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At least 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Structural basis of Gabija anti-phage defence and viral immune evasion

Bacteria encode hundreds of diverse defence systems that protect them from viral infection and inhibit phage propagation. Gabija is one of the most prevalent anti-phage defence systems, occurring in more than 15% of all sequenced bacterial and archaeal genomes, but the molecular basis of how Gabija defends cells from viral infection remains poorly understood. Here we use X-ray crystallography and cryo-electron microscopy (cryo-EM) to define how Gabija proteins assemble into a supramolecular complex of around 500 kDa that degrades phage DNA. Gabija protein A (GajA) is a DNA endonuclease that tetramerizes to form the core of the anti-phage defence complex. Two sets of Gabija protein B (GajB) dimers dock at opposite sides of the complex and create a 4:4 GajA–GajB assembly (hereafter, GajAB) that is essential for phage resistance in vivo. We show that a phage-encoded protein, Gabija anti-defence 1 (Gad1), directly binds to the Gabija GajAB complex and inactivates defence. A cryo-EM structure of the virally inhibited state shows that Gad1 forms an octameric web that encases the GajAB complex and inhibits DNA recognition and cleavage. Our results reveal the structural basis of assembly of the Gabija anti-phage defence complex and define a unique mechanism of viral immune evasion.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Surfactant-like peptide gels are based on cross-β amyloid fibrils

Surfactant-like peptides, in which hydrophilic and hydrophobic residues are encoded within different domains in the peptide sequence, undergo facile self-assembly in aqueous solution to form supramolecular hydrogels. These peptides have been explored extensively as substrates for the creation of functional materials since a wide variety of amphipathic sequences can be prepared from commonly available amino acid precursors. The self-assembly behavior of surfactant-like peptides has been compared to that observed for small molecule amphiphiles in which nanoscale phase separation of the hydrophobic domains drives the self-assembly of supramolecular structures. Here, we investigate the relationship between sequence and supramolecular structure for a pair of bola-amphiphilic peptides, Ac-KLIIIK-NH 2 (L2) and Ac-KIIILK-NH 2 (L5). Despite similar length, composition, and polar sequence pattern, L2 and L5 form morphologically distinct assemblies, nanosheets and nanotubes, respectively. Cryo-EM helical reconstruction was employed to determine the structure of the L5 nanotube at near-atomic resolution. Rather than displaying self-assembly behavior analogous to conventional amphiphiles, the packing arrangement of peptides in the L5 nanotube displayed steric zipper interfaces that resembled those observed in the structures of β-amyloid fibrils. Like amyloids, the supramolecular structures of the L2 and L5 assemblies were sensitive to conservative amino acid substitutions within an otherwise identical amphipathic sequence pattern. This study highlights the need to better understand the relationship between sequence and supramolecular structure to facilitate the development of functional peptide-based materials for biomaterials applications.

Das, Abhinaba [Emory University, Atlanta, GA (Unit↗
DOE OSTI2020

Designing Imidazolium Poly(amide-amide) and Poly(amide-imide) Ionenes and Their Interactions with Mono- and Tris(imidazolium) Ionic Liquids

Here we introduce the synthesis and thermal properties of a series of sophisticated imidazolium ionenes with alternating amide-amide or amide-imide backbone functionality, and investigate the structural effects of mono(imidazolium) and unprecedented tris(imidazolium) ionic liquids (ILs) in these ionenes. The new set of poly(amide-amide) (PAA) and poly(amide-imide) (PAI) ionenes represent the intersection of conventional high-performance polymers with the ionene archetype–presenting polymers with alternating functional and ionic elements precisely sequenced along the backbone. The effects of polymer composition on the thermal properties and morphology were analyzed. Five distinct polymer backbones were synthesized and combined with a stoichiometric equivalent of the IL 1-benzyl-3-methylimidazolium bistriflimide ([Bnmim][Tf 2 N]), which were studied to probe the self-assembly, structuring, and contributions of intermolecular forces when IL is added. Furthermore, three polyamide (PA) or polyimide (PI) ionenes with simpler xylyl linkages were interfaced with [Bnmim][Tf 2 N] as well as a novel amide-linked tris(imidazolium) IL, to demonstrate the structural changes imparted by the inclusion of functional, ionic additives dispersed within the ionene matrix. This work highlights the possibilities for utilizing concepts from small molecules which exhibit supramolecular self-assembly to guide creative design and manipulate the structuring of ionenes.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Peptide programming of supramolecular vinylidene fluoride ferroelectric phases

