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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Structurally Ordered Nanowire Formation from Co-Assembly of DNA Origami and Collagen-Mimetic Peptides

In this paper, we describe the co-assembly of two different building units: collagen-mimetic peptides and DNA origami. Two peptides CP ++ and sCP ++ are designed with a sequence comprising a central block (Pro-Hyp-Gly) and two positively charged domains (Pro-Arg-Gly) at both N- and C-termini. Co-assembly of peptides and DNA origami two-layer (TL) nanosheets affords the formation of one-dimensional nanowires with repeating periodicity of similar to 10 nm. Structural analyses suggest a face-to-face stacking of DNA nanosheets with peptides aligned perpendicularly to the sheet surfaces. We demonstrate the potential of selective peptide-DNA association between face-to-face and edge-to-edge packing by tailoring the size of DNA nanostructures. Finally, this study presents an attractive strategy to create hybrid biomolecular assemblies from peptide and DNA-based building blocks that takes advantage of the intrinsic chemical and physical properties of the respective components to encode structural and, potentially, functional complexity within readily accessible biomimetic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Folding and Assembly of Short α, β, γ -Hybrid Peptides: Minor Variations in Sequence and Drastic Differences in Higher-Level Structures

Multilevel protein structures typically involve polypeptides of sufficient lengths. Here we report the folding and assembly of seven short tetrapeptides sharing the same types of α-, β-, and aromatic γ-amino acid residues. These are two sets of hybrid peptides, with three members in one set and four in the other, having complementary hydrogen-bonding sequences that were hypothesized to pair into linear H-bonded duplexes. However, instead of undergoing the anticipated pairing, the initially examined three oligomers, 1 and 2a or 2b, differing only in their central αβ hybrid dipeptide sequence, do not associate with each other and exhibit distinctly different folding behavior. Experiments based on NMR and mass spectrometry, along with computational studies and systematic inference, reveal that oligomer 1 folds into an expanded β-turn containing an unusual hybrid α/β-amino acid sequence composed of glycine and β-alanine, two α- and β-amino acid residues that are conformationally most flexible, and peptides 2a and 2b adopt a noncanonical, extended helical conformation and dimerize into double helices undergoing rapid conformational exchange or helix inversion. The different central dipeptide sequences, αβ vs βα, result in drastically different intramolecular H-bonding patterns that are responsible for the observed folding behavior of 1 and 2. The revealed turn and double helix have few natural or synthetic counterparts, and provide novel and unique folding prototypes based on which chiral α- and β-amino acids are incorporated. The resultant derivatives 1a, 1b, 2c, and 2d follow the same folding and assembling behavior and demonstrate the generality of this system with the formation of expanded β-turns and double helices with enhanced folding stabilities, hampered helix inversion, as well as defined and dominant helical sense. This work has demonstrated the unique capability of synthetic foldamers in generating structures with fascinating folding and assembling behavior. As a result, the revealed systems offer ample opportunity for further structural optimization and applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Insight into the Mechanisms Driving the Self-Assembly of Functional Interfaces: Moving from Lipids to Charged Amphiphilic Oligomers

Polymer-stabilized liquid/liquid interfaces are an important and growing class of bioinspired materials that combine the structural and functional capabilities of advanced synthetic materials with naturally evolved biophysical systems. These platforms have the potential to serve as selective membranes for chemical separations and molecular sequencers and to even mimic neuromorphic computing elements. Despite the diversity in function, basic insight into the assembly of well-defined amphiphilic polymers to form functional structures remains elusive, which hinders the continued development of these technologies. In this work, we provide new mechanistic insight into the assembly of an amphiphilic polymer-stabilized oil/aqueous interface, in which the headgroups consist of positively charged methylimidazolium ionic liquids, and the tails are short, monodisperse oligodimethylsiloxanes covalently attached to the headgroups. We demonstrate using vibrational sum frequency generation spectroscopy and pendant drop tensiometery that the composition of the bulk aqueous phase, particularly the ionic strength, dictates the kinetics and structures of the amphiphiles in the organic phase as they decorate the interface. These results show that H-bonding and electrostatic interactions taking place in the aqueous phase bias the grafted oligomer conformations that are adopted in the neighboring oil phase. The kinetics of self-assembly were ionic strength dependent and found to be surprisingly slow, being composed of distinct regimes where molecules adsorb and reorient on relatively fast time scales, but where conformational sampling and frustrated packing takes place over longer time scales. These results set the stage for understanding related chemical phenomena of bioinspired materials in diverse technological and fundamental scientific fields and provide a solid physical foundation on which to design new functional interfaces.

