Casting metal nanowires within discrete self-assembled peptide nanotubes

Metal-Directed Self-Assembly of Minimal Heterochiral Peptides into Metallo-Supramolecular β-Helical Tubules for Artificial Transmembrane Water Channels

Transmembrane selective transport of metabolites controls essential biological functions. During the last two decades, artificial channels have been developed and cyclic peptides have emerged as ideal platforms for efficient ion, sugar, and nucleic acid channel translocation. Despite these tremendous developments, cyclic peptides have eluded selective water transport. Herein, we report the formation of narrow artificial β-helical tubules with diameters ranging from 2.80 to 3.25 Å that selectively control the water translocation, akin to natural aquaporin channels. The tubular assemblies resulted from the metal-driven folding and assembly of minimal heterochiral metal-binding 3-pyridyl-terminated peptides. The bent ultrashort peptide ligand coordinates with Ag+ metal ions in a head-to-tail manner, which undergoes subsequent polymerization into a β-helical tubular structure stabilized by interstrand hydrogen bonds (H-bonds) between the β-strands and π-π staking interactions between terminal pyridyl moieties. Furthermore, sequence engineering of the heterochiral peptide and subsequent Ag+ ion coordination of the tailored peptides enabled the formation of distinct synthetic double β-barrel and artificial β-helical tubular assemblies, with water molecules encapsulated in the hydrophilic core of the tubes. These water-encapsulated tubes were further explored as artificial water channels in lipid bilayers. Our findings suggest that such β-helical tubular channels achieve a single-channel permeability of 106 water molecules/second/channel, which is within 1-2 orders of magnitude lower than that of aquaporins, with a rather good ability to sterically reject ions and prevent proton transport. These assemblies present significant potential for engineering efficient membranes for water purification and separation sciences.

Biocatalytic Regulation of Peptide Self-Assembly for Biomineralization

The production of functional hierarchical architectures through the biomineralization of a continuously secreted protein matrix is prevalent in nature; however, it remains challenging to mimic this dynamic aspect of the biomineralization process, especially in biological systems. Here we report the use of dynamically generated supramolecular assemblies of peptides for in situ biomimetic mineralization in live cells. Specifically, by integrating enzymatic regulation of inorganic phosphate concentration and enzyme-instructed self-assembly, we demonstrate a phosphorylated tripeptide that self-assembles into dynamic supramolecular nanofibers via enzymatic dephosphorylation to template biomineralization with the inorganic phosphate. This biomimetic mineralization results in the formation of peptide-inorganic hybrid nanocrystals, with tunable crystal size and calcium-to-phosphorus (Ca:P) ratio, regulated by enzyme activity. Cellular enzymes can instruct in situ biomineralization around mammalian cells, inducing cell aggregation and osteogenic differentiation. This work presents a novel strategy for mimicking the dynamic biomineralization of a protein matrix and regulating biomimetic mineralization in live cells to control the cell fate.

Programming two-component peptide self-assembly by tuning the hydrophobic linker

Molecular self-assembly enables the formation of intricate networks through non-covalent interactions, serving as a key strategy for constructing structures ranging from molecules to macroscopic forms. While zero-dimensional and one-dimensional nanostructures have been widely achieved, two-dimensional nanostrip structures present unique advantages in biomedical and other applications due to their high surface area and potential for functionalization. However, their efficient design and precise regulation remain challenging. This study systematically explores how different hydrophobic amino acid linkers impact the microscopic morphology in two-component co-assembly systems with strong electrostatic interactions. The introduction of the AA linker resulted in distinctive 2D nanostrips, which stacked to form bilayer sheets, whereas VV, LL, and NleNle linkers formed one-dimensional fibers. In contrast, GG and PP linkers did not produce stable aggregates. Our findings highlight the role of intermolecular interactions in the development of 2D assemblies, providing new insights into the design and application of 2D materials.

Self-assembled peptide microtubes (SPMTs)/SnO2 sensors for enhanced room-temperature gas detection under visible light illumination

Nitrogen dioxide (NO2) is an important contaminant that poses a severe threat to environmental sustainability. Traditional inorganic NO2 gas detectors are generally used under harsh operating conditions and employ environmentally unfriendly resources, thus preventing widespread practical applications. Herein, self-assembled peptide microtubes (SPMTs) are combined with SnO2 nanoparticles (NPs) to develop a bioinspired NO2 gas sensor. The sensor incorporated with SPMTs exhibits a lower resistance and a stronger response under visible light irradiation. Under exposure to 4.7-mW/cm2 white light irradiation, the device exhibits a response of 412 and a resistance of only 97 MΩ, contrast to 318 and 340 MΩ for the bare SnO2-based counterpart under the same test conditions. This work exemplifies the feasibility of using bioinspired approach employing peptides self-assembly strategy to engineer comprehensive pollution detectors, potentially enabling development in the environmentally friendly sensing field.

Steric Complementarity Drives Strong Co-Assembly of Short Peptide Stereoisomers

Steric complementarity plays an essential role in maintaining protein architecture and recognition. In supramolecular chemistry and material science, however, it remains a major challenge to precisely control steric complementarity and associated interactions across different length scales for the construction of higher-order peptide and protein nanostructures and nanomaterials. Through coassembly of designed aromatic short peptide stereoisomers, we here incorporate specific π-π stacking interactions into facial complementarity between peptide strands within a β-sheet in a controllable manner. The high steric complementarity between aromatic side chains leads to strong coassembly capabilities of these peptide stereoisomers and dramatic changes in supramolecular morphology and size. We also unravel suprastructural handedness codes for their coassemblies and relate them to the side chain geometric complementarity and distribution on the two faces of the β-sheet. This work not only highlights the importance of steric complementarity in peptide folding but also provides a paradigm for the fabrication of intricate peptide β-sheet assemblies via steric complementarity at the subsheet level.

Self-Assembly of Noncanonical Peptides: A New Frontier in Cancer Therapeutics and Beyond

In addition to the 20 standard amino acids that form the building blocks of proteins, nature employs alternative amino acids to create specialized "noncanonical peptides." These unique peptides, found in organisms from bacteria to humans, often exhibit unconventional structures and functionalities, playing critical roles in modulating cellular processes, particularly as antibiotics. Their potential has attracted significant interest for designing novel functional materials based on noncanonical peptides. This review highlights recent advances in the generation and application of noncanonical peptide assemblies. It begins with a definition of noncanonical peptides, including classic examples that showcase their distinct structures and useful biological activities. Then the applications of noncanonical peptide assemblies in developing anticancer therapeutics are discussed, focusing on recent and representative studies that demonstrate their efficacy and versatility in targeting tumor cells. Beyond oncology, it is explored how noncanonical peptide assemblies have been utilized in biomaterials, regenerative medicine, molecular imaging and catalysis. Finally, perspectives are offered on future directions in this rapidly evolving field, emphasizing exciting opportunities and remaining challenges that will drive continued innovation in designing and applying noncanonical peptide-based assemblies.

Inhibition and Modulation of the Self-Assembly of Single Amino Acids and Dipeptides in the Presence of Chitosan-Derived Fluorescent Nanographene Oxide: Dye-Based White Light Generation in Micellar Media

Fluorescent carbon nanoparticles from various biomass and biowastes can be very much useful. In this work, we have successfully synthesized fluorescent carbon dot-type nanographene oxide (nGO). The emission properties of these nGOs were modulated in the presence of different stimuli and aqueous binary mixtures. Further, we have seen that nGOs showed aggregation-induced quenching in the presence of cationic surfactant up to its premicellar concentration. Two lipophilic dyes in micellar media can also generate excellent white light in combination with these nGOs. Further, fluorescence imaging showed that these nGOs could inhibit the usual self-assembly of l-tyrosine, L-tryptophan, and diphenylalanine and modulate the self-assembly of l-methionine and aspartame. Therefore, these nGOs have potential use in light-emitting and therapeutic applications.

