Residue-Specific Solvation-Directed Thermodynamic and Kinetic Control over Peptide Self-Assembly with 1D/2D Structure Selection

Designing Pathway-Controlled Multicomponent Ultrashort Peptide Hydrogels with Diverse Functionalities at the Nanoscale for Directing Cellular Behavior

Tuning self-assembling pathways by implementing different external stimuli has been extensively studied, owing to their effective control over structural and mechanical properties. Consequently, multicomponent peptide hydrogels with high structural tunability and stimuli responsiveness are crucial in dictating cellular behavior. Herein, we have implemented both coassembly approach and pathway-dependent self-assembly to design nonequilibrium nanostructures to understand the thermodynamic and kinetic aspects of peptide self-assembly toward controlling cellular response. Our system involved an ultrashort peptide gelator and a hydrophilic surfactant which coassembled through different pathways, i.e., heat-cool and sonication methods with variable energy input. Interestingly, it was possible to access diverse structural and mechanical properties at the nanoscale in a single coassembled system. Further, the hydrophilic surfactant provided additional surface functionalities, thus creating an efficient hydrophilic matrix for cellular interaction. Such diverse functionalities in a single coassembled system could lead to the development of advanced scaffolds, with applications in various biomedical fields.

Boron-Nitrogen-Embedded Polycyclic Aromatic Hydrocarbon-Based Controllable Hierarchical Self-Assemblies through Synergistic Cation-π and C-H···π Interactions for Bifunctional Photo- and Electro-Catalysis

Boron-Nitrogen-embedded polycyclic aromatic hydrocarbons (BN-PAHs) as novel π-conjugated systems have attracted immense attention owing to their superior optoelectronic properties. However, constructing long-range ordered supramolecular assemblies based on BN-PAHs remains conspicuously scarce, primarily attributed to the constraints arising from coordinating multiple noncovalent interactions and the intrinsic characteristics of BN-PAHs, which hinder precise control over delicate self-assembly processes. Herein, we achieve the successful formation of BN-PAH-based controllable hierarchical assemblies through synergistically leveraged cation-π and C-H···π interactions. By carefully adjusting the solvent conditions in two progressive assembly hierarchies, the one-dimensional (1D) supramolecular assemblies with "rigid yet flexible" assembled units are first formed by cation-π interactions, and then they can be gradually fused into two-dimensional (2D) structures under specific C-H···π interactions, thus realizing the precise control of the transformation process from BN-PAH-based 1D primary structures to 2D higher-order assemblies. The resulting 2D-BNSA, characterized by enhanced electrical conductivity and ordered 2D layered structure, provides anchoring and dispersion sites for loading two appropriate nanocatalysts, thus facilitating the efficient photocatalytic CO2 reduction (with a remarkable CH4 evolution rate of 938.7 μmol g-1 h-1) and electrocatalytic acetylene semihydrogenation (reaching a Faradaic efficiency for ethylene up to 98.5%).

3,4-Ethylenedioxythiophene Hydrogels: Relating Structure and Charge Transport in Supramolecular Gels

Ionic charge transport is a ubiquitous language of communication in biological systems. As such, bioengineering is in constant need of innovative, soft, and biocompatible materials that facilitate ionic conduction. Low molecular weight gelators (LMWGs) are complex self-assembled materials that have received increasing attention in recent years. Beyond their biocompatible, self-healing, and stimuli responsive facets, LMWGs can be viewed as a "solid" electrolyte solution. In this work, we investigate 3,4-ethylenedioxythiophene (EDOT) as a capping group for a small peptide library, which we use as a system to understand the relationship between modes of assembly and charge transport in supramolecular gels. Through a combination of techniques including small-angle neutron scattering (SANS), NMR-based Van't Hoff analysis, atomic force microscopy (AFM), rheology, four-point probe, and electrochemical impedance spectroscopy (EIS), we found that modifications to the peptide sequence result in distinct assembly pathways, thermodynamic parameters, mechanical properties, and ionic conductivities. Four-point probe conductivity measurements and electrochemical impedance spectroscopy suggest that ionic conductivity is approximately doubled by programmable gel assemblies with hollow cylinder morphologies relative to gels containing solid fibers or a control electrolyte. More broadly, it is hoped this work will serve as a platform for those working on charge transport of aqueous soft materials in general.

