Role of water in directing diphenylalanine assembly into nanotubes and nanowires

Amino-Acid-Encoded Bioinspired Supramolecular Self-Assembly of Multimorphological Nanocarriers

Supramolecular self-assembly has emerged as an efficient tool to construct well-organized nanostructures for biomedical applications by small organic molecules. However, the physicochemical properties of self-assembled nanoarchitectures are greatly influenced by their morphologies, mechanical properties, and working mechanisms, making it challenging to design and screen ideal building blocks. Herein, using a biocompatible firefly-sourced click reaction between the cyano group of 2-cyano-benzothiazole (CBT) and the 1,2-aminothiol group of cysteine (Cys), an amino-acid-encoded supramolecular self-assembly platform Cys(SEt)-X-CBT (X represents any amino acid) is developed to incorporate both covalent and noncovalent interactions for building diverse morphologies of nanostructures with bioinspired response mechanism, providing a convenient and rapid strategy to construct site-specific nanocarriers for drug delivery, cell imaging, and enzyme encapsulation. Additionally, it is worth noting that the biodegradation of Cys(SEt)-X-CBT generated nanocarriers can be easily tracked via bioluminescence imaging. By caging either the thiol or amino groups in Cys with other stimulus-responsive sites and modifying X with probes or drugs, a variety of multi-morphological and multifunctional nanomedicines can be readily prepared for a wide range of biomedical applications.

Applications of peptide-based nanomaterials in targeting cancer therapy

To meet the demand for precision medicine, researchers are committed to developing novel strategies to reduce systemic toxicity and side effects in cancer treatment. Targeting peptides are widely applied due to their affinity and specificity, and their ability to be high-throughput screened, chemically synthesized and modified. More importantly, peptides can form ordered self-assembled structures through non-covalent supramolecular interactions, which can form nanostructures with different morphologies and functions, playing crucial roles in targeted diagnosis and treatment. Among them, in targeted immunotherapy, utilizing targeting peptides to block the binding between immune checkpoints and ligands, thereby activating the immune system to eliminate cancer cells, is an advanced therapeutic strategy. In this mini-review, we summarize the screening, self-assembly, and biomedical applications of targeting peptide-based nanomaterials. Furthermore, this mini-review summarizes the potential and optimization strategies of targeting peptides.

Peptide Supramolecular Self-Assembly: Regulatory Mechanism, Functional Properties, and Its Application in Foods

Peptide self-assembly, due to its diverse supramolecular nanostructures, excellent biocompatibility, and bright application prospects, has received wide interest from researchers in the fields of biomedicine and green life technology and the food industry. Driven by thermodynamics and regulated by dynamics, peptides spontaneously assemble into supramolecular structures with different functional properties. According to the functional properties derived from peptide self-assembly, applications and development directions in foods can be found and explored. Therefore, in this review, the regulatory mechanism is elucidated from the perspective of self-assembly thermodynamics and dynamics, and the functional properties and application progress of peptide self-assembly in foods are summarized, with a view to more adaptive application scenarios of peptide self-assembly in the food industry.

Protein Nanotubes as Advanced Material Platforms and Delivery Systems

Protein nanotubes (PNTs) as state-of-the-art nanocarriers are promising for various potential applications both in the food and pharmaceutical industries. Derived from edible starting sources like α-lactalbumin, lysozyme, and ovalbumin, PNTs bear properties of biocompatibility and biodegradability. Their large specific surface area and hydrophobic core facilitate chemical modification and loading of bioactive substances, respectively. Moreover, their enhanced permeability and penetration ability across biological barriers such as intestinal mucus, extracellular matrix, and thrombus clot, make it promising platforms for health-related applications. Most importantly, their simple preparation processes enable large-scale production, supporting applications in the biomedical and nanotechnological fields. Understanding the self-assembly principles is crucial for controlling their morphology, size, and shape, and thus provides the ground to a multitude of applications. Here, the current state-of-the-art of PNTs including their building materials, physicochemical properties, and self-assembly mechanisms are comprehensively reviewed. The advantages and limitations, as well as challenges and prospects for their successful applications in biomaterial and pharmaceutical sectors are then discussed and highlighted. Potential cytotoxicity of PNTs and the need of regulations as critical factors for enabling in vivo applications are also highlighted. In the end, a brief summary and future prospects for PNTs as advanced platforms and delivery systems are included.

New Insight into the Structural Nature of Diphenylalanine Nanotube through Comparison with Amyloid Assemblies

Diphenylalanine (FF) nanotubes are a star material in the field of peptide self-assembly and have demonstrated numerous intriguing applications. Due to its resemblance to amyloid assembly, the FF nanotube is widely regarded as a simplified mimic of amyloids. Yet, whether FF nanotube truly possesses amyloid structure remains an open question. To better understand the structural nature of FF nanotube, we herein performed a comparative structural investigation between FF nanotube and typical amyloid systems by Aβ1-40, Aβ1-42, Aβ16-22, Aβ13-23, α-synuclein, and lysozyme using Fourier transform infrared spectroscopy. Through this comparative investigation, we obtained clear evidence to support that the FF nanotube does not possess a β-sheet structure, a key structural characteristic of amyloid assembly, thus revealing the non-amyloid structural nature of the FF nanotube. At last, in light of our new finding, we further discussed the unique self-assembly behaviors of FF during nanotube formation and the implications of our work for FF nanotube related applications.

