Self-Assembly of an α-Helical Peptide into a Crystalline Two-Dimensional Nanoporous Framework

Exo-chirality of the α-helix

The structure of helical polymers is dictated by the molecular chirality of their monomer units. Particularly, macromolecular helices with monomer sequence control have the potential to generate chiral topologies. In α-helical folded peptides, the sequential repetition of amino acids generates a chiral layer defined by the amino acid side chains projected outside the amide backbone. Despite being closely related to peptides' structural and functional properties, to the best of our knowledge, a general exo-helical symmetry model has not been yet described for the α-helix. Here, we perform the theoretical, computational, and spectroscopic elucidation of the α-helix principal exo-helical topologies. Non-canonical labeled amino acids are employed to spectroscopically characterize the different exo-helical topologies in solution, which precisely match the theorical prediction. Backbone-to-chromophore distance also shows the expected impact in the exo-helices' geometry and spectroscopic fingerprint. Theoretical prediction and spectroscopic validation of this exo-helical topological model provides robust experimental evidence of the chiral potential on the surface of helical peptides and outlines an entirely new structural scenario for the α-helix.

Genetically Fusing Order-Promoting and Thermoresponsive Building Blocks to Design Hybrid Biomaterials

The unique biophysical and biochemical properties of intrinsically disordered proteins (IDPs) and their recombinant derivatives, intrinsically disordered protein polymers (IDPPs) offer opportunities for producing multistimuli-responsive materials; their sequence-encoded disorder and tendency for phase separation facilitate the development of multifunctional materials. This review highlights the strategies for enhancing the structural diversity of elastin-like polypeptides (ELPs) and resilin-like polypeptides (RLPs), and their self-assembled structures via genetic fusion to ordered motifs such as helical or beta sheet domains. In particular, this review describes approaches that harness the synergistic interplay between order-promoting and thermoresponsive building blocks to design hybrid biomaterials, resulting in well-structured, stimuli-responsive supramolecular materials ordered on the nanoscale.

Unnatural Peptide Assemblies Rapidly Deplete Cholesterol and Potently Inhibit Cancer Cells

Cholesterol-rich membranes play a pivotal role in cancer initiation and progression, necessitating innovative approaches to target these membranes for cancer inhibition. Here we report the first case of unnatural peptide (1) assemblies capable of depleting cholesterol and inhibiting cancer cells. Peptide 1 self-assembles into micelles and is rapidly taken up by cancer cells, especially when combined with an acute cholesterol-depleting agent (MβCD). Click chemistry has confirmed that 1 depletes cell membrane cholesterol. It localizes in membrane-rich organelles, including the endoplasmic reticulum, Golgi apparatus, and lysosomes. Furthermore, 1 potently inhibits malignant cancer cells, working synergistically with cholesterol-lowering agents. Control experiments have confirmed that C-terminal capping and unnatural amino acid residues (i.e., BiP) are essential for both cholesterol depletion and potent cancer cell inhibition. This work highlights unnatural peptide assemblies as a promising platform for targeting the cell membrane in controlling cell fates.

Pore Restructuring of Peptide Frameworks by Mutations at Distal Packing Residues

Porous framework materials are highly useful for catalysis, adsorption, and separations. Though they are usually made from inorganic and organic building blocks, recently, folded peptides have been utilized for constructing frameworks, opening up an enormous structure-space for exploration. These peptides assemble in a metal-free fashion using π-stacking, H-bonding, dispersion forces, and the hydrophobic effect. Manipulation of pore-defining H-bonding residues is known to generate new topologies, but the impact of mutations in the hydrophobic packing region facing away from the pores is less obvious. To explore their effects, we synthesized variants of peptide frameworks with mutations in the hydrophobic packing positions and found by single-crystal X-ray crystallography (SC-XRD) that they induce significant changes to the framework pore structure. These structural changes are driven by a need to maximize van der Waals interactions of the nonpolar groups, which are achieved by various mechanisms including helix twisting, chain flipping, chain offsetting, and desymmetrization. Even subtle changes to the van der Waals interface, such as the introduction of a methyl group or isomeric replacement, result in significant pore restructuring. This study shows that the dispersion interactions upholding a peptide material are a rich area for structural engineering.

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

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

Streamlined construction of robust heteroprotein complexes by self-induced in-cell disulfide pairing

Biomolecules and their functional subdomains are essential building blocks in the creation of multifunctional nanocomplexes. Methyl-binding domain protein 2 (MBD2) and p66α stand out as small α-helical motifs with an ability to self-assemble into a heterodimeric coiled-coil, making them promising building units. Yet, their practical use is hindered by rapid dissociation upon dilution. In this study, novel fusion tags, MBD2 and p66α variants, were developed to covalently link during co-expression in E. coli SHuffle. Through strategic placement of cysteine at each α-helix's terminus, intracellular crosslinking occurred with high specificity and yield, facilitated by preserved α-helical interactions. This instant disulfide bonding in the oxidative cytoplasm of E. coli SHuffle efficiently overcame the need for inefficient in vitro oxidation and protein extraction prone to creating non-specific adducts and suboptimal bioprocesses. In contrast to their wild-type counterparts, the GFP-mCherry protein complex cross-linked by the fusion tags maintained the heterodimeric state even under extensive dilution. The fusion tags, when combined with the E. coli SHuffle system, allowed for the streamlined co-expression of a stable protein complex through self-induced intracellular cysteine coupling. The approach demonstrated herein holds great promise for producing multifunctional and robust heteroprotein complexes.