Self-assembly of cyclic peptide monolayers by hydrophobic supramolecular hinges

Supramolecular polymerisation of two-dimensional (2D) materials requires monomers with non-covalent binding motifs that can control the directionality of both dimensions of growth. A tug of war between these propagation forces can bias polymerisation in either direction, ultimately determining the structure and properties of the final 2D ensemble. Deconvolution of the assembly dynamics of 2D supramolecular systems has been widely overlooked, making monomer design largely empirical. It is thus key to define new design principles for suitable monomers that allow the control of the direction and the dynamics of two-dimensional self-assembled architectures. Here, we investigate the sequential assembly mechanism of new monolayer architectures of cyclic peptide nanotubes by computational simulations and synthesised peptide sequences with selected mutations. Rationally designed cyclic peptide scaffolds are shown to undergo hierarchical self-assembly and afford monolayers of supramolecular nanotubes. The particular geometry, the rigidity and the planar conformation of cyclic peptides of alternating chirality allow the orthogonal orientation of hydrophobic domains that define lateral supramolecular contacts, and ultimately direct the propagation of the monolayers of peptide nanotubes. A flexible 'tryptophan hinge' at the hydrophobic interface was found to allow lateral dynamic interactions between cyclic peptides and thus maintain the stability of the tubular monolayer structure. These results unfold the potential of cyclic peptide scaffolds for the rational design of supramolecular polymerisation processes and hierarchical self-assembly across the different dimensions of space.

Multistep, site-selective noncovalent synthesis of two-dimensional block supramolecular polymers

Although the principles of noncovalent bonding are well understood and form the basis for the syntheses of many intricate supramolecular structures, supramolecular noncovalent synthesis cannot yet achieve the levels of precision and complexity that are attainable in organic and/or macromolecular covalent synthesis. Here we show the stepwise synthesis of block supramolecular polymers from metal-porphyrin derivatives (in which the metal centre is Zn, Cu or Ni) functionalized with fluorinated alkyl chains. These monomers first undergo a one-dimensional supramolecular polymerization and cyclization process to form a toroidal structure. Subsequently, successive secondary nucleation, elongation and cyclization steps result in two-dimensional assemblies with concentric toroidal morphologies. The site selectivity endowed by the fluorinated chains, reminiscent of regioselectivity in covalent synthesis, enables the precise control of the compositions and sequences of the supramolecular structures, as demonstrated by the synthesis of several triblock supramolecular terpolymers.

Lipidation Alters the Structure and Hydration of Myristoylated Intrinsically Disordered Proteins

Lipidated proteins are an emerging class of hybrid biomaterials that can integrate the functional capabilities of proteins into precisely engineered nano-biomaterials with potential applications in biotechnology, nanoscience, and biomedical engineering. For instance, fatty-acid-modified elastin-like polypeptides (FAMEs) combine the hierarchical assembly of lipids with the thermoresponsive character of elastin-like polypeptides (ELPs) to form nanocarriers with emergent temperature-dependent structural (shape or size) characteristics. Here, we report the biophysical underpinnings of thermoresponsive behavior of FAMEs using computational nanoscopy, spectroscopy, scattering, and microscopy. This integrated approach revealed that temperature and molecular syntax alter the structure, contact, and hydration of lipid, lipidation site, and protein, aligning with the changes in the nanomorphology of FAMEs. These findings enable a better understanding of the biophysical consequence of lipidation in biology and the rational design of the biomaterials and therapeutics that rival the exquisite hierarchy and capabilities of biological systems.

