Nucleation and Growth of Amino Acid and Peptide Supramolecular Polymers through Liquid–Liquid Phase Separation

From Fundamental Amyloid Protein Self-Assembly to Development of Bioplastics

Proteins can self-assemble into a range of nanostructures as a result of molecular interactions. Amyloid nanofibrils, as one of them, were first discovered with regard to the relevance of neurodegenerative diseases but now have been exploited as building blocks to generate multiscale materials with designed functions for versatile applications. This review interconnects the mechanism of amyloid fibrillation, the current approaches to synthesizing amyloid protein-based materials, and the application in bioplastic development. We focus on the fundamental structures of self-assembled amyloid fibrils and how external factors can affect protein aggregation to optimize the process. Protein self-assembly is essentially the autonomous congregation of smaller protein units into larger, organized structures. Since the properties of the self-assembly can be manipulated by changing intrinsic factors and external conditions, protein self-assembly serves as an excellent building block for bioplastic development. Building on these principles, general processing methods and pathways from raw protein sources to mature state materials are proposed, providing a guide for the development of large-scale production. Additionally, this review discusses the diverse properties of protein-based amyloid nanofibrils and how they can be utilized as bioplastics. The economic feasibility of the protein bioplastics is also compared to conventional plastics in large-scale production scenarios, supporting their potential as sustainable bioplastics for future applications.

Side-Chain Chemistry Governs Hierarchical Order of Charge-Complementary β-sheet Peptide Coassemblies

Self-assembly of proteinaceous biomolecules into functional materials with ordered structures that span length scales is common in nature yet remains a challenge with designer peptides under ambient conditions. This report demonstrates how charged side-chain chemistry affects the hierarchical co-assembly of a family of charge-complementary β-sheet-forming peptide pairs known as CATCH(X+/Y-) at physiologic pH and ionic strength in water. In a concentration-dependent manner, the CATCH(6K+) (Ac-KQKFKFKFKQK-Am) and CATCH(6D-) (Ac-DQDFDFDFDQD-Am) pair formed either β-sheet-rich microspheres or β-sheet-rich gels with a micron-scale plate-like morphology, which were not observed with other CATCH(X+/Y-) pairs. This hierarchical order was disrupted by replacing D with E, which increased fibril twisting. Replacing K with R, or mutating the N- and C-terminal amino acids in CATCH(6K+) and CATCH(6D-) to Qs, increased observed co-assembly kinetics, which also disrupted hierarchical order. Due to the ambient assembly conditions, active CATCH(6K+)-green fluorescent protein fusions could be incorporated into the β-sheet plates and microspheres formed by the CATCH(6K+/6D-) pair, demonstrating the potential to endow functionality.

Emergent properties of melanin-inspired peptide/RNA condensates

Most biocatalytic processes in eukaryotic cells are regulated by subcellular microenvironments such as membrane-bound or membraneless organelles. These natural compartmentalization systems have inspired the design of synthetic compartments composed of a variety of building blocks. Recently, the emerging field of liquid-liquid phase separation has facilitated the design of biomolecular condensates composed of proteins and nucleic acids, with controllable properties including polarity, diffusivity, surface tension, and encapsulation efficiency. However, utilizing phase-separated condensates as optical sensors has not yet been attempted. Here, we were inspired by the biosynthesis of melanin pigments, a key biocatalytic process that is regulated by compartmentalization in organelles, to design minimalistic biomolecular condensates with emergent optical properties. Melanins are ubiquitous pigment materials with a range of functionalities including photoprotection, coloration, and free radical scavenging activity. Their biosynthesis in the confined melanosomes involves oxidation-polymerization of tyrosine (Tyr), catalyzed by the enzyme tyrosinase. We have now developed condensates that are formed by an interaction between a Tyr-containing peptide and RNA and can serve as both microreactors and substrates for tyrosinase. Importantly, partitioning of Tyr into the condensates and subsequent oxidation-polymerization gives rise to unique optical properties including far-red fluorescence. We now demonstrate that individual condensates can serve as sensors to detect tyrosinase activity, with a limit of detection similar to that of synthetic fluorescent probes. This approach opens opportunities to utilize designer biomolecular condensates as diagnostic tools for various disorders involving abnormal enzymatic activity.

