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At least 289 records · Page 16

Hierarchical Self‐Assembly of Multidimensional Functional Materials from Sequence‐Defined Peptoids

Abstract Hierarchical self‐assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular‐level understanding of the hierarchical assembly of sequence‐defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron‐based powder X‐ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence‐defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Protein Assembly by Design

Proteins are nature’s primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Furthermore, our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Insight into the β-Sheet Twist and Related Morphology of Self-Assembled Peptide Amphiphile Ribbons

Self-assembly of high-aspect-ratio filaments containing β-sheets has attracted much attention due to potential use in bioengineering and biomedicine. However, precisely predicting the assembled morphologies remains a grand challenge because of insufficient understanding of the self-assembly process. We employed an atomistic model to study the self-assembly of peptide amphiphiles (PAs) containing valine–glutamic acid (VE) dimeric repeats. By changing of the sequence length, the assembly morphology changes from flat ribbon to left-handed twisted ribbon, implying a relationship between β-sheet twist and strength of interstrand hydrogen bonds. The calculations are used to quantify this relationship including both magnitude and sign of the ribbon twist angle. Interestingly, a change in chirality is observed when we introduce the RGD epitope into the C-terminal of VE repeats, suggesting arginine and glycine’s role in suppressing right-handed β-sheet formation. Furthermore, this study provides insight into the relationship between β-sheet twist and self-assembled nanostructures including a possible design rule for PA self-assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Role of Cations in the Cation-Driven Assembly Process and their Effect on the Charge Storage Properties of Bilayered Vanadium Oxide and Reduced Graphene Oxide Heterostructures in Alkali Ion Systems

Exfoliated δ-Li x V 2 O 5 ·nH 2 O (ex-LVO) and reduced graphene oxide (rGO) heterostructures were constructed using different assembling cations (i.e., Li⁺, Na⁺, and K⁺ ions). The ex-LVO and rGO nanoflakes were stacked together using a concentrated chloride solution of each assembling cation and vacuum annealed at 200 °C to form three distinct two-dimensional (2D) layered architectures. X-ray diffraction and thermogravimetric analysis confirmed that the assembling ions can control the interlayer spacing of the bilayered vanadium oxide (BVO) phase as well as impact the crystallographic water content, which in turn affects the electrochemical performance. Scanning electron microscopy, scanning transmission electron microscopy (STEM), electron energy-loss spectroscopy (EELS), and X-ray photoelectron spectroscopy confirmed that a 2D heterointerface formed between LVO and rGO and that the cations used to assemble the heterostructure are trapped in the interlayer BVO region. High-resolution STEM imaging also showed the rGO dispersion throughout the LVO layers. Moreover, STEM-EELS identified a V 2 O 3 phase that forms along the rGO interface and can stabilize the materials during cycling. A charge storage mechanism analysis, combined with the galvanostatic intermittent titration technique, found that increased interlayer spacings of the BVO phase and using the assembling cations to define intercalation sites for identical charge-carrying ions lead to improved ion diffusion and increased capacities during cycling. Therefore, the Li⁺ and Na⁺ ion assembled heterostructures showed improved charge-carrying ion diffusion and charge storage capacities in each of their respective charge storage systems (i.e., Li-ion and Na-ion half-cells). In total, the cation used for heterostructure assembly can modify the final material structure and tailor the ion diffusion and charge storage capacity to tune its properties for the desired electrochemical system using a variety of 2D materials.

25 ENERGY STORAGE↗

Self-Assembly of Metallo-Supramolecules under Kinetic or Thermodynamic Control: Characterization of Positional Isomers Using Scanning Tunneling Spectroscopy