Unveiling the Assembly Transition of Diphenylalanine and Its Analogs: from Oligomer Equilibrium to Nanocluster Formation

Peptide self-assembly is fundamental to various biological processes and holds significant potential for nanotechnology and biomedical applications. Despite progress in understanding larger-scale assemblies, the early formation of low-molecular-weight oligomers remains poorly understood. In this study, we investigate the aggregation behavior of the self-assembling diphenylalanine (FF) peptide and its analogs. Utilizing single-nanopore analysis, we detected and characterized the low-molecular-oligomer formation of FF, N-tert-butoxycarbonyl-diphenylalanine (BocFF), fluorenylmethyloxycarbonyl-diphenylalanine (FmocFF), and fluorenylmethyloxycarbonyl-pentafluoro-phenylalanine (Fmoc-F5-Phe) in real time. This approach provided detailed insights into the early stages of peptide self-assembly, revealing the dynamic behavior and formation kinetics of low-molecular-weight oligomeric species. Analysis revealed that the trimer is the key nucleus for FF, while the dimer is the primary nucleus for FmocFF and Fmoc-F5-Phe aggregation, whereas both the dimer and trimer serve as nuclei for BocFF. Mass photometry was employed to track the evolution of these oligomers, revealing the transition from low- to high-molecular-weight species, thereby elucidating intermediate phases in the aggregation process. Transmission electron microscopy and Fourier transform infrared spectroscopy were further employed to characterize the final assembly states, offering high-resolution imaging of morphological structures and detailed information on secondary structures. Based on these analyses, we constructed a comprehensive graph that correlates the entire aggregation processes of the tested self-assembling peptides across multiple scales. This integrative approach provides a holistic understanding of peptide self-assembly, particularly in the formation of low-molecular-weight oligomers toward mature supramolecular structures. These findings shed light on their assembly pathways and structural properties, advancing our understanding of their assembly pathways for nanotechnology and biomedical applications.

Fragment-Based Approach for Hierarchical Nanotube Assembly of Small Molecules in Aqueous Phase

A fragment-based approach has proven successful in drug design and protein assemblies, yet its potential for constructing biomaterials from simple organic building blocks remains underexplored, particularly for self-assembly in aqueous phases, where water disrupts intermolecular hydrogen bonding. To the best of our knowledge, this study introduces the first case of integrating fragments from self-assembling molecules to design a small organic molecule that forms novel hierarchical nanotubes with polymorphism. The molecule's compact design incorporates three structural motifs derived from known nanotube assemblies, enabling a hierarchical assembly process: individual molecules with two conformations form dimers, which organize into hexameric units. These hexamers further assemble into nanotubes comprising 2-, 5-, and 6-protofilament fibers. The nanofibers share a nearly identical asymmetric unit - a hexameric triangular plate - with similar axial and lateral interfaces. The lateral interface, involving interactions between phosphate groups and aromatic rings, exhibits plasticity, allowing slight rotational variations between adjacent units. This adaptability facilitates the formation of diverse nanofiber architectures, showcasing the flexibility of these systems in aqueous environments. By leveraging fragments of self-assembling molecules, this work demonstrates a straightforward strategy that combines conformational flexibility and self-assembling fragments to construct advanced supramolecular biomaterials from small organic building blocks in aqueous settings.

An Injectable Multifunctional Nanosweeper Eliminates Cardiac Mitochondrial DNA to Reduce Inflammation

Myocarditis, a leading cause of sudden cardiac death and heart transplantation, poses significant treatment challenges. The study of clinical samples from myocarditis patients reveals a correlation between the pathogenesis of myocarditis and cardiomyocyte mitochondrial DNA (mtDNA). During inflammation, the concentration of mtDNA in cardiomyocytes increases. Hence, it is hypothesized that the combined clearance of mtDNA and its downstream STING pathway can treat myocarditis. However, clearing mtDNA is problematic. An innovative mtDNA scavenger is introduced, Nanosweeper (NS), which utilizes its nanostructure to facilitate the transport of NS-mtDNA co-assemblies for degradation, achieving mtDNA clearance. The fluorescent mtDNA probe on NS, bound to functional peptides, enhances the stability of NS. NS also exhibits robust stability in human plasma with a half-life of up to 10 hours. In a murine myocarditis model, NS serves as a drug delivery vehicle, targeting the delivery of the STING pathway inhibitor C-176 to the myocardium. This approach synergistically modulates the cGAS-STING axis with NS, effectively attenuating myocarditis- associated inflammatory cascade. This evaluation of NS in porcine models corroborated its superior biosafety profile and cardiac targeting capability. This strategic approach of targeted mtDNA clearance couple with STING pathway inhibition, significantly augments therapeutic efficacy against myocarditis, outperforming the conventional drug C-176, indicating its clinical potential.

Learning the rules of peptide self-assembly through data mining with large language models

Peptides are ubiquitous and important biomolecules that self-assemble into diverse structures. Although extensive research has explored the effects of chemical composition and exterior conditions on self-assembly, a systematic study consolidating these data to uncover global rules is lacking. In this work, we curate a peptide assembly database through a combination of manual processing by human experts and large language model-assisted literature mining. As a result, we collect over 1000 experimental data entries with information about peptide sequence, experimental conditions, and corresponding self-assembly phases. Using the data, machine learning models are developed, demonstrating excellent accuracy (>80%) in assembly phase classification. Moreover, we fine-tune a GPT model for peptide literature mining with the developed dataset, which markedly outperforms the pretrained model in extracting information from academic publications. This workflow can improve efficiency when exploring potential self-assembling peptide candidates, through guiding experimental work, while also deepening our understanding of the governing mechanisms.

2D Interfacial Crystallization Stabilized by Short-Chain Aliphatic Interfaces

We report the discovery and in-depth investigation of interfacial crystallization (IFC), the assembly and formation of membrane-like crystalline sheets from both chiral amino acid and achiral N-substituted glycine "peptoid" amide monomers selectively at vapor-liquid and liquid-liquid interfaces. This is the first assembly process known to be shared by two peptidomimic families of molecules with crucial backbone differences. A series of AFM, SEM, TOF-SIMS, FTIR, X-ray crystallography, counterion screening experiments, QM calculations, and MD simulation studies identified that IFC is based on the assembly of single monomer layers with alternating molecular orientations, which results in bilayers of unit thickness 1.2-1.6 nm consisting of internal hydrophobic planes and ionic interfaces cocrystallized with halide salt ions. The assembly is underpinned by, paradoxically, the dynamic freedom of attached side chains, especially those of aliphatic designs. Growth of these bilayers then fills entire interfaces, limited only by the size of the container. The fundamental observation of the interface-filling nanostructures and the simplicity of the monomer chemistry involved suggest that IFC may have applications in the convenient formation of interface-sealing supramolecular barriers and, more broadly, tunable 2D layered materials.

Racemic peptide assembly boosts biocatalysis

Racemic assembly of minimalistic heterochiral tripeptides boosts their biocatalytic activity for ester hydrolysis. The amino acidic sequences are bioinspired and feature histidine (His) as a catalytically active residue, and the diphenylalanine (Phe-Phe) motif to drive self-assembly into anisotropic nanostructures that gel. This study thus provides key insights for the design of green biocatalysts with improved activity.