The interface of condensates of the hnRNPA1 low-complexity domain promotes formation of amyloid fibrils

The maturation of liquid-like protein condensates into amyloid fibrils has been associated with several neurodegenerative diseases. However, the molecular mechanisms underlying this liquid-to-solid transition have remained largely unclear. Here we analyse the amyloid formation mediated by condensation of the low-complexity domain of hnRNPA1, a protein involved in amyotrophic lateral sclerosis. We show that phase separation and fibrillization are connected but distinct processes that are modulated by different regions of the protein sequence. By monitoring the spatial and temporal evolution of amyloid formation we demonstrate that the formation of fibrils does not occur homogeneously inside the droplets but is promoted at the interface of the condensates. We further show that coating the interface of the droplets with surfactant molecules inhibits fibril formation. Our results reveal that the interface of biomolecular condensates of hnRNPA1 promotes fibril formation, therefore suggesting interfaces as a potential novel therapeutic target against the formation of aberrant amyloids mediated by condensation.

Designing ECM-inspired supramolecular scaffolds by utilizing the interactions between a minimalistic neuroactive peptide and heparin

Short bioactive peptide-based supramolecular hydrogels are emerging as interesting candidates for developing scaffolds for tissue engineering applications. However, proteins and peptides represent only a single class of molecules present in the native ECM, thus, recapitulating the complete ECM microenvironment via only peptide-based biomaterials is extremely challenging. In this direction, complex multicomponent-based biomaterials have started gaining importance for achieving the biofunctional complexity and structural hierarchy of the native ECM. Sugar-peptide complexes can be explored in this direction as they provide essential biological signaling required for cellular growth and survival in vivo. In this direction, we explored the fabrication of an advanced scaffold by employing heparin and short bioactive peptide interactions at the molecular level. Interestingly, the addition of heparin into the peptide has significantly modulated the supramolecular organization, nanofibrous morphology and the mechanical properties of the scaffold. Additionally, the combined hydrogels demonstrated superior biocompatibility as compared to the peptide counterpart at certain ratios. These newly developed scaffolds were also observed to be stable under 3-D cell culture conditions and supported cellular adhesion and proliferation. Most importantly, the inflammatory response was also minimized in the case of combined hydrogels as compared to heparin. We expect that this approach of using simple non-covalent interactions between the ECM-inspired small molecules to fabricate biomaterials with improved mechanical and biological properties could advance the current knowledge on designing ECM mimetic biomaterials. Such an attempt would create a novel, adaptable and simplistic bottom-up strategy for the invention of new and more complex biomaterials of ECM origin with advanced functions.

Fmoc-diphenylalanine gelating nanoarchitectonics: A simplistic peptide self-assembly to meet complex applications

9-fluorenylmethoxycarbonyl-diphenylalanine (Fmoc-FF), has been has been extensively explored due to its ultrafast self-assembly kinetics, inherent biocompatibility, tunable physicochemical properties, and especially, the capability of forming self-sustained gels under physiological conditions. Consequently, various methodologies to develop Fmoc-FF gels and their corresponding applications in biomedical and industrial fields have been extensively studied. Herein, we systemically summarize the mechanisms underlying Fmoc-FF self-assembly, discuss the preparation methodologies of Fmoc-FF hydrogels, and then deliberate the properties as well as the diverse applications of Fmoc-FF self-assemblies. Finally, the contemporary shortcomings which limit the development of Fmoc-FF self-assembly are raised and the alternative solutions are proposed, along with future research perspectives.

LLPS vs. LLCPS: analogies and differences

We compare the process of Liquid-Liquid Phase Separation (LLPS) of flexible macromolecular solutions, with the Liquid-Liquid Crystalline Phase Separation (LLCPS) of semiflexible polymers and rigid filamentous colloids, which involves the formation of a liquid phase that possesses a directional alignment. Although the observed phase separation follows a similar dynamic path, namely nucleation and growth or spinodal decomposition separating two phases of dilute and concentrated compositions, the underlying physics that defines the theoretical framework of LLCPS is completely different from the one of LLPS. We review the main theories that describe the phase separation processes and relying on thermodynamics and dynamical arguments, we highlight the differences and analogies between these two phase separation phenomena, attempting to clarify the inner mechanisms that regulate those two processes. A particular focus is given to metastable phases, as these intermediate states represent a key element in understanding how phase separation works.

Revealing the Formation Mechanism and Optimizing the Synthesis Conditions of Layered Double Hydroxides for the Oxygen Evolution Reaction

Layered double hydroxides (LDHs), whose formation is strongly related to OH^- concentration, have attracted significant interest in various fields. However, the effect of the real-time change of OH^- concentration on LDHs' formation has not been fully explored due to the unsuitability of the existing synthesis methods for in situ characterization. Here, the deliberately designed combination of NH₃ gas diffusion and in situ pH measurement provides a solution to the above problem. The obtained results revealed the formation mechanism and also guided us to synthesize a library of LDHs with the desired attributes in water at room temperature without using any additives. After evaluating their oxygen evolution reaction performance, we found that FeNi-LDH with a Fe/Ni ratio of 25/75 exhibits one of the best performances so far reported.