Coordination-driven self-assembly has been extensively employed to construct a variety of discrete structures as a bottom-up strategy. However, mechanistic understanding regarding whether self-assembly is under kinetic or thermodynamic control is less explored. To date, such mechanistic investigation has been limited to distinct, assembled structures. It still remains a formidable challenge to study the kinetic and thermodynamic behavior of self-assembly systems with multiple assembled isomers due to the lack of characterization methods. Herein, we use a stepwise strategy which combined self-recognition and self-assembly processes to construct giant metallo-supramolecules with 8 positional isomers in solution. With the help of ultrahigh-vacuum, low-temperature scanning tunneling microscopy and scanning tunneling spectroscopy, we were able to unambiguously differentiate 14 isomers on the substrate which correspond to 8 isomers in solution. Through measurement of 162 structures, the experimental probability of each isomer was obtained and compared with the theoretical probability. Finally, such a comparison along with density functional theory (DFT) calculation suggested that although both kinetic and thermodynamic control existed in this self-assembly, the increased experimental probabilities of isomers compared to theoretical probabilities should be attributed to thermodynamic control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sequence Programmable Order–Disorder Transitions in Supramolecular Assembly of Peptide Nanofibers

Protein–protein interactions determine the assembly of complexes that are responsible for numerous key biological processes. The assembly of many natural protein complexes is mediated by post-translational structural changes and environmental stimuli. In this study, we show that incorporation of adjacent lysine residues results in the pH-tunable stability of peptide secondary structure and assembly, allowing for the incorporation of complementary order-inducing motifs. The strategic placement of cysteine pairs in the same peptide sequence results in redox-dependent disulfide staple formation, inducing a transition from random coil to β-sheet conformation and subsequent supramolecular nanofiber assembly from otherwise disordered peptide monomers. Spectroscopic, imaging, molecular dynamics, and kinetic studies highlight the critical role of sequence motif location, oligomerization, and the competitive interplay between intra- and interpeptide disulfide bonding in determining assembly outcomes. We extend this approach to demonstrate phosphorylation-dependent assembly from the design of the same parent peptide sequence, suggesting a general approach to the design of diverse stimulus-responsive peptide sequences for supramolecular assembly. Furthermore, these findings also provide a framework for investigating sequence-dependent pathways in amyloid fiber formation with potential implications for neurodegenerative disease research.

Disulfides↗

Microscopic origin of tunable assembly forces in chiral active environments

Across a variety of spatial scales, from nanoscale biological systems to micron-scale colloidal systems, equilibrium self-assembly is entirely dictated by—and therefore limited by—the thermodynamic properties of the constituent materials. In contrast, nonequilibrium materials, such as self-propelled active matter, expand the possibilities for driving the assemblies that are inaccessible in equilibrium conditions. Recently, a number of works have suggested that active matter drives or accelerates self-organization, but the emergent interactions that arise between solutes immersed in actively driven environments are complex and poorly understood. Here, we analyze and resolve two crucial questions concerning actively driven self-assembly: (i) how, mechanistically, do active environments drive self-assembly of passive solutes? (ii) Under which conditions is this assembly robust? We employ the framework of odd hydrodynamics to theoretically explain numerical and experimental observations that chiral active matter, i.e., particles driven with a directional torque, produces robust and long-ranged assembly forces. Overall, these developments constitute an important step towards a comprehensive theoretical framework for controlling self-assembly in nonequilibrium environments.

36 MATERIALS SCIENCE↗

Tailoring multi-dimensional hierarchical self-assembly of metallacages through balancing non-covalent interactions

Despite advances in non-covalent interactions and complex self-assembly, precise control of multi-dimensional hierarchical self-assembly (HSA) from the molecular level to larger scales remains challenging. Herein, we designed and synthesized two rigid tetratopic ligands with multiple preset driving forces, and assembled them with Zn(II) ions to obtain metallacages SC6 and SC12 . Through balancing multiple non-covalent interactions, including metal–organic coordination, hydrophobic, and π–π interactions, SC6 can hierarchically self-assemble driven by a poor solvent, from one-dimensional nanowires to super-helical nanostructures via non-equilibrium self-assembly, progressing continuously with time and the increasing proportion of the poor solvent. However, for SC12 with enhanced hydrophobic interactions, two-dimensional monolayer nanogrids were formed by hierarchical self-assembly. Notably, these structures can be recycled back to primary metallacages through simple dissolution, highlighting their potential for efficient recycling and reuse. These results demonstrate that multi-dimensional hierarchical structures enable precise construction by balancing non-covalent interactions through a bottom-up self-assembly approach. This study provides deeper insight into the mechanisms of HSA and a promising strategy for the tailored creation of complex structures and sustainable porous materials.