Designer Helical Fibers and Tubes: Self-assembling Hybrid Peptides via Leu/Ile-Phe Zipper

Here, we present a family of simple peptides that show diverse self-assembling behaviors. We used aliphatic (Leu/Ile) and aromatic (Phe) amino acids to delineate our design. The design consists of phenylene urea at the N-terminus of the peptide. The urea peptides with sequence Phe-LeuOMe (1) or Phe-IleOMe (2) associate to form polygonal peptide tubes via zipper arrangements, supported by microscopic and single crystal X-ray diffraction studies. The peptide with Phe placed away from the phenylene urea (3 and 4), showed fibrous assembly. All the peptides showed autofluorescence and red edge excitation behavior upon self-assembly.

Deciphering the self-assembly mechanisms of three diphenylalanine derivatives using infrared probe technique and scanning electron microscopy

Understanding the nucleation mechanism of peptide self-assembly is fundamental for the design and application of peptide-based materials. To this end, we herein explored the self-assembly processes of three diphenylalanine (FF) derivatives, Boc-XF, Boc-FX, and Boc-FF, where X is p-cyanophenylalanine with the cyano group being an infrared (IR) probe. Using IR probe technique and scanning electron microscopy (SEM), we revealed that the self-assembly of Boc-XF followed a three-step non-classical nucleation mechanism. Such a complex mechanism involved the presence of metastable spherical and fibrillar intermediates towards the final mature fibril phase. We further compared the self-assembly mechanism of Boc-XF with that of Boc-FF and Boc-FX and explored the potential impact of side-chain mutation on the peptide self-assembly mechanism. Our research provided a nice example of how to use a combined approach of IR probe technique and SEM to reveal the complex nucleation mechanism of peptide self-assembly.

Electrospinning of Self-Assembling Oligopeptides into Nanofiber Mats: The Impact of Peptide Composition and End Groups

Low-molecular-weight oligopeptides can be electrospun into nanofiber mats. However, the mechanism underlying their electrospinnability is not well-understood. In this study, we used solid-phase peptide synthesis to produce the oligopeptide FFKK, to which the aromatic end-capping groups naphthalene, pyrene, and tetraphenylporphyrin were attached. Nuclear magnetic resonance, circular dichroism, and electrospray ionization mass spectrometry were used to characterize the oligopeptide structures. We investigated the effect of end-caps and oligopeptide concentration on their self-assembly as well as on their electrospinnability in fluorinated solvents. All oligopeptides with aromatic end-caps were amenable to electrospinning. Attenuated total reflectance Fourier transform infrared spectroscopy and microrheology results support the hypothesis that at sufficiently high concentrations, the self-assembled structures interact strongly, which facilitates electrospinning. Moreover, the results from this fundamental study can be extended to nonpeptidic small molecules possessing strong intermolecular interactions.

Mechanistic role of proteins and peptides in Management of Neurodegenerative Disorders

Proteins and peptides have emerged as significant contributors in the management of neurodegenerative disorders due to their diverse biological functions. These biomolecules influence various cellular processes, including cellular repair, inflammation reduction, and neuronal survival, which are crucial for mitigating the effects of diseases such as Alzheimer's, Parkinson's, and Amyotrophic Lateral Sclerosis (ALS). By interacting with specific cellular receptors, proteins and peptides like neurotrophic factors, cytokines, and enzyme inhibitors promote neurogenesis, reduce oxidative stress, and enhance synaptic plasticity. Nevertheless, till certain limitations and challenges do exist to deliver these fragile therapeutic bioactives. Moreover, targeted delivery systems, such as nanoparticles and biomolecular carriers, are being developed to improve the bioavailability and specificity of these protein-based therapeutics, ensuring efficient crossing of the blood-brain barrier. This review explores the mechanistic pathways through which these biomolecules act, emphasizing their potential to modify disease progression and improve the quality of life in patients with neurodegenerative conditions. Overall, proteins and peptides are not only seen as promising therapeutic agents but also as foundational tools in advancing personalized medicine in the field of neurodegenerative disorders.

Designing highly tunable nanostructured peptide hydrogels using differential thermal histories to achieve variable cellular responses

In this study, we demonstrate a unique and promising approach to access peptide-based diverse nanostructures in a single gelator regime that is capable of exhibiting different surface topographies and variable physical properties, which, in turn, can effectively mimic the extracellular matrix (ECM) and regulate variable cellular responses. These diverse nanostructures represent different energy states in the free energy landscape, which have been created through different self-assembling pathways by providing variable energy inputs by simply altering the gelation induction temperature from 40 °C to 90 °C. The highly entangled network structure with long fibers was created by higher energy inputs, i.e., inducing the gelation at a higher temperature in the 70-90 °C range, whereas the less entangled nanoscale network with short fibers was obtained at a lower gelation induction temperature of 40-60 °C. It is worth mentioning that the highly entangled network structures with long fibers can be easily obtained by heating the less ordered structure, as evidenced by the thermoreversibility study. In addition, tuneable mechanical properties were achieved by merely adjusting the self-assembly pathways; the gels formed at high gelation induction temperatures showed high mechanical strengths in contrast to the gels formed at low gelation induction temperatures. Further, a detailed comparison was made with one of the important ECM proteins, i.e., collagen, to elucidate the potential of the hydrogels in mimicking the structural and mechanical properties of ECM. Interestingly, the highly entangled network structures with long fibers enhanced cellular survival as well as adhesion, comparable to that of the collagen gel, while a considerable proportion of cells were unable to adhere to the less entangled structures with short fibers. Such diverse nanostructures in a single gelator regime can be instrumental in controlling different cellular behaviours and could further pave the path for the development of responsive biomaterials.

Host-Guest Adduct as a Stimuli-Responsive Prodrug: Enzyme-Triggered Self-Assembly Process of a Short Peptide Within Mitochondria to Induce Cell Apoptosis

To address the issue of nonspecific biodistribution of a chemotherapeutic drug, stable [2]pseudorotaxane complexes (PK@CAOPP and PR@CAOPP) are used to demonstrate a proof of concept. Cationic -PPh3 + moiety in CAOPP allows specific localization of the PK@CAOPP/ PR@CAOPP in the mitochondrial membrane (MM). Electrostatic interaction between the cationic LysinePK or ArgininePR moiety and the negatively charged phosphoesterCAOPP functionality in CAOPP favours strong adduct formation. The ALP-induced hydrolytic cleavage of the phosphoester moiety in cancer cells triggers dephosphorylation and releases PK/ PR moiety from PK@CAOPP/PR@CAOPP. PK or PR, derived from the Phe-Phe dipeptide, formed fibril-like molecular aggregates in the MM to induce dysfunction, depolarization, ROS generation and apoptotic MCF7 cell death. Such phenomena were not observed in ALP-negative HEK293 normal cells. These propositions were confirmed through control studies using NBDK and PE, other guest molecules. Smaller size and inclusion of the short peptides (PK or PR) within the hydrophobic interior of CAOPP, were attributed to their stability in blood serum. Thus, we have demonstrated the use of supramolecular adducts as a potential therapeutic option for treating cancer cells without affecting healthy cells. The efficacy was also established with an in-vivo MCF7 tumour xenograft model using Balb/c nude mice.