Ionic supramolecular polymerization of water-soluble porphyrins: balancing ionic attraction and steric repulsion to govern stacking

We have synthesized novel water-soluble anionic porphyrin monomers that undergo pH-regulated ionic supramolecular polymerization in aqueous media. By tuning the total charge of the monomer, we selectively produced two different supramolecular polymers: J- and H-stacked. The main driving force toward the J-aggregated supramolecular polymers was the ionic interactions between the sulfonate and protonated pyrrole groups, ultimately affording neutral supramolecular polymers. In these J-aggregated supramolecular polymers, amide groups were aligned regularly along polymer wedges, which further assembled in an edge-to-edge manner to afford nanosheets. In contrast, the H-aggregated supramolecular polymers remained anionic, with their amide NH moieties acting as anion receptors along the polymer chains, thereby minimizing repulsion. For both polymers, varying the steric bulk of the peripheral ethylene glycol (EG) units controlled the rates of self-assembly as well as the degrees of polymerization. This steric effect was further tunable, depending on the solvation state of the EG chains. Accordingly, this new family of supramolecular polymers was created by taking advantage of unique driving forces that depended on both the pH and solvent.

Kinetic Mechanism of Amyloid-β-(16-22) Peptide Fibrillation

The kinetic mechanism of amyloid fibril formation by a peptide fragment containing seven residues of the amyloid-β protein Aβ-(16-22) was investigated. We found that the N- and C-terminal unprotected Aβ-(16-22), containing no aggregation nuclei, showed rapid fibrillation within seconds to minutes in a neutral aqueous buffer solution. The fibrillation kinetics were well described by the nucleation-elongation model, suggesting that primary nucleation was the rate-limiting step. On the basis of both experimental and theoretical analyses, the aggregated nucleus was estimated to be composed of 6-7 peptide molecules, wherein the two β-sheets were associated with their hydrophobic surfaces. Thin fibers with widths of 10-20 nm were formed, which increased their length and thickness, attaining a width of >20 nm over several tens of minutes, probably owing to the lateral association of the fibers. Electrostatic and hydrophobic interactions play important roles in aggregation. These results provide a basis for understanding the fibrillation of short peptides.

Collagen-Binding Peptide-Enabled Supramolecular Hydrogel Design for Improved Organ Adhesion and Sprayable Therapeutic Delivery

Spraying serves as an attractive, minimally invasive means of administering hydrogels for localized delivery, particularly due to high-throughput deposition of therapeutic depots over an entire target site of uneven surfaces. However, it remains a great challenge to design systems capable of rapid gelation after shear-thinning during spraying and adhering to coated tissues in wet, physiological environments. We report here on the use of a collagen-binding peptide to enable a supramolecular design of a biocompatible, bioadhesive, and sprayable hydrogel for sustained release of therapeutics. After spraying, the designed peptide amphiphile-based supramolecular filaments exhibit fast, physical cross-linking under physiological conditions. Our ex vivo studies suggest that the hydrogelator strongly adheres to the wet surfaces of multiple organs, and the extent of binding to collagen influences release kinetics from the gel. We envision that the sprayable organ-adhesive hydrogel can serve to enhance the efficacy of incorporated therapeutics for many biomedical applications.

Impact of Nanoparticle Size and Surface Chemistry on Peptoid Self-Assembly

Self-assembled organic nanomaterials can be generated by bottom-up assembly pathways where the structure is controlled by the organic sequence and altered using pH, temperature, and solvation. In contrast, self-assembled structures based on inorganic nanoparticles typically rely on physical packing and drying effects to achieve uniform superlattices. By combining these two chemistries to access inorganic-organic nanostructures, we aim to understand the key factors that govern the assembly pathway and structural outcomes in hybrid systems. In this work, we outline two assembly regimes between quantum dots (QDs) and reversibly binding peptoids. These regimes can be accessed by changing the solubility and size of the hybrid (peptoid-QD) monomer unit. The hybrid monomers are prepared via ligand exchange and assembled, and the resulting assemblies are studied using ex-situ transmission electron microscopy as a function of assembly time. In aqueous conditions, QDs were found to stabilize certain morphologies of peptoid intermediates and generate a final product consisting of multilayers of small peptoid sheets linked by QDs. The QDs were also seen to facilitate or inhibit assembly in organic solvents based on the relative hydrophobicity of the surface ligands, which ultimately dictated the solubility of the hybrid monomer unit. Increasing the size of the QDs led to large hybrid sheets with regions of highly ordered square-packed QDs. A second, smaller QD species can also be integrated to create binary hybrid lattices. These results create a set of design principles for controlling the structure and structural evolution of hybrid peptoid-QD assemblies and contribute to the predictive synthesis of complex hybrid matter.