Controlling the Assembly of Cellulose-Based Oligosaccharides through Sequence Modifications

Peptides and nucleic acids with programmable sequences are widely explored for the production of tunable, self-assembling functional materials. Herein we demonstrate that the primary sequence of oligosaccharides can be designed to access materials with tunable shapes and properties. Synthetic cellulose-based oligomers were assembled into 2D or 3D rod-like crystallites. Sequence modifications within the oligosaccharide core influenced the molecular packing and led to the formation of square-like assemblies based on the rare cellulose IVII allomorph. In contrast, modifications at the termini generated elongated aggregates with tunable surfaces, resulting in self-healing supramolecular hydrogels.

Hierarchical Assembly of Intrinsically Disordered Short Peptides

The understanding on how short peptide assemblies transit from disorder to order remains limited due to the lack of atomistic structures. Here we report cryo-EM structure of the nanofibers short intrinsically disordered peptides (IDPs). Upon lowering pH or adding calcium ions, the IDP transitions from individual nanoparticles to nanofibers containing an aromatic core and a disordered periphery comprised of 2 to 5 amino acids. Protonating the phosphate or adding more metal ions further assembles the nanofibers into filament bundles. The assemblies of the IDP analogs with controlled chemistry, such as phosphorylation site, hydrophobic interactions, and sequences indicate that metal ions interact with the flexible periphery of the nanoparticles of the IDPs to form fibrils and enhance the interfibrillar interactions to form filament bundles. Illustrating that an IDP self-assembles from disorder to order, this work offers atomistic molecular insights to understand assemblies of short peptides driven by noncovalent interactions.

A class of peptides designed to replicate and enhance the Receptor for Hyaluronic Acid Mediated Motility binding domain

The extra-cellular matrix (ECM) is a complex and rich microenvironment that is exposed and over-expressed across several injury or disease pathologies. Biomaterial therapeutics are often enriched with peptide binders to target the ECM with greater specificity. Hyaluronic acid (HA) is a major component of the ECM, yet to date, few HA adherent peptides have been discovered. A class of HA binding peptides was designed using B(X₇)B hyaluronic acid binding domains inspired from the helical face of the Receptor for Hyaluronic Acid Mediated Motility (RHAMM). These peptides were bioengineered using a custom alpha helical net method, allowing for the enrichment of multiple B(X₇)B domains and the optimisation of contiguous and non-contiguous domain orientations. Unexpectedly, the molecules also exhibited the behaviour of nanofiber forming self-assembling peptides and were investigated for this characteristic. Ten 23-27 amino acid residue peptides were assessed. Simple molecular modelling was used to depict helical secondary structures. Binding assays were performed with varying concentrations (1-10 mg/mL) and extra-cellular matrices (HA, collagens I-IV, elastin, and Geltrex). Concentration mediated secondary structures were assessed using circular dichroism (CD), and higher order nanostructures were visualized using transmission electron microscopy (TEM). All peptides formed the initial apparent 3₁₀/alpha-helices, yet peptides 17x-3, 4, BHP3 and BHP4 were HA specific and potent (i.e., a significant effect) binders at increasing concentrations. These peptides shifted from apparent 3₁₀/alpha-helical structures at low concentration to beta-sheets at increasing concentration and also formed nanofibers which are noted as self-assembling structures. Several of the HA binding peptides outperformed our positive control (mPEP35) at 3-4 times higher concentrations, and were enhanced by self-assembly as each of these groups had observable nanofibers. STATEMENT OF SIGNIFICANCE: Specific biomolecules or peptides have played a crucial role in developing materials or systems to deliver key drugs and therapeutics to a broad spectrum of diseases and disorders. In these diseased tissues, cells build protein/sugar networks, which are uniquely exposed and great targets to deliver drugs to. Hyaluronic acid (HA) is involved in every stage of injury and is abundant in cancer. To date, only two HA specific peptides have been discovered. In our work, we have designed a way to model and trace binding regions as they appear on the face of a helical peptide. Using this method we have created a family of peptides enriched with HA binding domains that stick with 3-4 higher affinity than those previously discovered.

