Super-resolution microscopy reveals structural diversity in molecular exchange among peptide amphiphile nanofibres

Multivalent Clustering of Adhesion Ligands in Nanofiber-Nanoparticle Composites

Because the positioning and clustering of biomolecules within the extracellular matrix dictates cell behaviors, the engineering of biomaterials incorporating bioactive epitopes with spatial organization tunable at the nanoscale is of primary importance. Here we used a highly modular composite approach combining peptide amphiphile (PA) nanofibers and silica nanoparticles, which are both easily functionalized with one or several bioactive signals. We show that the surface of silica nanoparticles allows the clustering of RGDS bioactive signals leading to improved adhesion and spreading of fibroblast cells on composite hydrogels at an epitope concentration much lower than in PA-only based matrices. Most importantly, by combining the two integrin-binding sequences RGDS and PHSRN on nanoparticle surfaces, we improved cell adhesion on the PA nanofiber/particle composite hydrogels, which is attributed to synergistic interactions known to be effective only for peptide intermolecular distance of ca. 5 nm. Such composites with soft and hard nanostructures offer a strategy for the design of advanced scaffolds to display multiple signals and control cell behavior.

The impact of chemical structure on the formation of the medium-range order and dynamical properties of selected antifungal APIs

In this paper, we have analyzed structural, thermal, and dynamical properties of four azole antifungals: itraconazole (ITZ), posaconazole (POS), terconazole (TER) and ketoconazole (KET), differing mainly in the length of the rod-like backbone and slightly in side groups. Our investigations clearly demonstrated that the changes in the chemical structure result in a different ability to form the medium-range order (MRO) and variation in thermal and dynamical properties of these pharmaceuticals. Direct comparison of the diffractograms collected for glassy and crystalline materials indicated that the MRO observed in the former phases is related to maintaining the local molecular arrangement of the crystal structure. Moreover, it was shown that once the MRO-related diffraction peaks appear, additional mobility (δ- or α' relaxation), slower than the structural (α)-process, is also detected in dielectric spectra. This new mode is connected to the motions within supramolecular nanoaggregates. Detailed analysis of dielectric and calorimetric data also revealed that the variation in the internal structure and MRO of the examined pharmaceuticals have an impact on the glass transition temperature (Tg) shape of the α-process, isobaric fragility, molecular dynamics in the glassy state and number of dynamically correlated molecules. These findings could be helpful in an understanding the influence of different types of intermolecular MRO on the properties of substances having a similar chemical backbone.

Supramolecular self-assembling peptides to deliver bone morphogenetic proteins for skeletal regeneration

Recombinant human bone morphogenetic proteins (BMPs) have shown clinical success in promoting bone healing, but they are also associated with unwanted side effects. The development of improved BMP carriers that can retain BMP at the defect site and maximize its efficacy would decrease the therapeutic BMP dose and thus improve its safety profile. In this review, we discuss the advantages of using self-assembling peptides, a class of synthetic supramolecular biomaterials, to deliver recombinant BMPs. Peptide amphiphiles (PAs) are a broad class of self-assembling peptides, and the use of PAs for BMP delivery and bone regeneration has been explored extensively over the past decade. Like many self-assembling peptide systems, PAs can be designed to form nanofibrous supramolecular biomaterials in which molecules are held together by non-covalent bonds. Chemical and biological functionality can be added to PA nanofibers, through conjugation of chemical moieties or biological epitopes to PA molecules. For example, PA nanofibers have been designed to bind heparan sulfate, a natural polysaccharide that is known to bind BMPs and potentiate their signal. Alternatively, PA nanofibers have been designed to synthetically mimic the structure and function of heparan sulfate, or to directly bind BMP specifically. In small animal models, these bio-inspired PA materials have shown the capacity to promote bone regeneration using BMP at doses 10-100 times lower than established therapeutic doses. These promising results have motivated further evaluation of PAs in large animal models, where their safety and efficacy must be established before clinical translation. We conclude with a discussion on the possiblity of combining PAs with other materials used in orthopaedic surgery to maximize their utility for clinical translation.

In Situ, Noncovalent Labeling and Stimulated Emission Depletion-Based Super-Resolution Imaging of Supramolecular Peptide Nanostructures

Supramolecular materials have gained substantial interest for a number biological and nonbiological applications. However, for optimum utilization of these dynamic self-assembled materials, it is important to visualize and understand their structures at the nanoscale, in solution and in real time. Previous approaches for imaging these structures have utilized super-resolution optical imaging methods such as STORM, which has provided important insights, but suffers from drawbacks of complex sample preparation and slow acquisition times, thus limiting real-time in situ imaging of dynamic processes. We demonstrate a noncovalent fluorescent labeling design for STED-based super-resolution imaging of self-assembling peptides. This is achieved by in situ, electrostatic binding of anionic sulfonates of Alexa-488 dye to the cationic sites of lysine (or arginine) residues exposed on the peptide nanostructure surface. A direct, multiscale visualization of static structures reveals hierarchical organization of supramolecular fibers with sub-60 nm resolution. In addition, the degradation of nanofibers upon enzymatic hydrolysis of peptide could be directly imaged in real time, and although resolution was compromised in this dynamic process, it provided mechanistic insights into the enzymatic degradation process. Noncovalent Alexa-488 labeling and subsequent imaging of a range of cationic self-assembling peptides and peptide-functionalized gold nanoparticles demonstrated the versatility of the methodology for the imaging of cationic supramolecular structures. Overall, our approach presents a general and simple method for the electrostatic fluorescent labeling of cationic peptide nanostructures for nanoscale imaging under physiological conditions and probe dynamic processes in real time and in situ.