Chowdhury, Azhad↗
DOE OSTI2017

Evolution of protein-coupled RNA dynamics during hierarchical assembly of ribosomal complexes

Assembly of 30S ribosomes involves the hierarchical addition of ribosomal proteins that progressively stabilize the folded 16S rRNA. Here, we use three-color single molecule FRET to show how combinations of ribosomal proteins uS4, uS17 and bS20 in the 16S 5' domain enable the recruitment of protein bS16, the next protein to join the complex. Analysis of real-time bS16 binding events shows that bS16 binds both native and non-native forms of the rRNA. The native rRNA conformation is increasingly favored after bS16 binds, explaining how bS16 drives later steps of 30S assembly. Chemical footprinting and molecular dynamics simulations show that each ribosomal protein switches the 16S conformation and dampens fluctuations at the interface between rRNA subdomains where bS16 binds. The results suggest that specific protein-induced changes in the rRNA dynamics underlie the hierarchy of 30S assembly and simplify the search for the native ribosome structure.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Designable and dynamic single-walled stiff nanotubes assembled from sequence-defined peptoids

Despite recent advances in assembly of organic nanotubes, conferral of sequence-defined engineering and dynamic response characteristics to the tubules remains a challenge. Here we report a new family of highly-designable and dynamic single-walled nanotubes assembled from sequence-defined peptoids through a unique “rolling-up and closure of nanosheet” mechanism. During the assembly process, amorphous spherical particles of amphiphilic peptoid oligomers (APOs) crystallized to form well-defined nanosheets which were then folded to form single-walled peptoid nanotubes (SW-PNTs). These SW-PNTs undergo a pH-triggered, reversible contraction-expansion motion. By varying the number of hydrophobic residues of APOs, we demonstrate the tuning of PNT wall thickness and diameter, and mechanical properties. AFM-based mechanical measurements indicate that PNTs are highly stiff (Young’s Modulus ~13-17 GPa), comparable to the stiffest known biological materials. We further demonstrate that the precise incorporation of functional groups within PNTs and the application of functional PNTs in water decontamination. We believe these SW-PNTs can provide a robust platform for development of biomimetic materials tailored to specific applications.

36 MATERIALS SCIENCE↗
DOE OSTI2018

Crystal structure of an assembly intermediate of respiratory Complex II

Flavin is covalently attached to the protein scaffold in ~10% of flavoenzymes. However, the mechanism of covalent modification is unclear, due in part to challenges in stabilizing assembly intermediates. Here, we capture the structure of an assembly intermediate of the Escherichia coli Complex II (quinol:fumarate reductase (FrdABCD)). The structure contains the E. coli FrdA subunit bound to covalent FAD and crosslinked with its assembly factor, SdhE. The structure contains two global conformational changes as compared to prior structures of the mature protein: the rotation of a domain within the FrdA subunit, and the destabilization of two large loops of the FrdA subunit, which may create a tunnel to the active site. We infer a mechanism for covalent flavinylation. As supported by spectroscopic and kinetic analyses, we suggest that SdhE shifts the conformational equilibrium of the FrdA active site to disfavor succinate/fumarate interconversion and enhance covalent flavinylation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Molecular architecture of a cylindrical self-assembly at human centrosomes

The cell is constructed by higher-order structures and organelles through complex interactions among distinct structural constituents. The centrosome is a membraneless organelle composed of two microtubule-derived structures called centrioles and an amorphous mass of pericentriolar material. Super-resolution microscopic analyses in various organisms revealed that diverse pericentriolar material proteins are concentrically localized around a centriole in a highly organized manner. However, the molecular nature underlying these organizations remains unknown. Here we show that two human pericentriolar material scaffolds, Cep63 and Cep152, cooperatively generate a heterotetrameric α-helical bundle that functions in conjunction with its neighboring hydrophobic motifs to self-assemble into a higher-order cylindrical architecture capable of recruiting downstream components, including Plk4, a key regulator for centriole duplication. Mutations disrupting the self-assembly abrogate Plk4-mediated centriole duplication. Because pericentriolar material organization is evolutionarily conserved, this work may offer a paradigm for investigating the assembly and function of centrosomal scaffolds in various organisms.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