Structural Elucidation of a Polypeptoid Chain in a Crystalline Lattice Reveals Key Morphology-Directing Role of the N-Terminus

The ability to engineer synthetic polymers with the same structural precision as biomacromolecules is crucial to enable the de novo design of robust nanomaterials with biomimetic function. Peptoids, poly(N-substituted) glycines, are a highly controllable bio-inspired polymer family that can assemble into a variety of functional, crystalline nanostructures over a wide range of sequences. Extensive investigation on the molecular packing in these lattices has been reported; however, many key atomic-level details of the molecular structure remain underexplored. Here, we use cryo-TEM 3D reconstruction to directly visualize the conformation of an individual polymer chain within a peptoid nanofiber lattice in real space at 3.6 Å resolution. The backbone in the N-decylglycine hydrophobic core is shown to clearly adopt an extended, all-cis-sigma strand conformation, as previously suggested in many peptoid lattice models. We also show that packing interactions (covalent and noncovalent) at the solvent-exposed N-termini have a dominant impact on the local chain ordering and hence the ability of the chains to pack into well-ordered lattices. Peptoids in pure water form fibers with limited growth in the a direction (<14 molecules in width), whereas in the presence of formamide, they grow to over microns in length in the a direction. This dependence points to the significant role of the chain terminus in determining the long-range order in the packing of peptoid lattices and provides an opportunity to modulate lattice stability and nanoscale morphology by the addition of exogenous small molecules. These findings help resolve a major challenge in the de novo structure-based design of sequence-defined biomimetic nanostructures based on crystalline domains and should accelerate the design of functional nanostructures.

Understanding a protein fold: the physics, chemistry, and biology of α-helical coiled coils

Protein science is being transformed by powerful computational methods for structure prediction and design: AlphaFold2 can predict many natural protein structures from sequence, and other AI methods are enabling the de novo design of new structures. This raises a question: how much do we understand the underlying sequence-to-structure/function relationships being captured by these methods? This perspective presents our current understanding of one class of protein assembly, the α-helical coiled coils. At first sight, these are straightforward: sequence repeats of hydrophobic (h) and polar (p) residues, (hpphppp)_n, direct the folding and assembly of amphipathic α helices into bundles. However, many different bundles are possible: they can have two or more helices (different oligomers); the helices can have parallel, antiparallel or mixed arrangements (different topologies); and the helical sequences can be the same (homomers) or different (heteromers). Thus, sequence-to-structure relationships must be present within the hpphppp repeats to distinguish these states. I discuss the current understanding of this problem at three levels: First, physics gives a parametric framework to generate the many possible coiled-coil backbone structures. Second, chemistry provides a means to explore and deliver sequence-to-structure relationships. Third, biology shows how coiled coils are adapted and functionalized in nature, inspiring applications of coiled coils in synthetic biology. I argue that the chemistry is largely understood; the physics is partly solved, though the considerable challenge of predicting even relative stabilities of different coiled-coil states remains; but there is much more to explore in the biology and synthetic biology of coiled coils.

Facile preparation of hexagonal nanosheets via polyion complex formation from α-helical polypeptides and polyphosphate-based molecules

The polyion complex-based supramolecular self-assembly of hexagonal nanosheets was achieved via the complexation of a PEGylated block catiomer with ATP and other polyphosphate-containing small molecules. The formation of hexagonal nanosheets required the presence of a polyethylene glycol block and α-helix formation in the catiomer block, which was induced by complexation with the polyphosphate moiety.

Peptide-based assembled nanostructures that can direct cellular responses

Natural originated materials have been well-studied over the past several decades owing to their higher biocompatibility compared to the traditional polymers. Peptides, consisting of amino acids, are among the most popular programable building blocks, which is becoming a growing interest in nanobiotechnology. Structures assembled using those biomimetic peptides allow the exploration of chemical sequences beyond those been routinely used in biology. In this Review, we discussed the most recent experimental discoveries on the peptide-based assembled nanostructures and their potential application at the cellular level such as drug delivery. In particular, we explored the fundamental principles of peptide self-assembly and the most recent development in improving their interactions with biological systems. We believe that as the fundamental knowledge of the peptide assemblies evolves, the more sophisticated and versatile nanostructures can be built, with promising biomedical applications.

Intrinsically Disordered Protein Micelles as Vehicles for Convection-Enhanced Drug Delivery to Glioblastoma Multiforme

Lipid and micelle-based nanocarriers have been explored for anticancer drug delivery to improve accumulation and uptake in tumor tissue. As an experimental opportunity in this area, our lab has developed a protein-based micelle nanocarrier consisting of a hydrophilic intrinsically disordered protein (IDP) domain bound to a hydrophobic tail, termed IDP-2Yx2A. This construct can be used to encapsulate hydrophobic chemotherapeutics that would otherwise be too insoluble in water to be administered. In this study, we evaluate the in vivo efficacy of IDP-2Yx2A by delivering a highly potent but water-insoluble cancer drug, SN38, into glioblastoma multiforme (GBM) tumors via convection-enhanced delivery (CED). The protein carriers alone are shown to elicit minimal toxicity effects in mice; furthermore, they can encapsulate and deliver concentrations of SN38 that would otherwise be lethal without the carriers. CED administration of these drug-loaded micelles into mice bearing U251-MG GBM xenografts resulted in slowed tumor growth and significant increases in median survival times compared to nonencapsulated SN38 and PBS controls.