Silver-Nanoparticle-Embedded Short Amphiphilic Peptide Nanostructures and Their Plausible Application to Reduce Bacterial Infections

The microbiota-gut-brain axis (GBA) plays a critical role in the development of neurodegenerative diseases. Dysbiosis of the intestinal microbiome causes a significant alteration in the gut microbiota of Alzheimer's disease (AD) patients, followed by neuroinflammatory processes. Thus, AD beginning in the gut is closely related to an imbalance in gut microbiota, and hence a multidomain approach to reduce this imbalance by exerting positive effects on the gut microbiota is needed. In one example, a tyrosine-based short peptide amphiphile (sPA) was used to synthesize antibacterial AgNPs-sPA nanostructures. Such nanostructures showed high biocompatibility and low cytotoxicity, and therefore work as model drug delivery agents for addressing local bacterial infections. These may have therapeutic value for the treatment of microbiota-triggered progression of neurodegenerative diseases.

Biomolecular condensates formed by designer minimalistic peptides

Inspired by the role of intracellular liquid-liquid phase separation (LLPS) in formation of membraneless organelles, there is great interest in developing dynamic compartments formed by LLPS of intrinsically disordered proteins (IDPs) or short peptides. However, the molecular mechanisms underlying the formation of biomolecular condensates have not been fully elucidated, rendering on-demand design of synthetic condensates with tailored physico-chemical functionalities a significant challenge. To address this need, here we design a library of LLPS-promoting peptide building blocks composed of various assembly domains. We show that the LLPS propensity, dynamics, and encapsulation efficiency of compartments can be tuned by changes to the peptide composition. Specifically, with the aid of Raman and NMR spectroscopy, we show that interactions between arginine and aromatic amino acids underlie droplet formation, and that both intra- and intermolecular interactions dictate droplet dynamics. The resulting sequence-structure-function correlation could support the future development of compartments for a variety of applications.

Modulating Nanodroplet Formation En Route to Fibrillization of Amyloid Peptides with Designed Flanking Sequences

Soluble oligomers populating early amyloid aggregation can be regarded as nanodroplets of liquid-liquid phase separation (LLPS). Amyloid peptides typically contain hydrophobic aggregation-prone regions connected by hydrophilic linkers and flanking sequences, and such a sequence hydropathy pattern drives the formation of supramolecular structures in the nanodroplets and modulates subsequent fibrillization. Here, we studied LLPS and fibrillization of coarse-grained amyloid peptides with increasing flanking sequences. Nanodroplets assumed lamellar, cylindrical micellar, and spherical micellar structures with increasing peptide hydrophilic/hydrophobic ratios, and such morphologies governed subsequent fibrillization processes. Adding glycine-serine repeats as flanking sequences to Aβ16-22, the amyloidogenic core of amyloid-β, our computational predictions of morphological transitions were corroborated experimentally. The uncovered inter-relationships between the peptide sequence pattern, oligomer/nanodroplet morphology, and fibrillization pathway, kinetics, and structure may contribute to our understanding of pathogenic amyloidosis in aging, facilitate future efforts ameliorating amyloidosis through peptide engineering, and aid in the design of novel amyloid-based functional nanobiomaterials and nanocomposites.

Self-assembly and Hydrogelation Properties of Peptides Derived from Peptic Cleavage of Aggregation-prone Regions of Ovalbumin

Egg white protein hydrolysate generated with pepsin was investigated for the presence of peptides with self-assembly and hydrogelation properties. Incubation of the hydrolysates for 16 h resulted in aggregates with significantly (p < 0.05) lower free amino nitrogen and sulfhydryl contents, and higher particle diameter and surface hydrophobicity compared to the hydrolysates. LC-MS/MS analysis of the aggregates resulted in identification of 429 ovalbumin-derived peptides, among which the top-six aggregation-prone peptides IFYCPIAIM, NIFYCPIAIM, VLVNAIVFKGL, YCPIAIMSA, MMYQIGLF, and VYSFSLASRL were predicted using AGGRESCAN by analysis of the aggregation “Hot Spots”. NIFYCPIAIM had the highest thioflavin T fluorescence intensity, particle diameter (5611.3 nm), and polydispersity index (1.0) after 24 h, suggesting the formation of β-sheet structures with heterogeneous particle size distribution. Transmission electron microscopy of MMYQIGLF, and VYSFSLASRL demonstrated the most favorable peptide self-assembly, based on the formation of densely packed, intertwined fibrils. Rheological studies confirmed the viscoelastic and mechanical properties of the hydrogels, with IFYCPIAIM, NIFYCPIAIM, VLVNAIVFKGL, and VYSFSLASRL forming elastic solid hydrogels (tan δ < 1), while YCPIAIMSA and MMYQIGLF formed viscous liquid-like hydrogels (tan δ > 1). The results provide valuable insight into the influence of peptide sequence on hydrogelation and self-assembly progression, and prospects of food peptides in biomaterial applications.