TASOR is a pseudo-PARP that directs HUSH complex assembly and epigenetic transposon control

The HUSH complex represses retroviruses, transposons and genes to maintain the integrity of vertebrate genomes. HUSH regulates deposition of the epigenetic mark H3K9me3, but how its three core subunits — TASOR, MPP8 and Periphilin — contribute to assembly and targeting of the complex remains unknown. Here, we define the biochemical basis of HUSH assembly and find that its modular architecture resembles the yeast RNA-induced transcriptional silencing complex. TASOR, the central HUSH subunit, associates with RNA processing components. TASOR is required for H3K9me3 deposition over LINE-1 repeats and repetitive exons in transcribed genes. In the context of previous studies, this suggests that an RNA intermediate is important for HUSH activity. We dissect the TASOR and MPP8 domains necessary for transgene repression. Structure-function analyses reveal TASOR bears a catalytically-inactive PARP domain necessary for targeted H3K9me3 deposition. We conclude that TASOR is a multifunctional pseudo-PARP that directs HUSH assembly and epigenetic regulation of repetitive genomic targets.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Self-assembly and regulation of protein cages from pre-organised coiled-coil modules

Coiled-coil protein origami (CCPO) is a modular strategy for the de novo design of polypeptide nanostructures. CCPO folds are defined by the sequential order of concatenated orthogonal coiled-coil (CC) dimer-forming peptides, where a single-chain protein is programmed to fold into a polyhedral cage. Self-assembly of CC-based nanostructures from several chains, similarly as in DNA nanotechnology, could facilitate the design of more complex assemblies and the introduction of functionalities. Here, we show the design of a de novo triangular bipyramid fold comprising 18 CC-forming segments and define the strategy for the two-chain self-assembly of the bipyramidal cage from asymmetric and pseudo-symmetric pre-organised structural modules. In addition, by introducing a protease cleavage site and masking the interfacial CC-forming segments in the two-chain bipyramidal cage, we devise a proteolysis-mediated conformational switch. This strategy could be extended to other modular protein folds, facilitating the construction of dynamic multi-chain CC-based complexes.

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

Flexible and high-performance electrochromic devices enabled by self-assembled 2D TiO 2 /MXene heterostructures

Transition metal oxides (TMOs) are promising electrochromic (EC) materials for applications such as smart windows and displays, yet the challenge still exists to achieve good flexibility, high coloration efficiency and fast response simultaneously. MXenes (e.g. Ti 3 C 2 T x ) and their derived TMOs (e.g. 2D TiO 2 ) are good candidates for high-performance and flexible EC devices because of their 2D nature and the possibility of assembling them into loosely networked structures. Here we demonstrate flexible, fast, and high-coloration-efficiency EC devices based on self-assembled 2D TiO 2 /Ti 3 C 2 T x heterostructures, with the Ti 3 C 2 T x layer as the transparent electrode, and the 2D TiO 2 layer as the EC layer. Benefiting from the well-balanced porosity and connectivity of these assembled nanometer-thick heterostructures, they present fast and efficient ion and electron transport, as well as superior mechanical and electrochemical stability. We further demonstrate large-area flexible devices which could potentially be integrated onto curved and flexible surfaces for future ubiquitous electronics.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly

The programmable synthesis of rationally engineered crystal architectures for the precise arrangement of molecular species is a foundational goal in nanotechnology, and DNA has become one of the most prominent molecules for the construction of these materials. In particular, branched DNA junctions have been used as the central building block for the assembly of 3D lattices. Here, crystallography is used to probe the effect of all 36 immobile Holliday junction sequences on self-assembling DNA crystals. Contrary to the established paradigm in the field, most junctions yield crystals, with some enhancing the resolution or resulting in unique crystal symmetries. Unexpectedly, even the sequence adjacent to the junction has a significant effect on the crystal assemblies. Six of the immobile junction sequences are completely resistant to crystallization and thus deemed “fatal,” and molecular dynamics simulations reveal that these junctions invariably lack two discrete ion binding sites that are pivotal for crystal formation. The structures and dynamics detailed here could be used to inform future designs of both crystals and DNA nanostructures more broadly, and have potential implications for the molecular engineering of applied nanoelectronics, nanophotonics, and catalysis within the crystalline context.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Fragment-based drug nanoaggregation reveals drivers of self-assembly