Design of materials with supramolecular polymers

One hundred years ago Hermann Staudinger was strongly criticized by his scientific peers for his macromolecular hypothesis, but today it is hard to imagine a world without polymers. His hypothesis described polymers as macromolecules composed of large numbers of structural units connected by covalent bonds. In the 1990s the concept of supramolecular polymers emerged in the scientific literature as discrete entities of large molar mass comparable to that of classical polymers but built through non-covalent bonds among monomers. Supramolecular polymers exist in biological systems, and potentially blend the physical properties of covalent polymers with unique features such as high degrees of internal order within the polymeric structure, defined shapes, and novel dynamics. This trend article provides a summary of seminal contributions in supramolecular polymerization and provides recent examples from the Stupp laboratory to demonstrate the potential applications of an exciting class of materials composed fully or partially of supramolecular polymers. In closing, we provide our perspective on future opportunities provided by this field at the onset of a second century of polymers. It is our objective here to demonstrate that this second century could be as prosperous, if not more so, than the preceding one.

Current Progress in Cross-Linked Peptide Self-Assemblies

Peptide-based fibrous supramolecular assemblies represent an emerging class of biomaterials that can realize various bioactivities and structures. Recently, a variety of peptide fibers with attractive functions have been designed together with the discovery of many peptide-based self-assembly units. Cross-linking of the peptide fibers is a key strategy to improve the functions of these materials. The cross-linking of peptide fibers forming three-dimensional networks in a dispersion can lead to changes in physical and chemical properties. Hydrogelation is a typical change caused by cross-linking, which makes it applicable to biomaterials such as cell scaffold materials. Cross-linking methods, which have been conventionally developed using water-soluble covalent polymers, are also useful in supramolecular peptide fibers. In the case of peptide fibers, unique cross-linking strategies can be designed by taking advantage of the functions of amino acids. This review focuses on the current progress in the design of cross-linked peptide fibers and their applications.

Enzyme-responsive chiral self-sorting in amyloid-inspired minimalistic peptide amphiphiles

Self-sorting is a spontaneous phenomenon that ensures the formation of complex yet ordered multicomponent systems and conceptualizes the design of artificial and orthogonally functional compartments. In the present study, we envisage chirality-mediated self-sorting in β-amyloid-inspired minimalistic peptide amphiphile (C₁₀-l/d-VFFAKK)-based nanofibers. The fidelity and stereoselectivity of chiral self-sorting was ascertained by Förster resonance energy transfer (FRET) by the judicious choice of a pyrene (Py)-hydroxy coumarin (HOCou) donor-acceptor pair tethered to the peptide sequences. Seed-promoted elongation of the homochiral peptide amphiphiles investigated by AFM image analyses and Thioflavin-T (ThT) binding study further validated the chiral recognition of the l/d peptide nanofibers. Moreover, direct visualization of the chirality-driven self-sorted nanofibers is reported using super-resolution microscopy that exhibits enantioselective enzymatic degradation for l-peptide fibers. Such enantioselective weakening of the hydrogels may be used for designing stimuli-responsive orthogonal compartments for delivery applications.

Non-Viral Targeted Nucleic Acid Delivery: Apply Sequences for Optimization

In nature, genomes have been optimized by the evolution of their nucleic acid sequences. The design of peptide-like carriers as synthetic sequences provides a strategy for optimizing multifunctional targeted nucleic acid delivery in an iterative process. The optimization of sequence-defined nanocarriers differs for different nucleic acid cargos as well as their specific applications. Supramolecular self-assembly enriched the development of a virus-inspired non-viral nucleic acid delivery system. Incorporation of DNA barcodes presents a complementary approach of applying sequences for nanocarrier optimization. This strategy may greatly help to identify nucleic acid carriers that can overcome pharmacological barriers and facilitate targeted delivery in vivo. Barcode sequences enable simultaneous evaluation of multiple nucleic acid nanocarriers in a single test organism for in vivo biodistribution as well as in vivo bioactivity.

100th Anniversary of Macromolecular Science Viewpoint: Enabling Advances in Fluorescence Microscopy Techniques

In the past few decades there has been a revolution in the field of optical microscopy with emerging capabilities such as super-resolution and single-molecule fluorescence techniques. Combined with the classical advantages of fluorescence imaging, such as chemical labeling specificity, and noninvasive sample preparation and imaging, these methods have enabled significant advances in our polymer community. This Viewpoint discusses several of these capabilities and how they can uniquely offer information where other characterization techniques are limited. Several examples are highlighted that demonstrate the ability of fluorescence microscopy to understand key questions in polymer science such as single-molecule diffusion and orientation, 3D nanostructural morphology, and interfacial and multicomponent dynamics. Finally, we briefly discuss opportunities for further advances in techniques that may allow them to make an even greater contribution in polymer science.

Molecularly Engineered "Janus GroEL": Application to Supramolecular Copolymerization with a Higher Level of Sequence Control

Herein we report the synthesis and isolation of a shape-persistent Janus protein nanoparticle derived from the biomolecular machine chaperonin GroEL (^AGroEL^B) and its application to DNA-mediated ternary supramolecular copolymerization. To synthesize ^AGroEL^B with two different DNA strands A and B at its opposite apical domains, we utilized the unique biological property of GroEL, i.e., Mg²⁺/ATP-mediated ring exchange between ^AGroEL^A and ^BGroEL^B with their hollow cylindrical double-decker architectures. This exchange event was reported more than 24 years ago but has never been utilized for molecular engineering of GroEL. We leveraged DNA nanotechnology to purely isolate Janus ^AGroEL^B and succeeded in its precision ternary supramolecular copolymerization with two DNA comonomers, A** and B*, that are partially complementary to A and B in ^AGroEL^B, respectively, and programmed to self-dimerize on the other side. Transmission electron microscopy allowed us to confirm the formation of the expected dual-periodic copolymer sequence -(^B*/BGroEL^A/A**/A**/AGroEL^B/B*)- in the form of a laterally connected lamellar assembly rather than a single-chain copolymer.

