Controlled patterning of aligned self-assembled peptide nanotubes

Exploring the temperature dependence of β-hairpin peptide self-assembly

Herein, we study the role that hydrophobicity plays in the temperature-dependent self-assembly of a family of β-hairpin peptide amphiphiles through the lens of thermally folding a protein from its cold-denatured state. This was facilitated by the development of new computational tools to measure solvent-accessible charge (SAC) and solvent-accessible hydrophobicity (SAH) at the resolution of atomic groups. Peptides in their disordered states are characterized by large SAH values that shift their thermal assembly transitions to observable temperatures, which is not possible for most native proteins, allowing comparisons amongst peptides to be made. We find that peptides with large SAH values assemble into β-sheet-rich fibers at lower temperatures and at faster rates than peptides having smaller SAH values. This is consistent with peptide assembly being driven by the hydrophobic effect, which involves the release of ordered water from hydrophobic moieties during assembly. We also find that peptide SAH values correlate linearly with Tg, the midpoint of the transition defining monomeric peptide transitioning to fibrils, for peptides of similar charge. Interestingly, the data also suggest that although entropy drives assembly, the exact temperature at which the assembly transition takes place is likely influenced by additional thermodynamic considerations.

Hierarchical Self-Assembly of Short Peptides: Nanostructure Formation, Function Tailoring, and Applications

This article explores the hierarchical self-assembly of short peptides, which refers to the structured spatial arrangements of these molecules over long distances. This phenomenon is commonly found in nature and has important implications for biological structure and function. Short peptides are preferred for self-assembly because they have the ability to spontaneously create various nanostructures. This process, known as bottom-up assembly, allows for the addition of functional groups at the carboxyl or amine ends of the peptides. These functional groups enable specific functions that are extremely valuable in the fields of biotechnology and biomedicine. This text discusses the basic processes involved in the self-assembly of short peptides, such as the characteristics of amino acid side chains, the categorization of short peptides according to their chemical structure, the influence of intermolecular forces, and the dynamic nature of the self-assembly process. In addition, the paper discusses the various uses of short peptides in the disciplines of biomedicine and optoelectronics, including stimulus-responsive hydrogels, tissue engineering, and drug delivery. The article also suggests rational design principles for controlling the hierarchical self-assembly of short peptides, creating new commercial applications, particularly with functional hydrogels, and offers insights into the future of the discipline.

Molecular Propeller Tethering on a Dipeptide Induces a One-Step Conversion of Its Secondary Structure on Water Surface Promoted by Chiral Supramolecular Assembly

Water provides a unique surface for the formation of directed self-assembly and transformation of secondary structures of peptides and proteins as witnessed in the biological systems. Herein a one-step transformation of an amyloid-derived dipeptide is reported from β-sheet to α-helix structures on the water surface, facilitated by chiral supramolecular assembly. The study utilizes various analytical techniques to elucidate the structural transformation and the supramolecular packing of the peptide assemblies. Organizations such as spherical aggregates and molecular nanowires containing β-sheet structure are converted into (2D) molecular sheets comprising a larger planar area yet with a molecular level thickness of α-helix structure. The conformational features of the β-sheet to α-helix structural transformation are dominated by the intermolecular H-bonding, π-π stacking, and C─H···π interactions. Strikingly, the dynamic changes in the dihedral (intramolecular) angle between the aromatic rings of the dipeptide at the water surface alter the molecular packing and shorten the intermolecular H-bonds with larger binding energies required for the secondary structural transformation. Thus, the novel one-step strategy reports herein offers a simple, efficient, and hitherto unprecedented way of chiral supramolecular assembly directed total secondary structural transformation of the dipeptide on water surface.