Protein conformation and biomolecular condensates

Protein conformation and cell compartmentalization are fundamental concepts and subjects of vast scientific endeavors. In the last two decades, we have witnessed exciting advances that unveiled the conjunction of these concepts. An avalanche of studies highlighted the central role of biomolecular condensates in membraneless subcellular compartmentalization that permits the spatiotemporal organization and regulation of myriads of simultaneous biochemical reactions and macromolecular interactions. These studies have also shown that biomolecular condensation, driven by multivalent intermolecular interactions, is mediated by order-disorder transitions of protein conformation and by protein domain architecture. Conceptually, protein condensation is a distinct level in protein conformational landscape in which collective folding of large collections of molecules takes place. Biomolecular condensates arise by the physical process of phase separation and comprise a variety of bodies ranging from membraneless organelles to liquid condensates to solid-like conglomerates, spanning lengths from mesoscopic clusters (nanometers) to micrometer-sized objects. In this review, we summarize and discuss recent work on the assembly, composition, conformation, material properties, thermodynamics, regulation, and functions of these bodies. We also review the conceptual framework for future studies on the conformational dynamics of condensed proteins in the regulation of cellular processes.

A study of bioactive glass-ceramic's mechanical properties, apatite formation, and medical applications

Apparently, bioactive glass-ceramics are made by doing a number of steps, such as creating a microstructure from dispersed crystals within the residual glass, which provides high bending strength, and apatite crystallizes on surfaces of glass-ceramics when calcium ions are present in the blood. Apatite crystals grow on the glass and ceramic surfaces due to the hydrated silica. These materials are biocompatible with living bone in a matter of weeks, don't weaken mechanically or histologically, and exhibit good osteointegration as well as mechanical properties that are therapeutically relevant, such as fracture toughness and flexural strength. As part of this study, we examined mechanical properties, process mechanisms involved in apatite formation, and potential applications for bioactive glass-ceramic in orthopedic surgery, including load-bearing devices.

Temporal Stimulus Patterns Drive Differentiation of a Synthetic Dipeptide-Based Coacervate

The fate of living cells often depends on their processing of temporally modulated information, such as the frequency and duration of various signals. Synthetic stimulus-responsive systems have been intensely studied for >50 years, but it is still challenging for chemists to create artificial systems that can decode dynamically oscillating stimuli and alter the systems' properties/functions because of the lack of sophisticated reaction networks that are comparable with biological signal transduction. Here, we report morphological differentiation of synthetic dipeptide-based coacervates in response to temporally distinct patterns of the light pulse. We designed a simple cationic diphenylalanine peptide derivative to enable the formation of coacervates. The coacervates concentrated an anionic methacrylate monomer and a photoinitiator, which provided a unique reaction environment and facilitated light-triggered radical polymerization─even in air. Pulsed light irradiation at 9.0 Hz (but not at 0.5 Hz) afforded anionic polymers. This dependence on the light pulse patterns is attributable to the competition of reactive radical intermediates between the methacrylate monomer and molecular oxygen. The temporal pulse pattern-dependent polymer formation enabled the coacervates to differentiate in terms of morphology and internal viscosity, with an ultrasensitive switch-like mode. Our achievements will facilitate the rational design of smart supramolecular soft materials and are insightful regarding the synthesis of sophisticated chemical cells.

Recent Advances in Microgels: From Biomolecules to Functionality

The emerging applications of hydrogel materials at different length scales, in areas ranging from sustainability to health, have driven the progress in the design and manufacturing of microgels. Microgels can provide miniaturized, monodisperse, and regulatable compartments, which can be spatially separated or interconnected. These microscopic materials provide novel opportunities for generating biomimetic cell culture environments and are thus key to the advances of modern biomedical research. The evolution of the physical and chemical properties has, furthermore, highlighted the potentials of microgels in the context of materials science and bioengineering. This review describes the recent research progress in the fabrication, characterization, and applications of microgels generated from biomolecular building blocks. A key enabling technology allowing the tailoring of the properties of microgels is their synthesis through microfluidic technologies, and this paper highlights recent advances in these areas and their impact on expanding the physicochemical parameter space accessible using microgels. This review finally discusses the emerging roles that microgels play in liquid-liquid phase separation, micromechanics, biosensors, and regenerative medicine.