Caught in the Act: Mechanistic Insight into Supramolecular Polymerization-Driven Self-Replication from Real-Time Visualization

Self-assembly features prominently in fields ranging from materials science to biophysical chemistry. Assembly pathways, often passing through transient intermediates, can control the outcome of assembly processes. Yet, the mechanisms of self-assembly remain largely obscure due to a lack of experimental tools for probing these pathways at the molecular level. Here, the self-assembly of self-replicators into fibers is visualized in real-time by high-speed atomic force microscopy (HS-AFM). Fiber growth requires the conversion of precursor molecules into six-membered macrocycles, which constitute the fibers. HS-AFM experiments, supported by molecular dynamics simulations, revealed that aggregates of precursor molecules accumulate at the sides of the fibers, which then diffuse to the fiber ends where growth takes place. This mechanism of precursor reservoir formation, followed by one-dimensional diffusion, which guides the precursor molecules to the sites of growth, reduces the entropic penalty associated with colocalizing precursors and growth sites and constitutes a new mechanism for supramolecular polymerization.

NMR Studies of Block Copolymer-Based Supramolecules in Solution

Hierarchical assemblies from block copolymer (BCP)-based supramolecules have shown immense potential as programmable materials owing to their versatility for incorporating functional molecules and provide access to arrays of hierarchical structures. However, there remains a knowledge gap on the formation of the supramolecule in solution. Here, we applied NMR techniques to investigate the solution-phase behavior of the most studied supramolecular systems, polystyrene-block-poly(4-vinylpyridine)(3-pentadecylphenol) (PS-b-P4VP(PDP)_r). The results show that the supramolecule likely adopts a coil-comb conformation, despite the small molecule's (PDP) rapid exchange between the bonded and free states. The exchange rate (>10⁴ s^-1) exceeds the NMR time scale at the frequency of interest. The supramolecules form under dilute conditions (∼2 vol %) and are attributed to the enthalpic gain of the hydrogen bonding between the PDP and 4VP. As the solute concentration increases (>10 vol %), the supramolecule forms micelle-like aggregates with PDP accumulated within the comb-block's pervaded volume based on analysis of the apparent molecular weight, viscosity, and chain dynamics. This work sheds light on the long-standing question regarding the evolution of the constituents in the BCP-based supramolecule in solution and provides valuable guidance toward their solution-based processing and morphological control.

Membrane active Janus-oligomers of β3-peptides

Self-assembly of an acyclic β³-hexapeptide with alternating side chain chirality, into nanometer size oligomeric bundles showing membrane activity and hosting capacity for hydrophobic small molecules.

Self-assembling peptides offer a versatile set of tools for bottom-up construction of supramolecular biomaterials. Among these compounds, non-natural peptidic foldamers experience increased focus due to their structural variability and lower sensitivity to enzymatic degradation. However, very little is known about their membrane properties and complex oligomeric assemblies – key areas for biomedical and technological applications. Here we designed short, acyclic β³-peptide sequences with alternating amino acid stereoisomers to obtain non-helical molecules having hydrophilic charged residues on one side, and hydrophobic residues on the other side, with the N-terminus preventing formation of infinite fibrils. Our results indicate that these β-peptides form small oligomers both in water and in lipid bilayers and are stabilized by intermolecular hydrogen bonds. In the presence of model membranes, they either prefer the headgroup regions or they insert between the lipid chains. Molecular dynamics (MD) simulations suggest the formation of two-layered bundles with their side chains facing opposite directions when compared in water and in model membranes. Analysis of the MD calculations showed hydrogen bonds inside each layer, however, not between the layers, indicating a dynamic assembly. Moreover, the aqueous form of these oligomers can host fluorescent probes as well as a hydrophobic molecule similarly to e.g. lipid transfer proteins. For the tested, peptides the mixed chirality pattern resulted in similar assemblies despite sequential differences. Based on this, it is hoped that the presented molecular framework will inspire similar oligomers with diverse functionality.

Self-Assembly Propensity Dictates Lifetimes in Transient Naphthalimide-Dipeptide Nanofibers

Transient self-assembly of dipeptide nanofibers with lifetimes that are predictably variable through dipeptide sequence design are presented. This was achieved using 1,8-naphthalimide (NI) amino acid methyl-esters (Phe, Tyr, Leu) that are biocatalytically coupled to amino acid-amides (Phe, Tyr, Leu, Val, Ala, Ser) to form self-assembling NI-dipeptides. However, competing hydrolysis of the dipeptides results in disassembly. It was demonstrated that the kinetic parameters like lifetimes of these nanofibers can be predictably regulated by the thermodynamic parameter, namely the self-assembly propensity of the constituent dipeptide sequence. These lifetimes could vary from minutes, to hours, to permanent gels that do not degrade. Moreover, the in-built NI fluorophore was utilized to image the transient nanostructures in solution with stimulated emission depletion (STED) based super-resolution fluorescence microscopy.