Assembly of π-Stacking Helical Peptides into a Porous and Multivariable Proteomimetic Framework

The evolution of proteins from simpler, self-assembled peptides provides a powerful blueprint for the design of complex synthetic materials. Previously, peptide-metal frameworks using short sequences (≤3 residues) have shown great promise as proteomimetic materials that exhibit sophisticated capabilities. However, their development has been hindered due to few variable residues and restricted choice of side-chains that are compatible with metal ions. Herein, we developed a noncovalent strategy featuring π-stacking bipyridyl residues to assemble much longer peptides into crystalline frameworks that tolerate even previously incompatible acidic and basic functionalities and allow an unprecedented level of pore variations. Single-crystal X-ray structures are provided for all variants to guide and validate rational design. These materials exhibit hallmark proteomimetic behaviors such as guest-selective induced fit and assembly of multimetallic units. Significantly, we demonstrate facile optimization of the framework design to substantially increase affinity toward a complex organic molecule.

Bottom-up supramolecular assembly in two dimensions

The self-assembly of molecules in two dimensions (2D) is gathering attention from all disciplines across the chemical sciences. Attracted by the interesting properties of two-dimensional inorganic analogues, monomers of different chemical natures are being explored for the assembly of dynamic 2D systems. Although many important discoveries have been already achieved, great challenges are still to be addressed in this field. Hierarchical multicomponent assembly, directional non-covalent growth and internal structural control are a just a few of the examples that will be discussed in this perspective about the exciting present and the bright future of two-dimensional supramolecular assemblies.

The self-assembly of molecules in two dimensions (2D) is gathering attention from all disciplines across the chemical sciences. This perspective discusses the main strategies to direct the supramolecular self-assembly of organic monomers in 2D.

Biomaterials via peptide assembly: Design, characterization, and application in tissue engineering

A core challenge in biomaterials, with both fundamental significance and technological relevance, concerns the rational design of bioactive microenvironments. Designed properly, peptides can undergo supramolecular assembly into dynamic, physical hydrogels that mimic the mechanical, topological, and biochemical features of native tissue microenvironments. The relatively facile, inexpensive, and automatable preparation of peptides, coupled with low batch-to-batch variability, motivates the expanded use of assembling peptide hydrogels for biomedical applications. Integral to realizing dynamic peptide assemblies as functional biomaterials for tissue engineering is an understanding of the molecular and macroscopic features that govern assembly, morphology, and biological interactions. In this review, we first discuss the design of assembling peptides, including primary structure (sequence), secondary structure (e.g., α-helix and β-sheets), and molecular interactions that facilitate assembly into multiscale materials with desired properties. Next, we describe characterization tools for elucidating molecular structure and interactions, morphology, bulk properties, and biological functionality. Understanding of these characterization methods enables researchers to access a variety of approaches in this ever-expanding field. Finally, we discuss the biological properties and applications of peptide-based biomaterials for engineering several important tissues. By connecting molecular features and mechanisms of assembling peptides to the material and biological properties, we aim to guide the design and characterization of peptide-based biomaterials for tissue engineering and regenerative medicine. STATEMENT OF SIGNIFICANCE: Engineering peptide-based biomaterials that mimic the topological and mechanical properties of natural extracellular matrices provide excellent opportunities to direct cell behavior for regenerative medicine and tissue engineering. Here we review the molecular-scale features of assembling peptides that result in biomaterials that exhibit a variety of relevant extracellular matrix-mimetic properties and promote beneficial cell-biomaterial interactions. Aiming to inspire and guide researchers approaching this challenge from both the peptide biomaterial design and tissue engineering perspectives, we also present characterization tools for understanding the connection between peptide structure and properties and highlight the use of peptide-based biomaterials in neural, orthopedic, cardiac, muscular, and immune engineering applications.

Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials

Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.

Protein Assembly by Design

Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.

Enzyme mimics based membrane reactor for di(2-ethylhexyl) phthalate degradation

Di(2-ethylhexyl) phthalate (DEHP), the most abundantly used plasticizer, was considered to be a hazardous chemical that was difficult to be degraded naturally. In this study, inspired by the "catalytic triad'' in serine proteases, an enzyme mimic material was developed by combining the proteases's active sites of serine, histidine and aspartate (S-H-D) with the self-assembling sequence of LKLKLKL and the aromatic group of fluorenylmethyloxycarbonyl (Fmoc). By mixing the monomer of peptides containing separate S, H and D residues with a ratio of 2:1:1, the enzyme mimics were found to co- assemble into nanofibers (Co-HSD) and showed the highest activity towards DEHP degradation because of the synergistic effects of active sites, orderly secondary structure and stable molecular conformation. To further improve ability and applicability, the high active mimetic enzyme was immobilized onto regenerated cellulose (RC) membranes for DEHP degradation in a continuous recycling mode. The RC membranes were first functionalized by the NaIO₄ oxidation method to form aldehyde groups and then conjugated with the enzyme mimics via Schiff-base reaction. As a biocatalytic membrane, this membrane could not only effectively degrade DEHP, but also showed good stability, thus establishing a promising biomaterial for large scale biodegradation of DEHP in water decontamination and liquid food depollution.