Sticky tubes co-assembled by functionalised diphenylalanine and polydopamine nanoparticles form biocompatible antifouling coating

The persistent challenge of biofouling, driven by the accumulation of microorganisms and biological residues on surfaces, undermines operational efficiency and safety across multiple industries. Functionalized peptide based biocompatible and supramolecular coating can provide a substantial solution to this crucial issue. This present study describes the formation of polydopamine-comprised sticky tubes through the co-assembly of an antifouling peptide P1 (FF-PFB) and Polydopamine Nanoparticles (PDA NPs) with an adhesive catechol moiety. To overcome the synthetic complications associated with the attachment of adhesive l-DOPA or dopamine with antifouling peptides, we have employed a simple co-assembly strategy. These co-assembled sticky tubes form a stable, biocompatible coating on desired surfaces (glass and aluminium) and resist fouling. The design consists of a diphenylalanine-based antifouling peptide covalently coupled with pentafluoro benzaldehyde (PFB), which could self-assemble into a stable functional coating through the adhesive catechol moiety of PDA NPs. This functional coating effectively resists bacterial and protein adhesion. These sticky tubes coated desired surfaces (glass and aluminium) exhibit excellent antifouling activity against both tested Gram (+)ve (S. aureus) and Gram (-)ve (E. coli) bacterial strains. More importantly, this simple co-assembly and drop-coating method has significant promise, primarily attributed to its simplicity of operation, which reduces production costs and expands the potential for widespread commercialization. This study not only contributes to the fundamental understanding of the antifouling process but also offers a practical and sustainable solution to the challenges caused by biofouling. Our findings, achieved through the simple and effective co-assembly strategy with two different functional components, pave the way for developing promising antifouling materials with broad applications in industries where effective biofouling resistance is crucial.

Fabrication of Hierarchical Nanostructures Featuring Amplified Asymmetry Through Co-Assembly of Liquid Crystalline Block Copolymer and Chiral Amphiphiles

The widespread presence of hierarchical asymmetric structures in nature has sparked considerable interest because of their unique functionalities. These ingenious structures across multiple scales often emerge from the transfer and amplification of asymmetry from chiral molecules under various synergistic effects. However, constructing artificial chiral asymmetric structures, particularly in developing hierarchical multicomponent structures analogous to those formed in nature through synergistic non-covalent interactions, still presents tremendous challenges. Herein, we propose a co-assembly strategy to fabricate hierarchical chiral mesostructures by combining a liquid crystalline block copolymer (LC-BCP) with a small molecular amphiphile containing chiral alanine or phenylalanine as a linker. Through a classic solvent-exchange process, chiral amphiphiles embedded within LC-BCP finely regulate the LC ordering effect and facilitate transfer and amplification of asymmetry. Consequently, various co-assembled structures with significant hierarchical chirality features are obtained through synergetic effects. Remarkably, subtle alterations to the side groups of amino acids in the amphiphiles effectively adjust the hierarchical morphology transition. Moreover, the covalent bonding sequence of amino acids in the amphiphiles emerges as a critical factor governing the formation of hierarchical nanofibers and multilayered vesicles exhibiting a superhelical sense.

Peptide-based nanomaterials and their diverse applications

The supramolecular self-assembly of peptides offers a promising avenue for both materials science and biological applications. Peptides have garnered significant attention in molecular self-assembly, forming diverse nanostructures with α-helix, β-sheet, and random coil conformations. These self-assembly processes are primarily driven by the amphiphilic nature of peptides and stabilized by non-covalent interactions, leading to complex nanoarchitectures responsive to environmental stimuli. While extensively studied in biomedical applications, including drug delivery and tissue engineering, their potential applications in the fields of piezoresponsive materials, conducting materials, catalysis and energy harvesting remain underexplored. This review comprehensively elucidates the diverse material characteristics and applications of self-assembled peptides. We discuss the multi-stimuli-responsiveness of peptide self-assemblies and their roles as energy harvesters, catalysts, liquid crystalline materials, glass materials and contributors to electrical conductivity. Additionally, we address the challenges and present future perspectives associated with peptide nanomaterials. This review aims to provide insights into the versatile applications of peptide self-assemblies while concisely summarizing their well-established biomedical roles that have previously been extensively reviewed by various research groups, including our group.

A Discrete Four-Stranded β-Sheet through Catenation of M2L2 Metal-Peptide Rings

Methods for precisely constructing a β-sheet assembly with number-defined strands in solution remains quite limited due to its intense aggregation property. Here, we report the precise construction of a four-stranded anti-parallel β-sheet by utilizing a non-covalent approach. This was achieved by folding and assembly of Ag+ and a pentapeptide (1) with the Ala-D3pa-Gly-3pa-Val (3pa: β-(3-pyridyl)-alanine) sequence, which was designed to form an interlocking Ag2(1)2 ring through metal cross-linking of the side chains. NMR analyses and X-ray crystallographic studies characterized the structure of the discrete β-sheet assembly as well as the remarkable structural selectivity in terms of strands' number, orientation and the sheet type.

From experimental studies to computational approaches: recent trends in designing novel therapeutics for amyloidogenesis

Amyloidosis is a condition marked by misfolded proteins that build up in tissues and eventually destroy organs. It has been connected to a number of fatal illnesses, including non-neuropathic and neurodegenerative conditions, which in turn have a significant influence on the worldwide health sector. The inability to identify the underlying etiology of amyloidosis has hampered efforts to find a treatment for the condition. Despite the identification of a multitude of putative pathogenic variables that may operate independently or in combination, the molecular mechanisms responsible for the development and progression of the disease remain unclear. A thorough investigation into protein aggregation and the impacts of toxic aggregated species will help to clarify the cytotoxicity of aggregation-mediated cellular apoptosis and lay the groundwork for future studies aimed at creating effective treatments and medications. This review article provides a thorough summary of the combination of various experimental and computational approaches to modulate amyloid aggregation. Further, an overview of the latest developments of novel therapeutic agents is given, along with a discussion of the possible obstacles and viewpoints on this developing field. We believe that the information provided by this review will help scientists create innovative treatment strategies that affect the way proteins aggregate.

Self-Assembly of Homo Phenylalanine Oligopeptides: Role of Oligopeptide Chain Length

The self-assembly of phenylalanine (F)-based peptides is a critical area of research with potential implications for the development of advanced biomaterials and technologies. Previous studies indicate that homo-oligopeptides with F-X residues (X = 1 to 6) can self-assemble into diverse nano-microstructures, but the role of oligopeptide chain length on this process remains unclear. This review investigates the role of F-X chain length on self-assembly processes and morphologies, considering the effect of incubation conditions and the capping group at the N and/or C terminals. Morphologies, such as fibrils or tubes, are typical structures that result from the self-assembly of F-X oligopeptides, especially, with an even number of residues. When one or two termini of the F-X oligopeptide are capped, the tendency to form such structures is altered. Highly aromatic F-X oligopeptides display a wide range of morphologies due to hydrophobic cores created by stacked aromatic groups leading to slow formation of poor aggregates without well-defined morphologies. The terminal charges and capping groups on the oligopeptide backbone affect the atomic-level structure of self-assembled F-Xs (X > 1) by driving parallel or antiparallel β-strand associations between F-X monomers. We conclude that oligopeptide chain length plays a critical role in the self-assembly process of F-based peptides and that shorter chains may lead to the formation of more stable and ordered structures. Besides chain length, several other factors influence the structures, including solvent type, cosolvent properties (polarity and volatility), oligopeptide concentrations, and temperature. A significant challenge in investigating self-assembly processes is the lack of a solvent that promotes self-assembly under identical incubation conditions due to solubility variations among F-X oligopeptides. Consequently, additional experimental and mathematical studies are required to examine the self-assembly of F-X oligopeptides under the same incubation conditions (solvent type, cosolvent, peptide concentration, pH, and temperature) to produce viable F-based materials with potential applications in advanced biomaterials and technologies.