Transition of Nano-Architectures Through Self-Assembly of Lipidated β3-Tripeptide Foldamers

β³-peptides consisting exclusively of β³-amino acids adopt a variety of non-natural helical structures and can self-assemble into well-defined hierarchical structures by axial head-to-tail self-assembly resulting in fibrous materials of varying sizes and shapes. To allow control of fiber morphology, a lipid moiety was introduced within a tri-β³-peptide sequence at each of the three amino acid positions and the N-terminus to gain finer control over the lateral assembly of fibers. Depending on the position of the lipid, the self-assembled structures formed either twisted ribbon-like fibers or distinctive multilaminar nanobelts. The nanobelt structures were comprised of multiple layers of peptide fibrils as revealed by puncturing the surface of the nanobelts with an AFM probe. This stacking phenomenon was completely inhibited through changes in pH, indicating that the layer stacking was mediated by electrostatic interactions. Thus, the present study is the first to show controlled self-assembly of these fibrous structures, which is governed by the location of the acyl chain in combination with the 3-point H-bonding motif. Overall, the results demonstrate that the nanostructures formed by the β³-tripeptide foldamers can be tuned via sequential lipidation of N-acetyl β³-tripeptides which control the lateral interactions between peptide fibrils and provide defined structures with a greater homogeneous population.

Impact of NDI-Core Substitution on the pH-Responsive Nature of Peptide-Tethered Luminescent Supramolecular Polymers

The pH-responsive nature of two self-assembled NDI-peptide amphiphile conjugates is reported. The diethoxy substituted NDI showed a pH-dependent assembly behaviour, as expected. In contrast, the isopropylamino- and ethoxy-substituted NDI based supramolecular polymer was stable at acidic and basic aqueous conditions. This finding highlights how subtle changes in the molecular design of π-stacked chromophore-peptide conjugates have a drastic impact on their equilibrium structure and ultimately functional properties.

Supramolecular materials based on AIE luminogens (AIEgens): construction and applications

The emergence of aggregation-induced emission luminogens (AIEgens) has significantly stimulated the development of luminescent supramolecular materials because their strong emissions in the aggregated state have resolved the notorious obstacle of the aggregation-caused quenching (ACQ) effect, thereby enabling AIEgen-based supramolecular materials to have a promising prospect in the fields of luminescent materials, sensors, bioimaging, drug delivery, and theranostics. Moreover, in contrast to conventional fluorescent molecules, the configuration of AIEgens is highly twisted in space. Investigating AIEgens and the corresponding supramolecular materials provides fundamental insights into the self-assembly of nonplanar molecules, drastically expands the building blocks of supramolecular materials, and pushes forward the frontiers of supramolecular chemistry. In this review, we will summarize the basic concepts, seminal studies, recent trends, and perspectives in the construction and applications of AIEgen-based supramolecular materials with the hope to inspire more interest and additional ideas from researchers and further advance the development of supramolecular chemistry.

Soft-Matter Nanotubes: A Platform for Diverse Functions and Applications

Self-assembled organic nanotubes made of single or multiple molecular components can be classified into soft-matter nanotubes (SMNTs) by contrast with hard-matter nanotubes, such as carbon and other inorganic nanotubes. To date, diverse self-assembly processes and elaborate template procedures using rationally designed organic molecules have produced suitable tubular architectures with definite dimensions, structural complexity, and hierarchy for expected functions and applications. Herein, we comprehensively discuss every functions and possible applications of a wide range of SMNTs as bulk materials or single components. This Review highlights valuable contributions mainly in the past decade. Fifteen different families of SMNTs are discussed from the viewpoints of chemical, physical, biological, and medical applications, as well as action fields (e.g., interior, wall, exterior, whole structure, and ensemble of nanotubes). Chemical applications of the SMNTs are associated with encapsulating materials and sensors. SMNTs also behave, while sometimes undergoing morphological transformation, as a catalyst, template, liquid crystal, hydro-/organogel, superhydrophobic surface, and micron size engine. Physical functions pertain to ferro-/piezoelectricity and energy migration/storage, leading to the applications to electrodes or supercapacitors, and mechanical reinforcement. Biological functions involve artificial chaperone, transmembrane transport, nanochannels, and channel reactors. Finally, medical functions range over drug delivery, nonviral gene transfer vector, and virus trap.

The Power of Confocal Laser Scanning Microscopy in Supramolecular Chemistry: In situ Real-time Imaging of Stimuli-Responsive Multicomponent Supramolecular Hydrogels

Multicomponent supramolecular hydrogels are promising scaffolds for applications in biosensors and controlled drug release due to their designer stimulus responsiveness. To achieve rational construction of multicomponent supramolecular hydrogel systems, their in-depth structural analysis is essential but still challenging. Confocal laser scanning microscopy (CLSM) has emerged as a powerful tool for structural analysis of multicomponent supramolecular hydrogels. CLSM imaging enables real-time observation of the hydrogels without the need of drying and/or freezing to elucidate their static and dynamic properties. Through multiple, selective fluorescent staining of materials of interest, multiple domains formed in supramolecular hydrogels (e. g. inorganic materials and self-sorting nanofibers) can also be visualized. CLSM and the related microscopic techniques will be indispensable to investigate complex life-inspired supramolecular chemical systems.

Quantification of functional crosslinker reaction kinetics via super-resolution microscopy of swollen microgels

Super resolution microscopy (SRM) brings the advantages of optical microscopy to the imaging of nanostructured soft matter, and in colloidal microgels, promises to quantify variations of crosslink densities at unprecedented length scales. However, the distribution of all crosslinks does not coincide with that of dye-tagged crosslinks, and density quantification in SRM is not guaranteed due to over/under-counting dye molecules. Here we demonstrate that SRM images of microgels encode reaction rate constants of functional cross linkers, which hold the key to correlating these distributions. Combined with evolution of microgel particle radii, the functional cross linker distributions predict consumption versus time with high fidelity. Using a Bayesian regression approach, we extract reaction rate constants for homo and cross propagation of the functional crosslinker, which should be widely useful for predicting spatial variations in crosslink density of gels.