36 MATERIALS SCIENCE↗

polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies

Long-read sequencing has revolutionized genome assembly, yielding highly contiguous, chromosome-level contigs. However, assemblies from some third generation long read technologies, such as Pacific Biosciences (PacBio) continuous long reads (CLR), have a high error rate. Such errors can be corrected with short reads through a process called polishing. Although best practices for polishing non-model de novo genome assemblies were recently described by the Vertebrate Genome Project (VGP) Assembly community, there is a need for a publicly available, reproducible workflow that can be easily implemented and run on a conventional high performance computing environment. Here, we describe polishCLR (https://github.com/isugifNF/polishCLR), a reproducible Nextflow workflow that implements best practices for polishing assemblies made from CLR data. PolishCLR can be initiated from several input options that extend best practices to suboptimal cases. It also provides re-entry points throughout several key processes, including identifying duplicate haplotypes in purge_dups, allowing a break for scaffolding if data are available, and throughout multiple rounds of polishing and evaluation with Arrow and FreeBayes. PolishCLR is containerized and publicly available for the greater assembly community as a tool to complete assemblies from existing, error-prone long-read data.

59 BASIC BIOLOGICAL SCIENCES↗

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗

Hierarchical Self‐Assembly of Multidimensional Functional Materials from Sequence‐Defined Peptoids

Abstract Hierarchical self‐assembly represents a powerful strategy for the fabrication of functional materials across various length scales. However, achieving precise formation of functional hierarchical assemblies remains a significant challenge and requires a profound understanding of molecular assembly interactions. In this study, we present a molecular‐level understanding of the hierarchical assembly of sequence‐defined peptoids into multidimensional functional materials, including twisted nanotube bundles serving as a highly efficient artificial light harvesting system. By employing synchrotron‐based powder X‐ray diffraction and analyzing single crystal structures of model compounds, we elucidated the molecular packing and mechanisms underlying the assembly of peptoids into multidimensional nanostructures. Our findings demonstrate that incorporating aromatic functional groups, such as tetraphenyl ethylene (TPE), at the termini of assembling peptoid sequences promotes the formation of twisted bundles of nanotubes and nanosheets, thus enabling the creation of a highly efficient artificial light harvesting system. This research exemplifies the potential of leveraging sequence‐defined synthetic polymers to translate microscopic molecular structures into macroscopic assemblies. It holds promise for the development of functional materials with precisely controlled hierarchical structures and designed functions.

Shao, Li↗

The Metal Effect on Self-Assembling of Oxalamide Gelators Explored by Mass Spectrometry and DFT Calculations

Gels formed by self-assembly of small organic molecules are of wide interest as dynamic soft materials with numerous possible applications, especially in terms of nanotechnology for functional and responsive biomaterials, biosensors, and nanowires. Four bis-oxalamides were chosen to show if electrospray ionization mass spectrometry (ESI-MS) could be used as a prediction of a good gelator and also to shed light on the gelation processes. By inspecting the gelation of several solvent, we showed that bis(amino acid)oxalamide 1 proved to be the most efficient, also being able of forming the largest observable assemblies in the gas phase. The formation of singly charged assemblies holding from one up to six monomer units is the outcome of the strong intermolecular H-bonds, particularly among terminal carboxyl groups. The variation of solvents from polar aprotic towards polar protic did not have any significant effects on the size of the assemblies. The addition of a salt such as NaOAc or Mg(OAc){sub 2}, depending on the concentration, altered the assembling. Computational analysis at the DFT level aided in the interpretation of the observed trends and revealed that individual gelator molecules spontaneously assemble to higher aggregates, but the presence of the Na{sup +} cation disrupts any gelator organization since it becomes significantly more favorable for gelator molecules to bind Na{sup +} cations up to the 3:1 ratio than to self-assemble, being fully in line with experimental observations reported here. .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Key Intermediate Nanostructures in the Self-Assembly of Amphiphilic Polypeptoids Revealed by Cryo-TEM