Multiscale Simulations to Discover Self-Assembled Oligopeptides: A Benchmarking Study

Peptide self-assembly is critical for biomedical and material discovery and production. While it is costly to experimentally test every possible peptide design, computational assessment provides an affordable solution to evaluate many designs and prioritize synthesis and characterization. Following a theoretical investigation, we present a systematic analysis of all-atom and coarse-grained simulations to predict peptide self-assembly. Benchmarking studies of two model dipeptides allow us to assess the impacts of intrinsic properties (such as amino acids and terminal modifications) and external environment (such as salinity) on the simulated aggregation. Further examination of 20 oligopeptides containing two to five amino acids shows good agreement among our theory, simulations, and prior experimental observations. The success rate of our prediction is 90%. Therefore, our theory, simulation, and analysis can be useful to identify peptide designs that can self-assemble and predict the potential nanostructures. These findings lay the ground for future virtual screening of peptide-assembled nanostructures and computer-aided biologics design.

Piezoactive Bioorganic Diphenylalanine Films: Mechanism of Phase Formation

Self-organized peptides are unique materials with various applications in biology, medicine, and nanotechnology. Many of these applications require fabrication of homogeneous thin films having high piezoelectric effect and sufficiently low roughness. Recently, a facile method for the controlled deposition of flat solid films of the most studied peptide, diphenylalanine (FF), has been proposed, which is based on the crystallization of FF in the amorphous phase under the action of water vapor. This method is very advantageous compared with crystallization from a liquid phase reported previously. Here, we thoroughly investigate the mechanism of solid-state transformation from the amorphous to crystalline phase. The study revealed that the process proceeds in two distinct stages, maintaining clamped condition of self-assembling building blocks that preserve the films' morphology and high piezoelectric activity. We emphasize the critical role of water diffusion that governs two-dimensional growth of crystalline domains in FF films, merging in very dense, flat, and homogeneous films. These findings open a wide perspective for using this methodology for the direct fabrication of biofilms from the amorphous phase. We thus expect the application of these films to various nanotechnological applications of self-assembled structures.

Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes

Diphenylalanine (FF) peptides exhibit a unique ability to self-assemble into nanotubes with confined water molecules playing pivotal roles in their structure and function. This study investigates the structure and dynamics of diphenylalanine peptide nanotubes (FFPNTs) using all-atom molecular dynamics (MD) and grand canonical Monte Carlo combined with MD (GCMC/MD) simulations with both the CHARMM additive and Drude polarizable force fields. The occupancy and dynamics of confined water molecules were also examined. It was found that less than 2 confined water molecules per FF help stabilize the FFPNTs on the x-y plane. Analyses of the kinetics of confined water molecules revealed distinctive transport behaviors for bound and free water, and their respective diffusion coefficients were compared. Our results validate the importance of polarizable force field models in studying peptide nanotubes and provide insights into our understanding of nanoconfined water.

RAFT-synthesis and self-assembly-induced emission of pendant diphenylalanine-tetraphenylethylene copolymers

Manipulation of the properties of aggregation-induced emission luminogens (AIEgens) by combining self-assembling motifs has attracted significant interest as a promising approach to developing various advanced materials. In this study, pendant diphenylalanine-tetraphenylethylene (TPE) copolymers exhibiting the ability for self-assembly and AIE properties were synthesized via reversible addition-fragmentation chain-transfer (RAFT) copolymerization. The resulting anionic and non-ionic amphiphilic copolymers with a carbon-carbon main chain bearing diphenylalanine-TPE through-space interactions self-assembled into nanorods and nanofibers, showing blue emissions originating from the aggregation of TPE side chains in the assembled structures. Suitable tuning of the comonomer composition, monomer structure, and environmental conditions (e.g., solvent polarity) enables manipulation of the self-assembled structures, AIE properties, and aggregation-induced circular dichroism by achiral TPE units via through-space interactions with diphenylalanine moieties.

Machine Learning-Guided Adaptive Parametrization for Coupling Terms in a Mixed United-Atom/Coarse-Grained Model for Diphenylalanine Self-Assembly in Aqueous Ionic Liquids