Interface-Enrichment-Induced Instability and Drug-Loading-Enhanced Stability in Inhalable Delivery of Supramolecular Filaments

Filamentous microorganisms traveling in aerosol particles display enhanced deposition and retention in the lungs. Inspired by this shape-related biological effect, we report here on the use of supramolecular filaments as potential inhalable drug carriers within aerosols via jet nebulization. We found that the peptide design and supramolecular stability play a crucial role in the interfacial stability and aerosolization properties of the supramolecular filaments. Monomeric units with a positively charged C-terminus produced filaments with reduced aerosol stability, promoting morphological changes after nebulization. Conversely, having a neutral or negatively charged terminus yielded filaments with enhanced stability, where supramolecular integrity is maintained with only reduced length. Our results suggest that molecular enrichment at the air-liquid interface during nebulization is the primary factor to deplete the monomeric peptide amphiphiles in solution, accounting for the observed morphological disruption/transitions. Importantly, encapsulation of drugs and dyes within filaments notably stabilize their supramolecular structure during nebulization, and the loaded filaments exhibit a linear release profile from a nebulizer device. We envision the use of this supramolecular carrier system as an effective platform for the inhalation-based treatment of many lung diseases.

Designing stable, hierarchical peptide fibers from block co-polypeptide sequences

Here we report the pH induced self-assembly of equilibrium zwitterionically charged block co-polypeptide nanotubes into hierarchical nanotube fibers.

Natural materials, such as collagen, can assemble with multiple levels of organization in solution. Achieving a similar degree of control over morphology, stability and hierarchical organization with equilibrium synthetic materials remains elusive. For the assembly of peptidic materials the process is controlled by a complex interplay between hydrophobic interactions, electrostatics and secondary structure formation. Consequently, fine tuning the thermodynamics and kinetics of assembly remains extremely challenging. Here, we synthesized a set of block co polypeptides with varying hydrophobicity and ability to form secondary structure. From this set we select a sequence with balanced interactions that results in the formation of high-aspect ratio thermodynamically favored nanotubes, stable between pH 2 and 12 and up to 80 °C. This stability permits their hierarchical assembly into bundled nanotube fibers by directing the pH and inducing complementary zwitterionic charge behavior. This block co-polypeptide design strategy, using defined sequences, provides a straightforward approach to creating complex hierarchical peptide-based assemblies with tunable interactions.

Tuning the matrix metalloproteinase-1 degradability of peptide amphiphile nanofibers through supramolecular engineering

Matrix metalloproteinases (MMPs) are a family of endopeptidases capable of degrading extracellular matrix (ECM) components. They are known to play crucial roles during the ECM turnover in both physiological and pathological processes. As such, their activities are utilized as biological stimuli to engineer MMP-responsive peptide-based biomaterials such as self-assembled peptide amphiphiles (PAs). Although previous studies have unveiled the role of PAs secondary structure on the mechanical and biological properties of their self-assembled nanostructures, the effect on the degradability of their assemblies by MMP-1 has not been reported. Herein, a series of PAs are designed and synthesized, all comprising the same MMP-1 cleavable domain but with variable structural segments, to decipher the role of PA's secondary structure on the MMP-1 degradability of their assemblies. This study reveals a correlation between the MMP-1 degradation efficiency and the β-sheet content of the self-assembled PA nanofibers, with the MMP-1 cleavability being significantly reduced in the PA nanofibers with stronger β-sheet characteristics. These results shed light on the role of supramolecular cohesion in PA assemblies on their hydrolysis by MMP-1 and open up the possibility to control the degradation rate of PA-based nanostructures by MMP-1 through tweaking their molecular sequences.

DNA-Peptide Amphiphile Nanofibers Enhance Aptamer Function

The single stranded DNA oligonucleotides known as aptamers have the capacity to bind proteins and other molecules and offer great therapeutic potential. Further work is required to optimize their function and to diminish their susceptibility to nuclease degradation. We report here on the synthesis and supramolecular self-assembly of DNA-peptide amphiphiles that form high aspect ratio nanofibers and display aptamers for platelet-derived growth factor. The nanofibers were found to bind the growth factor with an affinity that was fivefold greater than the free aptamer. We also observed that the aptamer displayed by the supramolecular nanostructures was eight times more nuclease resistant than free aptamer. In order to highlight the therapeutic potential of these supramolecular systems, we demonstrated the improved inhibition of proliferation when the growth factor was bound to aptamers displayed by the nanofibers.

A stochastic view on surface inhomogeneity of nanoparticles

The interactions between and with nanostructures can only be fully understood when the functional group distribution on their surfaces can be quantified accurately. Here we apply a combination of direct stochastic optical reconstruction microscopy (dSTORM) imaging and probabilistic modelling to analyse molecular distributions on spherical nanoparticles. The properties of individual fluorophores are assessed and incorporated into a model for the dSTORM imaging process. Using this tailored model, overcounting artefacts are greatly reduced and the locations of dye labels can be accurately estimated, revealing their spatial distribution. We show that standard chemical protocols for dye attachment lead to inhomogeneous functionalization in the case of ubiquitous polystyrene nanoparticles. Moreover, we demonstrate that stochastic fluctuations result in large variability of the local group density between particles. These results cast doubt on the uniform surface coverage commonly assumed in the creation of amorphous functional nanoparticles and expose a striking difference between the average population and individual nanoparticle coverage.

