Assembly Motif Research Articles

Dynamic fibrillar assembly of αB-crystallin induced by perturbation of the conserved NT-IXI motif resolved by cryo-EM

αB-crystallin is an archetypical member of the small heat shock proteins (sHSPs) vital for cellular proteostasis and mitigating protein misfolding diseases. Gaining insights into the principles defining their molecular organization and chaperone function have been hindered by intrinsic dynamic properties and limited high-resolution structural analysis. To disentangle the mechanistic underpinnings of these dynamical properties, we ablate a conserved IXI-motif located within the N-terminal (NT) domain of human αB-crystallin implicated in subunit exchange dynamics and client sequestration. This results in a profound structural transformation, from highly polydispersed caged-like native assemblies into an elongated fibril state amenable to high-resolution cryo-EM analysis. The reversible nature of this variant facilitates interrogation of functional effects due to perturbation of the NT-IXI motif in both the native-like oligomer and fibril states. Together, our investigations unveil several features thought to be key mechanistic attributes to sHSPs and point to a critical significance of the NT-IXI motif in αB-crystallin assembly, polydispersity, and chaperone activity.

Enhanced Molecular Imaging through a Versatile Peptide Nanofiber for Self-Assembly and Precise Recognition.

Designing molecules for multivalent targeting of specific disease markers can enhance binding stability which is critical in molecular imaging and targeted therapy. Through rational molecular design, the nanostructures formed by self-assembly of targeting peptides are expected to achieve multivalent targeting by increasing the density of recognition ligands. However, the balance between targeting peptide self-assembly and molecular recognition remains elusive. In this study, we designed a targeting-peptide-based imaging probe system TAP which consist of the signal unit, the recognition motif, the assembly motif and a Pro-leverage. It is verified that TAP could specifically binds to PD-L1-positive tumor cells in a multivalent manner to produce biological effects, and could also be combined with imaging probes through unique self-assembly strategies. By the balance between the peptide self-assembly and targeting recognition, the specificity and stability can be improved while the accumulation capacity of the probes at the tumor site can be greatly enhanced compared with the conventional strategy, thus reducing side effects, providing an effective tool for diagnostic and therapeutic integration of tumors.

Recent Progress in Synthetic Chemistry and Biological Activities of Pyrimido[ 4,5-b] Quinoline Derivatives (Part III)

Abstract: Amongst heterocyclic compounds, quinoline and pyrimidine are advantaged scaffolds that appear as significant assembly motifs for the development of new drug entities. Moreover, quinolinepyrimidine- inspired hybrids have a number of biological characteristics that are known. In addition, many pyrimido[4,5-b]quinoline ring systems (PyQs4,5-b), specifically concerning medicinal chemistry, have been reported over the past decade. The synthesis of (PyQs4,5-b) using barbituric acid, thiobarbituric acid, pyrimidine, and their derivatives is presented in this review. The preparation of PyQs4,5-b was clarified through the following chemical reactions: Friedländer, Vilsmeier-Haack formylation, Hantzsch-like reaction, and one-pot three-component reaction.

FGF‐Mimicking Triphen[3]arene Peptide Self‐Assembly to Accelerate Muscle Regeneration and Repair

AbstractBioactive peptides play crucial roles in the biomedicine fields including cancer therapy and regenerative medicine due to their favorable biocompatibility, low immunogenicity, and excellent biological activity. However, their low stability greatly limits their clinical application. Herein, a novel bioactive peptide delivery strategy is reported that utilizes triphen[3]arene polyvalent‐conjugated bioactive peptides to induce self‐assembly and form nanofibers to enhance the in vivo stability and bioactivity of bioactive peptides. Specifically, a water‐soluble triphen[3]arene (WTP3(YRSRK)6, Comp. 2) containing six FGF‐mimicking peptides, primarily comprising two components: triphen[3]arene serves as a skeleton molecule and an assembly motif with multiple customizable sites, while YRSRK is a pentapeptide with fibroblast growth factor 2 (FGF‐2) biological activity. Despite the presence of the inhibitor dexamethasone (Dex), Comp. 2 continued to enhance cell proliferation by 15% and rescued 17% of cells from apoptosis. The administration of Comp. 2 resulted in improved restoration of skeletal muscle atrophy and functional damage in mice. The mean grip strength increased by 42%, and the calf muscle volume increased by 17%. This innovative approach of utilizing macrocycle polyvalent conjugated bioactive peptides offers a universal method for enabling bioactive peptides to produce sustained and efficient biological effects, potentially advancing the development of promising peptide‐based nanomedicines.

