The Role of Hydrogen Bonds in Thermally Responsive Crystallization-Driven Template Autocatalysis

Autocatalysis has been recognized to be involved in the emergence of life and intrinsic to biomolecular replication. Recently, an efficient template autocatalysis driven by solvent-free crystallization has been reported. Herein, we unveil the role of intermolecular hydrogen bonds formed by amides in crystallization-driven template autocatalysis (CDTA), which involves the autocatalytic activity, template selectivity, and thermal responsiveness. We found that the thermal-induced cis-trans isomerization of amides possibly affects the H-bonding-mediated template ability of products for autocatalytic transformation. As a result, CDTA can be reversibly inhibited and activated by tuning the reaction temperatures. Our work sheds light on the significance of noncovalent H-bonding interactions in artificial self-replicators.

Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production

Self-assembling peptides represent a captivating area of study in nanotechnology and biomaterials. This interest is largely driven by their unique properties and the vast application potential across various fields such as catalytic functions. However, design complexities, including high-dimensional sequence space and structural diversity, pose significant challenges in the study of such systems. In this work, we explored the possibility of self-assembled peptides to catalyze the hydrolysis of hydrosilane for hydrogen production using ab initio calculations and carried out wet-lab experiments to confirm the feasibility of these catalytic reactions under ambient conditions. Further, we delved into the nuanced interplay between sequence, structural conformation, and catalytic activity by combining modeling with experimental techniques such as transmission electron microscopy and nuclear magnetic resonance and proposed a dual mode of the microstructure of the catalytic center. Our results reveal that although research in this area is still at an early stage, the development of self-assembled peptide catalysts for hydrogen production has the potential to provide a more sustainable and efficient alternative to conventional hydrogen production methods. In addition, this work also demonstrates that a computation-driven rational design supplemented by experimental validation is an effective protocol for conducting research on functional self-assembled peptides.

Stimuli-responsive peptide assemblies: Design, self-assembly, modulation, and biomedical applications

Peptide molecules have design flexibility, self-assembly ability, high biocompatibility, good biodegradability, and easy functionalization, which promote their applications as versatile biomaterials for tissue engineering and biomedicine. In addition, the functionalization of self-assembled peptide nanomaterials with other additive components enhances their stimuli-responsive functions, promoting function-specific applications that induced by both internal and external stimulations. In this review, we demonstrate recent advance in the peptide molecular design, self-assembly, functional tailoring, and biomedical applications of peptide-based nanomaterials. The strategies on the design and synthesis of single, dual, and multiple stimuli-responsive peptide-based nanomaterials with various dimensions are analyzed, and the functional regulation of peptide nanomaterials with active components such as metal/metal oxide, DNA/RNA, polysaccharides, photosensitizers, 2D materials, and others are discussed. In addition, the designed peptide-based nanomaterials with temperature-, pH-, ion-, light-, enzyme-, and ROS-responsive abilities for drug delivery, bioimaging, cancer therapy, gene therapy, antibacterial, as well as wound healing and dressing applications are presented and discussed. This comprehensive review provides detailed methodologies and advanced techniques on the synthesis of peptide nanomaterials from molecular biology, materials science, and nanotechnology, which will guide and inspire the molecular level design of peptides with specific and multiple functions for function-specific applications.

Autonomic self-regulating systems based on polyelectrolyte microcapsules and microgel particles

Biological systems possess unique non-equilibrium functions, maintaining tight manipulation of their surroundings through inter-communication of multiple components and self-regulatory capability organized over different length scales. However, most artificial materials are incapable of communicating and self-regulating behavior due to their limited number of component and direct responsive modes. Herein, a new integrated self-regulation system is developed utilizing stimuli-responsive polyelectrolyte capsules as building blocks. The combination of stimuli-responsive capsules and enzyme immobilized microgels is designed to mimic life systems and its programmable interactive communications and self-regulation behavior is demonstrated through communication-feedback mechanism. Polyelectrolyte capsules can sense changes of their surrounding, then start the internal communication by releasing energy-rich cargo mimicking the behavior of the cells. The microgel particles subsequently complete closed-loop communication through providing negative feedback on capsules by enzymatic reaction and actuating pH-regulation of the whole system. Different communication modes and pH-regulation behaviors could be achieved by adjusting spatial and kinetic conditions. Proposed intelligent system is highly customizable due to the wide selection of encapsulated cargos, stimuli-responsive blocks and reaction networks, and would have broad influences in areas ranging from medical implants that assist in stabilizing body functions to microreactor system that regulate catalytic reactions.