Recent Progress in Ionic Coassembly of Cationic Peptides and Anionic Species

Peptide assembly has been extensively exploited as a promising platform for the creation of hierarchical nanostructures and tailor-made bioactive materials. Ionic coassembly of cationic peptides and anionic species is paving the way to provide particularly important contribution to this topic. In this review, the recent progress of ionic coassembly soft materials derived from the electrostatic coupling between cationic peptides and anionic species in aqueous solution is systematically summarized. The presentation of this review starts from a brief background on the general importance and advantages of peptide-based ionic coassembly. After that, diverse combinations of cationic peptides with small anions, macro- and/or oligo-anions, anionic polymers, and inorganic polyoxometalates are described. Emphasis is placed on the hierarchical structures, value-added properties, and applications. The molecular design of cationic peptides and the general principles behind the ionic coassembled structures are discussed. It is summarized that the combination of interesting and unique characteristics that arise both from the chemical diversity of peptides and the wide range of anionic species may contribute in a variety of output, including drug delivery, tissue engineering, gene transfection, and antibacterial activity. The emergent new phenomena and findings are illustrated. Finally, the outlook for the peptide-based ionic coassembly systems is also presented.

Nanoarchitectonics beyond Self-Assembly: Challenges to Create Bio-Like Hierarchic Organization

Incorporation of non-equilibrium actions in the sequence of self-assembly processes would be an effective means to establish bio-like high functionality hierarchical assemblies. As a novel methodology beyond self-assembly, nanoarchitectonics, which has as its aim the fabrication of functional materials systems from nanoscopic units through the methodological fusion of nanotechnology with other scientific disciplines including organic synthesis, supramolecular chemistry, microfabrication, and bio-process, has been applied to this strategy. The application of non-equilibrium factors to conventional self-assembly processes is discussed on the basis of examples of directed assembly, Langmuir-Blodgett assembly, and layer-by-layer assembly. In particular, examples of the fabrication of hierarchical functional structures using bio-active components such as proteins or by the combination of bio-components and two-dimensional nanomaterials, are described. Methodologies described in this review article highlight possible approaches using the nanoarchitectonics concept beyond self-assembly for creation of bio-like higher functionalities and hierarchical structural organization.

Cucurbit[7]uril-Mediated 2D Single-Layer Hybrid Frameworks Assembled by Tetraphenylethene and Polyoxometalate toward Modulation of the α-Chymotrypsin Activity

Construction of large-scale single-layer two-dimensional (2D) frameworks in water is significant due to their utilities in various fields. Utilizing macrocycle-mediated supramolecular self-assembly represents a promising approach; however, challenges still remain in their practical preparation. Here, we exploited a two-step supramolecular strategy to build 2D organic-inorganic hybrid frameworks at a micrometer scale in water. Taking advantage of the high binding affinity to cucurbit[7]uril (CB[7]), mono-quaternary ammonium tetraphenylethene (MQATPE) derivatives were first included with CB[7] to form a 1:1 complex (MQATPE@CB[7]). Then, just mixing the complex with anionic polyoxometalate Na₉[EuW₁₀O₃₆]·32H₂O (denoted as Eu-POM) in a 3:1 molar ratio leads to the formation of single-layer 2D films with tens of micrometers via electrostatic and π-π stacking interactions. The most unique feature of this strategy is that the steric effect imposed by CB[7] would not only lead the modules to adopt a periodic hexagonal assembly but also forbid stacking between layers through comparison with the merely multilayered 2D nanosheets self-assembled by MQATPE/Eu-POM. Interestingly, the charge interactions between MQATPE and Eu-POM would lead to the aggregation-induced emission (AIE) fluorescence of MQATPE, and white light emission could be obtained through the simple regulation of the contents of Eu-POM and MQATPE. Furthermore, due to the high surface areas and more accessible active sites, the single-layer films can act as an effective enzyme inhibitor to modulate the activity of α-chymotrypsin (ChT). These findings suggest a simple but universal approach for single-layer hybrid materials, which may hold promise for practical applications in photophysical and biomedical fields.

Enzyme mimics based on self-assembled peptides for di(2-ethylhexyl)phthalate degradation

Enzyme mimics inspired by serine proteases are developed through self-assembled peptides to degrade di(2-ethylhexyl)phthalate (DEHP).