Engineering Nanobelt Structure via Sulphur and Oxygen Doping: Synthesis, Structural Characterization, and Complexation with Fullerenes.

This study explores the synthesis, structural characterization, and host-guest interactions of heteroatom bridged nanobelts, focusing on a cyclothianthrene nanobelt and a fused nanobelt incorporating thianthrene and phenoxathiin. Utilizing a cyclization-followed-by-bridging synthetic approach, both molecular belts were successfully synthesized, and their structures confirmed through NMR and MALDI-TOF-MS analysis. Crystallographic studies revealed that the cyclothianthrene nanobelt adopts an octagonal column-like conformation, while the hybrid belt forms an oval tub-shaped shape, both exhibiting distinct assembly motifs. The host-guest chemistry of these nanobelts was investigated with fullerenes (C60, C70, and PC61BM). The cyclothianthrene belt showed no interaction with these fullerenes, whereas the other belt demonstrated adaptive binding capabilities, forming stable complexes with C60 and C70 through π-π interactions and C-H⋅⋅⋅S hydrogen bonds. The binding constants indicated that the hybrid belt has a stronger affinity for C70 due to better size complementarity. Additionally, its interaction with PC61BM showcased a specific 1 : 1 binding mode despite exhibiting a smaller binding constant. This study underscores the impact of heteroatom incorporation on the structural and functional properties of nanobelts, offering insights for future molecular design strategies.

TRAMP assembly alters the conformation and RNA binding of Mtr4 and Trf4-Air2.

The TRAMP complex contains two enzymatic activities essential for RNA processing upstream of the nuclear exosome. Within TRAMP, RNA is 3' polyadenylated by a sub-complex of Trf4/5 and Air1/2 and unwound 3' to 5' by Mtr4, a DExH helicase. The molecular mechanisms of TRAMP assembly and RNA shuffling between the two TRAMP catalytic sites are poorly understood. Here, we report solution hydrogen-deuterium exchange data with thermodynamic and functional assays to uncover these mechanisms for yeast TRAMP with Trf4 and Air2 homologs. We show that TRAMP assembly constrains RNA-recognition motifs that are peripheral to catalytic sites. These include the Mtr4 Arch and Air2 zinc knuckles 1, 2, and 3. While the Air2 Arch-interacting motif likely constrains the Mtr4 Arch via transient interactions, these do not fully account for the importance of the Mtr4 Arch in TRAMP assembly. We further show that tRNA binding by single active-site subunits, Mtr4 and Trf4-Air2, differs from the double active-site TRAMP. TRAMP has reduced tRNA binding on the Mtr4 Fist and RecA2 domains, offset by increased tRNA binding on Air2 zinc knuckles 2 and 3. Competition between these RNA-binding sites may drive tRNA transfer between TRAMP subunits. We identify dynamic changes upon TRAMP assembly and RNA-recognition motifs that transfer RNA between TRAMP catalytic sites.

Predicting the Geometry of Core-Shell Structures: How a Shape Changes with Constant Added Thickness.

The core-shell assembly motif is ubiquitous in chemistry. While the most obvious examples are core/shell-type nanoparticles, many other examples exist. The shape of the core/shell constructs is poorly understood, making it impossible to separate chemical effects from geometric effects. Here, we create a model for the core/shell construct and develop proof for how the eccentricity is expected to change as a function of the shell. We find that the addition of a constant thickness shell always creates a relatively more spherical shape for all shapes covered by our model unless the shape is already spherical or has some underlying radial symmetry. We apply this work to simulated AOT reverse micelles and demonstrate that it is remarkably successful at explaining the observed shapes of the chemical systems. We identify the three specific cases where the model breaks down and how this impacts eccentricity.