Ferroelectric structures have spontaneous macroscopic polarization that can be inverted using external electric fields and have potential applications including information storage, energy transduction, ultralow-power nanoelectronics and biomedical devices. These functions would benefit from nanoscale control of ferroelectric structure, the ability to switch polarization with lower applied fields (low coercive field) and biocompatibility. Soft ferroelectrics based on poly(vinylidene fluoride) (PVDF) have a thermodynamically unstable ferroelectric phase in the homopolymer, complex semi-crystalline structures, and high coercive fields. Here, in this work, we report on ferroelectric materials formed by water-soluble molecules containing only six VDF repeating units covalently conjugated to a tetrapeptide, with the propensity to assemble into the β-sheet structures that are ubiquitous in proteins. This led to the discovery of ribbon-shaped ferroelectric supramolecular assemblies that are thermodynamically stable with their long axes parallel to both the preferred hydrogen-bonding direction of β-sheets and the bistable polar axes of VDF hexamers. Relative to a commonly used ferroelectric copolymer, the biomolecular assemblies exhibit a coercive field that is two orders of magnitude lower, as the result of supramolecular dynamics, and a similar level of remnant polarization, despite having a peptide content of 49 wt%. Furthermore, the Curie temperature of the assemblies is about 40 °C higher than that of a copolymer containing a similar amount of VDF. This supramolecular system was created using a biologically inspired strategy that is attractive in terms of sustainability and that could lead to new functions for soft ferroelectrics.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Emerged Metallicity in Molecular Ferromagnetic Wires

Supramolecular engineering bridges molecular assembly with macromolecular charge-transfer salts, promising the design to construct supramolecular architectures that integrate cooperative properties difficult or impossible to find in conventional lattices. Here, we report the crystal engineering design and kinetic growth of one-dimensional supramolecular wires composed of bis(ethylenedithio)tetrathiafulvalene (ET + ) cation and polymeric Cu[N(CN) 2 ] 2 – anion. A bulk ferromagnetic order is discovered for filling up the gap where strong ferromagnetism is missing in such ET molecule-based charge-transfer salts. Metallicity is induced by electric current from the semiconducting wire, which is attributed to strain effect by tuning its close molecular contact. This structural feature is evidenced through the combination of various mechanistic spectroscopic studies. Further, electric dipole is established from the close molecular contacts and is suggestive to stabilize ferromagnetic spin interaction through anions bridging spin sites. The breakthrough shown here provides a pathway to explore low-dimensional supramolecular materials exhibiting strong electron correlation, metallicity, and ferromagnetism.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Peptoid-Based Programmable 2D Nanomaterial Sensor for Selective and Sensitive Detection of H 2 S in Live Cells

During the past decades, a variety of two-dimensional (2D) nanosheets have been developed through supramolecular self-assembly. Among them, those assembled from sequence-defined molecules have received particularly attention because they enable a precise displaying of functional groups, including fluorescent dyes, within nanosheet surfaces. On the other hand, due to the fluorescence self-quenching, synthesis of organic 2D nanosheets exhibiting high fluorescence quantum yields is a significant challenge. Herein, we report the utilization of H 2 S-responsive probes as peptoid sidechains to design and synthesize crystalline 2D nanomembranes (2DNMs) as selective and sensitive H 2 S sensors. These 2DNM sensors exhibit a high quantum yield as a result of high crystallinity and tunable probe density. Compared with amorphous state of peptoid assembly and pre-assembled peptoid-probe conjugates, these crystalline 2DNM sensors exhibit a significantly strong fluorescence intensity and a high sensitivity (~ 0.36 nM). By sonication-cutting these 2DNM sensors into a colloidal form in aqueous solution, we further demonstrated the use of colloidal 2DNMs for detecting both exogenous and endogenous H 2 S inside cells or targeted cell organelles. As far as we know, this is the first example of using sequence-defined 2D nanomaterials for selective and sensitive detection of H 2 S. Because peptoids are biocompatible and peptoid-based 2DNMs are highly programmable, we expect that this new class of 2DNM sensors offer great potentials for detecting H 2 S and for biological applications.