Unveiling the multifaceted potential of amyloid fibrils: from pathogenic myths to biotechnological marvels

Amyloid fibrils, historically stigmatized due to their association with diseases like Alzheimer's and Parkinson's, are now recognized as a distinct class of functional proteins with extraordinary potential. These highly ordered, cross-β-sheet protein aggregates are found across all domains of life, playing crucial physiological roles. In bacteria, functional amyloids like curli fibers are essential for surface adhesion, biofilm formation, and viral DNA packaging. Fungal prions exploit amyloid conformations to regulate translation, metabolism, and virulence, while mammalian amyloids are integral to melanin synthesis, hormone storage, and antimicrobial defense. The stability and hydrophobic nature of amyloid scaffolds underpin these diverse biological functions. Beyond their natural roles, amyloid fibrils offer unique capabilities in biomedicine, nanotechnology, and materials science. Their exceptional mechanical strength and biocompatibility make them ideal for controlled drug delivery, tissue engineering scaffolds, and enzyme immobilization. The intrinsic fluorescence and optical properties of certain amyloids open up innovative applications in biosensors, molecular probes, and optoelectronic devices. Furthermore, amyloid fibrils can template metal nanowires, enhance conducting materials, and form nanocomposites by integrating with polymers. This newfound appreciation for the functional diversity of amyloids has ignited intense research efforts to elucidate their molecular mechanisms, stability, and tunable properties. By unraveling the structural intricacies of functional amyloids, researchers aim to harness their remarkable attributes for groundbreaking biomedical therapies, advanced nanomaterials, and sustainable biotechnological innovations. This review explores the transformative journey of amyloids from pathological entities to biotechnological marvels, highlighting their vast potential across agriculture, environmental remediation, and industrial processes.

3D Cryo-Electron Microscopy Reveals the Structure of a 3-Fluorenylmethyloxycarbonyl Zipper Motif Ensuring the Self-Assembly of Tripeptide Nanofibers

Short peptide-based supramolecular hydrogels appeared as highly interesting materials for applications in many fields. The optimization of their properties relies mainly on the design of a suitable hydrogelator through an empirical trial-and-error strategy based on the synthesis of various types of peptides. This approach is in part due to the lack of prior structural knowledge of the molecular architecture of the various families of nanofibers. The 3D structure of the nanofibers determines their ability to interact with entities present in their surrounding environment. Thus, it is important to resolve the internal structural organization of the material. Herein, using Fmoc-FFY tripeptide as a model amphiphilic hydrogelator and cryo-EM reconstruction approach, we succeeded to obtain a 3.8 Å resolution 3D structure of a self-assembled nanofiber with a diameter of approximately 4.1 nm and with apparently "infinite" length. The elucidation of the spatial organization of such nano-objects addresses fundamental questions about the way short amphiphilic N-Fmoc peptides lacking secondary structure can self-assemble and ensure the cohesion of such a lengthy nanostructure. This nanofiber is organized into a triple-stranded helix with an asymmetric unit composed of two Fmoc-FFY peptides per strand. The three identical amphiphilic strands are maintained together by strong lateral interactions coming from a 3-Fmoc zipper motif. This hydrophobic core of the nanofiber is surrounded by 12 phenyl groups from phenylalanine residues, nonplanar with the six Fmoc groups. Polar tyrosine residues at the C-term position constitute the hydrophilic shell and are exposed all around the external part of the assembly. This fiber has a highly hydrophobic central core with an internal diameter of only 2.4 Å. Molecular dynamics simulations highlight van der Waals and hydrogen bonds between peptides placed on top of each other. We demonstrate that the self-assembly of Fmoc-FFY, whether induced by annealing or by the action of a phosphatase on the phosphorylated precursor Fmoc-FFpY, results in two nanostructures with minor differences that we are unable to distinguish.

Advanced Antibacterial Strategies for Combatting Biomaterial-Associated Infections: A Comprehensive Review

Biomaterial-associated infections (BAIs) pose significant challenges in modern medical technologies, being a major postoperative complication and leading cause of implant failure. These infections significantly risk patient health, resulting in prolonged hospitalization, increased morbidity and mortality rates, and elevated treatment expenses. This comprehensive review examines the mechanisms driving bacterial adhesion and biofilm formation on biomaterial surfaces, offering an in-depth analysis of current antimicrobial strategies for preventing BAIs. We explore antimicrobial-eluting biomaterials, contact-killing surfaces, and antifouling coatings, emphasizing the application of antifouling polymer brushes on medical devices. Recent advancements in multifunctional antimicrobial biomaterials, which integrate multiple mechanisms for superior protection against BAIs, are also discussed. By evaluating the advantages and limitations of these strategies, this review aims to guide the design and development of highly efficient and biocompatible antimicrobial biomaterials. We highlight potential design routes that facilitate the transition from laboratory research to clinical applications. Additionally, we provide insights into the potential of synthetic biology as a novel approach to combat antimicrobial resistance. This review aspires to inspire future research and innovation, ultimately improving patient outcomes and advancing medical device technology.