Precise regulation of the peptide self-assembly into ordered nanostructures with intriguing properties has attracted intense attention. However, predicting peptide assembly at atomic resolution is a challenge due to both the structural flexibility of peptides and the associated huge computational costs. A machine learning-guided adaptive parametrization method was proposed for developing a mixed atomic and coarse-grained (CG) model through a multiobjective optimization strategy. Our model incorporates the united-atom (UA) model for diphenylalanine (P) and the polarizable electrostatic-variable coarse-grained (VaCG) model for aqueous ionic liquid [BMIM]+[BF4]- solution. In this mixed model, the coupling van der Waals (vdW) interaction is addressed by introducing virtual sites (VS) in the UA model to interact with solvent CG beads. The coupling parameters, including the electrostatic parameter and vdW parameters, are automatically optimized through ML-guided adaptive parametrization. The performance of this model was tested by some microstructural properties, e.g., the average number of P-P intermolecular hydrogen bonds (HBs) and radius distribution functions (RDFs) between P and different fragments of IL, in comparison with all-atom (AA) simulations. The computational cost is significantly reduced using such a parametrization scheme, which could search tens of thousands of force-field parameter sets, while needing only a small fraction of them to be assessed with molecular dynamics (MD) simulations. We used such a mixed resolution model to investigate the self-assembly in IL-water mixtures with variants of IL concentration (X). The long-range-ordered fibril structure is formed in a pure water system (X = 0). With an increase of IL concentrations, the formation of an ordered self-assembly nanostructure is prohibited, instead forming branched fibril at X = 2 mol % or amorphous aggregates when X > 10 mol %, resulting from the interplay between π-stacking and HB interactions between P and IL. The qualitative agreement between the simulated structures and the observed morphologies in experiments indicates the applicability of ML-guided parametrization strategy in the study of complex systems, such as polymers, lipid bilayers, and polysaccharides.

Influence of pH on the self-assembly of diphenylalanine peptides: molecular insights from coarse-grained simulations

Nanostructures fabricated from peptide self-assemblies are attracting increasing attention owing to their possible applications in biology and nanotechnology. A known example is an aromatic dipeptide (diphenylalanine, FF) which is extracted from Alzheimer's β-amyloid polypeptide as the core recognition motif for molecular self-assembly. Many studies have been carried out to organize FF peptides into various functional ordered nanostructures. For potential applications of self-assembled FF-based nanomaterials, it becomes important to consider some influencing factors (e.g., solvents, peptide concentrations, pH, temperature, etc.) on the self-assembly process. Among these factors, the effect of pH on the self-assembly process of FF peptides into assembled nanostructures through simulation studies is the main focus of the present work. In the current study, we have investigated the assembly pathway of 1000 FF peptides and qualitatively evaluated the morphological changes of FF-based nanostructures at different pH values by performing extensive coarse-grained molecular dynamics (CG-MD) simulations. Structural analyses suggest that FF peptides can spontaneously assemble into nanotubes with different shapes under acidic, neutral and basic conditions. Based on the analysis of FF nanostructure formation pathways in different pH solutions, the self-assembly of the nanotube involves the aggregation of molecules to form a bilayer, the curling of a bilayer to form a vesicle and the transformation of a vesicle into a tubular structure. It is noted that a flat hollow columnar structure is observed as a special intermediate state during the transformation process of a vesicle-like to a tube-like structure. Energetic analysis suggests that the aggregation of FF peptides is driven by the vdW interactions but the aggregation shape is mainly affected by the electrostatic interactions. Overall, this study provides further understanding of the self-assembly behavior of aromatic short peptide derivatives in different pH solutions.

Kinetic Controlled Chirality Transfer and Induction in 2D Hydrogen-Bonding Assemblies of Glycylglycine on Au(111)

Chirality transfer is of vital importance that dominates the structure and functionality of biological systems and living matters. External physical stimulations, e.g. polarized light and mechanical forces, can trigger the chirality symmetry breaking, leading to the appearance of the enantiomeric entities created from a chiral self-assembly of achiral molecule. Here, several 2D assemblies with different chirality, synthesized on Au(111) surface by using achiral building blocks - glycylglycine (digly), the simplest polypeptide are reported. By delicately tuning the kinetic factors, i.e., one-step slow/rapid deposition, or stepwise slow deposition with mild annealing, achiral square hydrogen-bond organic frameworks (HOF), homochiral rhombic HOF and racemic rectangular assembly are achieved, respectively. Chirality induction and related symmetry broken in assemblies are introduced by the handedness (H-bond configurations in principle) of the assembled motifs and then amplified to the entire assemblies via the interaction between motifs. The results show that the chirality transfer and induction of biological assemblies can be tuned by altering the kinetic factors instead of applying external forces, which may offer an in-depth understanding and practical approach to peptide chiral assembly on the surfaces and can further facilitate the design of desired complex biomolecular superstructures.