Alcohol-perturbed self-assembly of the tobacco mosaic virus coat protein

The self-assembly of the tobacco mosaic virus coat protein is significantly altered in alcohol-water mixtures. Alcohol cosolvents stabilize the disk aggregate and prevent the formation of helical rods at low pH. A high alcohol content favours stacked disk assemblies and large rafts, while a low alcohol concentration favours individual disks and short stacks. These effects appear to be caused by the hydrophobicity of the alcohol additive, with isopropyl alcohol having the strongest effect and methanol the weakest. We discuss several effects that may contribute to preventing the protein-protein interactions between disks that are necessary to form helical rods.

Molecular Engineering of Peptide–Drug Conjugates for Therapeutics

In recent years, hundreds of novel small molecular drugs used for different treatments have been studied in the three phases of clinical trials around the world. However, less than 10% of them are eventually used due to diverse problems. Even some traditional drugs that have been approved by the Food and Drug Administration (FDA) have faced similar dilemmas. For instance, many drugs have poor water solubility, are easily hydrolyzed, or possess undesirable toxicity, while a variety of cancer cells develop drug resistance (DR) or multiple drug resistance (MDR) towards chemotherapeutic agents after long-term therapy. In order to improve the efficacy and efficiency of drugs, research has been directed forward towards the creation of assemblies of peptide–drug conjugates (PDCs) which have proven to possess wide potential for overcoming such complications based on their excellent biocompatibility, controllable biodegradability, site-selective targeting, and comparably low cytotoxicity. In this review, we focus on the recent developments and advances made in the creation of self-assembled nanostructures of PDCs for cancer therapy, on the chemical and physical properties of such drugs and peptides, and how they are arranged together to form diverse supramolecular nanostructures. Additionally, we cover certain mechanisms regarding how peptides or their derivatives enhance the efficiency and efficacy of those selected drugs and provide a brief discussion regarding the perspectives and remaining challenges in this intriguing field.

Aggregation of Amphiphilic Carbocyanines: Fluorination Favors Cylindrical Micelles over Bilayered Tubes

The synthesis of a new amphiphilic 5,5',6,6'-tetrachlorobenzimidacarbocyanine dye derivative with -(CH₂)₂-(CF₂)₅-CF₃ chains attached to the nitrogen atoms in the 1,1'-position, CF8O3, is reported. Depending on the dye concentration and the addition of MeOH, CF8O3 forms J- and H-aggregates in aqueous solutions. The aggregation behavior was investigated using steady-state absorption, linear dichroism, and fluorescence spectroscopy, as well as by cryogenic transmission electron microscopy (cryo-TEM). The J-band of the MeOH-free solution is monomer-like, rather broad, and less red-shifted with respect to the monomer absorption, indicating weak excitonic coupling and disorder effects. Cryo-TEM reveals a diversity of supramolecular structures, wherein linear and branched cylindrical micelles dominate. It is concluded that the high stiffness of fluoroalkyl chains does not allow the chains to splay and completely fill up the hydrophobic gap between opposing chromophores. This destabilizes the bilayers and favors the micellar structure motifs instead. The aggregates appearing at 30% MeOH show a split absorption spectrum consisting of a broad blue-shifted H-band and an accompanying sharp red-shifted J-band with perpendicular polarizations. These HJ-type aggregates are also composed of micellar fibers, but these bundle into rope-like strands. For 10% MeOH, a narrow bilayered tube is the dominating morphology. The observed MeOH dependence of aggregation reveals a clear cosolvent effect.