One-step high-speed thermal-electric aerosol printing of piezoelectric bio-organic films for wirelessly powering bioelectronics

Piezoelectric biomaterials hold a pivotal role in the progression of bioelectronics and biomedicine, owing to their remarkable electromechanical properties, biocompatibility, and bioresorbability. However, their technological potential is restrained by certain challenges, including precise manipulation of nanobiomolecules, controlling their growth across nano-to-macro hierarchy, and tuning desirable mechanical properties. We report a high-speed thermal-electric driven aerosol (TEA) printing method capable of fabricating piezoelectric biofilms in a singular step. Electrohydrodynamic aerosolizing and in situ electrical poling allow instantaneous tuning of the spatial organization of biomolecular inks. We demonstrate TEA printing of β-glycine/polyvinylpyrrolidone films, and such films exhibit the piezoelectric voltage coefficient of 190 × 10-3 volt-meters per newton, surpassing that of industry-standard lead zirconate titanate by approximately 10-fold. Furthermore, these films demonstrate nearly two orders of magnitude improvement in mechanical flexibility compared to glycine crystals. We also demonstrate the ultrasonic energy harvesters based on the biofilms, providing the possibility of wirelessly powering bioelectronics.

Molecular self-assembled helix peptide nanotubes based on some amino acid molecules and their dipeptides: molecular modeling studies

CONTEXT

The paper considers the features of the structure and dipole moments of several amino acids and their dipeptides which play an important role in the formation of the peptide nanotubes based on them. The influence of the features of their chirality (left L and right D) and the alpha-helix conformations of amino acids are taken into account. In particular, amino acids with aromatic rings, such as phenylalanine (Phe/F), and branched-chain amino acids (BCAAs)-leucine (Leu/L) and isoleucine (Ile/I)-as well as corresponding dipeptides (diphenylalanine (FF), dileucine (LL), and diisoleucine (II)) are considered. The main features and properties of these dipeptide structures and peptide nanotubes (PNTs), based on them, are investigated using computational molecular modeling and quantum-chemical semi-empirical calculations. Their polar, piezoelectric, and photoelectronic properties and features are studied in detail. The results of calculations of dipole moments and polarization, as well as piezoelectric coefficients and band gap width, for different types of helical peptide nanotubes are presented. The calculated values of the chirality indices of various nanotubes are given, depending on the chirality of the initial dipeptides-the results obtained are consistent with the law of changes in the type of chirality as the hierarchy of molecular structures becomes more complex. The influence of water molecules in the internal cavity of nanotubes on their physical properties is estimated. A comparison of the results of these calculations by various computational methods with the available experimental data is presented and discussed.

METHOD

The main tool for molecular modeling of all studied nanostructures in this work was the HyperChem 8.01 software package. The main approach used here is the Hartree-Fock (HF) self-consistent field (SCF) with various quantum-chemical semi-empirical methods (AM1, PM3, RM1) in the restricted Hartree-Fock (RHF) and in the unrestricted Hartree-Fock (UHF) approximations. Optimization of molecular systems and the search for their optimal geometry is carried out in this work using the Polak-Ribeire algorithm (conjugate gradient method), which determines the optimized geometry at the point of their minimum total energy. For such optimized structures, dipole moments D and electronic energy levels (such as EHOMO and ELUMO), as well as the band gap Eg = ELUMO - EHOMO, were then calculated. For each optimized molecular structure, the volume was calculated using the QSAR program implemented also in the HyperChem software package.