Graphene exfoliation using multidomain peptides.

Liquid-phase exfoliation using biomolecules in aqueous solution is a promising approach to obtain high quality 2D nanosheets. For example, the well-studied graphene-binding peptide, P1 (sequence HSSYWYAFNNKT), has been previously investigated and shown to have a good ability to exfoliate graphene sheets in aqueous conditions under sonication, maintaining colloidal stability. Building on this, the biomolecular exfoliant and assembly motif (BEAM) peptide, that features a graphene-binding domain at one end and a hexagonal boron nitride (h-BN) binding domain at the other, separated by a 10-carbon fatty acid chain in the centre, is shown to exfoliate graphene sheets from bulk graphite in aqueous media. An in-depth examination of the ability of the BEAM to both facilitate sheet exfoliation under sonication conditions and also maintain colliodal stability is provided through molecular dynamics simulations. These findings open new possibilities for designing multi-functional molecules that can both exfoliate and organise 2D materials into heterostructures under ambient conditions in aqueous media.

A peptide selectively recognizes Gram-negative bacteria and forms a bacterial extracellular trap (BET) through interfacial self-assembly.

An innate immune system intricately leverages unique mechanisms to inhibit colonization of external invasive Bacteria, for example human defensin-6, through responsive encapsulation of bacteria. Infection and accompanying antibiotic resistance stemming from Gram-negative bacteria aggregation represent an emerging public health crisis, which calls for research into novel anti-bacterial therapeutics. Herein, inspired by naturally found host-defense peptides, we design a defensin-like peptide ligand, bacteria extracellular trap (BET) peptide, with modular design composed of targeting, assembly, and hydrophobic motifs with an aggregation-induced emission feature. The ligand specifically recognizes Gram-negative bacteria via targeting cell wall conserved lipopolysaccharides (LPS) and transforms from nanoparticles to nanofibrous networks in situ to trap bacteria and induce aggregation. Importantly, treatment of the BET peptide was found to have an antibacterial effect on the Pseudomonas aeruginosa strain, which is comparable to neomycin. Animal studies further demonstrate its ability to trigger aggregation of bacteria in vivo. This biomimetic self-assembling BET peptide provides a novel approach to fight against pathogenic Gram-negative bacteria.

Preserving Structurally Labile Peptide Nanosheets After Molecular Functionalization of the Self-Assembling Peptides.

A significant challenge in creating supramolecular materials is that conjugating molecular functionalities to building blocks often results in dissociation or undesired morphological transformation of their assemblies. Here we present a facile strategy to preserve structurally labile peptide assemblies after molecular modification of the self-assembling peptides. Sheet-forming peptides are designed to afford a staggered alignment with the segments bearing chemical modification sites protruding from the sheet surfaces. The staggered assembly allows for simultaneous separation of attached molecules from each other and from the underlying assembly motifs. Strikingly, using PEGs as the external molecules, PEG400 - and PEG700 -peptide conjugates directly self-associate into nanosheets with the PEG chains localized on the sheet surfaces. In contrast, the sheet formation based on in-register lateral packing of peptides does not recur upon the peptide PEGylation. This strategy allows for fabrication of densely modified assemblies with a variety of molecules, as demonstrated using biotin (hydrophobic molecule), c(RGDfK) (cyclic pentapeptide), and nucleic acid aptamer (negatively charged ssDNA). The staggered co-assembly also enables extended tunability of the amount/density of surface molecules, as exemplified by screening ligand-appended assemblies for cell targeting. This study paves the way for functionalization of historically challenging fragile assemblies while maintaining their overall morphology.