Self-Assembled Peptide Hydrogels PPI45 and PPI47: Novel Drug Candidates for Staphylococcus aureus Infection Treatment

Staphylococcus aureus, a prevalent zoonotic pathogen, poses a significant threat to skin wound infections. This study evaluates the bactericidal efficacy of self-assembled peptide hydrogels, PPI45 and PPI47, derived from the defensin-derived peptide PPI42, against S. aureus ATCC43300. The high-level preparation of PPI45 and PPI47 was achieved with yields of 1.82 g/L and 2.13 g/L, which are 2.19 and 2.60 times the yield of PPI42. Additionally, the critical micelle concentrations (CMCs) of the peptides at pH 7.4 for PPI42, PPI45, and PPI47 were determined to be 245 µg/mL, 973 µg/mL, and 1016 µg/mL, respectively. At a concentration of 3 mg/mL, the viscosities of the gels were 52,500 mPa·s, 33,700 mPa·s, and 3480 mPa·s for PPI42, PPI45, and PPI47. Transmission electron microscopy (TEM) revealed that all peptides exhibited long, pearl necklace-like protofibrils. These peptides demonstrated potent bactericidal activity, with a minimal inhibitory concentration (MIC) of 4-16 µg/mL against S. aureus, and a sustained effect post-drug clearance. Flow cytometry analysis after 2×MIC peptides treatment for 2 h revealed a 20-38% membrane disruption rate in bacteria, corroborated by scanning electron microscopy (SEM) observations of membrane damage and bacterial collapse. The peptide treatment also led to reduced hyperpolarized membrane potential. In vitro safety assessments indicated minimal hemolytic activity on murine red blood cells and low cytotoxicity on human immortalized epidermal cells (HaCaT). In summary, this work lays a valuable cornerstone for the future design and characterization of self-assembling antimicrobial peptides hydrogels to combat S. aureus infection.

Molecular Propeller Tethering on a Dipeptide Induces a One-Step Conversion of Its Secondary Structure on Water Surface Promoted by Chiral Supramolecular Assembly

Water provides a unique surface for the formation of directed self-assembly and transformation of secondary structures of peptides and proteins as witnessed in the biological systems. Herein a one-step transformation of an amyloid-derived dipeptide is reported from β-sheet to α-helix structures on the water surface, facilitated by chiral supramolecular assembly. The study utilizes various analytical techniques to elucidate the structural transformation and the supramolecular packing of the peptide assemblies. Organizations such as spherical aggregates and molecular nanowires containing β-sheet structure are converted into (2D) molecular sheets comprising a larger planar area yet with a molecular level thickness of α-helix structure. The conformational features of the β-sheet to α-helix structural transformation are dominated by the intermolecular H-bonding, π-π stacking, and C─H···π interactions. Strikingly, the dynamic changes in the dihedral (intramolecular) angle between the aromatic rings of the dipeptide at the water surface alter the molecular packing and shorten the intermolecular H-bonds with larger binding energies required for the secondary structural transformation. Thus, the novel one-step strategy reports herein offers a simple, efficient, and hitherto unprecedented way of chiral supramolecular assembly directed total secondary structural transformation of the dipeptide on water surface.

Metal‐coordinated amino acid/peptide/protein‐based supramolecular self‐assembled nanomaterials for anticancer applications

Biomolecules with metals can form supramolecular nanomaterials through coordination assembly, opening new avenues for cancer theranostics and bringing unique insights into personalized nanomedicine. These biomaterials have been considered versatile and innovative nanoagents due to their structure‒function control, biological nature, and simple preparation methods. This review article summarized the recent developments in multicomponent nanomaterials formed from metal coordination interactions with amino acids, peptides, and proteins, together with anticancer drugs, for cancer theranostics. We discussed the role of functional groups anchored in building blocks for coordination interactions, and subsequently, the types of interactions were examined from a structure‒function perspective. Amino acids with different metals and anticancer drugs forming supramolecular nanomaterials and their anticancer mechanisms were highlighted. Peptides with different metals and anticancer drugs, proteins with metals and anticancer drugs used for material formations, and anticancer activity have been discussed. Ultimately, the conclusion and future outlook for multicomponent supramolecular nanomaterials offer fundamental insights into fabrication design and precision medicine.

Metal-Free Peptide Semiconductor-Enhanced Raman Scattering

There is a growing demand for sustainable and safe materials in developing technological systems and devices, including those that enhance Raman scattering. Organic (bio) materials based on simple peptides are one class of such materials. This study investigates self-assembled semiconducting peptides as metal-free substrates for surface-enhanced Raman scattering. Our results reveal significant variations in Raman enhancement factors, spanning up to 2 orders of magnitude. We examined specific Raman enhancement selection rules related to the energy levels and structural configurations of the probe molecules. The effectiveness of these rules underscores the importance of strong molecule-peptide coupling and efficient charge transfer for achieving optimal Raman enhancement factors. These insights offer a foundational understanding of peptide-molecule interactions and the underlying chemical mechanisms driving Raman enhancement, highlighting the potential of organic semiconductor-based materials as highly effective platforms for enhancing Raman scattering in chemical sensing applications.

Coarse-Grained Simulation Study of the Association of Selected Dipeptides

The association of 55 dipeptides extracted from aggregation-prone regions of selected proteins was studied by means of multiplexed replica-exchange molecular dynamics simulations with the coarse-grained UNRES model of polypeptide chains. Each simulation was carried out with 320 dipeptide molecules in a periodic box at 0.24 mol/dm3 concentration, in the 260-370 K temperature range. The temperature profiles of the degree of association, distributions of dipeptide cluster size, and structures of clusters were examined. It has been found that the dipeptides composed of strongly nonpolar (aromatic or aliphatic) residues associate nearly completely at all temperatures to form tight clusters, while those composed of charged or polar residues exhibited no or residual association. The dipeptides composed of nonpolar and small polar residues and those composed of less hydrophobic residues formed single clusters, gradually dissolving with increasing temperature, while those composed of phenylalanine or tryptophan and polar or charged residues formed multiple irregular clusters with room to accommodate water inside, suggesting the formation of liquid droplets or gels. The logarithms of the average degree of association and the free energy of aggregation per monomer were found to correlate with the dipeptide hydrophobicity.

De novo design of a mechano-pharmaceutical screening platform against formation of individual beta-amyloid oligomers

Small molecules that can reduce the neurotoxic beta-amyloid (Aβ) aggregates in the brain provide a potential treatment for Alzheimer disease (AD). Most screening methods for small-molecule hits focus on the overall Aβ aggregations without a specific target, such as the very first association step (i.e., nucleation) en route to the Aβ oligomers. Located in the middle of a full-length Aβ peptide, Aβ19-20 (diphenylalanine or FF) nucleates the neurotoxic Aβ oligomer formation. Here, we innovate a single-molecule screen method in optical tweezers by targeting the nucleation process in Aβ aggregation, namely FF-dimerization. With a 121-compound National Institutes of Health (NIH) library, we identify 12 inhibitors and 8 stimulants that can inhibit/promote Aβ19-20 dimerization significantly. The representative hits are subjected to the thioflavin T and cell toxicity assays to confirm their inhibiting or stimulating activities. By replacing FF with longer Aβ sequences, our single-molecule platform may identify more specific and potent small molecules to fight AD.

A water playground for peptide re-assembly from fibrils to plates

Short-peptide amyloid assembly and disassembly play crucial roles in various research fields, which range from addressing pathologies that lack therapeutic solutions to the development of innovative soft (bio)materials. Hydrogels from short peptides typically show thermo-reversible gel-to-sol transition, whereby fibrils disassemble upon heating, and re-assemble upon cooling down to room temperature (rt). Despite ongoing intense research studies in this area, the majority focus on peptide-peptide interaction and neglect the structuring role of water in peptide supramolecular behavior. This study describes an unprotected tetrapeptide gelator that forms highly stable fibrils which, upon heating, re-organize into plates that persist upon cooling to rt. All-atom molecular dynamics (MD) simulations and experimental methods reveal water as a key player in the thermodynamics that accompany this irreversible morphological transition, and advance our understanding of supramolecular structures.