Robust and Versatile Coatings Engineered via Simultaneous Covalent and Noncovalent Interactions

Interfacial modular assembly has emerged as an adaptable strategy for engineering the surface properties of substrates in biomedicine, photonics, and catalysis. Herein, we report a versatile and robust coating (pBDT-TA), self-assembled from tannic acid (TA) and a self-polymerizing aromatic dithiol (i.e., benzene-1,4-dithiol, BDT), that can be engineered on diverse substrates with a precisely tuned thickness (5-40 nm) by varying the concentration of BDT used. The pBDT-TA coating is stabilized by covalent (disulfide) bonds and supramolecular (π-π) interactions, endowing the coating with high stability in various harsh aqueous environments across ionic strength, pH, temperature (e.g., 100 mM NaCl, HCl (pH 1) or NaOH (pH 13), and water at 100 °C), as well as surfactant solution (e.g., 100 mM Triton X-100) and biological buffer (e.g., Dulbecco's phosphate-buffered saline), as validated by experiments and simulations. Moreover, the reported pBDT-TA coating enables secondary reactions on the coating for engineering hybrid adlayers (e.g., ZIF-8 shells) via phenolic-mediated adhesion, and the facile integration of aromatic fluorescent dyes (e.g., rhodamine B) via π interactions without requiring elaborate synthetic processes.

Fluorinated peptide biomaterials

Fluorinated compounds, while rarely used by nature, are emerging as fundamental ingredients in biomedical research, with applications in drug discovery, metabolomics, biospectroscopy, and, as the focus of this review, peptide/protein engineering. Leveraging the fluorous effect to direct peptide assembly has evolved an entirely new class of organofluorine building blocks from which unique and bioactive materials can be constructed. Here, we discuss three distinct peptide fluorination strategies used to design and induce peptide assembly into nano-, micro-, and macrosupramolecular states that potentiate high-ordered organization into material scaffolds. These fluorine-tailored peptide assemblies employ the unique fluorous environment to boost biofunctionality for a broad range of applications, from drug delivery to antibacterial coatings. This review provides foundational tactics for peptide fluorination and discusses the utility of these fluorous-directed hierarchical structures as material platforms in diverse biomedical applications.

Pushing and Pulling: A Dual pH Trigger Controlled by Varying the Alkyl Tail Length in Heme Coordinating Peptide Amphiphiles

Some organisms in nature that undergo anaerobic respiration utilize 1D nanoscale arrays of densely packed cytochromes containing the molecule heme. The assemblies can be mimicked with 1D nanoscale fibrils composed of peptide amphiphiles designed to coordinate heme in dense arrays. To create such materials and assemblies, it is critical to understand the assembly process and what controls the various aspects of hierarchical assembly. MD simulations suggest that shorter alkyl chains on the peptide lead to more dynamic structures than the peptides with longer chains that yield kinetically trapped states. The hydration parameters manifest themselves experimentally through the observation of a dual pH trigger, which controls the peptide assembly rate, the heme binding affinity, and heme organization kinetics. Great strides in understanding the relative complexity of the self-assembly process in relation to incorporating a functional moiety like heme opens up many possibilities in developing abiotic assemblies for bioelectronic devices and assemblies.

Pathogen-specific antimicrobials engineered de novo through membrane-protein biomimicry

Precision antimicrobials aim to kill pathogens without damaging commensal bacteria in the host, and thus to cure disease without antibiotic-associated dysbiosis. Here, we report the de novo design of a synthetic host defence peptide that targets a specific pathogen by mimicking key molecular features of the pathogen’s channel-forming membrane proteins. By exploiting physical and structural vulnerabilities within the pathogen’s cellular envelope, we designed a peptide sequence that undergoes instructed tryptophan-zippered assembly within the mycolic-acid rich outer membrane of Mycobacterium tuberculosis (Mtb) to specifically kill the pathogen without collateral toxicity towards lung commensal bacteria or host tissue. These ‘mycomembrane-templated’ assemblies elicit rapid mycobactericidal activity, and enhance the potency of antibiotics by improving their otherwise poor diffusion across the rigid Mtb envelope with respect to agents that exploit transmembrane protein channels for antimycobacterial activity. This biomimetic strategy may aid the design of other narrow-spectrum antimicrobial peptides.