Drug nanoaggregates are particles that can deleteriously cause false positive results during drug screening efforts, but alternatively, they may be used to improve pharmacokinetics when developed for drug delivery purposes. The structural features of molecules that drive nanoaggregate formation remain elusive, however, and the prediction of intracellular aggregation and rational design of nanoaggregate-based carriers are still challenging. We investigate nanoaggregate self-assembly mechanisms using small molecule fragments to identify the critical molecular forces that contribute to self-assembly. We find that aromatic groups and hydrogen bond acceptors/donors are essential for nanoaggregate formation, suggesting that both π-π stacking and hydrogen bonding are drivers of nanoaggregation. We apply structure-assembly-relationship analysis to the drug sorafenib and discover that nanoaggregate formation can be predicted entirely using drug fragment substructures. We also find that drug nanoaggregates are stabilized in an amorphous core-shell structure. These findings demonstrate that rational design can address intracellular aggregation and pharmacologic/delivery challenges in conventional and fragment-based drug development processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2024

p14 ARF forms meso-scale assemblies upon phase separation with NPM1

NPM1 is an abundant nucleolar chaperone that, in addition to facilitating ribosome biogenesis, contributes to nucleolar stress responses and tumor suppression through its regulation of the p14 Alternative Reading Frame tumor suppressor protein (p14 ARF ). Oncogenic stress induces p14 ARF to inhibit MDM2, stabilize p53 and arrest the cell cycle. Under non-stress conditions, NPM1 stabilizes p14 ARF in nucleoli, preventing its degradation and blocking p53 activation. However, the mechanisms underlying the regulation of p14 ARF by NPM1 are unclear because the structural features of the p14 ARF -NPM1 complex were elusive. Here we show that p14 ARF assembles into a gel-like meso-scale network upon phase separation with NPM1. This assembly is mediated by intermolecular contacts formed by hydrophobic residues in an α-helix and β-strands within a partially folded N-terminal portion of p14 ARF . These hydrophobic interactions promote phase separation with NPM1, enhance p14 ARF nucleolar partitioning, restrict NPM1 diffusion within condensates and nucleoli, and reduce cellular proliferation. Our structural analysis provides insights into the multifaceted chaperone function of NPM1 in nucleoli by mechanistically linking the nucleolar localization of p14 ARF to its partial folding and meso-scale assembly upon phase separation with NPM1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Supramolecular assembly of molecular wires alternating crown ethers and metal–halide complexes

Metal–halide complexes serve as key emissive centres in halide perovskites; however, precise control over their spatial organization through bottom-up assembly is challenging. Here we show that a crown-ether-assisted supramolecular assembly strategy can alternatingly connect metal–halide complexes and (crown ether@A) 2+ (where ‘A’ is an alkaline earth metal cation) complexes into a one-dimensional molecular wire, which can then be packed into a hexagonal crystal structure. This process resulted in the creation of an (18C6@Ba)MnBr 4 single crystal with green emission, achieving over 80% photoluminescence quantum yield and a narrow full width at half maximum. In addition, the non-centrosymmetric crystal structure gave rise to strong nonlinear optical responses, including second-harmonic generation. This versatile supramolecular assembly approach could be generalized to create various [M(I)X 2 ] − , [M(I)X 3 ] 2− , [M(II)X 4 ] 2− and [M(III)X 5 ] 2− molecular wires, broadening the potential for diverse emission colours and distinct optical properties. This strategy provides a general design principle for constructing supramolecular metal–halide building blocks with diverse optical functionalities.