Localized Enzyme-Assisted Self-Assembly of low molecular weight hydrogelators. Mechanism, applications and perspectives

Nature uses systems of high complexity coordinated by the precise spatial and temporal control of associated processes, working from the molecular to the macroscopic scale. This living organization is mainly ensured by enzymatic actions. Herein, we review the concept of Localized Enzyme-Assisted Self-Assembly (LEASA). It is defined and presented as a straightforward and insightful strategy to achieve high levels of control in artificial systems. Indeed, the use of immobilized enzymes to drive self-assembly events leads not only to the local formation of supramolecular structures but also to tune their kinetics and their morphologies. The possibility to design tailored complex systems taking advantage of self-assembled networks through their inherent and emergent properties offers new perspectives for the design of novel, more adaptable materials. As a result, some applications have already been developed and are gathered in this review. Finally, challenges and perspectives of LEASA are introduced and discussed.

Ion-Triggered Hydrogels Self-Assembled from Statistical Copolypeptides

Statistical copolypeptides comprising lysine and tyrosine with unprecedented ion-induced gelation behavior are reported. Copolypeptides are obtained by one-step N-carboxyanhydride (NCA) ring-opening polymerization. The gelation mechanism is studied by in situ SAXS analyses, in addition to optical spectroscopy and transmission electron microscopy (TEM). It is found that the gelation of these statistically polymerized polypeptides is due to the formation of stable intermolecular β-sheet secondary structures induced by the presence of salt ions as well as the aggregation of an α-helix between the copolypeptides. This behavior is unique to the statistical lysine/tyrosine copolypeptides and was not observed in any other amino acid combination or arrangement. Furthermore, the diffusion and mechanical properties of these hydrogels can be tuned through tailoring the polypeptide chain length and ion strength.

Injectable Tripeptide/Polymer Nanoparticles Supramolecular Hydrogel: A Candidate for the Treatment of Inflammatory Pathologies

Supramolecular peptide-based hydrogels attract great attention in several fields, i.e., biomedicine, catalysis, energy, and materials chemistry, due to the noncovalent nature of the self-assembly and functional tunable properties defined by the amino acid sequence. In this work, we developed an injectable hybrid supramolecular hydrogel whose formation was triggered by electrostatic interactions between a phosphorylated tripeptide, Fmoc-FFpY (F: phenylalanine, pY: phosphorylated tyrosine), and cationic polymer nanoparticles made of vinylimidazole and ketoprofen (poly(HKT-co-VI) NPs). Hydrogel formation was assessed through inverted tube tests, and its fibrillary structure, around polymer NPs, was observed by transmission electron microscopy. Interestingly, peptide self-assembly yields the formation of nontwisted and twisted fibers, which could be attributed to β-sheets and α-helix structures, respectively, as characterized by circular dichroism and infrared spectroscopies. An increase of the elastic modulus of the Fmoc-FFpY/polymer NPs hybrid hydrogels was observed with peptide concentration as well as its injectability property, due to its shear thinning behavior and self-healing ability. After checking their stability under physiological conditions, the cytotoxicity properties of these hybrid hydrogels were evaluated in contact with human dermal fibroblasts (FBH) and murine macrophages (RAW 264.7). Finally, the Fmoc-FFpY/polymer NPs hybrid hydrogels exhibited a great nitric oxide reduction (∼67%) up to basal values of pro-inflammatory RAW 264.7 cells, thus confirming their excellent anti-inflammatory properties for the treatment of localized inflammatory pathologies.

Hierarchical self-assembly of aromatic peptide conjugates into supramolecular polymers: it takes two to tango

Supramolecular polymers are self-assembled materials displaying adaptive and responsive "life-like" behaviour which are often made of aromatic compounds capable of engaging in π-π interactions to form larger assemblies. Major advances have been made recently in controlling their mode of self-assembly, from thermodynamically-controlled isodesmic to kinetically-controlled living polymerization. Dynamic covalent chemistry has been recently implemented to generate dynamic covalent polymers which can be seen as dynamic analogues of biomacromolecules. On the other hand, peptides are readily-available and structurally-rich building blocks that can lead to secondary structures or specific functions. In this context, the past decade has seen intense research activity in studying the behaviour of aromatic-peptide conjugates through supramolecular and/or dynamic covalent chemistries. Herein, we review those impressive key achievements showcasing how aromatic- and peptide-based self-assemblies can be combined using dynamic covalent and/or supramolecular chemistry, and what it brings in terms of the structure, self-assembly pathways, and function of supramolecular and dynamic covalent polymers.