Mechanistic Insights into Hyaluronic Acid Induced Peptide Nanofiber Organization in Supramolecular Hydrogels

Composite hydrogels composed of low-molecular-weight peptide self-assemblies and polysaccharides are gaining great interest as new types of biomaterials. Interactions between polysaccharides and peptide self-assemblies are well reported, but a molecular picture of their impact on the resulting material is still missing. Using the phosphorylated tripeptide precursor Fmoc-FFpY (Fmoc, fluorenylmethyloxycarbonyl; F, phenylalanine; Y, tyrosine; p, phosphate group), we investigated how hyaluronic acid (HA) influences the enzyme-assisted self-assembly of Fmoc-FFY generated in situ in the presence of alkaline phosphatase (AP). In the absence of HA, Fmoc-FFY peptides are known to self-assemble in nanometer thick and micrometer long fibers. The presence of HA leads to the spontaneous formation of bundles of several micrometers thickness. Using fluorescence recovery after photobleaching (FRAP), we find that in the bundles both (i) HA colocalizes with the peptide self-assemblies and (ii) its presence in the bundles is highly dynamic. The attractive interaction between negatively charged peptide fibers and negatively charged HA chains is explained through molecular dynamic simulations that show the existence of hydrogen bonds. Whereas the Fmoc-FFY peptide self-assembly itself is not affected by the presence of HA, this polysaccharide organizes the peptide nanofibers in a nematic phase visible by small-angle X-ray scattering (SAXS). The mean distance d between the nanofibers decreases by increasing the HA concentration c, but remains always larger than the diameter of the peptide nanofibers, indicating that they do not interact directly with each other. At a high enough HA concentration, the nematic organization transforms into an ordered 2D hexagonal columnar phase with a nanofiber distance d of 117 Å. Depletion interaction generated by the polysaccharides can explain the experimental power law variation d ∼ c - 1 / 4 and is responsible for the bundle formation and organization. Such behavior is thus suggested for the first time on nano-objects using polymers partially adsorbing on self-assembled peptide nanofibers.

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.

Impact of flexibility on the aggregation of polymeric macromolecules

Dependence of the dimerization probability and the aggregation behavior of polymeric macromolecules on their flexibility is studied using Langevin dynamics simulations. It is found that the dimerization probability is a non-monotonic function of the polymers persistence length. For a given value of inter-polymer attraction strength, semiflexible polymers have lower dimerization probability relative to flexible and rigid polymers of the same length. The threshold temperature of the formation of aggregates in a many-polymer system and its dependence on the polymers persistence length is also investigated. The simulation results of two- and many-polymer systems are in good agreement and show how the amount of flexibility affects the dimerization and the aggregation behaviors of polymeric macromolecules.

Advancements in Biosensors Based on the Assembles of Small Organic Molecules and Peptides

Over the past few decades, molecular self-assembly has witnessed tremendous progress in a variety of biosensing and biomedical applications. In particular, self-assembled nanostructures of small organic molecules and peptides with intriguing characteristics (e.g., structure tailoring, facile processability, and excellent biocompatibility) have shown outstanding potential in the development of various biosensors. In this review, we introduced the unique properties of self-assembled nanostructures with small organic molecules and peptides for biosensing applications. We first discussed the applications of such nanostructures in electrochemical biosensors as electrode supports for enzymes and cells and as signal labels with a large number of electroactive units for signal amplification. Secondly, the utilization of fluorescent nanomaterials by self-assembled dyes or peptides was introduced. Thereinto, typical examples based on target-responsive aggregation-induced emission and decomposition-induced fluorescent enhancement were discussed. Finally, the applications of self-assembled nanomaterials in the colorimetric assays were summarized. We also briefly addressed the challenges and future prospects of biosensors based on self-assembled nanostructures.

Molecular Dynamics Simulation of Self-Assembly Processes of Diphenylalanine Peptide Nanotubes and Determination of Their Chirality

In this work, we further developed a new approach for modeling the processes of the self-assembly of complex molecular nanostructures using molecular dynamics methods; in particular, using a molecular dynamics manipulator. Previously, this approach was considered using the example of the self-assembly of a phenylalanine helical nanotube. Now, a new application of the algorithm has been developed for implementing a similar molecular dynamic self-assembly into helical structures of peptide nanotubes (PNTs) based on other peptide molecules-namely diphenylalanine (FF) molecules of different chirality L-FF and D-FF. In this work, helical nanotubes were assembled from linear sequences of FF molecules with these initially different chiralities. The chirality of the obtained nanotubes was calculated by various methods, including calculation by dipole moments. In addition, a statistical analysis of the results obtained was performed. A comparative analysis of the structures of nanotubes was also performed using the method of visual differential analysis. It was found that FF PNTs obtained by the MD self-assembly method form helical nanotubes of different chirality. The regimes that form nanotubes of right chirality D from initial L-FF dipeptides and nanotubes of left chirality L from D-FF dipeptides are revealed. This corresponds to the law of changing the sign of the chirality of molecular helical structures as the level of their hierarchical organization becomes more complicated.