Manipulating Reaction Intermediates to Aqueous-Phase ZnSe Magic-Size Clusters and Quantum Dots at Room Temperature

It is not resolved which model describes better the aqueous-phase nucleation and growth of semiconductor quantum dots (QDs), the classical one-step one or the nonclassical multi-step one. Here, we design a room-temperature reaction to trap reaction intermediates in the prenucleation stage of ZnSe QDs (as a model system). We show that the trapped intermediate can transform to magic-size clusters (MSCs) via intra-molecular reorganization and can fragment to enable the growth of QDs. The MSCs exhibit a sharp optical absorption peaking at 299 nm, labelled MSC-299. The intermediate, the precursor compound (PC-299) of MSC-299, is optically transparent at 299 nm and to longer wavelengths. This intermediate forms in various Zn and Se reaction systems. The present study provides unambiguous evidence that the nonclassical and classical pathways are both necessary to explain the nucleation and growth of aqueous-phase QDs, with the former pathway favored more by high reaction concentrations.

Amyloid-β Inspired Short Peptide Amphiphile Facilitates Synthesis of Silver Nanoparticles as Potential Antibacterial Agents

An amyloid-β inspired biocompatible short peptide amphiphile (sPA) molecule was used for controlled and targeted delivery of bioactive silver nanoparticles via transforming sPA nanostructures. Such sPA-AgNPs hybrid structures can be further used to develop antibacterial materials to combat emerging bacterial resistance. Due to the excellent antibacterial activity of silver, the growth of clinically relevant bacteria was inhibited in the presence of AgNPs-sPA hybrids. Bacterial tests demonstrated that the high biocompatibility and low cytotoxicity of the designed sPA allow it to work as a model drug delivery agent. It therefore shows great potential in locally addressing bacterial infections. The results of our study suggest that these nanodevices have the potential to trap and then engage in the facile delivery of their chemical payload at the target site, thereby working as potential delivery materials. This system has potential therapeutic value for the treatment of microbiota triggered progression of neurodegenerative diseases.

2D Polymer Nanonets: Controllable Constructions and Functional Applications

Two-dimensional (2D) polymer nanonets have demonstrated great potential in various application fields due to their integrated advantages of ultrafine diameter, small pore size, high porosity, excellent interconnectivity, and large specific surface area. Here, a comprehensive overview of the controlled constructions of the polymer nanonets derived from electrospinning/netting, direct electronetting, self-assembly of cellulose nanofibers, and nonsolvent-induced phase separation is provided. Then, the widely researched multifunctional applications of polymer nanonets in filtration, sensor, tissue engineering, and electricity are also given. Finally, the challenges and possible directions for further developing the polymer nanonets are also intensively highlighted. This article is protected by copyright. All rights reserved.

Exploring the TEMPO-Oxidized Nanofibrillar Cellulose and Short Ionic-Complementary Peptide Composite Hydrogel as Biofunctional Cellular Scaffolds

Multicomponent self-assembly is an emerging approach in peptide nanotechnology to develop nanomaterials with superior physical and biological properties. Inspired by the multicomponent nature of the native extracellular matrix (ECM) and the well-established advantages of co-assembly in the field of nanotechnology, we have attempted to explore the noncovalent interactions among the sugar and peptide-based biomolecular building blocks as an approach to design and develop advanced tissue scaffolds. We utilized TEMPO-oxidized nanofibrillar cellulose (TO-NFC) and a short ionic complementary peptide, Nap-FEFK, to fabricate highly tunable supramolecular hydrogels. The differential doping of the peptide into the TO-NFC hydrogel was observed to tune the surface hydrophobicity, microporosity, and mechanical stiffness of the scaffold. Interestingly, a differential cellular response was observed toward composite scaffolds with a variable ratio of TO-NFC versus Nap-FEFK. Composite scaffolds having a 10:1 (w/w) ratio of TO-NFC and the Nap-FEFK peptide showed enhanced cellular survival and proliferation under two-dimensional cell culture conditions. More interestingly, the cellular proliferation on the 10:1 matrix was found to be similar to that of Matrigel in three-dimensional culture conditions, which clearly indicated the potential of these hydrogels in advanced tissue engineering applications. Additionally, these composite hydrogels did not elicit any significant inflammatory response in Raw cells and supported their survival and proliferation, which further emphasized their ability to form versatile scaffolds for tissue regeneration. This multicomponent assembly approach to construct biomolecular composite hydrogels to access superior physical and biological properties within the scaffold is expected to improve the scope for designing novel ECM-mimicking biomaterials for regenerative medicine.