Preserving Structurally Labile Peptide Nanosheets After Molecular Functionalization of the Self‐Assembling Peptides

AbstractA significant challenge in creating supramolecular materials is that conjugating molecular functionalities to building blocks often results in dissociation or undesired morphological transformation of their assemblies. Here we present a facile strategy to preserve structurally labile peptide assemblies after molecular modification of the self‐assembling peptides. Sheet‐forming peptides are designed to afford a staggered alignment with the segments bearing chemical modification sites protruding from the sheet surfaces. The staggered assembly allows for simultaneous separation of attached molecules from each other and from the underlying assembly motifs. Strikingly, using PEGs as the external molecules, PEG400‐ and PEG700‐peptide conjugates directly self‐associate into nanosheets with the PEG chains localized on the sheet surfaces. In contrast, the sheet formation based on in‐register lateral packing of peptides does not recur upon the peptide PEGylation. This strategy allows for fabrication of densely modified assemblies with a variety of molecules, as demonstrated using biotin (hydrophobic molecule), c(RGDfK) (cyclic pentapeptide), and nucleic acid aptamer (negatively charged ssDNA). The staggered co‐assembly also enables extended tunability of the amount/density of surface molecules, as exemplified by screening ligand‐appended assemblies for cell targeting. This study paves the way for functionalization of historically challenging fragile assemblies while maintaining their overall morphology.

RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles

RAD51C is an enigmatic predisposition gene for breast, ovarian, and prostate cancer. Currently, missing structural and related functional understanding limits patient mutation interpretation to homology-directed repair (HDR) function analysis. Here we report the RAD51C-XRCC3 (CX3) X-ray co-crystal structure with bound ATP analog and define separable RAD51C replication stability roles informed by its three-dimensional structure, assembly, and unappreciated polymerization motif. Mapping of cancer patient mutations as a functional guide confirms ATP-binding matching RAD51 recombinase, yet highlights distinct CX3 interfaces. Analyses of CRISPR/Cas9-edited human cells with RAD51C mutations combined with single-molecule, single-cell and biophysics measurements uncover discrete CX3 regions for DNA replication fork protection, restart and reversal, accomplished by separable functions in DNA binding and implied 5’ RAD51 filament capping. Collective findings establish CX3 as a cancer-relevant replication stress response complex, show how HDR-proficient variants could contribute to tumor development, and identify regions to aid functional testing and classification of cancer mutations.

Domains required for the interaction of the central negative element FRQ with its transcriptional activator WCC within the core circadian clock of Neurospora

In the negative feedback loop composing the Neurospora circadian clock, the core element, FREQUENCY (FRQ), binds with FRQ-interacting RNA helicase (FRH) and casein kinase 1 to form the FRQ-FRH complex (FFC) which represses its own expression by interacting with and promoting phosphorylation of its transcriptional activators White Collar-1 (WC-1) and WC-2 (together forming the White Collar complex, WCC). Physical interaction between FFC and WCC is a prerequisite for the repressive phosphorylations, and although the motif on WCC needed for this interaction is known, the reciprocal recognition motif(s) on FRQ remains poorly defined. To address this, we assessed FFC-WCC in a series of frq segmental-deletion mutants, confirming that multiple dispersed regions on FRQ are necessary for its interaction with WCC. Biochemical analysis shows that interaction between FFC and WCC but not within FFC or WCC can be disrupted by high salt, suggesting that electrostatic forces drive the association of the two complexes. As a basic sequence on WC-1 was previously identified as a key motif for WCC-FFC assembly, our mutagenetic analysis targeted negatively charged residues of FRQ, leading to identification of three Asp/Glu clusters in FRQ that are indispensable for FFC-WCC formation. Surprisingly, in several frq Asp/Glu-to-Ala mutants that vastly diminish FFC-WCC interaction, the core clock still oscillates robustly with an essentially wildtype period, indicating that the interaction between the positive and negative elements in the feedback loop is required for the operation of the circadian clock but is not a determinant of the period length.