Atomic Insight on Inhibition of Fibrillization of Dipeptides by Replacement of Phenylalanine with Tryptophan

Tryptophan (Trp) conjugates destabilize amyloid fibrils responsible for amyloidoses. However, the mechanism of such destabilization is obscure. Herein the self-assembly of four synthesized Trp-containing dipeptides Boc-xxx-Trp-OMe (xxx: Val, Leu, Ile, and Phe) has been investigated and compared with the existing report on their Phe congeners. Two among them are the C-terminal tryptophan analogs of Boc-Val-Phe-OMe (VF, Aβ_18-19) and Boc-Phe-Phe-OMe (FF, Aβ_19-20), part of the central hydrophobic region of amyloid-β (Aβ_1-42). While Boc-Val-Trp-OMe (VW), Boc-Leu-Trp-OMe (LW), Boc-Ile-Trp-OMe (IW), and Boc-Phe-Trp-OMe (FW) displayed a spherical morphology in FESEM and AFM images, the corresponding phenylalanine-containing dipeptides displayed various fibrous structures. Single-crystal X-ray diffraction (SC-XRD) indicated that peptides VW and IW exhibited structures containing parallel β-sheet, cross-β-structure, sheet-like layer structure, and helical arrangement in the solid state. Interestingly, peptide FW displayed inverse γ-turn conformation (similar to open-turn structure), antiparallel β-sheet structure, columnar structure, supramolecular nanozipper structure, sheet-like layer arrangement, and helical architecture in the solid state. The open-turn conformation and nanozipper structure formation by FW may be the first example of a dipeptide that forms such structures. The minute but consistent differences in molecular packing at the atomic level between Trp and Phe congeners may be responsible for their remarkably different supramolecular structure generation. This molecular-level structural analysis may be helpful for the de novo design of peptide nanostructures and therapeutics. Similar studies by the Debasish Haldar group are reported, but they investigated the inhibition of fibrillization of dipeptides by tyrosine and interactions are expectedly different.

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

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

Engineering Multi-Scale Organization for Biotic and Organic Abiotic Electroactive Systems

Multi-scale organization of molecular and living components is one of the most critical parameters that regulate charge transport in electroactive systems-whether abiotic, biotic, or hybrid interfaces. In this article, an overview of the current state-of-the-art for controlling molecular order, nanoscale assembly, microstructure domains, and macroscale architectures of electroactive organic interfaces used for biomedical applications is provided. Discussed herein are the leading strategies and challenges to date for engineering the multi-scale organization of electroactive organic materials, including biomolecule-based materials, synthetic conjugated molecules, polymers, and their biohybrid analogs. Importantly, this review provides a unique discussion on how the dependence of conduction phenomena on structural organization is observed for electroactive organic materials, as well as for their living counterparts in electrogenic tissues and biotic-abiotic interfaces. Expansion of fabrication capabilities that enable higher resolution and throughput for the engineering of ordered, patterned, and architecture electroactive systems will significantly impact the future of bioelectronic technologies for medical devices, bioinspired harvesting platforms, and in vitro models of electroactive tissues. In summary, this article presents how ordering at multiple scales is important for modulating transport in both the electroactive organic, abiotic, and living components of bioelectronic systems.

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.