Self-assembly of a benzothiazolone conjugate into panchromatic fluorescent fibres and their application in cellular imaging

We report self assembly of a benzothiazolone conjugate (CBT) into fluorescent panchromatic fibres and their application as a panchromatic dye in bioimaging.

Solvent Effects on the Self-Assembly of an Amphiphilic Polypeptide Incorporating α-Helical Hydrophobic Blocks

The self-assembly of biological molecules is an important pathway to understanding the molecular basis of complex metabolic events. The presence of a cosolvent in an aqueous solution during the self-assembly process can promote the formation of kinetically trapped metastable intermediates. In nature, a category of cosolvents termed osmolytes can work to strengthen the hydrogen-bond network of water such that the native states of certain proteins are favored, thus modulating their function and stability. However, identifying cosolvents that act as osmolytes in biomimetic applications, such as the self-assembly of soft materials, remains challenging. The present work examined the effects of ethanol (EtOH) and acetonitrile (ACN) as cosolvents on the self-assembly of the amphiphilic polypeptide PSar₃₀-(l-Leu-Aib)₆ (S30L12), which incorporates α-helical hydrophobic blocks, in aqueous solution. The results provided a direct observation of morphological behavior of S30L12 as a function of solvent composition. Morphological transitions were investigated using transmission electron microscopy, while the packing of peptide molecules was assessed using circular dichroism analyses and evaluations of membrane fluidity. In the EtOH/H₂O mixtures, the EtOH strengthened the hydrogen-bond network of the water, thus limiting the hydrophobic hydration of S30L12 assemblies and enhancing hydrophobic interactions between assemblies. In contrast, ACN formed self-associated nanoclusters in water and at the hydrophobic cores of peptide assemblies to stabilize the edges exposed to bulk water and enhance the assembly kinetics. Fourier transform infrared (FT-IR) analysis indicated that both EtOH and ACN can modify the self-assembly of biomaterials in the same manner as osmolyte protectants or denaturants.

Pathway-Dependent Preferential Selection and Amplification of Variable Self-Assembled Peptide Nanostructures and Their Biological Activities

We demonstrate the formation of diverse peptide nanostructures, which are "out of equilibrium" based on a single dipeptide gelator. These structures represent the differential energy states of the free energy landscape, which are accessed by differential energy inputs provided by variable self-assembly pathways, that is, heat-cool method or ultrasonication. A higher energy input by the heat-cool method created a thermodynamically favored long entangled nanofibrillar network, while twisted ribbonlike structures were prevalent by ultrasonication. Interestingly, the nanofibrillar network representing the global thermodynamic minima could be accessed by simply melting the kinetically trapped structures as indicated by the thermoreversibility studies. The impact on the material strength was remarkable; gels with an order of magnitude difference in mechanical properties could be fabricated by simply modulating the self-assembly pathways. Interestingly, the thermodynamically favored nanofibrous network promoted cellular adhesion and survival, while a significant number of cells fail to adhere on the kinetically trapped twisted ribbons. Thus, nonequilibrium nanostructures open up new directions to develop advanced functional materials with diverse functions.

Solute-Solvent Interactions in Modern Physical Organic Chemistry: Supramolecular Polymers as a Muse

Interactions between solvents and solutes are a cornerstone of physical organic chemistry and have been the subject of investigations over the last century. In recent years, a renewed interest in fundamental aspects of solute-solvent interactions has been sparked in the field of supramolecular chemistry in general and that of supramolecular polymers in particular. Although solvent effects in supramolecular chemistry have been recognized for a long time, the unique opportunities that supramolecular polymers offer to gain insight into solute-solvent interactions have become clear relatively recently. The multiple interactions that hold the supramolecular polymeric structure together are similar in strength to those between solute and solvent. The cooperativity found in ordered supramolecular polymers leads to the possibility of amplifying these solute-solvent effects and will shed light on extremely subtle solvation phenomena. As a result, many exciting effects of solute-solvent interactions in modern physical organic chemistry can be studied using supramolecular polymers. Our aim is to put the recent progress into a historical context and provide avenues toward a more comprehensive understanding of solvents in multicomponent supramolecular systems.