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

Tunable assembly of hybrid colloids induced by regioselective depletion

Assembling colloidal particles using site-selective directional interactions into predetermined colloidal superlattices with desired properties is broadly sought-after, but challenging to achieve. Here in this paper, we exploit regioselective depletion interactions to engineer the directional bonding and assembly of non-spherical colloidal hybrid microparticles. We report that the crystallization of a binary colloidal mixture can be regulated by tuning the depletion conditions. Subsequently, we fabricate triblock biphasic colloids with controlled aspect ratios to achieve regioselective bonding. Without any surface treatment, these biphasic colloids assemble into various colloidal superstructures and superlattices featuring optimized pole-to-pole or center-to-center interactions. Additionally, we observe polymorphic crystallization, quantify the abundancy of each form using algorithms we developed, and investigate the crystallization process in real time. We demonstrate selective control of attractive interactions between specific regions on an anisotropic colloid with no need of site-specific surface functionalization, leading to a general method for achieving colloidal structures with yet unforeseen arrangements and properties.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Material assembly from collective action of shape-changing polymers

Some animals form transient, responsive and solid-like ensembles through dynamic structural interactions. These ensembles demonstrate emergent responses such as spontaneous self-assembly, which are difficult to achieve in synthetic soft matter. In this work, we use shape-morphing units comprising responsive polymers to create solids that self-assemble, modulate their volume and disassemble on demand. The ensemble is composed of a responsive hydrogel, liquid crystal elastomer or semicrystalline polymer ribbons that reversibly bend or twist. The dispersions of these ribbons mechanically interlock, inducing reversible aggregation. The aggregated liquid crystal elastomer ribbons have a 12-fold increase in the yield stress compared with cooled dispersion and contract by 34% on heating. Ribbon type, concentration and shape dictate the aggregation and govern the global mechanical properties of the solid that forms. Coating liquid crystal elastomer ribbons with a liquid metal begets photoresponsive and electrically conductive aggregates, whereas seeding cells on hydrogel ribbons enables self-assembling three-dimensional scaffolds, providing a versatile platform for the design of dynamic materials.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Elastic colloidal monopoles and reconfigurable self-assembly in liquid crystals

Monopole-like electrostatic interactions are ubiquitous in condensed matter, but they are often screened by counter-ions and cannot be switched from attractive to repulsive. In colloidal science, where the main goal is to develop colloidal particles that mimic and exceed the diversity and length scales of atomic and molecular assembly, electrostatically charged particles cannot change the sign of their surface charge or transform from monopoles to higher-order multipoles. In liquid-crystal colloids, elastic interactions between particles arise to minimize the free energy associated with elastic distortions in the long-range alignment of rod-like molecules around the particles. In dipolar quadrupolar and hexadecapolar nematic colloids, the symmetries of such elastic distortions mimic both electrostatic multipoles and the outermost occupied electron shells of atoms. Electric and magnetic switching, spontaneous transformations and optical control of elastic multipoles, as well as their interactions with topological defects and surface boundary conditions, have been demonstrated in such colloids. However, it has long been understood that elastic monopoles should relax to uniform or higher-order multipole states because of the elastic torques that they induce. We develop nematic colloids with strong elastic monopole moments and with elastic torques balanced by the optical torques induced by ambient light. We demonstrate the monopole-to-quadrupole reconfiguration of these colloidal particles by unstructured light, which resembles the driving of atoms between the ground state and various excited states. We show that the sign of the elastic monopoles can be switched, and that like-charged monopoles attract whereas oppositely charged ones repel, unlike in electrostatics. We also demonstrate the out-of-equilibrium dynamic assembly of these colloidal particles. This diverse and surprising behaviour is explained using a model that considers the balance of the optical and elastic torques that are responsible for the excited-state elastic monopoles and may lead to light-powered active-matter systems and self-assembled nanomachines.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Structural basis for intermodular communication in assembly-line polyketide biosynthesis

Assembly-line polyketide synthases (PKSs) are modular multi-enzyme systems with considerable potential for genetic reprogramming. Understanding how they selectively transport biosynthetic intermediates along a defined sequence of active sites could be harnessed to rationally alter PKS product structures. Here, to investigate functional interactions between PKS catalytic and substrate acyl carrier protein (ACP) domains, we employed a bifunctional reagent to crosslink transient domain–domain interfaces of a prototypical assembly line, the 6-deoxyerythronolide B synthase, and resolved their structures by single-particle cryogenic electron microscopy (cryo-EM). Together with statistical per-particle image analysis of cryo-EM data, we uncovered interactions between ketosynthase (KS) and ACP domains that discriminate between intra-modular and inter-modular communication while reinforcing the relevance of conformational asymmetry during the catalytic cycle. Our findings provide a foundation for the structure-based design of hybrid PKSs comprising biosynthetic modules from different naturally occurring assembly lines.

59 BASIC BIOLOGICAL SCIENCES↗