Controllable hierarchical self-assembly of porphyrin-derived supra-amphiphiles

Control of self-assembly is significant to the preparation of supramolecular materials and illustration of diversities in either natural or artificial systems. Supra-amphiphiles have remarkable advantages in the construction of nanostructures but control of shape and size of supramolecular nanostructures is still a great challenge. Here, we fabricate a series of supra-amphiphiles by utilizing the recognition motifs based on a heteroditopic porphyrin amphiphile and its zinc complex. These porphyrin amphiphiles can bind with a few guests including Cl^-, coronene, C₆₀, 4,4'-bipyridine and 2,4,6-tri(pyridin-4-yl)-1,3,5-triazine, which are further applied to facilitate the controllable self-assembly. Addition of these guests result in the formation of various supra-amphiphiles with well-defined structures, thus induce the generation of different aggregates. A diverse of aggregation morphologies including nanospheres, nanorods, films, spheric micelles, vesicles and macrowires are constructed upon the influence of specific complexation, which highlights the present work with abundant control on the shapes and dimensions of self-assemblies.

DNA-Functionalized Supramolecular Polymers: Dynamic Multicomponent Assemblies with Emergent Properties

Recent years have witnessed an increasing interest in hybrid molecular systems in which the programmability of DNA hybridization is used to introduce enhanced molecular control in synthetic systems. The first examples of DNA-functionalized supramolecular polymers have been reported only recently, but have already revealed structural and functional properties that are not easily obtained in either synthetic supramolecular polymers or DNA-only based systems. In this Topical Review, we provide an overview of the various forms of additional control offered by DNA hybridization for different types of supramolecular polymers and discuss how orthogonal supramolecular interactions in these hybrid systems can give rise to emergent structural and functional properties.

Self-assembly in elastin-like recombinamers: a mechanism to mimic natural complexity

The topic of self-assembled structures based on elastin-like recombinamers (ELRs, i.e., elastin-like polymers recombinantly bio-produced) has released a noticeable amount of references in the last few years. Most of them are intended for biomedical applications. In this review, a complete revision of the bibliography is carried out. Initially, the self-assembly (SA) concept is considered from a general point of view, and then ELRs are described and characterized based on their intrinsic disorder. A classification of the different self-assembled ELR-based structures is proposed based on their morphologies, paying special attention to their tentative modeling. The impact of the mechanism of SA on these biomaterials is analyzed. Finally, the implications of ELR SA in biological systems are considered.

Super-resolution Imaging of Proton Sponge-Triggered Rupture of Endosomes and Cytosolic Release of Small Interfering RNA

The intracellular delivery of nucleic acids and proteins remains a key challenge in the development of biological therapeutics. In gene therapy, the inefficient delivery of small interfering RNA (siRNA) to the cytosol by lipoplexes or polyplexes is often ascribed to the entrapment and degradation of siRNA payload in the endosomal compartments. A possible mechanism by which polyplexes rupture the endosomal membrane and release their nucleic acid cargo is commonly defined as the "proton sponge effect". This is an osmosis-driven process triggered by the proton buffering capacity of polyplexes. Herein, we investigate the molecular basis of the "proton sponge effect" through direct visualization of the siRNA trafficking process, including analysis of individual polyplexes and endosomes, using stochastic optical reconstruction microscopy. We probe the sequential siRNA trafficking steps through single molecule super-resolution analysis of subcellular structures, polyplexes, and silencing RNA molecules. Specifically, individual intact polyplexes released in the cytosol upon rupture of the endosomes, the damaged endosomal vesicles, and the disassembly of the polyplexes in the cytosol are examined. We find that the architecture of the polyplex and the rigidity of the cationic polymer chains are crucial parameters that control the mechanism of endosomal escape driven by the proton sponge effect. We provide evidence that in highly branched and rigid cationic polymers, such as glycogen or polyethylenimine, immobilized on silica nanoparticles, the proton sponge effect is effective in inducing osmotic swelling and rupture of endosomes.

Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) with Graphene Oxide

Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) was demonstrated with graphene oxide sheets, peptides and bacteria; a method of contrast enhancement with super-resolution fluorescence microscopy. Individual sheets of graphene oxide (GO) were imaged with a resolution of 16 nm using the quenching of fluorescence emission by GO via its large Resonant Energy Transfer (RET) efficiency. The method was then extended to image self-assembled peptide aggregates (resolution 19 nm) and live bacterial cells (resolution 55 nm, the capsular structure of E. coli from urinary tract infections) with extremely low backgrounds and high contrasts (between one and two orders of magnitude contrast factor improvements that depended on the thickness of the graphene oxide layer used). Graphene oxide films combined with STORM imaging thus provide an extremely convenient method to image samples with large backgrounds due to non-specifically bound fluorophores (either due to excess labelling or autofluorescent molecules), which is a common occurrence in studies of both biological cells and soft-condensed matter. The GO quenches the fluorescence across a thin layer at distances of less than 15 nm. Graphene oxide films coated with thin layers (≤15 nm) of polystyrene, polymethylmethacrylate and polylysine are shown to be effective in producing high contrast qSTORM images, providing a convenient modulation of sample/substrate interactions. The GO coatings can also provide an increased image resolution and a factor of 2.3 improvement was observed with the peptide fibres using a feature of interest metric,when there was a large non-specifically bound background.