Biomimetic mineralization based on self-assembling peptides

Biomimetic science has attracted great interest in the fields of chemistry, biology, materials science, and energy. Biomimetic mineralization is the process of synthesizing inorganic minerals under the control of organic molecules or biomolecules under mild conditions. Peptides are the motifs that constitute proteins, and can self-assemble into various hierarchical structures and show a high affinity for inorganic substances. Therefore, peptides can be used as building blocks for the synthesis of functional biomimetic materials. With the participation of peptides, the morphology, size, and composition of mineralized materials can be controlled precisely. Peptides not only provide well-defined templates for the nucleation and growth of inorganic nanomaterials but also have the potential to confer inorganic nanomaterials with high catalytic efficiency, selectivity, and biotherapeutic functions. In this review, we systematically summarize research progress in the formation mechanism, nanostructural manipulation, and applications of peptide-templated mineralized materials. These can further inspire researchers to design structurally complex and functionalized biomimetic materials with great promising applications.

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.

Dipeptide nanostructures: Synthesis, interactions, advantages and biomedical applications

Short peptides are important in the design of self-assembled materials due to their versatility and flexibility. Self-assembled dipeptides, a group of peptide nanostructures, have highly attractive uses in the field of biomedicine. Recently these materials have proved to be important nanostructures because of their biocompatibility, low-cost and simplicity of synthesis, functionality/easy tunability and nano dimensions. Although there are different studies on peptide and protein-based nanostructures, more information about self-assembled nanostructures for dipeptides is still required to discover the advantages, challenges, importance, synthesis, interactions, and applications. This review describes and discusses the self-assembled dipeptide nanostructures especially for biomedical applications.

Cell Adhesion Motif-Functionalized Lipopeptides: Nanostructure and Selective Myoblast Cytocompatibility

The conformation and self-assembly of four lipopeptides, peptide amphiphiles comprising peptides conjugated to lipid chains, in aqueous solution have been examined. The peptide sequence in all four lipopeptides contains the integrin cell adhesion RGDS motif, and the cytocompatibility of the lipopeptides is also analyzed. Lipopeptides have either tetradecyl (C₁₄, myristyl) or hexadecyl (C₁₆, palmitoyl) lipid chains and peptide sequence WGGRGDS or GGGRGDS, that is, with either a tryptophan-containing WGG or triglycine GGG tripeptide spacer between the bioactive peptide motif and the alkyl chain. All four lipopeptides self-assemble above a critical aggregation concentration (CAC), determined through several comparative methods using circular dichroism (CD) and fluorescence. Spectroscopic methods [CD and Fourier transform infrared (FTIR) spectroscopy] show the presence of β-sheet structures, consistent with the extended nanotape, helical ribbon, and nanotube structures observed by cryogenic transmission electron microscopy (cryo-TEM). The high-quality cryo-TEM images clearly show the coexistence of helically twisted ribbon and nanotube structures for C₁₄-WGGRGDS, which highlight the mechanism of nanotube formation by the closure of the ribbons. Small-angle X-ray scattering shows that the nanotapes comprise highly interdigitated peptide bilayers, which are also present in the walls of the nanotubes. Hydrogel formation was observed at sufficiently high concentrations or could be induced by a heat/cool protocol at lower concentrations. Birefringence due to nematic phase formation was observed for several of the lipopeptides, along with spontaneous flow alignment of the lyotropic liquid crystal structure in capillaries. Cell viability assays were performed using both L929 fibroblasts and C2C12 myoblasts to examine the potential uses of the lipopeptides in tissue engineering, with a specific focus on application to cultured (lab-grown) meat, based on myoblast cytocompatibility. Indeed, significantly higher cytocompatibility of myoblasts was observed for all four lipopeptides compared to that for fibroblasts, in particular at a lipopeptide concentration below the CAC. Cytocompatibility could also be improved using hydrogels as cell supports for fibroblasts or myoblasts. Our work highlights that precision control of peptide sequences using bulky aromatic residues within "linker sequences" along with alkyl chain selection can be used to tune the self-assembled nanostructure. In addition, the RGDS-based lipopeptides show promise as materials for tissue engineering, especially those of muscle precursor cells.

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.