Surface-controlled spatially heterogeneous physical properties of a supramolecular gel with homogeneous chemical composition

Controlling supramolecular self-assembly across multiple length scales to prepare gels with localised properties is challenging. Most strategies concentrate on fabricating gels with heterogeneous components, where localised properties are generated by the stimuli-responsive component. Here, as an alternative approach, we use a spiropyran-modified surface that can be patterned with light. We show that light-induced differences in surface chemistry can direct the bulk assembly of a low molecular weight gelator, 2-NapAV, meaning that mechanical gel properties can be controlled by the surface on which the gel is grown. Using grazing incidence X-ray diffraction and grazing incidence small angle X-ray scattering, we demonstrate that the origin of the different gel properties relates to differences in the architectures of the gels. This provides a new method to prepare a single domain (i.e., chemically homogeneous) hydrogel with locally controlled (i.e., mechanically heterogeneous) properties.

Impact of transposable elements on the evolution of complex living systems and their epigenetic control

Transposable elements (TEs) contribute to genomic innovations, as well as genome instability, across a wide variety of species. Popular designations such as 'selfish DNA' and 'junk DNA,' common in the 1980s, may be either inaccurate or misleading, while a more enlightened view of the TE-host relationship covers a range from parasitism to mutualism. Both plant and animal hosts have evolved epigenetic mechanisms to reduce the impact of TEs, both by directly silencing them and by reducing their ability to transpose in the genome. However, TEs have also been co-opted by both plant and animal genomes to perform a variety of physiological functions, ranging from TE-derived proteins acting directly in normal biological functions to innovations in transcription factor activity and also influencing gene expression. Their presence, in fact, can affect a range of features at genome, phenotype, and population levels. The impact TEs have had on evolution is multifaceted, and many aspects still remain unexplored. In this review, the epigenetic control of TEs is contextualized according to the evolution of complex living systems.

Feedback and Communication in Active Hydrogel Spheres with pH Fronts: Facile Approaches to Grow Soft Hydrogel Structures

Compartmentalized reaction networks regulating signal processing, communication and pattern formation are central to living systems. Towards achieving life-like materials, we compartmentalized urea-urease and more complex urea-urease/ester-esterase pH-feedback reaction networks into hydrogel spheres and investigate how fuel-driven pH fronts can be sent out from these spheres and regulated by internal reaction networks. Membrane characteristics are installed by covering urease spheres with responsive hydrogel shells. We then encapsulate the two networks (urea-urease and ester-esterase) separately into different hydrogel spheres to devise communication, pattern formation and attraction. Moreover, these pH fronts and patterns can be used for self-growing hydrogels, and for developing complex geometries from non-injectable hydrogels without 3D printing tools. This study opens possibilities for compartmentalized feedback reactions and their use in next generation materials fabrication.

Wet spinning of a library of carbohydrate low molecular weight gels

HYPOTHESIS

Recently, a low molecular weight hydrogel based on a carbohydrate alkyl amide has been successfully used as biomaterial for neuron cell culture and for 3D printing. Varying the molecular structure should make it possible to extend the library of carbohydrate low molecular weight hydrogels available for these applications and to improve their performances.

EXPERIMENTS

Thirteen molecules easy to synthetize and designed to be potentially biocompatible were prepared. They are based on gluconamide, glucoheptonamide, galactonamide, glucamide, aliphatic chains and glycine. Their gelation in water was investigated in thermal conditions and wet spinning conditions, namely by dimethylsulfoxide-water exchange under injection.

FINDINGS

Nine molecules give hydrogels in thermal conditions. By wet spinning, six molecules self-assemble fast enough, within few seconds, to form continous hydrogel filaments. Therefore, the method enables to shape by injection these mechanically fragile hydrogels, notably in the perspective of 3D printing. Depending on the molecular structure, persistent or soluble gel filaments are obtained. The microstructures are varied, featuring entangled ribbons, platelets or particles. In thermal gelation, molecules with a symmetrical polar head (galacto, glucoheptono) give flat ribbons and molecules with an asymmetrical polar head (gluco) give helical ribbons. The introduction of an extra glycine linker disturbs this trend.