Self-Repair of Structure and Bioactivity in a Supramolecular Nanostructure

Supramolecular nanostructures formed through self-assembly can have energy landscapes, which determine their structures and functions depending on the pathways selected for their synthesis and processing and on the conditions they are exposed to after their initial formation. We report here on the structural damage that occurs in supramolecular peptide amphiphile nanostructures, during freezing in aqueous media, and the self-repair pathways that restore their functions. We found that freezing converts long supramolecular nanofibers into shorter ones, compromising their ability to support cell adhesion, but a single heating and cooling cycle reverses the damage and rescues their bioactivity. Thermal energy in this cycle enables noncovalent interactions to reconfigure the nanostructures into the thermodynamically preferred long nanofibers, a repair process that is impeded by kinetic traps. In addition, we found that nanofibers disrupted during freeze-drying also exhibit the ability to undergo thermal self-repair and recovery of their bioactivity, despite the extra disruption caused by the dehydration step. Following both freezing and freeze-drying, which shorten the 1D nanostructures, their self-repair capacity through thermally driven elongation is inhibited by kinetically trapped states, which contain highly stable noncovalent interactions that are difficult to rearrange. These states decrease the extent of thermal nanostructure repair, an observation we hypothesize applies to supramolecular systems in general and is mechanistically linked to suppressed molecular exchange dynamics.

Peptide supramolecular materials for therapeutics

Supramolecular assembly of peptide-based monomers into nanostructures offers many promising applications in advanced therapies. In this Tutorial Review, we introduce molecular designs to control the structure and potential biological function of supramolecular assemblies. An emphasis is placed on peptide-based supramolecular nanostructures that are intentionally designed to signal cells, either directly through the incorporation of amino acid sequences that activate receptors or indirectly by recruiting native signals such as growth factors. Additionally, we describe the use and future potential of hierarchical structures, such as single molecules that assemble into nanoscale fibers which then align to form macroscopic strings; the strings can then serve as scaffolds for cell growth, proliferation, and differentiation.

Reversible self-assembly of superstructured networks

Soft structures in nature, such as protein assemblies, can organize reversibly into functional and often hierarchical architectures through noncovalent interactions. Molecularly encoding this dynamic capability in synthetic materials has remained an elusive goal. We report on hydrogels of peptide-DNA conjugates and peptides that organize into superstructures of intertwined filaments that disassemble upon the addition of molecules or changes in charge density. Experiments and simulations demonstrate that this response requires large-scale spatial redistribution of molecules directed by strong noncovalent interactions among them. Simulations also suggest that the chemically reversible structures can only occur within a limited range of supramolecular cohesive energies. Storage moduli of the hydrogels change reversibly as superstructures form and disappear, as does the phenotype of neural cells in contact with these materials.

Polyprodrug Antimicrobials: Remarkable Membrane Damage and Concurrent Drug Release to Combat Antibiotic Resistance of Methicillin-Resistant Staphylococcus aureus

The increased threat of antibiotic resistance has created an urgent need for new strategies. Herein, polyprodrug antimicrobials are proposed to mimic antimicrobial peptides appended with a concurrent drug release property, exhibiting broad-spectrum antibacterial activity and especially high potency to inhibit methicillin-resistant Staphylococcus aureus (MRSA) without inducing resistance. Two series of polyprodrug antimicrobials are fabricated by facile polymerization of triclosan prodrug monomer (TMA) and subsequent quaternization of hydrophilic poly(N,N-dimethylaminoethyl methacrylate) (PDMAEMA), affording PDMAEMA-b-PTMA and PQDMA-b-PTMA, respectively. Optimized samples with proper hydrophobic ratio are screened out, which exhibit remarkable bacterial inhibition and low hemolysis toward red blood cells. Furthermore, synergistic antibacterial mechanisms contribute to the bacteria killing, including serious membrane damage, increased out-diffusion of cytosolic milieu across the membrane, and intracellular reductive milieu-mediated triclosan release. No detectable resistance is observed for polyprodrug antimicrobials against MRSA, which is demonstrated to be better than commercial triclosan and vancomycin against in vivo MRSA-infected burn models and a promising approach to the hurdle of antibiotic resistance in biomedicine.

Functional Control of Peptide Amphiphile Assemblies via Modulation of Internal Cohesion and Surface Chemistry Switch

Understanding the impacts of the internal cohesion and surface chemistry of supramolecular systems on the collective behaviors in the contacts between the systems and biomolecules can greatly expand the functional diversity and adaptivity of supramolecular nanostructures. Here we show how the tuned molecular interactions modulate the morphologies and internal cohesion of peptide amphiphile (PA) self-assemblies and their resultant functions. Circular dichroism spectroscopy, fluorescence probing, atomic force and electron microscopy, along with molecular dynamics simulations, revealed that the PA self-assembly formed compact long fibers when surface charge repulsion was screened, but formed loose short fibers or micelle-like assemblies when hydrogen bonding was disrupted or hydrophobic core was enhanced. More importantly, depending on the strength of the phospholipid affinity for the cationic segment of the PA, the same internal cohesion of PA nanostructures can lead to either cell death or cell survival, providing unique insights into the design of supramolecular materials.