Stimuli-Responsive Membrane Anchor Peptide Nanofoils for Tunable Membrane Association and Lipid Bilayer Fusion

Self-assembled peptide nanostructures with stimuli-responsive features are promising as functional materials. Despite extensive research efforts, water-soluble supramolecular constructs that can interact with lipid membranes in a controllable way are still challenging to achieve. Here, we have employed a short membrane anchor protein motif (GLFD) and coupled it to a spiropyran photoswitch. Under physiological conditions, these conjugates assemble into ∼3.5 nm thick, foil-like peptide bilayer morphologies. Photoisomerization from the closed spiro (SP) form to the open merocyanine (MC) form of the photoswitch triggers rearrangements within the foils. This results in substantial changes in their membrane-binding properties, which also varies sensitively to lipid composition, ranging from reversible nanofoil reformation to stepwise membrane adsorption. The formed peptide layers in the assembly are also able to attach to various liposomes with different surface charges, enabling the fusion of their lipid bilayers. Here, SP-to-MC conversion can be used both to trigger and to modulate the liposome fusion efficiency.

Three-Dimensional Printing of Dipeptides with Spatioselective Programming of Crystallinity for Multilevel Anticounterfeiting

The functionalities of peptide microstructures and nanostructures can be enhanced by controlling their crystallinity. Gaining control over the crystallinity within the desired structure, however, remains a challenge. We have developed a three-dimensional (3D) printing method that enables spatioselective programming of the crystallinity of diphenylalanine (FF) dipeptide microarchitectures. A femtoliter ink meniscus is used to spatially control reprecipitation self-assembly, enabling the printing of a freestanding FF microstructure with programmed shape and crystallinity. The self-assembly crystallization of FF can be switched on and off at will by controlling the evaporation of the binary solvent. The evaporation-dependent crystallization was theoretically studied by the numerical simulation of supersaturation fields in the meniscus. We found that a 3D-printed FF microarchitecture with spatially programmed crystallinity can carry a 3D digital optical anisotropy pattern, applicable to generating polarization-encoded anticounterfeiting labels. This crystallinity-controlled additive manufacturing will pave the new way for facilitating the creation of peptide-based devices.

Enhancing the optical response and biosensing capabilities of bioinspired peptide micro-waveguides exploiting chromatic aberration

Bioinspired peptide waveguides of mesoscopic length scales have established a new paradigm in photonics with possible applications in precision bioimaging, sensing, and diagnostics. Here, we improve the efficiency of coupling various constituent colors of a white light source into single self-assembled microtube-shaped passive peptide waveguides by employing chromatic aberration. Thus, we use a chromatically aberrated microscope objective lens to couple light into peptide waveguides. Using both numerical simulation and experiments, we show that the waveguide response displays higher quality factor, wavelength selectivity, and axial coupling range compared to a chromatically corrected standard plan-fluoritic objective lens. We also demonstrate absorption and refractive index-based sensing by studying the changes in the optical responses of the peptide tubes in the presence of a wide concentration range of the absorptive Congo red, and the nonabsorptive Coumarin dyes. The former understandably display a much higher response than the latter due to the low finesse of the waveguides. We obtain a detection limit of around 10 nM for Congo red, and 10 mM for Coumarin. Our study opens up possibilities for deploying such peptide microtubes for various biosensing applications utilizing spectral and waveguide characteristics.

Controlled-Alignment Patterns of Dipeptide Micro- and Nanofibers

Ordered assemblies of the peptide diphenylalanine (FF) are produced and deposited on planar substrates. The FF aggregate growth is achieved through precipitation from aqueous ammonia solutions induced by solvent evaporation. The applied dip-coating technique confines the FF assembly growth to a narrow zone near the three-phase contact. The growth was observed online by optical microscopy and was investigated systematically as a function of the process parameters. Depending on the external gas flow (to influence solvent evaporation), the withdrawal speed, the initial FF, and the initial ammonia concentrations, FF forms long, straight, and rigid microfibers and/or shorter, curved nanofibers. Under certain process conditions, the FF fibers can also aggregate into stripes. These can be deposited as large arrays of uniform stripes with regular widths and spacings. Scenarios leading to the various types of fibers and the stripe formation are presented and discussed in view of the experimental findings.