Amphiphilic copolypeptoids are known to form a variety of nanostructures (fibers, tubes, sheets, etc.), but the assembly mechanisms and key intermediates remain underexplored. This study investigates the intermediate structures formed during the early stages of self-assembly in diblock copolypeptoids using cryo-transmission electron microscopy (cryo-TEM). Here we focused on two diblock copolypeptoids, one with a free N-terminus and the other with a capped N-terminus, which ultimately form less-ordered nanofibers and well-ordered nanosheets, respectively. Through cryo-TEM imaging of vitrified solutions at various time points during the self-assembly process, the study identified micelles and vesicles as key intermediate structures. Notably, the formation of vesicles as intermediates is unusual in crystallization-driven self-assembly and suggests a unique pathway in polypeptoid self-assembly. The study provides direct imaging evidence of key intermediates in polypeptoid self-assembly, advancing the understanding of their self-assembly mechanisms.

59 BASIC BIOLOGICAL SCIENCES↗

Modulating the Molecular Geometry and Solution Self-Assembly of Amphiphilic Polypeptoid Block Copolymers by Side Chain Branching Pattern

Solution self-assembly of coil-crystalline diblock copolypeptoids has attracted increasing attention due to its capability to form hierarchical nanostructures with tailorable morphologies and functionalities. While the N-substituent (or side chain) structures are known to affect the crystallization of polypeptoids, their roles in dictating the hierarchical solution self-assembly of diblock copolypeptoids are not fully understood. Herein, we designed and synthesized two types of diblock copolypeptoids, i.e., poly(N-methylglycine)-b-poly(N-octylglycine) (PNMG-b-PNOG) and poly(N-methylglycine)-b-poly(N-2-ethyl-1-hexylglycine) (PNMG-b-PNEHG), to investigate the influence of N-substituent structure on the crystalline packing and hierarchical self-assembly of diblock copolypeptoids in methanol. With a linear aliphatic N-substituent, the PNOG blocks pack into a highly ordered crystalline structure with a board-like molecular geometry, resulting in the self-assembly of PNMG-b-PNOG molecules into a hierarchical microflower morphology composed of radially arranged nanoribbon subunits. By contrast, the PNEHG blocks bearing bulky branched aliphatic N-substituents are rod-like and prefer to stack into a columnar hexagonal liquid crystalline mesophase, which drives PNMG-b-PNEHG molecules to self-assemble into symmetrical hexagonal nanosheets in solution. A combination of time-dependent small/wide-angle X-ray scattering and microscopic imaging analysis further revealed the self-assembly mechanisms for the formation of these microflowers and hexagonal nanosheets. These results highlight the significant impact of the N-substituent architecture (i.e., linear versus branched) on the supramolecular self-assembly of diblock copolypeptoids in solution, which can serve as an effective strategy to tune the geometry and hierarchical structure of polypeptoid-based nanomaterials.

99 GENERAL AND MISCELLANEOUS↗

Soil pH mediates the balance between stochastic and deterministic assembly of bacteria

Little is known about the factors affecting the relative influence of stochastic and deterministic processes that governs the assembly of microbial communities in successional soils. Here, we conducted a meta-analysis of bacterial communities using six different successional soils data sets, scattered across different regions, with different pH conditions in early and late successional soils. We found that soil pH was the best predictor of bacterial community assembly and the relative importance of stochastic and deterministic processes along successional soils. Extreme acidic or alkaline pH conditions lead to assembly of phylogenetically more clustered bacterial communities through deterministic processes, whereas pH conditions close to neutral lead to phylogenetically less clustered bacterial communities with more stochasticity. We suggest that the influence of pH, rather than successional age, is the main driving force in producing trends in phylogenetic assembly of bacteria, and that pH also influences the relative balance of stochastic and deterministic processes along successional soils. Given that pH had a much stronger association with community assembly than did successional age, we evaluated whether the inferred influence of pH was maintained when studying globally-distributed samples collected without regard for successional age. This dataset confirmed the strong influence of pH, suggesting that the influence of soil pH on community assembly processes occurs globally. Extreme pH conditions likely exert more stringent limits on survival and fitness, imposing strong selective pressures through ecological and evolutionary time. Taken together, these findings suggest that the degree to which stochastic vs. deterministic processes shape soil bacterial community assembly is a consequence of soil pH rather than successional age.