Facile Approach to Develop Peptide-Stabilized CdS/CdSe Quantum Dots for Cellular Imaging

This study presents a mild, one-pot synthetic approach for the synthesis of multicolor, water soluble, photo luminescent CdS and CdSe quantum dots (QDs). To achieve this goal, cyclic peptides containing cysteine residues are rationally designed and synthesized. Among the peptides tested, those containing two cysteine residues exhibit superior stabilizing properties, ensuring the solubility and long-term stability of the QDs in aqueous solutions for several months. The newly synthesized QDs exhibit unique excitation-dependent multicolor photoluminescence with a quantum yield of 20.55% and 45.50% for CdS and CdSe, respectively, providing versatility for imaging applications. Cellular uptake studies using HCT 116 cells reveal effective internalization of the QDs into both the cytoplasm and nucleus, highlighting their potential applications in bioimaging and drug delivery. This green synthesis approach underscores the crucial role of peptide chemistry in nanoparticle stabilization, paving the way for the development of functional nanomaterials tailored for specific uses in bioimaging and nanomedicine.

Application of metallic nanoparticles-amyloid protein supramolecular materials in tissue engineering and drug delivery: Recent progress and perspectives

Supramolecular medicine refers to the formulation of therapeutic and diagnostic agents through supramolecular techniques, amid treating, diagnosing, and preventing disease. Recently, there has been growing interest in developing metal nanoparticles (MNPs)-amyloid hybrid materials, which have the potential to revolutionize medical applications. Furthermore, the development of MNPs-amyloid hydrogel/scaffold supramolecules represents a promising new direction in amyloid nanotechnology, with potential applications in tissue engineering and biomedicine. This review first provides a brief introduction to the formation process of protein amyloid aggregates and their unique nanostructures. Subsequently, we focused on recent investigations into the use of MNPs-amyloid hybrid materials in tissue engineering and biomedicine. We anticipate that MNPs-amyloid supramolecular materials will pave the way for new functional materials in medical science, particularly in the field of tissue engineering.

Unveiling the multifaceted potential of amyloid fibrils: from pathogenic myths to biotechnological marvels

Amyloid fibrils, historically stigmatized due to their association with diseases like Alzheimer's and Parkinson's, are now recognized as a distinct class of functional proteins with extraordinary potential. These highly ordered, cross-β-sheet protein aggregates are found across all domains of life, playing crucial physiological roles. In bacteria, functional amyloids like curli fibers are essential for surface adhesion, biofilm formation, and viral DNA packaging. Fungal prions exploit amyloid conformations to regulate translation, metabolism, and virulence, while mammalian amyloids are integral to melanin synthesis, hormone storage, and antimicrobial defense. The stability and hydrophobic nature of amyloid scaffolds underpin these diverse biological functions. Beyond their natural roles, amyloid fibrils offer unique capabilities in biomedicine, nanotechnology, and materials science. Their exceptional mechanical strength and biocompatibility make them ideal for controlled drug delivery, tissue engineering scaffolds, and enzyme immobilization. The intrinsic fluorescence and optical properties of certain amyloids open up innovative applications in biosensors, molecular probes, and optoelectronic devices. Furthermore, amyloid fibrils can template metal nanowires, enhance conducting materials, and form nanocomposites by integrating with polymers. This newfound appreciation for the functional diversity of amyloids has ignited intense research efforts to elucidate their molecular mechanisms, stability, and tunable properties. By unraveling the structural intricacies of functional amyloids, researchers aim to harness their remarkable attributes for groundbreaking biomedical therapies, advanced nanomaterials, and sustainable biotechnological innovations. This review explores the transformative journey of amyloids from pathological entities to biotechnological marvels, highlighting their vast potential across agriculture, environmental remediation, and industrial processes.

Interfacial Assembly of Peptide Carbon Dot Hybrids Enables Photoinduced Electron Transfer with Improved Photoresponse

Assemblies at the interface represent a powerful tool for integrating organic and inorganic components into hybrid nanostructures. Carbon dots are both excellent electron donors and acceptors, offering opportunities for their potential uses in light-harvesting applications. To further improve their functions, integration of acceptor carbon dots into donor organic nanostructures is of great interest for improving photophysical properties useful for photoinduced electron transfer. Here, a one-step protocol for the interfacial assembly of a two-component hybrid consisting of carbon dots and perylene containing an l-phenylalanine-based dipeptide through noncovalent bonding is developed. The perylene-containing dipeptide derivative formed micrometer-long nanofibers on the water surface through J-aggregate formation. Spectroscopic studies reveal photoluminescence quenching of the donor dipeptide upon increasing the concentration of acceptor carbon dots in the hybrid, suggesting photoinduced electron transfer from the donor peptides to acceptor carbon dots. The hybrids integrated in a planar device architecture show a significantly improved photoresponse because of the favorable interactions between the donor-acceptor components. The one-step integration of donor-acceptor hybrids on the water surface offers opportunities for light harvesting and related applications.

Enantiomeric peptides self-assembling into fibrils with the same handedness

It is widely accepted that peptides with enantiomeric configurations would self-assemble into nanostructures with opposite supramolecular chirality. However, in this work, we found that the L-peptide polyphenylalanine F10 (FFFFFFFFFF) and its enantiomer f10 displayed mirror image CD spectra, yet both self-assembled into fibers with exclusive left-handedness, a phenomenon also observed in the other two enantiomeric pairs (F9f and f9F, F5f5 and f5F5). Our work provides new insights into the relationship between the molecular chirality of peptide building blocks and the supramolecular chirality of their self-assemblies.

Water-Vapor Responsive Metallo-Peptide Nanofibers

Short peptides are versatile molecules for the construction of supramolecular materials. Most reported peptide materials are hydrophobic, stiff, and show limited response to environmental conditions in the solid-state. Herein, we describe a design strategy for minimalistic supramolecular metallo-peptide nanofibers that, depending on their sequence, change stiffness, or reversibly assemble in the solid-state, in response to changes in relative humidity (RH). We tested a series of histidine (H) containing dipeptides with varying hydrophobicity, XH, where X is G, A, L, Y (glycine, alanine, leucine, and tyrosine). The one-dimensional fiber formation is supported by metal coordination and dynamic H-bonds. Solvent conditions were identified where GH/Zn and AH/Zn formed gels that upon air-drying gave rise to nanofibers. Upon exposure of the nanofiber networks to increasing RH, a reduction in stiffness was observed with GH/Zn fibers reversibly (dis-)assembled at 60-70 % RH driven by a rebalancing of hydrogen bonding interactions between peptides and water. When these metallo-peptide nanofibers were deposited on the surface of polyimide films and exposed to varying RH, peptide/water-vapor interactions in the solid-state mechanically transferred to the polymer film, leading to the rapid and reversible folding-unfolding of the films, thus demonstrating RH-responsive actuation.