Designing Self-Assembling Chimeric Peptide Nanoparticles with High Stability for Combating Piglet Bacterial Infections

As a novel type of antibiotic alternative, peptide-based antibacterial drug shows potential application prospects attributable to their unique mechanism for lysing the membrane of pathogenic bacteria. However, peptide-based antibacterial drugs suffer from a series of problems, most notably their immature stability, which seriously hinders their application. In this study, self-assembling chimeric peptide nanoparticles (which offer excellent stability in the presence of proteases and salts) are constructed and applied to the treatment of bacterial infections. In vitro studies are used to demonstrate that peptide nanoparticles NPs1 and NPs2 offer broad-spectrum antibacterial activity and desirable biocompatibility, and they retain their antibacterial ability in physiological salt environments. Peptide nanoparticles NPs1 and NPs2 can resist degradation under high concentrations of proteases. In vivo studies illustrate that the toxicity caused by peptide nanoparticles NPs1 and NPs2 is negligible, and these nanoparticles can alleviate systemic bacterial infections in mice and piglets. The membrane permeation mechanism and interference with the cell cycle differ from that of antibiotics and mean that the nanoparticles are at a lower risk of inducing drug resistance. Collectively, these advances may accelerate the development of peptide-based antibacterial nanomaterials and can be applied to the construction of supramolecular nanomaterials.

Deep Downregulation of PD-L1 by Caged Peptide-Conjugated AIEgen/miR-140 Nanoparticles for Enhanced Immunotherapy

Downregulating programmed cell death ligand 1(PD-L1) protein levels in tumor cells is an effective way to achieve immune system activation for oncology treatment, but current strategies are inadequate. Here, we design a caged peptide-AIEgen probe (GCP) to self-assemble with miR-140 forming GCP/miR-140 nanoparticles. After entering tumor cells, GCP/miR-140 disassembles in the presence of Cathepsin B (CB) and releases caged GO203 peptide, miR-140 and PyTPA. Peptide decages in the highly reductive intracellular environment and binds to mucin 1 (MUC1), thereby downregulating the expression of PD-L1. Meanwhile, miR-140 reduces PD-L1 expression by targeting downregulation of PD-L1 mRNA. Under the action of PyTPA-mediated photodynamic therapy (PDT), tumor-associated antigens are released, triggering immune cell attack on tumor cells. This multiple mechanism-based strategy of deeply downregulating PD-L1 in tumor cells activates the immune system and thus achieves effective immunotherapy.

Co-Assembly Induced Solid-State Stacking Transformation in Amino Acid-Based Crystals with Enhanced Physical Properties

The physical characteristics of supramolecular assemblies composed of small building blocks are dictated by molecular packing patterns in the solid-state. Yet, the structure-property correlation is still not fully understood. Herein, we report the unexpected cofacial to herringbone stacking transformation of a small aromatic bipyridine through co-assembly with acetylated glutamic acid. The unique solid-state structural transformation results in enhanced physical properties of the supramolecular organizations. The co-assembly methodology was further expanded to obtain diverse molecular packings by different bipyridine and acetylated amino acid derivatives. This study presents a feasible co-assembly approach to achieve the solid-state stacking transformation of supramolecular organization and opens up new opportunities to further explore the relationship between molecular arrangement and properties of supramolecular assemblies by crystal engineering.

Nucleobase Clustering Contributes to the Formation and Hollowing of Repeat-Expansion RNA Condensate

RNA molecules with repeat expansion sequences can phase separate into gel-like condensate, which could lead to neurodegenerative diseases. Here, we report that, in the presence of Mg²⁺, RNA molecules containing 20× CAG repeats self-assemble into three morphologically distinct droplets. Using hyperspectral stimulated Raman microscopy, we show that RNA phase separation is accompanied by the clustering of nucleobases while forfeiting the canonical base-paired structure. As the RNA/Mg²⁺ ratio increases, the RNA droplets first expand and then shrink to adopt hollow vesicle-like structures. Significantly, for both large and vesicle-like RNA droplets, the nucleobase-clustered structure is more prominent at the rim, suggesting a continuously hardening process. This mechanism may be implicated in the general aging processes of RNA-containing membrane-less organelles.