Identification of heterochirality-mediated stereochemical interactions in peptide architectures

In this work, we illustrate a strategy for constructing heterochiral peptide architectures with distinct structural, mechanical and thermal characteristics. A series of nanotube structures based on diphenylalanine (FF) and its chiral derivatives were examined. Pronounced effects relating to heterochirality on mechanostability and thermal stability can be identified. The homochiral peptide FF and its enantiomer ff formed nanotubes with high thermal and mechanical stabilities (Young's modulus: 20.3 ± 5.9 GPa for FF and 21.2 ± 4.7 GPa for ff). In contrast, heterochiral nanotubes formed by Ff and fF manifest superstructures along the axial direction with differed thermal and mechanical strength (Young's modulus: 7.3 ± 2.4 GPa for Ff and 8.3 ± 2.1 GPa for fF). Combining their single-crystal XRD structure and in silico results, it was demonstrated that the spatial orientations of aromatic moieties were subtly changed by heterochirality of peptide building blocks, which led to intramolecular face-to-face interactions. As the result, both intermolecular axial and interchannel interactions in heterochiral nanotubes were weakened as reflected in the strikingly deteriorated mechanical and thermal stabilities. Conversely, two aromatic side chains of the homochiral peptides were staggered and formed interdigitated steric zippers, which served as strong glues that secured the robustness of nanotubes in both axial and radial orientation. Furthermore, the generality of the heterochiral-mediated stereochemical effects was demonstrated in other "FF class" dipeptides, including fluorinated Ff, FW and FL. Our results unequivocally revealed the relationship between amino acid chirality, peptide molecule packing, and physical stabilities of "FF class" dipeptide self-assembled materials and provide valuable molecular insights into chirality-mediated stereochemical interactions in determining the properties of peptide architectures.

Nanotubes and water-channels from self-assembling dipeptides

Dipeptides are attractive building blocks for biomaterials in light of their inherent biocompatibility, biodegradability, and simplicity of preparation. Since the discovery of diphenylalanine (Phe-Phe) self-assembling ability into nanotubes, research efforts have been devoted towards the identification of other dipeptide sequences capable of forming these interesting nanomorphologies, although design rules towards nanotube formation are still elusive. In this review, we analyze the dipeptide sequences reported thus far for their ability to form nanotubes, which often feature water-filled supramolecular channels as revealed by single-crystal X-ray diffraction, as well as their properties, and their potential biological applications, which span from drug delivery and regenerative medicine, to bioelectronics and bioimaging.

Synthesis and self-assembly of a diphenylalanine–tetraphenylethylene hybrid monomer and RAFT polymers with aggregation-induced emission

A hybrid monomer consisting of diphenylalanine with the self-assembling ability and tetraphenylethylene with aggregation-induced emission properties was synthesized and employed for reversible addition–fragmentation chain transfer polymerization.

Hierarchical Materials from High Information Content Macromolecular Building Blocks: Construction, Dynamic Interventions, and Prediction

Hierarchical materials that exhibit order over multiple length scales are ubiquitous in nature. Because hierarchy gives rise to unique properties and functions, many have sought inspiration from nature when designing and fabricating hierarchical matter. More and more, however, nature's own high-information content building blocks, proteins, peptides, and peptidomimetics, are being coopted to build hierarchy because the information that determines structure, function, and interfacial interactions can be readily encoded in these versatile macromolecules. Here, we take stock of recent progress in the rational design and characterization of hierarchical materials produced from high-information content blocks with a focus on stimuli-responsive and "smart" architectures. We also review advances in the use of computational simulations and data-driven predictions to shed light on how the side chain chemistry and conformational flexibility of macromolecular blocks drive the emergence of order and the acquisition of hierarchy and also on how ionic, solvent, and surface effects influence the outcomes of assembly. Continued progress in the above areas will ultimately usher in an era where an understanding of designed interactions, surface effects, and solution conditions can be harnessed to achieve predictive materials synthesis across scale and drive emergent phenomena in the self-assembly and reconfiguration of high-information content building blocks.

Triboelectric Generator Based on Oriented Self-Assembled Peptide Microbelts

Along with piezoelectric nanogenerators, triboelectric nanogenerators (TENGs) collecting energy from mechanical vibrations proved to be simple, low-cost, and efficient sources of electricity for various applications. In view of possible biomedical applications, the search for TENGs made of biomolecular and biocompatible materials is demanding. Diphenylalanine (FF) microstructures are promising for these applications due to their unique characteristics and ability to form various morphologies (microribbons, spherical vesicles, fibrils, micro- and nanotubes, nanorods, etc.). In this work, we developed a contact-separate mode TENG based on arrays of oriented FF microbelts deposited by dip-coating technique and studied their performance under various temperature treatments. We show that these TENGs outperform piezoelectric nanogenerators based on FF microbelts in terms of short-circuit current (I_SC), open-circuit voltage (V_OC), and output power. It was found that bound water captured in FF nanochannels mainly affects V_OC, whereas mobile water increases I_SC. We also found that the cyclization of FF molecules increases the performance of TENG likely due to an increase in surface energy and surface flattening.

Looking into a crystal ball: printing and patterning self-assembled peptide nanostructures

The solution processability of organic semiconductors and conjugated polymers along with the advent of nanomaterials as conducting inks have revolutionized next-generation flexible consumer electronics. Another equally important class of nanomaterials, self-assembled peptides, heralded as next-generation materials for bioelectronics, have a lot of potential in printed technology. In this minireview, we address the self-assembly process in dipeptides, their application in electronics, and recent progress in three-dimensional printing. The prospect of a generalizable path for nanopatterning self-assembled peptides using ice lithography and its challenges are further discussed.