Functional Coiled-Coil-like Assembly by Knob-into-Hole Packing of Single Heptad Repeat

Coiled-coil peptides represent the principal building blocks for structure-based design of bionanomaterials. The sequence-structure relationship and precise nanoscale ordering of the coiled-coil helices originate from the knob-into-hole (KIH) packing of side chains. The helical interface stabilized by the KIH interaction is known to have chain lengths ranging from 30 to 1000 residues. Yet the shortest peptide required for oligomerization through KIH assembly is still unknown. Here, we report that through atomic resolution a minimal seven-residue amphipathic helix forms a different type of KIH motif, termed "supramolecular KIH packing", which confers an exceptional stability to the helical dimers. Significantly, at a low pH, the peptide self-assembles into nanofibers with coiled-coil architecture resembling the natural fibrous proteins. Furthermore, hierarchical ordering of the nanofibers affords lyotropic liquid crystals composed of a shortest natural helical sequence. Thus, this study expands the sequence space for a coiled-coil folding manifold and provides another paradigm for designer nanomaterials from minimal helical sequences.

Precise Self-Assembly of Nanoparticles into Ordered Nanoarchitectures Directed by Tobacco Mosaic Virus Coat Protein

Self-assembly guided by biological molecules is a promising approach for fabricating predesigned nanostructures. Protein is one such biomolecule possessing deterministic 3D crystal structure and peptide information, which acts as a good candidate for templating functional nanoparticles (fNPs). However, inadequate coordination efficacy during the establishment of interfacial interactions with fNPs makes it highly challenging to precisely fabricate designed nanostructures and functional materials. Here, a facile and robust strategy is reported for the hierarchical assembly of fNPs into ordered architectures, with unprecedentedly large sizes up to tens of micrometers, using a hollow cylinder-shaped tobacco mosaic virus coat protein (TMV disk). The rational design of the site-specific functional groups on the TMV disk not only demonstrates the powerful capability of directing various discrete fNP assemblies with high controllability but also assists in precise assembly of a TMV monolayer sheet structure for further organizing homogeneous and heterogeneous fNP periodic lattices by varying the types of fNPs. The high precision and adjustability of the pattern fashions of different fNPs unambiguously corroborate the validity of this innovative strategy, which provides a convenient route to design and assemble protein-based hierarchical ordered architectures for use in nanophotonics and nanodevices.

The de novo design of α-helical peptides for supramolecular self-assembly

One approach to designing de novo proteinaceous assemblies and materials is to develop simple, standardised building blocks and then to combine these symmetrically to construct more-complex higher-order structures. This has been done extensively using β-structured peptides to produce peptide fibres and hydrogels. Here, we focus on building with de novo α-helical peptides. Because of their self-contained, well-defined structures and clear sequence-to-structure relationships, α helices are highly programmable making them robust building blocks for biomolecular construction. The progress made with this approach over the past two decades is astonishing and has led to a variety of de novo assemblies, including discrete nanoscale objects, and fibrous, nanotube, sheet and colloidal materials. This body of work provides an exceptionally strong foundation for advancing the field beyond in vitro design and into in vivo applications including what we call protein design in cells.

Degradation of phthalic acid esters (PAEs) by an enzyme mimic and its application in the degradation of intracellular DEHP

An enzyme mimic inspired by serine proteases was developed for the degradation of PAEs and applied in the hydrolysis of intracellular DEHP.

The design and biomedical applications of self-assembled two-dimensional organic biomaterials

Self-assembling 2D organic biomaterials exhibit versatile abilities for structural and functional tailoring, as well as high potential for biomedical applications.

Biomolecular Assemblies: Moving from Observation to Predictive Design

Biomolecular assembly is a key driving force in nearly all life processes, providing structure, information storage, and communication within cells and at the whole organism level. These assembly processes rely on precise interactions between functional groups on nucleic acids, proteins, carbohydrates, and small molecules, and can be fine-tuned to span a range of time, length, and complexity scales. Recognizing the power of these motifs, researchers have sought to emulate and engineer biomolecular assemblies in the laboratory, with goals ranging from modulating cellular function to the creation of new polymeric materials. In most cases, engineering efforts are inspired or informed by understanding the structure and properties of naturally occurring assemblies, which has in turn fueled the development of predictive models that enable computational design of novel assemblies. This Review will focus on selected examples of protein assemblies, highlighting the story arc from initial discovery of an assembly, through initial engineering attempts, toward the ultimate goal of predictive design. The aim of this Review is to highlight areas where significant progress has been made, as well as to outline remaining challenges, as solving these challenges will be the key that unlocks the full power of biomolecules for advances in technology and medicine.