Rippled Sheets: The Early Polyglycine Days and Recent Developments in Nylons

The rippled sheet structure is a remarkable insight due to Pauling and Corey, that supplements the pleated sheet structure of homochiral proteins introduced in 1951. Whereas the pleated sheet was immediately adopted by the scientific community, the rippled sheet has remained more confidential since it applies only to blends of poly(L-peptides) and poly(D-peptides). The present account tells the intimate but patchy relationship developed by the author with the rippled sheet. In the 1970s, twenty years after Pauling and Corey's proposal, the rippled sheet was recognized as a valid model for the sheet structure of the achiral polyglycine, polyglycine I, which helped improve the structure of Bombyx mori silk fibroin. Very recently, pleated and rippled sheets were found to account for unsolved crystal structures of a variety of nylons. These structures help to explain a mysterious high temperature "Brill transition" first reported in nylon 6-6 by Brill in 1942.

An atomistic view of rigid crystalline supramolecular polymers derived from short amphiphilic, α,β hybrid peptide

The spontaneous self-association of an amphiphilic α, β-hybrid peptide into supramolecular fibers and atomic details of the fibrillar assembly are reported.

A bioinspired stimuli-responsive amino acid-based antibacterial drug delivery system in cancer therapy

Design of tyrosine based stimuli responsive antibacterial drug delivery system with potential application in cancer therapy.

Chemical Perspective of the Mechanism of Action of Antiamyloidogenic Compounds Using a Minimalistic Peptide as a Reductionist Model

The diphenylalanine (FF) residue which is present at the 19 and 20 positions of the amyloid beta (1-42) (Aβ42) peptide sequence is considered as a reductionist model for studying Aβ42 aggregation. FF self-assembles into well-ordered tubular structures via aromatic π-π stacking. Herein the manuscript, we have presented a chemical perspective on the mechanism of action of antiamyloid compounds by assessing their interaction with FF. Therefore, we first coincubated FF fibers with single amino acids, since they are constituted of different R side chains yet have a common structural unit. This study revealed a crucial role of aromatic rings and functional groups like thiol (-SH) in causing destabilization of FF assembly via their interaction with π-electrons participating in π-π stacking present in FF. We further studied the interaction of different nonsteroidal anti-inflammatory drugs (NSAIDs), other known antiamyloidogenic compounds, and host-guest inclusion compounds like cyclodextrin (CD) to assess their mechanism of action and to decipher the functional moiety present in these compounds which could cause destabilization of π-π stacking. From the coincubation experiments, we could surmise a crucial role of aromatic rings present in these compounds for causing interference in aromatic stacking. We further consolidated our observations through microscopy analysis by various spectroscopic methods such as aggregation-induced emission enhancement (AIEE), fluorescence spectroscopy, solution-state ¹H NMR, FTIR, and circular dichroism. The studies presented in the manuscript thus provide significant insights into the role of functional groups in imparting antiamyloid action and open new avenues for an efficient design of antiamyloid drugs in the future.

Liquid-Liquid Phase-Separated Systems from Reversible Gel-Sol Transition of Protein Microgels

Liquid-liquid phase-separated biomolecular systems are increasingly recognized as key components in the intracellular milieu where they provide spatial organization to the cytoplasm and the nucleoplasm. The widespread use of phase-separated systems by nature has given rise to the inspiration of engineering such functional systems in the laboratory. In particular, reversible gelation of liquid-liquid phase-separated systems could confer functional advantages to the generation of new soft materials. Such gelation processes of biomolecular condensates have been extensively studied due to their links with disease. However, the inverse process, the gel-sol transition, has been less explored. Here, a thermoresponsive gel-sol transition of an extracellular protein in microgel form is explored, resulting in an all-aqueous liquid-liquid phase-separated system with high homogeneity. During this gel-sol transition, elongated gelatin microgels are demonstrated to be converted to a spherical geometry due to interfacial tension becoming the dominant energetic contribution as elasticity diminishes. The phase-separated system is further explored with respect to the diffusion of small particles for drug-release scenarios. Together, this all-aqueous system opens up a route toward size-tunable and monodisperse synthetic biomolecular condensates and controlled liquid-liquid interfaces, offering possibilities for applications in bioengineering and biomedicine.

Supramolecular Nanodrugs Based on Covalent Assembly of Therapeutic Peptides toward In Vitro Synergistic Anticancer Therapy

Therapeutic peptides have attracted significant attention in clinical applications due to their advantages in biological origination and good biocompatibility. However, the therapeutic performance of peptides is usually hindered by their short half-lives in blood and inferior activity. Herein, supramolecular nanodrugs of therapeutic peptides are constructed by covalent assembly of chemotherapeutic peptides through genipin cross-linking. The resulting nanodrugs have intense absorbance in the near-infrared region and high photothermal conversion efficiencies, leading to the possibility of photothermal therapy. The combination of photothermal therapy and chemotherapy using the nanodrugs shows synergistic therapeutic effects on cancer cells. Hence, covalent assembly not only maintains the chemotherapeutic activities of the peptides but also triggers supramolecular photothermal effects, demonstrating that the covalent assembly of therapeutic peptides through genipin cross-linking is an efficient approach in constructing supramolecular nanodrugs toward synergistic anticancer therapy.