Structures of synthetic helical filaments and tubes based on peptide and peptido-mimetic polymers

Synthetic peptide and peptido-mimetic filaments and tubes represent a diverse class of nanomaterials with a broad range of potential applications, such as drug delivery, vaccine development, synthetic catalyst design, encapsulation, and energy transduction. The structures of these filaments comprise supramolecular polymers based on helical arrangements of subunits that can be derived from self-assembly of monomers based on diverse structural motifs. In recent years, structural analyses of these materials at near-atomic resolution (NAR) have yielded critical insights into the relationship between sequence, local conformation, and higher-order structure and morphology. This structural information offers the opportunity for development of new tools to facilitate the predictable and reproduciblede novodesign of synthetic helical filaments. However, these studies have also revealed several significant impediments to the latter process – most notably, the common occurrence of structural polymorphism due to the lability of helical symmetry in structural space. This article summarizes the current state of knowledge on the structures of designed peptide and peptido-mimetic filamentous assemblies, with a focus on structures that have been solved to NAR for which reliable atomic models are available.

Peptide Coassembly to Enhance Piezoelectricity for Energy Harvesting

The discovery of piezoelectricity in self-assembled peptide nanostructures opens an avenue to a new regime of piezoelectric materials and enables the fundamental investigation of electromechanical coupling in biomaterials. However, strategies for fabricating peptides with desired properties are still lacking. We find that a peptide-based coassembly process effectively controls the properties of peptide nanomaterials and demonstrates their application potential in nanogenerators. The composing peptides and their concentration influence the morphology, molecular property, and physical property of coassembled crystals. Compared with self-assembled diphenylalanine peptides, the coassembled peptides of diphenylalanine and phenylalanine-tryptophan show a 38% increase in piezoelectric coefficient, and the resulting harvesting device shows nearly a 3-fold increase in open-circuit voltage outputs.

Fabrication of self-assembled nanostructures for intracellular drug delivery from diphenylalanine analogues with rigid or flexible chemical linkers

Self-assembly of molecular building blocks is a simple and useful approach to generate supramolecular structures with varied morphologies and functions. By studying the chemical properties of the building blocks and tuning the parameters of their self-assembly process, the resultant supramolecular assemblies can be optimized for the required downstream applications. To this end, in the present study we have designed and synthesized three different molecular building blocks composed of two diphenylalanine (FF) units connected to each other through three different linkers: ethylenediamine, succinic acid, or terephthalaldehyde. Under identical conditions, all the three building blocks self-assemble into supramolecular architectures with distinct morphologies. However, by varying the polarity of the self-assembly medium, the nature of the non-covalent interactions changes in such a way as to generate additional self-assembled structures unique to each building block. Utilizing microscopic and spectroscopic techniques, we characterized the morphological variety generated by each building block/linker combination. These data represent the first report analysing the diversity of nanostructures that can be generated from identical dipeptide-based molecular backbones simply by varying the chemical linker. We also demonstrate that the spherical assemblies and nanorod structures fabricated from these dipeptide/linker pairs can act as drug delivery systems. More specifically, the spherical assembly generated by two FF dipeptides linked via ethylenediamine and nanorods fabricated from terephthalaldehyde linked FF dipeptides were able to encapsulate the cancer chemotherapeutic agent doxorubicin (DOX) and chaperone the drug into cells. Thus, these supramolecular assemblies represent a new platform for the development of efficient and effective intracellular drug delivery systems.

Expanding the Structural Diversity and Functional Scope of Diphenylalanine-Based Peptide Architectures by Hierarchical Coassembly

Modulation of the structural diversity of diphenylalanine-based assemblies by molecular modification and solvent alteration has been extensively explored for bio- and nanotechnology. However, regulation of the structural transition of assemblies based on this minimal building block into tunable supramolecular nanostructures and further construction of smart supramolecular materials with multiple responsiveness are still an unmet need. Coassembly, the tactic employed by natural systems to expand the architectural space, has been rarely explored. Herein, we present a coassembly approach to investigate the morphology manipulation of assemblies formed by N-terminally capped diphenylalanine by mixing with various bipyridine derivatives through intermolecular hydrogen bonding. The coassembly-induced structural diversity is fully studied by a set of biophysical techniques and computational simulations. Moreover, multiple-responsive two-component supramolecular gels are constructed through the incorporation of functional bipyridine molecules into the coassemblies. This study not only depicts the coassembly strategy to manipulate the hierarchical nanoarchitecture and morphology transition of diphenylalanine-based assemblies by supramolecular interactions but also promotes the rational design and development of smart hydrogel-based biomaterials responsive to various external stimuli.

Dipeptide Nanostructure Assembly and Dynamics via in Situ Liquid-Phase Electron Microscopy

In this paper, we report the in situ growth of FF nanotubes examined via liquid-cell transmission electron microscopy (LCTEM). This direct, high spatial, and temporal resolution imaging approach allowed us to observe the growth of peptide-based nanofibrillar structures through directional elongation. Furthermore, the radial growth profile of FF nanotubes through the addition of monomers perpendicular to the tube axis has been observed in real-time with sufficient resolution to directly observe the increase in diameter. Our study demonstrates that the kinetics, dynamics, structure formation, and assembly mechanism of these supramolecular assemblies can be directly monitored using LCTEM. The performance of the peptides and the assemblies they form can be verified and evaluated using post-mortem techniques including time-of-flight secondary ion mass spectrometry (ToF-SIMS).