Multistep sequence-controlled supramolecular polymerization by the combination of multiple self-assembly motifs

The precise sequence control of polymer chain is an important research topic of polymer chemistry. Although some methods such as iterative synthesis and supramolecular polymerization have been developed to fabricate sequence-controllable polymer, it is still a great challenge to consecutively prepare multiple supramolecular polymers with different sequence structures. In this work, through the reasonable utilization of assembly motifs, we integrated multiple host-guest recognitions and metal coordination interactions to prepare different sequence-controlled supramolecular polymers by a multistep assembly strategy. This research provides inspiration for the design and preparation of supramolecular polymers with different sequence structures.

Evolution of Transient Luminescent Assemblies Regulated by Trace Water in Organic Solvents.

Trace water in organic solvents can play a crucial role in the construction of supramolecular assemblies, which has not gained enough attention until very recent years. Herein, we demonstrate that residual water in organic solvents plays a decisive role in the regulation of the evolution of assembled structures and their functionality. By adding Mg(ClO4)2 into a multi-component organic solution containing terpyridine-based ligand 3Tpy and monodentate imidazole-based ligand M2, the system underwent an unexpected kinetic evolution. Metallo-supramolecular polymers (MSP) formed first by the coordination of 3Tpy and Mg2+, but they subsequently decomposed due to the interference of M2, resulting in a transient MSP system. Further investigation revealed that this occurred because residual water in the solvent and M2 cooperatively coordinated with Mg2+. This allowed M2 to capture Mg2+ from MSP, which led to depolymerization. However, owing to the slow reaction between trace water/M2/Mg2+, the formation of MSP still occurred first. Therefore, water regulated both the thermodynamics and kinetics of the system and was the key factor for constructing the transient MSP. Fine-tuning the water content and other assembly motifs regulated the assembly evolution pathway, tuned the MSP lifetime, and made the luminescent color of the system undergo intriguing transition processes over time.

The Chemical and Pharmacological Advancements of Quinoline: A Mini Review

Quinoline is a preferred scaffold that emerges as a prominent assembly motif for the creation of novel pharmacological molecules among heterocyclic compounds. An important family of chemicals includes quinoline and its derivatives that have been studied for various biological activities. Due to its wide range of bioactivity, quinoline, which is made up of benzene fused with N-heterocyclic pyridine, has drawn a lot of interest as a key template in drug creation. In order to demonstrate the quinoline motifs' significant efficacies for upcoming drug development, this review intends to provide the most current developments in chemistry, their medicinal potential, and their pharmacological applications. As a result, these compounds have been produced by several scientific groups as intentional structures, and their biological functions have been examined. The current study offers succinct information on quinoline's natural sources, as well as details on newly marketed medications that include quinoline. The pharmacological effects of quinoline derivatives, such as their anticonvulsant, antibacterial, antiviral, anti-protozoal, antimalarial, anticancer, anti-inflammatory, and anthelmintic properties, are also discussed in this study.
 Keywords: Nitrogen-Based Heterocycles, Quinoline, Synthesis, Biological Activities

Medial packing and elastic asymmetry stabilize the double-gyroid in block copolymers

Triply-periodic networks are among the most complex and functionally valuable self-assembled morphologies, yet they form in nearly every class of biological and synthetic soft matter building blocks. In contrast to simpler assembly motifs – spheres, cylinders, layers – networks require molecules to occupy variable local environments, confounding attempts to understand their formation. Here, we examine the double-gyroid network phase by using a geometric formulation of the strong stretching theory of block copolymer melts, a prototypical soft self-assembly system. The theory establishes the direct link between molecular packing, assembly thermodynamics and the medial map, a generic measure of the geometric center of complex shapes. We show that “medial packing” is essential for stability of double-gyroid in strongly-segregated melts, reconciling a long-standing contradiction between infinite- and finite-segregation theories. Additionally, we find a previously unrecognized non-monotonic dependence of network stability on the relative entropic elastic stiffness of matrix-forming to tubular-network forming blocks. The composition window of stable double-gyroid widens for both large and small elastic asymmetry, contradicting intuitive notions that packing frustration is localized to the tubular domains. This study demonstrates the utility of optimized medial tessellations for understanding soft-molecular assembly and packing frustration via an approach that is readily generalizable far beyond gyroids in neat block copolymers.