From Protein Building Blocks to Functional Materials

Proteins are the fundamental building blocks for high-performance materials in nature. Such materials fulfill structural roles, as in the case of silk and collagen, and can generate active structures including the cytoskeleton. Attention is increasingly turning to this versatile class of molecules for the synthesis of next-generation green functional materials for a range of applications. Protein nanofibrils are a fundamental supramolecular unit from which many macroscopic protein materials are formed. In this Review, we focus on the multiscale assembly of such protein nanofibrils formed from naturally occurring proteins into new supramolecular architectures and discuss how they can form the basis of material systems ranging from bulk gels, films, fibers, micro/nanogels, condensates, and active materials. We review current and emerging approaches to process and assemble these building blocks in a manner which is different to their natural evolutionarily selected role but allows the generation of tailored functionality, with a focus on microfluidic approaches. We finally discuss opportunities and challenges for this class of materials, including applications that can be involved in this material system which consists of fully natural, biocompatible, and biodegradable feedstocks yet has the potential to generate materials with performance and versatility rivalling that of the best synthetic polymers.

Non-Equilibrium Large-Scale Membrane Transformations Driven by MinDE Biochemical Reaction Cycles

The MinDE proteins from E. coli have received great attention as a paradigmatic biological pattern-forming system. Recently, it has surfaced that these proteins do not only generate oscillating concentration gradients driven by ATP hydrolysis, but that they can reversibly deform giant vesicles. In order to explore the potential of Min proteins to actually perform mechanical work, we introduce a new model membrane system, flat vesicle stacks on top of a supported lipid bilayer. MinDE oscillations can repeatedly deform these flat vesicles into tubules and promote progressive membrane spreading through membrane adhesion. Dependent on membrane and buffer compositions, Min oscillations further induce robust bud formation. Altogether, we demonstrate that under specific conditions, MinDE self-organization can result in work performed on biomimetic systems and achieve a straightforward mechanochemical coupling between the MinDE biochemical reaction cycle and membrane transformation.

Occurrence of Peptide-Peptide Interactions during the Purification of Self-Assembling Peptide f1-8 from a β-Lactoglobulin Tryptic Hydrolysate

Self-assembling peptides have gained attention because of their nanotechnological applications. Previous work demonstrated that the self-assembling peptide f1-8 (Pf1-8) that is generated from the tryptic hydrolysis of β-lactoglobulin can form a hydrogel after several purification steps, including membrane filtration and consecutive washes. This study evaluates the impact of each processing step on peptide profile, purity, and gelation capacity of each fraction to understand the purification process of Pf1-8 and the peptide-peptide interactions involved. We showed that peptide-peptide interactions mainly occurred through electrostatic and hydrophobic interactions, influencing the fraction compositions. Indeed, the purity of Pf1-8 did not correlate with the number of wash steps. In addition to Pf1-8, two other hydrophobic peptides were identified, peptide f15-20, and peptide f41-60. The gelation observed could be induced either through peptide-peptide interactions or through self-assembling, both being driven by non-covalent bond and more specifically hydrophobic interactions.

Biomolecular condensates undergo a generic shear-mediated liquid-to-solid transition

Membrane-less organelles resulting from liquid-liquid phase separation of biopolymers into intracellular condensates control essential biological functions, including messenger RNA processing, cell signalling and embryogenesis1-4. It has recently been discovered that several such protein condensates can undergo a further irreversible phase transition, forming solid nanoscale aggregates associated with neurodegenerative disease5-7. While the irreversible gelation of protein condensates is generally related to malfunction and disease, one case where the liquid-to-solid transition of protein condensates is functional, however, is that of silk spinning8,9. The formation of silk fibrils is largely driven by shear, yet it is not known what factors control the pathological gelation of functional condensates. Here we demonstrate that four proteins and one peptide system, with no function associated with fibre formation, have a strong propensity to undergo a liquid-to-solid transition when exposed to even low levels of mechanical shear once present in their liquid-liquid phase separated form. Using microfluidics to control the application of shear, we generated fibres from single-protein condensates and characterized their structural and material properties as a function of shear stress. Our results reveal generic backbone-backbone hydrogen bonding constraints as a determining factor in governing this transition. These observations suggest that shear can play an important role in the irreversible liquid-to-solid transition of protein condensates, shed light on the role of physical factors in driving this transition in protein aggregation-related diseases and open a new route towards artificial shear responsive biomaterials.