Oligomers of diphenylalanine examined using cold ion spectroscopy and neural network-based conformational search

Diphenylalanine (Phe2) is the primary building block of many self-assembling nanostructures that are important in biology and materials science. Understanding the detailed mechanism of their formation requires knowledge of the structural motives that the smallest oligomers attain at the very first steps of the process. Herein, we first employed high-resolution mass spectrometry to assign protonated Phe2 and its 2-13-unit oligomers formed in the gas phase from solution via electrospray ionization and then used cold ion spectroscopy to record UV and IR spectra for the monomer, dimer and hexamer. UV spectroscopy suggests the likely lack of specific strong proton-π interactions in oligomers larger than octamers, implying their certain structural stabilization. IR spectroscopy and quantum chemical calculations, enhanced by neural network-based conformational search, jointly determined the lowest-energy structures of the Phe2 monomer and dimer.

Synthetic Nanoassemblies for Regulating Organelles: From Molecular Design to Precision Therapeutics

Each organelle referring to a complex multiorder architecture executes respective biological processes via its distinct spatial organization and internal microenvironment. As the assembly of biomolecules is the structural basis of living cells, creating synthetic nanoassemblies with specific physicochemical and morphological properties in living cells to interfere or couple with the natural organelle architectures has attracted great attention in precision therapeutics of cancers. In this review, we give an overview of the latest advances in the synthetic nanoassemblies for precise organelle regulation, including the formation mechanisms, triggering strategies, and biomedical applications in precision therapeutics. We summarize the emerging material systems, including polymers, peptides, and deoxyribonucleic acids (DNAs), and their respective intermolecular interactions for intercellular synthetic nanoassemblies, and highlight their design principles in constructing precursors that assemble into synthetic nanoassemblies targeting specific organelles in the complex cellular environment. We further showcase the developed intracellular synthetic nanoassemblies targeting specific organelles including mitochondria, the endoplasmic reticulum, lysosome, Golgi apparatus, and nucleus and describe their underlying mechanisms for organelle regulation and precision therapeutics for cancer. Last, the essential challenges in this field and prospects for future precision therapeutics of synthetic nanoassemblies are discussed. This review should facilitate the rational design of organelle-targeting synthetic nanoassemblies and the comprehensive recognition of organelles by materials and contribute to the deep understanding and application of the synthetic nanoassemblies for precision therapeutics.

3D Cryo-Electron Microscopy Reveals the Structure of a 3-Fluorenylmethyloxycarbonyl Zipper Motif Ensuring the Self-Assembly of Tripeptide Nanofibers

Short peptide-based supramolecular hydrogels appeared as highly interesting materials for applications in many fields. The optimization of their properties relies mainly on the design of a suitable hydrogelator through an empirical trial-and-error strategy based on the synthesis of various types of peptides. This approach is in part due to the lack of prior structural knowledge of the molecular architecture of the various families of nanofibers. The 3D structure of the nanofibers determines their ability to interact with entities present in their surrounding environment. Thus, it is important to resolve the internal structural organization of the material. Herein, using Fmoc-FFY tripeptide as a model amphiphilic hydrogelator and cryo-EM reconstruction approach, we succeeded to obtain a 3.8 Å resolution 3D structure of a self-assembled nanofiber with a diameter of approximately 4.1 nm and with apparently "infinite" length. The elucidation of the spatial organization of such nano-objects addresses fundamental questions about the way short amphiphilic N-Fmoc peptides lacking secondary structure can self-assemble and ensure the cohesion of such a lengthy nanostructure. This nanofiber is organized into a triple-stranded helix with an asymmetric unit composed of two Fmoc-FFY peptides per strand. The three identical amphiphilic strands are maintained together by strong lateral interactions coming from a 3-Fmoc zipper motif. This hydrophobic core of the nanofiber is surrounded by 12 phenyl groups from phenylalanine residues, nonplanar with the six Fmoc groups. Polar tyrosine residues at the C-term position constitute the hydrophilic shell and are exposed all around the external part of the assembly. This fiber has a highly hydrophobic central core with an internal diameter of only 2.4 Å. Molecular dynamics simulations highlight van der Waals and hydrogen bonds between peptides placed on top of each other. We demonstrate that the self-assembly of Fmoc-FFY, whether induced by annealing or by the action of a phosphatase on the phosphorylated precursor Fmoc-FFpY, results in two nanostructures with minor differences that we are unable to distinguish.

Au(I) complexes installed on a self-assembled peptide efficiently catalyze intramolecular cyclization reactions

Self-assembled peptides are used for diverse applications in the biomedical and technological fields. The morphology and function of the assembled systems are dictated by the peptide sequence and length. In this work, a supramolecular catalyst was obtained upon self-assembly of the diphenylalanine peptide conjugated to a triphenylphosphine Au(I) complex in acetonitrile. The assembled molecules were characterized by spectroscopic techniques and by scanning electron microscopy. The activity of the catalyst was tested on two substrates in cyclization reactions. The morphology and the dimensions of the assembled systems vary depending on the presence of a carboxyl versus an amide C-terminal end. The catalyst efficiently promotes intramolecular cyclization reactions. Results obtained encourage the use of self-assembled peptides for the obtainment of new and efficient catalysts.

Super-Resolution Microscopy as a Versatile Tool in Probing Molecular Assembly

Molecular assembly is promising in the construction of advanced materials, obtaining structures with specific functions. In-depth investigation of the relationships between the formation, dynamics, structure, and functionality of the specific molecular assemblies is one of the greatest challenges in nanotechnology and chemistry, which is essential in the rational design and development of functional materials for a variety of applications. Super-resolution microscopy (SRM) has been used as a versatile tool for investigating and elucidating the structures of individual molecular assemblies with its nanometric resolution, multicolor ability, and minimal invasiveness, which are also complementary to conventional optical or electronic techniques that provide the direct observation. In this review, we will provide an overview of the representative studies that utilize SRM to probe molecular assemblies, mainly focusing on the imaging of biomolecular assemblies (lipid-based, peptide-based, protein-based, and DNA-based), organic-inorganic hybrid assemblies, and polymer assemblies. This review will provide guidelines for the evaluation of the dynamics of molecular assemblies, assembly and disassembly processes with distinct dynamic behaviors, and multicomponent assembly through the application of these advanced imaging techniques. We believe that this review will inspire new ideas and propel the development of structural analyses of molecular assemblies to promote the exploitation of new-generation functional materials.

Regulating H2S release from self-assembled peptide H2S-donor conjugates using cysteine derivatives

Self-assembled peptides provide a modular and diverse platform for drug delivery, and innovative delivery methods are needed for delivery of hydrogen sulfide (H2S), an endogenous signaling molecule (gasotransmitter) with significant therapeutic potential. Of the available types of H2S donors, peptide/protein H2S donor conjugates (PHDCs) offer significant versatility. Here we discuss the design, synthesis, and in-depth study of a PHDC containing three covalently linked components: a thiol-triggered H2S donor based on an S-aroylthiooxime (SATO), a GFFF tetrapeptide, and a tetraethylene glycol (TEG) dendron. Conventional transmission electron microscopy showed that the PHDC self-assembled into spherical structures without heat or stirring, but it formed nanofibers with gentle heat (37 °C) and stirring. Circular dichroism (CD) spectroscopy data collected during self-assembly under nanofiber-forming conditions suggested an increase in β-sheet character and a decrease in organization of the SATO units. Release of H2S from the nanofibers was studied through triggering with various thiols. The release rate and total amount of H2S released over both short (5 h) and long (7 d) time scales varied with the charge state: negatively charged and zwitterionic thiols (e.g., Ac-Cys-OH and H-Cys-OH) triggered release slowly while a neutral thiol (Ac-Cys-OMe) showed ∼10-fold faster release, and a positively charged thiol (H-Cys-OMe) triggered H2S release nearly 50-fold faster than the negatively charged thiols. CD spectroscopy studies monitoring changes in secondary structure over time during H2S release showed similar trends. This study sheds light on the driving forces behind self-assembling nanostructures and offers insights into tuning H2S release through thiol charge state modulation.