2D nanomaterials↗
DOE OSTI2022

3D structure and in situ arrangements of CatSper channel in the sperm flagellum

The sperm calcium channel CatSper plays a central role in successful fertilization as a primary Ca 2+ gateway. Here, we applied cryo-electron tomography to visualize the higher-order organization of the native CatSper complex in intact mammalian sperm. The repeating CatSper units form long zigzag-rows along mouse and human sperm flagella. Above each tetrameric channel pore, most of the extracellular domains form a canopy that interconnects to a zigzag-shaped roof. Murine CatSper contains an additional wing-structure connected to the tetrameric channel. The intracellular domains link two neighboring channels to a diagonal array, suggesting a dimer formation. Fitting of an atomic model of isolated monomeric CatSper to the in situ map reveals supramolecular interactions and assembly of the CatSper complex. Loss of EFCAB9-CATSPERζ alters the architecture and interactions of the channels, resulting in fragmentation and misalignment of the zigzag-rows and disruption of flagellar movement in Efcab9 -/- sperm. This work offers unique insights into the structural basis for understanding CatSper regulation of sperm motility.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Acid-Base Equilibrium and Dielectric Environment Regulate Charge in Supramolecular Nanofibers

Peptide amphiphiles are a class of molecules that can self-assemble into a variety of supramolecular structures, including high-aspect-ratio nanofibers. It is challenging to model and predict the charges in these supramolecular nanofibers because the ionization state of the peptides are not fixed but liable to change due to the acid-base equilibrium that is coupled to the structural organization of the peptide amphiphile molecules. Here, we have developed a theoretical model to describe and predict the amount of charge found on self-assembled peptide amphiphiles as a function of pH and ion concentration. In particular, we computed the amount of charge of peptide amphiphiles nanofibers with the sequence C 16 − V 2 A 2 E 2 . In our theoretical formulation, we consider charge regulation of the carboxylic acid groups, which involves the acid-base chemical equilibrium of the glutamic acid residues and the possibility of ion condensation. The charge regulation is coupled with the local dielectric environment by allowing for a varying dielectric constant that also includes a position-dependent electrostatic solvation energy for the charged species. We find that the charges on the glutamic acid residues of the peptide amphiphile nanofiber are much lower than the same functional group in aqueous solution. There is a strong coupling between the charging via the acid-base equilibrium and the local dielectric environment. Our model predicts a much lower degree of deprotonation for a position-dependent relative dielectric constant compared to a constant dielectric background. Furthermore, the shape and size of the electrostatic potential as well as the counterion distribution are quantitatively and qualitatively different. These results indicate that an accurate model of peptide amphiphile self-assembly must take into account charge regulation of acidic groups through acid–base equilibria and ion condensation, as well as coupling to the local dielectric environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Superstructured Biomaterials Formed by Exchange Dynamics and Host–Guest Interactions in Supramolecular Polymers

Dynamic and reversible assembly of molecules is ubiquitous in the hierarchical superstructures of living systems and plays a key role in cellular functions. Recent work from the laboratory reported on the reversible formation of such superstructures in systems of peptide amphiphiles conjugated to oligonucleotides and electrostatically complimentary peptide sequences. Here, a supramolecular system is reported upon where exchange dynamics and host–guest interactions between β-cyclodextrin and adamantane on peptide amphiphiles lead to superstructure formation. Superstructure formation with bundled nanoribbons generates a mechanically robust hydrogel with a highly porous architecture that can be 3D printed. Functionalization of the porous superstructured material with a biological signal results in a matrix with significant in vitro bioactivity toward neurons that could be used as a supramolecular model to design novel biomaterials.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Gated Molecular Diffusion at Liquid–Liquid Interfaces

Abstract The jamming of nanoparticle surfactants (NPSs) at liquid–liquid interface imparts attractive properties to the interfacial assemblies and enables the structuring of liquids. Herein, we report photoresponsive supramolecular microcapsules with jammed NPS assemblies at the oil‐water interface, taking advantage of host–guest molecular recognition. The permeability of the colloidal membrane can be effectively manipulated by switching the NPSs from a jammed state to an unjammed state with a photo trigger, leading to a controlled molecular diffusion and release, affording a versatile platform for the construction of next generation smart microcapsule systems.