Probing the formation of isolated cyclo-FF peptide clusters by far-infrared action spectroscopy

Small cyclic peptides containing phenylalanine residues are prone to aggregate in the gas phase into highly hydrophobic chains. A combination of laser desorption, mass spectrometry and conformational selective IR-UV action spectroscopy allows us to obtain detailed structural insights into the formation processes of the cyclic L-phenylalanyl-L-phenylalanine dipeptide (named cyclo-FF) aggregates. The rigid properties of cyclo-FF result in highly resolved IR spectra for the smaller clusters (n ≤ 3) and corresponding conformational assignments. For the higher order clusters (n > 3) the spectra are less resolved, however the observed ratios, peak positions and trends in IR shifts are key to make predictions on their structural details. Whereas the mid-IR spectral region between 1000-1800 cm^-1 turns out to be undiagnostic for these small aggregates and the 3 μm region only for specific calculated structures, the far-IR contains valuable information that allows for clear assignments.

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations

The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.

Gelation of a Pentapeptide in Alcohols

Properties of solvents such as polarity and H-bond-forming ability are critical for the formation of an organogel and have a significant impact on the gel behavior, as solvents are the majority of organogel systems. However, so far, there is still a lack of systematic studies regarding the effects of molecular structures of solvents on the characteristics of organogels. Motivated by revealing such a relationship, in this paper, we studied the morphologies of assemblies, gelation behaviors, and secondary structures of a pentapeptide termed EAF-5 in a wide variety of alcohols. The side chains and lengths of carbon chains of the solvent molecules were found to play a critical role in the self-assembly and gelation of EAF-5. EAF-5 was capable of self-assembling into fibers and entangling into a network in alcohols including ethanol, propanol, butanol, n-pentanol, and n-hexanol, which further immobilized the corresponding alcohols to form gels. In these organogels, increasing β-sheet secondary structures of the peptides were formed by introducing side chains and extending the length of primary alcohol molecules. We hypothesized that alcohol molecules with extended lengths and side chains reduced the gelator-solvent interactions and promoted the gelator-gelator interactions, resulting in the self-assembly of EAF-5 into fibril structures and development of gels. These findings provide a new sight into the interactions between gelators and solvents and are helpful for designing peptide-based organogelators.

A colored hydrophobic peptide film based on self-assembled two-fold topology

Structural colors are abundant in nature and bear advantages over pigment-based colors, such as higher durability, brilliance and often physical hydrophobicity, thus underlying their vast potential for technological applications. Recently, biomimetics of complex natural topologies resulting in such effects has been extensively studied, requiring advanced processing and fabrication techniques. Yet, artificial topologies combining structural coloration and hydrophobicity have not been reported. Herein, we present the bottom-up fabrication of short self-assembling peptides as surface covering films, resulting in an easily achievable multilevel morphology of primary structures in a foam-like enclosure, producing structural colors and hydrophobicity. We demonstrate simple techniques allowing controlled coloration of different surfaces while maintaining an >100° water contact angle (WCA). The new artificial topology is much simpler than the natural counterparts and is not limited to a specific peptide, thus allowing the design of modular materials with unparalleled multifunctionalities and potential for further tuning and modifications.

Janus Nanosheets with Face-Selective Molecular Recognition Properties from DNA-Peptide Conjugates

Chemical and functional anisotropy in Janus materials offer intriguing possibilities for constructing complex nanostructures and regulating chemical and biological reactions. Here, the authors report the fabrication of Janus nanosheets from molecular building blocks composed of two information-carrying biopolymers, DNA and peptides. Experimental and structural modeling studies reveal that DNA-peptide diblock conjugates assemble into Janus nanosheets with distinct DNA and peptide faces. The surprising level of structural control is attributed to the exclusive parallel β-sheet formation of phenylalanine-rich peptides. This approach is extended to triblock DNA1-peptide-DNA2 conjugates, which assemble into nanosheets presenting two different DNA on opposite faces. The Janus nanosheets with independently addressable faces are utilized to organize an enzyme pair for concerted enzymatic reactions, where enhanced catalytic activities are observed. These results demonstrate that the predictable and designable peptide interaction is a promising tool for creating Janus nanostructures with regio-selective and sequence-specific molecular recognition properties.

