SEIPIN via a conserved hydrophobic helix in SEIPIN and LDIP functions together with SEIPIN to modulate LD numbers and sizes in plants. Further, the co-expression of both proteins is required to restore normal LD production in SEIPIN-deficient yeast cells. These data, combined with the analogous function of LDIP to a mammalian protein called LD Assembly Factor 1, are discussed in the context of a new model for LD biogenesis in plant cells with evolutionary connections to LD biogenesis in other eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Packaging “vegetable oils”: Insights into plant lipid droplet proteins

Abstract Plant neutral lipids, also known as “vegetable oils”, are synthesized within the endoplasmic reticulum (ER) membrane and packaged into subcellular compartments called lipid droplets (LDs) for stable storage in the cytoplasm. The biogenesis, modulation, and degradation of cytoplasmic LDs in plant cells are orchestrated by a variety of proteins localized to the ER, LDs, and peroxisomes. Recent studies of these LD-related proteins have greatly advanced our understanding of LDs not only as steady oil depots in seeds but also as dynamic cell organelles involved in numerous physiological processes in different tissues and developmental stages of plants. In the past 2 decades, technology advances in proteomics, transcriptomics, genome sequencing, cellular imaging and protein structural modeling have markedly expanded the inventory of LD-related proteins, provided unprecedented structural and functional insights into the protein machinery modulating LDs in plant cells, and shed new light on the functions of LDs in nonseed plant tissues as well as in unicellular algae. Here, we review critical advances in revealing new LD proteins in various plant tissues, point out structural and mechanistic insights into key proteins in LD biogenesis and dynamic modulation, and discuss future perspectives on bridging our knowledge gaps in plant LD biology.

Cai, Yingqi (ORCID:0000000203575809)↗
DOE OSTI2023

Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflect pH

Many Archaea produce membrane-spanning lipids that enable life in extreme environments. These isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) may contain up to eight cyclopentyl and one cyclohexyl ring, where higher degrees of cyclization are associated with more acidic, hotter or energy-limited conditions. Recently, the genes encoding GDGT ring synthases, grsAB, were identified in two Sulfolobaceae; however, the distribution and abundance of grs homologs across environments inhabited by these and related organisms remain a mystery. To address this, we examined the distribution of grs homologs in relation to environmental temperature and pH, from thermal springs across Earth, where sequences derive from metagenomes, metatranscriptomes, single-cell and cultivar genomes. The abundance of grs homologs shows a strong negative correlation to pH, but a weak positive correlation to temperature. Archaeal genomes and metagenome-assembled genomes (MAGs) that carry two or more grs copies are more abundant in low pH springs. We also find grs in 12 archaeal classes, with the most representatives in Thermoproteia, followed by MAGs of the uncultured Korarchaeia, Bathyarchaeia and Hadarchaeia, while several Nitrososphaeria encodes >3 copies. Furthermore, our findings highlight the key role of grs-catalysed lipid cyclization in archaeal diversification across hot and acidic environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Lipid droplet-associated proteins in alcohol-associated fatty liver disease: A proteomic approach

The earliest manifestation of alcohol-associated liver disease (ALD) is steatosis characterized by deposition of fat in specialized organelles called lipid droplets (LDs). While alcohol administration causes a rise in LD numbers in the hepatocytes, little is known regarding their characteristics that allow their accumulation and size to increase. The aim of the present study is to gain insights into underlying pathophysiological mechanisms by investigating the ethanol-induced changes in hepatic LD proteome as a function of LD size. Adult male Wistar rats (180–200 g BW) were fed with ethanol liquid diet for 6 weeks. At sacrifice, large-, medium-, and small-sized hepatic LD subpopulations (LD1, LD2, and LD3, respectively) were isolated and subjected to morphological and proteomic analyses. Morphological analysis of LD1-LD3 fractions of ethanol-fed rats clearly demonstrated that LD1 contained larger LDs compared with LD2 and LD3 fractions. Our preliminary results from principal component analysis showed that the proteome of different-sized hepatic LD fractions was distinctly different. Proteomic data analysis identified over 2000 proteins in each LD fraction with significant alterations in protein abundance among the three LD fractions. Among the altered proteins, several were related to fat metabolism, including synthesis, incorporation of fatty acid, and lipolysis. Ingenuity pathway analysis revealed increased fatty acid synthesis, fatty acid incorporation, LD fusion, and reduced lipolysis in LD1 compared to LD3. Overall, the proteomic findings indicate that the increased level of protein that facilitates fusion of LDs combined with an increased association of negative regulators of lipolysis dictates the generation of large-sized LDs during the development of alcohol-associated hepatic steatosis. Several significantly altered proteins were identified in different-sized LDs isolated from livers of ethanol-fed rats. Ethanol-induced increases in specific proteins that hinder LD lipid metabolism led to the accumulation and persistence of large-sized LDs in the liver.

60 APPLIED LIFE SCIENCES↗