Selective Capture and Recovery of Monoclonal Antibodies by Self-Assembling Supramolecular Polymers of High Affinity for Protein Binding

The separation and purification of therapeutic proteins from their biological resources pose a great limitation for industrial manufacturing of biologics in an efficient and cost-effective manner. We report here a supramolecular polymeric system that can undergo multiple reversible processes for efficient capture, precipitation, and recovery of monoclonal antibodies (mAbs). These supramolecular polymers, namely immunofibers (IFs), are formed by coassembly of a mAb-binding peptide amphiphile with a rationally designed filler molecule of varying stoichiometric ratios. Under the optimized conditions, IFs can specifically capture mAbs with a precipitation yield greater than 99%, leading to an overall mAb recovery yield of 94%. We also demonstrated the feasibility of capturing and recovering two mAbs from clarified cell culture harvest. These results showcase the promising potential of peptide-based supramolecular polymers as reversible affinity precipitants for mAb purification.

A combined experimental and computational approach reveals how aromatic peptide amphiphiles self-assemble to form ion-conducting nanohelices

Reported here is a combined experimental-computational strategy to determine structure-property-function relationships in persistent nanohelices formed by a set of aromatic peptide amphiphile (APA) tetramers with the general structure K S XEK S , where KS= S-aroylthiooxime modified lysine, X = glutamic acid or citrulline, and E = glutamic acid. In low phosphate buffer concentrations, the APAs self-assembled into flat nanoribbons, but in high phosphate buffer concentrations they formed nanohelices with regular twisting pitches ranging from 9-31 nm. Coarse-grained molecular dynamics simulations mimicking low and high salt concentrations matched experimental observations, and analysis of simulations revealed that increasing strength of hydrophobic interactions under high salt conditions compared with low salt conditions drove intramolecular collapse of the APAs, leading to nanohelix formation. Analysis of the radial distribution functions in the final self-assembled structures led to several insights. For example, comparing distances between water beads and beads representing hydrolysable KS units in the APAs indicated that the KS units in the nanohelices should undergo hydrolysis faster than those in the nanoribbons; experimental results verified this hypothesis. Simulation results also suggested that these nanohelices might display high ionic conductivity due to closer packing of carboxylate beads in the nanohelices than in the nanoribbons. Experimental results showed no conductivity increase over baseline buffer values for unassembled APAs, a slight increase (0.4 × 102 μS/cm) for self-assembled APAs under low salt conditions in their nanoribbon form, and a dramatic increase (8.6 × 102 μS/cm) under high salt conditions in their nanohelix form. Remarkably, under the same salt conditions, these self-assembled nanohelices conducted ions 5-10-fold more efficiently than several charged polymers, including alginate and DNA. These results highlight how experiments and simulations can be combined to provide insight into how molecular design affects self-assembly pathways; additionally, this work highlights how this approach can lead to discovery of unexpected properties of self-assembled nanostructures.

Peptide-Driven Shape Control of Low-Dimensional DNA Nanostructures

We report the rational design and fabrication of unusual low-dimensional DNA nanostructures through programmable and sequence-specific peptide interactions. Dual-bioactive block copolymers composed of DNA and amino acid-based polymers (DNA-b-poly(amino acid)) were synthesized by coupling oligonucleotides to phenylalanine (Phe)-based polymers. Unlike prototypical DNA block copolymers, which typically form simple spherical micelles, DNA-b-poly(amino acid) assemble into various low-dimensional structures such as nanofibers, ribbons, and sheets through controllable amino acid interactions. Moreover, DNA-b-poly(amino acid) assemblies can undergo protease-induced fiber-to-sheet shape transformations, where the morphology change is dictated by the type of enzymes and amino acid sequences. The peptide-based self-assembly reported here provides a programmable approach to fabricate dynamic DNA assemblies with diverse and unusual low-dimensional structures.