Tripathi, Binu M.↗

Disordered-to-ordered transitions in assembly factors allow the complex II catalytic subunit to switch binding partners

Complex II (CII) activity controls phenomena that require crosstalk between metabolism and signaling, including neurodegeneration, cancer metabolism, immune activation, and ischemia-reperfusion injury. CII activity can be regulated at the level of assembly, a process that leverages metastable assembly intermediates. The nature of these intermediates and how CII subunits transfer between metastable complexes remains unclear. In this work, we identify metastable species containing the SDHA subunit and its assembly factors, and we assign a preferred temporal sequence of appearance of these species during CII assembly. Structures of two species show that the assembly factors undergo disordered-to-ordered transitions without the appearance of significant secondary structure. The findings identify that intrinsically disordered regions are critical in regulating CII assembly, an observation that has implications for the control of assembly in other biomolecular complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Inositol phosphates are assembly co-factors for HIV-1

A short, 14-amino-acid segment called SP1, located in the Gag structural protein, has a critical role during the formation of the HIV-1 virus particle. During virus assembly, the SP1 peptide and seven preceding residues fold into a six-helix bundle, which holds together the Gag hexamer and facilitates the formation of a curved immature hexagonal lattice underneath the viral membrane. Upon completion of assembly and budding, proteolytic cleavage of Gag leads to virus maturation, in which the immature lattice is broken down; the liberated CA domain of Gag then re-assembles into the mature conical capsid that encloses the viral genome and associated enzymes. Folding and proteolysis of the six-helix bundle are crucial rate-limiting steps of both Gag assembly and disassembly, and the six-helix bundle is an established target of HIV-1 inhibitors. Here, using a combination of structural and functional analyses, we show that inositol hexakisphosphate (InsP6, also known as IP 6 ) facilitates the formation of the six-helix bundle and assembly of the immature HIV-1 Gag lattice. IP 6 makes ionic contacts with two rings of lysine residues at the centre of the Gag hexamer. Proteolytic cleavage then unmasks an alternative binding site, where IP 6 interaction promotes the assembly of the mature capsid lattice. Furthermore, these studies identify IP6 as a naturally occurring small molecule that promotes both assembly and maturation of HIV-1.

59 BASIC BIOLOGICAL SCIENCES↗

Design of metal-mediated protein assemblies via hydroxamic acid functionalities

The self-assembly of proteins into sophisticated multicomponent assemblies is a hallmark of all living systems and has spawned extensive efforts in the construction of novel synthetic protein architectures with emergent functional properties. Protein assemblies in nature are formed via selective association of multiple protein surfaces through intricate noncovalent protein-protein interactions, a challenging task to accurately replicate in the de novo design of multiprotein systems. In this protocol, we describe the application of metal-coordinating hydroxamate (HA) motifs to direct the metal-mediated assembly of polyhedral protein architectures and 3D crystalline protein frameworks (protein-MOFs). This strategy has been implemented using an asymmetric cytochrome cb562 monomer through selective, concurrent association of Fe 3+ and Zn 2+ ions to form polyhedral cages. Furthermore, the use of ditopic HA linkers as bridging ligands with metal-binding protein nodes has allowed the construction of crystalline 3D protein-MOF lattices. The protocol is divided into two major sections: (1) the development of a Cys-reactive HA molecule for protein derivatization and self-assembly of protein-HA conjugates into polyhedral cages and (2) the synthesis of ditopic HA bridging ligands for the construction of ferritin-based protein-MOFs using symmetric metal-binding protein nodes. Furthermore, protein cages can be analyzed using analytical ultracentrifugation (AUC), transmission electron microscopy (TEM) and single-crystal X-ray diffraction (sc-XRD) techniques. HA-mediated protein-MOFs are formed in sitting-drop vapor diffusion crystallization trays and are probed via sc-XRD and multi-crystal small-angle X-ray scattering (SAXS) measurements. Ligand synthesis, construction of HA-mediated assemblies, and post-assembly analysis as described in this protocol can be performed by a graduate-level researcher within six weeks.

36 MATERIALS SCIENCE↗