Li, Lianshun↗
DOE OSTI2021

Gated Molecular Diffusion at Liquid–Liquid Interfaces

The jamming of nanoparticle surfactants (NPSs) at liquid-liquid interface imparts attractive properties to the interfacial assemblies and enables the structuring of liquids. Herein, we report photoresponsive supramolecular microcapsules with jammed NPS assemblies at the oil-water interface, taking advantage of host-guest molecular recognition. The permeability of the colloidal membrane can be effectively manipulated by switching the NPSs from a jammed state to an unjammed state with a photo trigger, leading to a controlled molecular diffusion and release, affording a versatile platform for the construction of next generation smart microcapsule systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Supramolecular Tuning Enables Selective Oxygen Reduction Catalyzed by Cobalt Porphyrins for Direct Electrosynthesis of Hydrogen Peroxide

Abstract We report a supramolecular strategy for promoting the selective reduction of O 2 for direct electrosynthesis of H 2 O 2 . We utilized cobalt tetraphenylporphyrin (Co‐TPP), an oxygen reduction reaction (ORR) catalyst with highly variable product selectivity, as a building block to assemble the permanently porous supramolecular cage Co‐PB‐1(6) bearing six Co‐TPP subunits connected through twenty‐four imine bonds. Reduction of these imine linkers to amines yields the more flexible cage Co‐rPB‐1(6). Both Co‐PB‐1(6) and Co‐rPB‐1(6) cages produce 90–100 % H 2 O 2 from electrochemical ORR catalysis in neutral pH water, whereas the Co‐TPP monomer gives a 50 % mixture of H 2 O 2 and H 2 O. Bimolecular pathways have been implicated in facilitating H 2 O formation, therefore, we attribute this high H 2 O 2 selectivity to site isolation of the discrete molecular units in each supramolecule. The ability to control reaction selectivity in supramolecular structures beyond traditional host–guest interactions offers new opportunities for designing such architectures for a broader range of catalytic applications.

Smith, Peter T.↗
DOE OSTI2020

Supramolecular Tuning Enables Selective Oxygen Reduction Catalyzed by Cobalt Porphyrins for Direct Electrosynthesis of Hydrogen Peroxide

Abstract We report a supramolecular strategy for promoting the selective reduction of O 2 for direct electrosynthesis of H 2 O 2 . We utilized cobalt tetraphenylporphyrin (Co‐TPP), an oxygen reduction reaction (ORR) catalyst with highly variable product selectivity, as a building block to assemble the permanently porous supramolecular cage Co‐PB‐1(6) bearing six Co‐TPP subunits connected through twenty‐four imine bonds. Reduction of these imine linkers to amines yields the more flexible cage Co‐rPB‐1(6). Both Co‐PB‐1(6) and Co‐rPB‐1(6) cages produce 90–100 % H 2 O 2 from electrochemical ORR catalysis in neutral pH water, whereas the Co‐TPP monomer gives a 50 % mixture of H 2 O 2 and H 2 O. Bimolecular pathways have been implicated in facilitating H 2 O formation, therefore, we attribute this high H 2 O 2 selectivity to site isolation of the discrete molecular units in each supramolecule. The ability to control reaction selectivity in supramolecular structures beyond traditional host–guest interactions offers new opportunities for designing such architectures for a broader range of catalytic applications.

Smith, Peter T.↗
DOE OSTI2021

Orbital Angular Momentum from Self‐Assembled Concentric Nanoparticle Rings

Abstract Ring‐shaped nanostructures can focus, filter, and manipulate electromagnetic waves, but are challenging to incorporate into devices using standard nanofabrication techniques. Directed self‐assembly (DSA) of block copolymers (BCPs) on lithographically patterned templates has successfully been used to fabricate concentric rings and spirals as etching masks. However, this method is limited by BCP phase behavior and material selection. Here, a straightforward approach to generate ring‐shaped nanoparticle assemblies in thin films of supramolecular nanocomposites is demonstrated. DSA is used to guide the formation of concentric rings with radii spanning 150–1150 nm and ring widths spanning 30–60 nm. When plasmonic nanoparticles are used, ring nanodevice arrays can be fabricated in one step, and the completed devices produce high‐quality orbital angular momentum (OAM). Nanocomposite DSA simplifies and streamlines nanofabrication by producing metal structures without etching or deposition steps; it also introduces interparticle coupling as a new design axis. Detailed analysis of the nanoparticle ring assemblies confirms that the supramolecular system self‐regulates the spatial distribution of its components, and thus exhibits a degree of flexibility absent in DSA of BCPs alone, where structures are determined by polymer‐pattern incommensurability. The present studies also provide guidelines for developing self‐regulating DSA as an alternative to incommensurability‐driven methods.