Resisting Bacteria and Attracting Cells: Spontaneous Formation of a Bifunctional Peptide-Based Coating by On-Surface Assembly Approach

Due to extension of life expectancy, millions of people suffer nowadays from bone and dental malfunctions that can only be treated by different types of implants. However, these implants tend to fail due to bacterial infection and lack of integration with the remaining tissue. Here, we demonstrate a new concept in which we use specifically designed peptides, in a "Lego-like" manner to endow multiple preprogrammed functions. We developed a bifunctional peptide-based coating that simultaneously rejects the adhesion of infecting bacteria and attracts cells that build the new connecting tissue. The peptide design contains fluorinated phenylalanine that mediates the self-assembly of the peptide into a coating that resists bacterial adhesion. It also includes an Arg-Gly-Asp (RGD) motif that attracts mammalian cells. The whole compound is attached to the surface using a third unit, the amino acid 3,4-dihydroxyphenylalanine (DOPA). This novel, yet very simple approach is significantly advantageous for practical use and synthesis. More importantly, this peptide design can serve as a general platform for generating functional coatings.

Ultralarge Single-Layer Porous Protein Nanosheet for Precise Nanosize Separation

Highly permeable and precisely size-selective membranes are the subject of continuous pursuit for energy-efficient separation of fine chemicals. However, challenges remain in the fabrication of an ultrathin selective layer with homogeneous pores, in particular, with the pore sizes in the 1-10 nm range. We report the design of a free-standing porous nanosheet assembled with a single layer of proteins. Tobacco mosaic virus mutant (TMVm), a cylinder-shaped protein containing an inner pore of 4 nm in diameter, was cross-linked via a Cu²⁺-catalyzed disulfide-bond-forming reaction along the 2D orientation. By such a design, ultralarge single-layer TMVm nanosheets extending over tens of micrometers in width and with well-defined nanopores were successfully developed. A ∼40 nm thick ultrafiltration membrane laminated by the single-layer TMVm nanosheets through simple vacuum filtration accomplished the precise separation of ∼4 nm sized substances. Meanwhile, the membrane exhibited water permeance up to ∼7000 L m^-2 h^-1 bar^-1, which is an order of magnitude improvement compared with traditional ultrafiltration membranes with a similar rejection profile.

A novel pillar[5]arene-based supramolecular organic framework gel to achieve an ultrasensitive response by introducing the competition of cationπ and ππ interactions

Ultrasensitive response properties are an intriguing concern for stimuli-responsive materials. Herein, we report a novel method to achieve an ultrasensitive response by introducing the competition of cationπ and ππ interactions into a pillar[5]arene-based supramolecular organic framework (SOF-AMP). SOF-AMP was constructed with a novel bis-naphthalimide functionalized pillar[5]arene, which was able to form a stable supramolecular gel (SOF-AMP-G) in cyclohexanol. Interestingly, SOF-AMP-G shows an ultrasensitive response to Fe3+ through the competition of cationπ and ππ interactions. Meanwhile, the Fe3+ coordinated SOF (MSOF-Fe) shows an ultrasensitive response to H2PO4-. SOF-AMP-G displayed yellow fluorescence whereas, after the addition of 0.5 equiv. of Fe3+ to SOF-AMP-G, the yellow fluorescence was quenched. The detection limit of SOF-AMP-G for Fe3+ is 7.54 × 10-9 M. More interestingly, the Fe3+ coordinated SOF gel (MSOF-Fe-G) could sense H2PO4- with a fluorescence "turn-on". The detection limit of MSOF-Fe-G for H2PO4- is 4.21 × 10-9 M. Simultaneously, the Fe3+ and H2PO4- responsive thin films based on these SOF gels were prepared. Moreover, these SOF gels could be used as ultrasensitive ion sensors, fluorescent display materials and sensitive logic gates.

Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition

Harnessing the self-assembly of peptide sequences has demonstrated great promise in the domain of creating high precision shape-tunable biomaterials. The unique properties of peptides allow for a building block approach to material design. In this study, self-assembly of mixed systems encompassing two peptide sequences with identical hydrophobic regions and distinct polar segments is investigated. The two peptide sequences are diphenylalanine and phenylalanine-asparagine-phenylalanine. The study examines the impact of molecular composition (namely, the total peptide concentration and the relative tripeptide concentration) on the morphology of the self-assembled hybrid biological material. We report a rich polymorphism in the assemblies of these peptides and explain the relationship between the peptide sequence, concentration and the morphology of the supramolecular assembly.

Pillar[5]arene-Based Supramolecular Organic Framework with Multi-Guest Detection and Recyclable Separation Properties

The selective detection and separation of target ions or molecules is an intriguing issue. Herein, a novel supramolecular organic framework (SOF-THBP) was constructed by bis-thioacetylhydrazine functionalized pillar[5]arenes. The SOF-THBP shows a fluorescent response for Fe³⁺ , Cr³⁺ , Hg²⁺ and Cu²⁺ ions. The xerogel of SOF-THBP shows excellent recyclable separation properties for these metal ions and the absorption rates were up to 99.29 %. More interestingly, by rationally introducing these metal ions into the SOF-THBP, a series of metal-ion-coordinated SOFs (MSOFs) such as MSOF-Fe, MSOF-Hg and MSOF-Cu were constructed. These metal ions coordinated MSOFs could selectively sense F^- , Br^- , and l-Cys, respectively. The detection limits of these MSOFs for F^- , Br^- and l-Cys were about 10^-8  m.