Recent advances in the fabrication and bio-medical applications of self-assembled dipeptide nanostructures

Molecular self-assembly is a widespread natural phenomenon and has inspired several researchers to synthesize a compendium of nano/microstructures with widespread applications. Biomolecules like proteins, peptides and lipids are used as building blocks to fabricate various nanomaterials. Supramolecular peptide self-assembly continue to play a significant role in forming diverse nanostructures with numerous biomedical applications; however, dipeptides offer distinctive supremacy in their ability to self-assemble and produce a variety of nanostructures. Though several reviews have articulated the progress in the field of longer peptides or polymers and their self-assembling behavior, there is a paucity of reviews or literature covering the emerging field of dipeptide-based nanostructures. In this review, our goal is to present the recent advancements in dipeptide-based nanostructures with their potential applications.

Self-assembly of diphenylalanine peptides on graphene via detailed atomistic simulations

The self-assembly of diphenylalanine peptides (FF) on a graphene layer, in aqueous solution, is investigated, through all atom molecular dynamics simulations. Two interfacial systems are studied, with different concentrations of dipeptides and the results are compared with an aqueous solution of FF at room temperature. Corresponding length and time scales of the formed structures are quantified providing important insight into the adsorption mechanism of FF onto the graphene surface. A hierarchical formation of FF structures is observed involving two sequential processes: first, a stabilized interfacial layer of dipeptides onto the graphene surface is formulated, which next is followed by the development of a structure of self-aggregated dipeptides on top of this layer. The whole procedure is completed in almost 200 ns, whereas self-assembly in the system without graphene is accomplished much faster; in less than 50 ns cylindrical structures, the microscopic signal of the macroscopic fibrillar ones, are formed. Strong π-π* interactions between FF and the graphene lead to a parallel orientation to the graphene layer of the phenyl rings within a characteristic time of 80 ns, similar to the one indicated by the time evolution of the number of adsorbed FF atoms at the surface. Reduction in the number of hydrogen bonds between FF peptides is observed because of the graphene layer, since it disturbs their self-assembly propensity. The self-assembly of dipeptides and their adsorption onto the graphene surface destruct the hydrogen bond network of water, in the vicinity of FF, however, the total number of hydrogen bonds in all systems increases, promoting the formed structures.

Self-Assembled Peptide Nanofibers with Voltage-Regulated Inverse Photoconductance

Inverse photoconductance is an uncommon phenomenon observed in selective low-dimensional materials, in which the electrical conductivity of the materials decreases under light illumination. The unique material property holds great promise for biomedical applications in photodetectors, photoelectric logic gates, and low-power nonvolatile memory, which remains a daunting challenge. Especially, tunable photoconductivity for biocompatible materials is highly desired for interfacing with biological systems but is less explored in organic materials. Here, we report nanofibers self-assembled with cyclo-tyrosine-tyrosine (cyclo-YY) having voltage-regulated inverse photoconductance and photoconductance. The peptide nanofibers can be switched back and forth by a bias voltage for imitating biological sensing in artificial vision and memory devices. A peptide optoelectronic resistive random access memory (PORRAM) device has also been fabricated using the nanofibers that can be electrically switched between long-term and short-term memory. The underlying mechanism of the reversible photoconductance is discussed in this paper. Due to the inherent biocompatibility of peptide materials, the reversible photoconductive nanofibers may have broad applications in sensing and storage for biotic and abiotic interfaces.

Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules

DFT (VASP) and semi-empirical (HyperChem) calculations for the L- and D-chiral diphenylalanine (L-FF and D-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. The results obtained show that after optimization, the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like-cluster obtained after optimization inside L-FF and D-FF PNT and total L-FF and D-FF PNT with embedded water/ice cluster are discussed.

Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like cluster, obtained after optimization inside L-FF and D-FF PNT, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed.

Self-Assembled Dipeptide Aerogels with Tunable Wettability

Constructing supramolecular materials with tunable properties and functions is a great challenge due to the complex competition between multiple assembly pathways. Herein, we report that dipeptides can self-assemble into aerogels with entirely different surface wettability through precisely controlling the assembly pathways. Charged groups or aromatic residues are selectively exposed on the surface of their nanoscale building blocks which results either in a superhydrophilic or highly hydrophobic surface. With this special property, single component dipeptide aerogels can play diverse roles in medical care applications. This study suggests great promise in the synthesis of supramolecular materials with different targeted functions from the same molecular unit.

Coassemble dopamine and GHK tripeptide into fluorescent nanoparticles for pH sensing

Fluorescent nanostructures have been widely applied to biomedical researches and clinical diagnosis such as biolabeling/imaging/sensing and have even acted as therapy reagents. Peptide-based fluorescent nanostructures attract recent interest from biomedical researchers. Inspired by the natural existence of GHK-Cu complex with a growth factor-like effect in human blood, here we have developed a novel approach for designing nanosensors through the co-assembling of two kinds of biomolecules. By making best use of both π-π stacking between carbon rings and the easy-oxidation property of an important transmitter molecule, dopamine (DA), we successfully built up a supersensitive and robust fluorescent pH nanosensor by co-assembling oxidized DA (DA_ox ) with a tripeptide GHK. The GHK-DA_ox nanostructures have a quantum yield of 20.82%, which might be the brightest one among all the current co-assembling structures merely through unmodified biomolecules. We envision this approach could open a new avenue for not only hybrid nanostructure construction, but also may inspire the bioengineering of in vivo luminescent probes.