Localized Enzyme-Assisted Self-Assembly in the Presence of Hyaluronic Acid for Hybrid Supramolecular Hydrogel Coating

Hydrogel coating is highly suitable in biomaterial design. It provides biocompatibility and avoids protein adsorption leading to inflammation and rejection of implants. Moreover, hydrogels can be loaded with biologically active compounds. In this field, hyaluronic acid has been largely studied as an additional component since this polysaccharide is naturally present in extracellular matrix. Strategies to direct hydrogelation processes exclusively from the surface using a fully biocompatible approach are rare. Herein we have applied the concept of localized enzyme-assisted self-assembly to direct supramolecular hydrogels in the presence of HA. Based on electronic and fluorescent confocal microscopy, rheological measurements and cell culture investigations, this work highlights the following aspects: (i) the possibility to control the thickness of peptide-based hydrogels at the micrometer scale (18–41 µm) through the proportion of HA (2, 5 or 10 mg/mL); (ii) the structure of the self-assembled peptide nanofibrous network is affected by the growing amount of HA which induces the collapse of nanofibers leading to large assembled microstructures underpinning the supramolecular hydrogel matrix; (iii) this changing internal architecture induces a decrease of the elastic modulus from 2 to 0.2 kPa when concentration of HA is increasing; (iv) concomitantly, the presence of HA in supramolecular hydrogel coatings is suitable for cell viability and adhesion of NIH 3T3 fibroblasts.

Biological functions of supramolecular assemblies of small molecules in cellular environment

Like biomacromolecules, certain small molecules (e.g., aggregators) are able to self-assemble in aqueous phase to form nanoscale aggregates. Though it is well-established that the aggregates may interact with enzymes in vitro, the study of the biological activities of the assemblies of small molecules in cellular environment is only at its beginning. This review summarizes the recent progresses in exploring the biological functions of supramolecular assemblies of small molecules (SASMs). We first discuss the use of SASMs to inhibit pathogenic cells, such as cancer cells and bacteria. The use of SASMs to target different parts of cancer cells, such as pericellular space, cytosol, and subcellular organelles, and to combine with other bioactive entities (e.g., proteins and clinically used drugs), is particularly promising for addressing the challenge of acquired multidrug resistance in cancer therapy. Then, we describe the use of SASMs to sustain physiological functions of normal cells, that is, promoting cells proliferation and differentiation for tissue regeneration. After that, we show the use of SASMs as a basic tool to research cell behaviors, for instance, identifying the specific cells, improving enzyme probes, revealing membrane dynamics, enhancing molecular imaging, and mimicking context-dependent signaling. Finally, we give the outlook of the research of SASMs. We expect that this review, by highlighting the biological functions of SASMs, provides a starting point to explore the chemical biology of SASMs.

Reciprocal Coupling in Chemically Fueled Assembly: A Reaction Cycle Regulates Self-Assembly and Vice Versa

In biology, self-assembly of proteins and energy-consuming reaction cycles are intricately coupled. For example, tubulin is activated and deactivated for assembly by a guanosine triphosphate (GTP)-driven reaction cycle, and the emerging microtubules catalyze this reaction cycle by changing the microenvironment of the activated tubulin. Recently, synthetic analogs of chemically fueled assemblies have emerged, but examples in which assembly and reaction cycles are reciprocally coupled remain rare. In this work, we report a peptide that can be activated and deactivated for self-assembly. The emerging assemblies change the microenvironment of their building blocks, which consequently accelerate the rates of building block deactivation and reactivation. We quantitatively understand the mechanisms at play, and we are thus able to tune the catalysis by molecular design of the peptide precursor.

Complex Cascade Reaction Networks via Cross β Amyloid Nanotubes

Biocatalytic reaction networks integrate complex cascade transformations via spatial localization of multiple enzymes confined within the cellular milieu. Inspired by nature's ingenuity, we demonstrate that short peptide-based cross-β amyloid nanotubular hybrids can promote different kinds of cascade reactions, from simple two-step, to multistep, to complex convergent cascades. The compartmentalizing ability of paracrystalline cross-β phases was utilized to colocalize sarcosine oxidase (SOX) and hemin as an artificial peroxidase. Further, the catalytic potential of the amyloid nanotubes with ordered arrays of imidazoles were used as hydrolase mimic. The SOX-hemin amyloid nanohybrids featuring a single extant enzyme could integrate different logic networks to access complex digital designs with the help of three concatenated AND gates and biologically relevant stimuli as inputs.