Hexagonally Ordered Arrays of α-Helical Bundles Formed from Peptide-Dendron Hybrids

Combining monodisperse building blocks that have distinct folding properties serves as a modular strategy for controlling structural complexity in hierarchically organized materials. We combine an α-helical bundle-forming peptide with self-assembling dendrons to better control the arrangement of functional groups within cylindrical nanostructures. Site-specific grafting of dendrons to amino acid residues on the exterior of the α-helical bundle yields monodisperse macromolecules with programmable folding and self-assembly properties. The resulting hybrid biomaterials form thermotropic columnar hexagonal mesophases in which the peptides adopt an α-helical conformation. Bundling of the α-helical peptides accompanies self-assembly of the peptide-dendron hybrids into cylindrical nanostructures. The bundle stoichiometry in the mesophase agrees well with the size found in solution for α-helical bundles of peptides with a similar amino acid sequence.

Self-Assembling Ability Determines the Activity of Enzyme-Instructed Self-Assembly for Inhibiting Cancer Cells

Enzyme-instructed self-assembly (EISA) represents a dynamic continuum of supramolecular nanostructures that selectively inhibits cancer cells via simultaneously targeting multiple hallmark capabilities of cancer, but how to design the small molecules for EISA from the vast molecular space remains an unanswered question. Here we show that the self-assembling ability of small molecules controls the anticancer activity of EISA. Examining the EISA precursor analogues consisting of an N-capped d-tetrapeptide, a phosphotyrosine residue, and a diester or a diamide group, we find that, regardless of the stereochemistry and the regiochemistry of their tetrapeptidic backbones, the anticancer activities of these precursors largely match their self-assembling abilities. Additional mechanistic studies confirm that the assemblies of the small peptide derivatives result in cell death, accompanying significant rearrangement of cytoskeletal proteins and plasma membranes. These results imply that the diester or diamide derivatives of the d-tetrapeptides self-assemble pericellularly, as well as intracellularly, to result in cell death. As the first case to correlate thermodynamic properties (e.g., self-assembling ability) of small molecules with the efficacy of a molecule process against cancer cells, this work provides an important insight for developing a molecular dynamic continuum for potential cancer therapy, as well as understanding the cytotoxicity of pathogenic assemblies.

Geometrical frustration as a potential design principle for peptide-based assemblies

Two-dimensional peptide and protein assemblies have been the focus of increased scientific research as they display significant potential for the creation of functional nanomaterials. Soluble subunits derived from a variety of protein motifs have been demonstrated to self-assemble into structurally defined nanosheets under environmentally benign conditions in which the components often retain their native structure and function. These types of two-dimensional assemblies may have an advantage for nanofabrication in that their extended planar shapes can be more straightforwardly incorporated into the current formats of nanoscale devices. However, significant challenges remain in the fabrication of these materials, particularly in devising methods to control the size, shape and internal structure of the resultant materials. Geometrical frustration may be envisioned as a possible mechanism to exert control over these structural parameters through rational design. While this objective has yet to be realized in practice, we discuss in this article the potential role of geometrical frustration as a principle to rationalize unusual self-assembly behaviour in several examples of two-dimensional peptide assemblies.

Strand Displacement in Coiled-Coil Structures: Controlled Induction and Reversal of Proximity

Coiled-coil peptides are frequently used to create new function upon the self-assembly of supramolecular complexes. A multitude of coil peptide sequences provides control over the specificity and stability of coiled-coil complexes. However, comparably little attention has been paid to the development of methods that allow the reversal of complex formation under non-denaturing conditions. Herein, we present a reversible two-state switching system. The process involves two peptide molecules for the formation of a size-mismatched coiled-coil duplex and a third, disruptor peptide that targets an overhanging end. A real-time fluorescence assay revealed that the proximity between two chromophores can be switched on and off, repetitively if desired. Showcasing the advantages provided by non-denaturing conditions, the method permitted control over the bivalent interactions of the tSH2 domain of Syk kinase with a phosphopeptide ligand.

SLADS: a parallel code for direct simulations of scattering of large anisotropic dense nanoparticle systems

SLADS(http://www.pims.ac.cn/Resources.html), a parallel code for direct simulations of X-ray scattering of large anisotropic dense nanoparticle systems of arbitrary species and atomic configurations, is presented. Particles can be of arbitrary shapes and dispersities, and interactions between particles are considered. Parallelization is achieved in real space for the sake of memory limitation. The system sizes attempted are up to one billion atoms, and particle concentrations in dense systems up to 0.36. Anisotropy is explored in terms of superlattices. One- and two-dimensional small-angle scattering or diffraction patterns are obtained.SLADSis validated self-consistently or against cases with analytical solutions.