Pharmaceutical Formulation and Characterization of Dipeptide Nanotubes for Drug Delivery Applications

Peptide nanotubes are promising materials for a variety of biomedical applications with ultrashort (≤7 amino acids) forms providing particular promise for clinical translation. The manufacture of peptide nanotubes has, however, been associated with toxic organic solvents restricting clinical use. The purpose of this work is to formulate dipeptide nanotubes using mild techniques easily translated to industrial upscale and to characterize their physiochemical and biological properties. Phenylalanine-phenylalanine variants can be successfully formulated using distilled water as demonstrated here. Formulations are homogenous in shape (tubular), with apparent size (50-260 nm) and a zeta potential of up to +30 mV. L-(H₂ N-FF-COOH), and D-enantiomers (H₂ N-ff-COOH) demonstrate no toxicity against glioblastoma cells and are explored for ability to deliver a model hydrophilic molecule, sodium fluorescein, at pH 5.5 (tumor) and 7.4 (physiological). Peptide nanotubes loaded with >85% sodium fluorescein, demonstrate burst release characteristics, fitting the Weibull model of drug release. This research provides important data contributing to the pharmaceutical formulation of peptide nanotubes as drug delivery platforms for hydrophilic drugs.

Molecular self-assembly of porphyrin and BODIPY chromophores connected with diphenylalanine moieties

In this study, a series of diphenylalanine tetra-substituted porphyrin derivatives were synthesized and their self-assembly ability was extensively studied. Apart from investigating the impact of incorporating many peptide moieties onto a porphyrin molecule; another perspective was investigated as well, namely the connection of two different chromophore entities (porphyrin and BODIPY) onto the same diphenylalanine molecule. Interestingly, various supra-molecular nanostructures were observed depending on the solvent mixture as well as the protecting group of the peptides, namely spheres, plaques and fibrils. The obtained self-assemblies were studied via UV-vis absorption and emission spectroscopies. Mainly red shifting was observed, indicating the formation of [Formula: see text]-aggregates in the self-assembled state. However, in one case a blue shifted UV-vis spectrum was obtained suggesting the formation of [Formula: see text]-type aggregates. Concerning the porphyrin-diphenylalanine-BODIPY derivative, additional fluorescence studies were performed in order to examine a possible interaction between the two chromophores in the excited state. Indeed, the emission measurements indicated that upon photo-excitation of the BODIPY entity, a very efficient energy or electron transfer process takes place from the BODIPY molecule to the porphyrin macrocycle.

Biopolymeric photonic structures: design, fabrication, and emerging applications

Biological photonic structures can precisely control light propagation, scattering, and emission via hierarchical structures and diverse chemistry, enabling biophotonic applications for transparency, camouflaging, protection, mimicking and signaling. Corresponding natural polymers are promising building blocks for constructing synthetic multifunctional photonic structures owing to their renewability, biocompatibility, mechanical robustness, ambient processing conditions, and diverse surface chemistry. In this review, we provide a summary of the light phenomena in biophotonic structures found in nature, the selection of corresponding biopolymers for synthetic photonic structures, the fabrication strategies for flexible photonics, and corresponding emerging photonic-related applications. We introduce various photonic structures, including multi-layered, opal, and chiral structures, as well as photonic networks in contrast to traditionally considered light absorption and structural photonics. Next, we summarize the bottom-up and top-down fabrication approaches and physical properties of organized biopolymers and highlight the advantages of biopolymers as building blocks for realizing unique bioenabled photonic structures. Furthermore, we consider the integration of synthetic optically active nanocomponents into organized hierarchical biopolymer frameworks for added optical functionalities, such as enhanced iridescence and chiral photoluminescence. Finally, we present an outlook on current trends in biophotonic materials design and fabrication, including current issues, critical needs, as well as promising emerging photonic applications.

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.

Self-assembly of dipeptide Boc-diphenylalanine nanotubes inside electrospun polymeric fibers with strong piezoelectric response

Dipeptide biomaterials are strong piezoelectric materials that can convert applied mechanical forces into electricity. We have developed large-scale hybrid electrospun arrays containing N-tert-butoxycarbonyl (Boc) diphenylalanine in the form of nanotubes embedded in biocompatible polymers. These nanofibers exhibit strong piezoelectric properties when a periodic mechanical force is applied. The nanostructured hybrid materials were produced by the electrospinning technique. Optical absorption measurements show four bands in the spectral region 240-280 nm indicating quantum confinement due to nanotube formation of Boc-diphenylalanine in dichloromethane solutions. A strong blue photoluminescence emission was observed from nanotubes crystallized inside the fiber arrays during the electrospinning process. These two dimensional hybrid biomaterial structures are able to generate voltage, current and density power of up to 30 V, 300 nA and 2.3 μW cm^-2, respectively, when a periodical force of 1.5 N is applied. The dipeptide-polymer electrospun arrays can power several liquid-crystal display panels and may be used for biomedical applications and as bio-energy sources.