Unveiling the Self-assembly and Therapeutic Efficacy of Antimicrobial Peptides SA4 Against Multidrug-Resistant A. baumannii

Infections linked to Acinetobacter baumannii are one of the main risks of modern medicine. Biofilms formed by A. baumannii due to a protective extracellular polysaccharide matrix make them highly tolerant to conventional antibiotics and raise the possibility of antibiotic resistance. Antimicrobial peptides (AMPs) are gaining popularity due to their broad-spectrum actions and key properties of peptide self-assembly, making them a promising alternative to antibiotics. Here, we demonstrate that 12-residue synthetic self-assembled peptide SA4 nanostructures have enough antibacterial action to prevent the growth of mature bacterial biofilms. The SA4 peptide was successfully synthesized by using the solid-phase peptide synthesis method, and its self-assembly was prepared in water. The self-assembled peptide hydrogel formed nanotube structure was observed under a scanning electron microscope and further characterized to confirm their physical and molecular properties. The resulting hydrogel exhibits significant antibacterial activity against MDR A. baumannii strains (MDR-1 and MDR-2), responsible for many nosocomial infections. In addition, at various gel concentrations, this hydrogel has the potential to inhibit about 30-80% of biofilms formed by MDR strains. Furthermore, under a microscope, it has been observed that the rupture of the bacterial cell membrane and cell wall of A. baumannii cells is caused by peptide nanotubes generated by self-assemblies. Thus, peptide-based nanotubes present intriguing avenues for various biomedical applications. This is the first report of bacterial biofilm removal with SA4 peptide nanotubes, and offering a unique treatment for infections linked to biofilms.

Amino-Acid-Encoded Supramolecular Nanostructures for Persistent Bioluminescence Imaging of Tumor

Bioluminescence imaging (BLI) is a powerful technique for noninvasive monitoring of biological processes and cell transplantation. Nonetheless, the application of D-luciferin, which is widely employed as a bioluminescent probe, is restricted in long-term in vivo tracking due to its short half-life. This study presents a novel approach using amino acid-encoded building blocks to accumulate and preserve luciferin within tumor cells, through a supramolecular self-assembly strategy. The building block platform called Cys(SEt)-X-CBT (CXCBT, with X representing any amino acid) utilizes a covalent-noncovalent hybrid self-assembly mechanism to generate diverse luciferin-containing nanostructures in tumor cells after glutathione reduction. These nanostructures exhibit efficient tumor-targeted delivery as well as sequence-dependent well-designed morphologies and prolonged bioluminescence performance. Among the selected amino acids (X = Glu, Lys, Leu, Phe), Cys(SEt)-Lys-CBT (CKCBT) exhibits the superior long-lasting bioluminescence signal (up to 72 h) and good biocompatibility. This study demonstrates the potential of amino-acid-encoded supramolecular self-assembly as a convenient and effective method for developing BLI probes for long-term biological tracking and disease imaging.

Mica Lattice Orientation of Epitaxially Grown Amyloid β25-35 Fibrils

β-amyloid (Aβ) peptides form self-organizing fibrils in Alzheimer's disease. The biologically active, toxic Aβ25-35 fragment of the full-length Aβ-peptide forms a stable, oriented filament network on the mica surface with an epitaxial mechanism at the timescale of seconds. While many of the structural and dynamic features of the oriented Aβ25-35 fibrils have been investigated before, the β-strand arrangement of the fibrils and their exact orientation with respect to the mica lattice remained unknown. By using high-resolution atomic force microscopy, here, we show that the Aβ25-35 fibrils are oriented along the long diagonal of the oxygen hexagon of mica. To test the structure and stability of the oriented fibrils further, we carried out molecular dynamics simulations on model β-sheets. The models included the mica surface and a single fibril motif built from β-strands. We show that a sheet with parallel β-strands binds to the mica surface with its positively charged groups, but the C-terminals of the strands orient upward. In contrast, the model with antiparallel strands preserves its parallel orientation with the surface in the molecular dynamics simulation, suggesting that this model describes the first β-sheet layer of the mica-bound Aβ25-35 fibrils well. These results pave the way toward nanotechnological construction and applications for the designed amyloid peptides.

Cell-Free Nonequilibrium Assembly for Hierarchical Protein/Peptide Nanopillars

Cells contain intricate protein nanostructures, but replicating them outside of cells presents challenges. One such example is the vertical fibronectin pillars observed in embryos. Here, we demonstrate the creation of cell-free vertical fibronectin pillar mimics using nonequilibrium self-assembly. Our approach utilizes enzyme-responsive phosphopeptides that assemble into nanotubes. Enzyme action triggers shape changes in peptide assemblies, driving the vertical growth of protein nanopillars into bundles. These bundles, with peptide nanotubes serving as a template to remodel fibronectin, can then recruit collagen, which forms aggregates or bundles depending on their types. Nanopillar formation relies on enzyme-catalyzed nonequilibrium self-assembly and is governed by the concentrations of enzyme, protein, peptide, the structure of the peptide, and peptide assembly morphologies. Cryo-EM reveals unexpected nanotube thinning and packing after dephosphorylation, indicating a complex sculpting process during assembly. Our study demonstrates a cell-free method for constructing intricate, multiprotein nanostructures with directionality and composition.

Designer pseudopeptides: autofluorescent polygonal tubes via Phe-zipper and triple helix

Chemists are increasingly turning to biology for inspiration to develop novel and superior synthetic materials. Here, we present an innovative peptide design strategy for tubular assembly. In this simple design, a phenylene urea unit is introduced as an aglet at the N-terminus of the peptide. When α-amino isobutyric acid (Aib) is the first residue and phenylalanine (Phe) is the second residue from the phenylene urea entity, it induces an edge-to-face π-π interaction resulting in a turn conformation. The peptides with a unique reverse turn conformation associate to form polygonal peptide tubes via a Phe-zipper arrangement, as evidenced by microscopic and single crystal X-ray studies. Ultra-microscopic imaging revealed that the tubular assembly is hexagonal, square, and triangular in shape. This hierarchical assembly reveals the interplay between π-π interactions and hydrogen bonding. In another design, pseudopeptide 5, wherein a Phe-Phe (FF) unit is linked to phenylene urea, formed polygonal tubes via a triple helical arrangement. Interestingly, the extension of this design to the bis-urea core resulted in vesicular assembly. These supramolecular polygonal tubes and vesicles showed autofluorescence, which allowed confocal imaging. The observed fluorescence is an additional advantage for applications in biological and medical sciences.

Exploring Macroscopic Dipoles of Designed Cyclic Peptide Ordered Assemblies to Harvest Piezoelectric Properties

Crystalline materials exhibiting non-centrosymmetry and possessing substantial surface dipole moments play a critical role in piezoelectricity. Designing biocompatible self-assembled materials with these attributes is particularly challenging when compared to inorganic materials and ceramics. In this study, we elucidate the crystal conformations of novel cyclic peptides that exhibit self-assembly into tubular structures characterized by unidirectional hydrogen bonding and piezoelectric properties. Unlike cyclic peptides derived from alternating L- and D-amino acids, those derived from new δ-amino acids demonstrate the formation of self-assembled tubes with unidirectional hydrogen bonds. Further, the tightly packed tubular assemblies and higher macrodipole moments result in superior piezoelectric coefficients compared to peptides with lower macrodipole moments. Our findings underscore the potential for designing cyclic peptides with unidirectional hydrogen bonds, thereby paving the way for their application in design of biocompatible piezo- and ferroelectric materials.