Three-dimensional visualization of nanoparticle lattices and multimaterial frameworks.

Advances in nanoscale self-assembly have enabled the formation of complex nanoscale architectures. However, the development of self-assembly strategies toward bottom-up nanofabrication is impeded by challenges in revealing these structures volumetrically at the single-component level and with elemental sensitivity. Leveraging advances in nano-focused hard x-rays, DNA-programmable nanoparticle assembly, and nanoscale inorganic templating, we demonstrate nondestructive three-dimensional imaging of complexly organized nanoparticles and multimaterial frameworks. In a three-dimensional lattice with a size of 2 micrometers, we determined the positions of about 10,000 individual nanoparticles with 7-nanometer resolution, and identified arrangements of assembly motifs and a resulting multimaterial framework with elemental sensitivity. The real-space reconstruction permits direct three-dimensional imaging of lattices, which reveals their imperfections and interfaces and also clarifies the relationship between lattices and assembly motifs.

Chaotropic Effect as an Assembly Motif to Construct Supramolecular Cyclodextrin-Polyoxometalate-Based Frameworks.

In aqueous solution, low-charged polyoxometalates (POMs) exhibit remarkable self-assembly properties with nonionic organic matter that have been recently used to develop groundbreaking advances in host-guest chemistry, as well as in soft matter science. Herein, we exploit the affinity between a chaotropic POM and native cyclodextrins (α-, β-, and γ-CD) to enhance the structural and functional diversity of cyclodextrin-based open frameworks. First, we reveal that the Anderson-Evans type polyoxometalate [AlMo6O18(OH)6]3- represents an efficient inorganic scaffold to design open hybrid frameworks built from infinite cyclodextrin channels connected through the disk-shaped POM. A single-crystal X-ray analysis demonstrates that the resulting supramolecular architectures contain large cavities (up to 2 nm) where the topologies are dictated by the rotational symmetry of the organic macrocycle, generating honeycomb (bnn net) and checkerboard-like (pcu net) networks for α-CD (C6) and γ-CD (C8), respectively. On the other hand, the use of β-CD, a macrocycle with C7 ideal symmetry, led to a distorted-checkerboard-like network. The cyclodextrin-based frameworks built from an Anderson-Evans type POM are easily functionalizable using the molecular recognition properties of the macrocycle building units. As a proof of concept, we successfully isolated a series of compartmentalized functional frameworks by the entrapment of polyiodides or superchaotropic redox-active polyanions within the macrocyclic host matrix. This set of results paves the way for designing multifunctional supramolecular frameworks whose pore dimensions are controlled by the size of inorganic entities.

Pharmacological Properties And Bioavailability Studies Of 3-Methyl Quinoline

Amongst heterocyclic compounds, quinoline is the privileged scaffold that appears as a significant assembly motif for the development of new drug entities. Quinoline and its derivatives tested with diverse biological activity constitute an important class of compounds for new drug development. Therefore, many scientific communities have developed these compounds as intent structures and evaluated their biological activities. Our goal is to discover bioavailability, relative bioavailability, definition and assembly factors that may influence the bioavailability of a medication item, physiologic and other factors influencing bioavailability, characteristics of medications with a high risk of bioavailability, and evaluation of bioavailability from pharmacologic just as a therapeutic reaction. From the GCMS analysis bioactive compound chosen was Quinoline compounds and it is further investigated. The compound 3-methyl Quinoline, solved Lipinski‟s rule and it showed drug resemblance (Mi Log P esteem < 5, TPSA < 140 Ǻ2, n infringement = 0, sub-atomic mass < 500, N rotb < 5, n HBD <5 and n HBA<8). As the bioavailability score is high it can be used for further studies. This finding revealed that the bulk of pharmacological characteristics and bioavailability investigations were conducted using ADME and toxicity, rather than the absence of viability. From mid-one, the substance 3-methyl Quinoline measures are being taken in the drug business to improve achievement rates by contemplating the ADME and toxicological perspectives in medication disclosure.