Vargo, Emma↗
DOE OSTI2021

Polymorphism and Optoelectronic Properties in Crystalline Supramolecular Polymers

Supramolecular polymers can emulate some of the physical properties of covalent polymers but offer new opportunities given the possibility of designing monomers that will form highly ordered assemblies with defined shapes. Internally ordered supramolecular polymers formed through nucleation–elongation self-assembly are well-known but highly crystalline examples which exhibit important properties such as light harvesting, charge transport, and ferroelectricity are not common. We report here on a detailed study of supramolecular polymers formed in water by carboxylated naphtho-p-quinodimethane amphiphiles. We found that supramolecular polymerization of these amphiphiles in aqueous media yields crystalline assemblies with morphologies that included ribbons, helically rolled ribbons, and twisted filaments. This polymorphism was found to be controlled exclusively by repulsive electrostatic interactions controlled by the degree of protonation of the carboxylic head groups which also dictates the nature of supramolecular packing. Substoichiometric amounts of base lead to highly crystalline ribbons due to a decreased surface charge density and less electrostatic repulsion. Increasing deprotonation results in helically rolled ribbons with a different polymorph crystal lattice, whereas excessive deprotonation leads to twisted filaments with maximum surface charge density. Ribbons, helical rolled ribbons, and twisted filaments revealed an increasing red shift in their visible absorption maxima. These crystalline assemblies could be potential candidates for solar energy materials and photocatalytic systems.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Self-Sorting vs Coassembly in Peptide Amphiphile Supramolecular Nanostructures

The functionality of supramolecular nanostructures can be expanded if systems containing multiple components are designed to either self-sort or mix into coassemblies. This is critical to gain the ability to craft self-assembling materials that integrate functions, and our understanding of this process is in its early stages. Here, in this work, we have utilized three different peptide amphiphiles with the capacity to form β-sheets within supramolecular nanostructures and found binary systems that self-sort and others that form coassemblies. This was measured using atomic force microscopy to reveal the nanoscale morphology of assemblies and confocal laser scanning microscopy to determine the distribution of fluorescently labeled monomers. We discovered that PA assemblies with opposite supramolecular chirality self-sorted into chemically distinct nanostructures. In contrast, the PA molecules that formed a mixture of right-handed, left-handed, and flat nanostructures on their own were able to coassemble with the other PA molecules. We attribute this phenomenon to the energy barrier associated with changing the handedness of a β-sheet twist in a coassembly of two different PA molecules. This observation could be useful for designing biomolecular nanostructures with dual bioactivity or interpenetrating networks of PA supramolecular assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Lattice Symmetry-Guided Charge Transport in 2D Supramolecular Polymers Promotes Triplet Formation

Singlet-to-triplet intersystem crossing (ISC) in organic molecules is intimately connected with their geometries: by modifying the molecular shape, symmetry selection rules pertaining to spin-orbit coupling can be partially relieved, leading to extra matrix elements for increased ISC. As an analog to this molecular design concept, the study finds that the lattice symmetry of supramolecular polymers also defines their triplet formation efficiencies. A supramolecular polymer self-assembled from weakly interacting molecules is considered. Its 2D oblique unit cell effectively renders it as a coplanar array of 1D molecular columns weakly bound to each other. Using momentum-resolved photoluminescence imaging in combination with Monte Carlo simulations, the study found that photogenerated charge carriers in the supramolecular polymer predominantly recombine as spin-uncorrelated carrier pairs through inter-column charge transfer states. This lattice-defined recombination pathway leads to a substantial triplet formation efficiency (≈60%) in the supramolecular polymer. These findings suggest that lattice symmetry of micro-/macroscopic structures relying on intermolecular interactions can be strategized for controlled triplet formation.

36 MATERIALS SCIENCE↗