Painting Supramolecular Polymers in Organic Solvents by Super-resolution Microscopy

Despite the rapid development of complex functional supramolecular systems, visualization of these architectures under native conditions at high resolution has remained a challenging endeavor. Super-resolution microscopy was recently proposed as an effective tool to unveil one-dimensional nanoscale structures in aqueous media upon chemical functionalization with suitable fluorescent probes. Building upon our previous work, which enabled photoactivation localization microscopy in organic solvents, herein, we present the imaging of one-dimensional supramolecular polymers in their native environment by interface point accumulation for imaging in nanoscale topography (iPAINT). The noncovalent staining, typical of iPAINT, allows the investigation of supramolecular polymers' structure in situ without any chemical modification. The quasi-permanent adsorption of the dye to the polymer is exploited to identify block-like arrangements within supramolecular fibers, which were obtained upon mixing homopolymers that were prestained with different colors. The staining of the blocks, maintained by the lack of exchange of the dyes, permits the imaging of complex structures for multiple days. This study showcases the potential of PAINT-like strategies such as iPAINT to visualize multicomponent dynamic systems in their native environment with an easy, synthesis-free approach and high spatial resolution.

Genetically encoded lipid-polypeptide hybrid biomaterials that exhibit temperature-triggered hierarchical self-assembly

Post-translational modification of proteins is a strategy widely used in biological systems. It expands the diversity of the proteome and allows for tailoring of both the function and localization of proteins within cells as well as the material properties of structural proteins and matrices. Despite their ubiquity in biology, with a few exceptions, the potential of post-translational modifications in biomaterials synthesis has remained largely untapped. As a proof of concept to demonstrate the feasibility of creating a genetically encoded biohybrid material through post-translational modification, we report here the generation of a family of three stimulus-responsive hybrid materials-fatty-acid-modified elastin-like polypeptides-using a one-pot recombinant expression and post-translational lipidation methodology. These hybrid biomaterials contain an amphiphilic domain, composed of a β-sheet-forming peptide that is post-translationally functionalized with a C14 alkyl chain, fused to a thermally responsive elastin-like polypeptide. They exhibit temperature-triggered hierarchical self-assembly across multiple length scales with varied structure and material properties that can be controlled at the sequence level.

Amyloid-like staining property of RADA16-I nanofibers and its potential application in detecting and imaging the nanomaterial

Background

Designer self-assembling peptide nanofibers (SAPNFs) as a novel kind of emerging nanomaterial have received more and more attention in the field of nanomedicine in recent years. However, a simple method to monitor and image SAPNFs is still currently absent.

Methods

RADA16-I, a well-studied ionic complementary peptide was used as a model to check potential amyloid-like staining properties of SAPNFs. Thioflavin-T (ThT) and Congo red (CR) as specific dyes for amyloid-like fibrils were used to stain RADA16-I nanofibers in solution, combined with drugs or cells, or injected in vivo as hydrogels. Fluorescent spectrometry and fluorescent microscopy were used to check ThT-binding property, and polarized light microscopy was used to check CR-staining property.

Results

ThT binding with the nanofibers showed enhanced and blue-shifted fluorescence, and specific apple-green birefringence could be observed after the nanofibers were stained with CR. Based on these properties we further showed that ThT-binding fluorescence intensity could be used to monitor the forming and changing of nanofibers in solution, while fluorescent microscopy and polarized light microscopy could be used to image the nanofibers as material for drug delivery, 3D cell culture, and tissue regeneration.

Conclusion

Our results may provide convenient and reliable tools for detecting SAPNFs, which would be helpful for understanding their self-assembling process and exploring their applications.

How the Dynamics of a Supramolecular Polymer Determines Its Dynamic Adaptivity and Stimuli-Responsiveness: Structure-Dynamics-Property Relationships From Coarse-Grained Simulations

The rational design of supramolecular polymers that can adapt or respond in time to specific stimuli in a controlled way is interesting for many applications, but this requires understanding the molecular factors that make the material faster or slower in responding to the stimulus. To this end, it is necessary to study the dynamic adaptive properties at submolecular resolution, which is difficult at an experimental level. Here we show coarse-grained molecular dynamics simulations (<5 Å resolution) demonstrating how the dynamic adaptivity and stimuli responsiveness of a supramolecular polymer is controlled by the intrinsic dynamics of the assembly, which is in turn determined by the structure of the monomers. As a representative case, we focus on a water-soluble 1,3,5-benzenetricarboxamide (BTA) supramolecular polymer incorporating (charged) receptor monomers, experimentally seen to undergo dynamic clustering following the superselective binding to a multivalent recruiter. Our simulations show that the dynamic reorganization of the supramolecular structure proceeds via monomer diffusion on the dynamic fiber surface (exchange within the fiber). Rationally changing the structure of the monomers to make the fiber surface more or less dynamic allows tuning the rate of response to the stimulus and of supramolecular reconfiguration. Simple in silico experiments draw a structure-dynamics-property relationship revealing the key factors underpinning the dynamic adaptivity and stimuli-responsiveness of these supramolecular polymers. We come out with clear evidence that to master the bioinspired properties of these fibers, it is necessary to control their intrinsic dynamics, while the high-resolution of our molecular models permits us to show how.

Structured illumination microscopy with interleaved reconstruction (SIMILR)

Structured illumination microscopy (SIM) is the commonly used super-resolution (SR) technique for imaging subcellular dynamics. However, due to its need for multiple illumination patterns, the frame rate is just a fraction of that of conventional microscopy and is thus too slow for fast dynamic studies. A new SR image reconstruction method that maximizes the use of each subframe of the acquisition series is proposed for improving the super-resolved frame rate by N times for N illumination directions. The method requires no changes in raw data and is appropriate for many versions of SIM setup, including those implementing fast illumination pattern generation mechanism based on spatial light modulator or digital micromirror device. The performance of the proposed method is demonstrated through imaging the highly dynamic endoplasmic reticulum where continuous rapid growths or shape changes of tiny structures are observed.