Microfabrication of peptide self-assemblies: inspired by nature towards applications

Peptide self-assemblies show intriguing and tunable physicochemical properties, and thus have been attracting increasing interest over the last two decades. However, the micro/nano-scale dimensions of the self-assemblies severely restrict their extensive applications. Inspired by nature, to genuinely realize the practical utilization of the bio-organic super-architectures, it is beneficial to further organize the peptide self-assemblies to integrate the properties of the individual supermolecules and fabricate higher-level organizations for smart functional devices. Therefore, cumulative studies have been reported on peptide microfabrication giving rise to diverse properties. This review summarizes the recent development of the microfabrication of peptide self-assemblies, discussing each methodology along with the diverse properties and practical applications of the engineered peptide large-scale, highly-ordered organizations. Finally, the current limitations of the state-of-the-art microfabrication strategies are critically assessed and alternative solutions are suggested.

Aromatic interactions directing peptide nano-assembly

Self-assembly is a process of spontaneous organization of molecules as a result of non-covalent interactions. Organized self-assembly at the nano level is emerging as a powerful tool in the bottom-up fabrication of functional nanostructures for targeted applications. Aromatic π-π stacking plays a significant role by facilitating the persistent supramolecular association of individual subunits to the self-assembled structures of high stability. Understanding, the supramolecular chemistry of the materials interacting through aromatic interactions, is of tremendous interest in not only constructing functional materials but also in revealing the mechanism of molecular assembly in living organisms. This chapter aims to focus on understanding the potential role of π-π interactions in directing and regulating the self-assembly of peptide nanostructures. The scope of the chapter starts with an outline of the history and mechanism of the aromatic π-π interactions. It progresses through the design strategy for the assembly of peptides containing aromatic rings, the conditions affecting the aromatic stacking interactions, their resulting nanoassemblies, properties, and applications. The properties and applications of the supramolecular materials formed through the aromatic stacking interactions are highlighted to provide an increased understanding of the role of weak interactions in the design and construction of novel functional materials.

Peptide-based nanomaterials: Self-assembly, properties and applications

Peptide-based materials that have diverse structures and functionalities are an important type of biomaterials. In former times, peptide-based nanomaterials with excellent stability were constructed through self-assembly. Compared with individual peptides, peptide-based self-assembly nanomaterials that form well-ordered superstructures possess many advantages such as good thermo- and mechanical stability, semiconductivity, piezoelectricity and optical properties. Moreover, due to their excellent biocompatibility and biological activity, peptide-based self-assembly nanomaterials have been vastly used in different fields. In this review, we provide the advances of peptide-based self-assembly nanostructures, focusing on the driving forces that dominate peptide self-assembly and assembly mechanisms of peptides. After that, we outline the synthesis and properties of peptide-based nanomaterials, followed by the applications of functional peptide nanomaterials. Finally, we provide perspectives on the challenges and future of peptide-based nanomaterials.

Optical Polarization-Based Measurement Methods for Characterization of Self-Assembled Peptides' and Amino Acids' Micro- and Nanostructures

In recent years, self-assembled peptides’ and amino acids’ (SAPA) micro- and nanostructures have gained much research interest. Here, description of how SAPA architectures can be characterized using polarization-based optical measurement methods is provided. The measurement methods discussed include: polarized Raman spectroscopy, polarized imaging microscopy, birefringence imaging, and fluorescence polarization. An example of linear polarized waveguiding in an amino acid Histidine microstructure is discussed. The implementation of a polarization-based measurement method for monitoring peptide self-assembly processes and for deriving molecular orientation of peptides is also described.

Molecular modelling and computational studies of peptide diphenylalanine nanotubes, containing waters: structural and interactions analysis

The work is devoted to computer studies of the structural and physical properties of such self-organizing structures as peptide nanotubes (PNT) based on diphenylalanine (FF) dipeptide with different initial isomers of the left (L-FF) and right (D-FF) chiralities of these dipeptides. The structures under study are considered both with empty anhydrous and with internal cavities filled with water molecules. Molecular models of both chiralities are investigated using quantum-chemical DFT and semi-empirical methods, which are in consistent with the known experimental data. To study the effect of nano-sized clusters of water molecules embedded in the inner hydrophilic cavity on the properties of nanotubes (including the changes in their dipole moments and polarizations), as well as the changes in the structure and properties of water clusters themselves (their own dipole moments and polarizations), the surfaces of internal cavities of nanotubes and outer surfaces of water cluster structures for both types of chirality are analyzed. A specially developed method of visual differential analysis of structural features of (bio)macromolecular structures is applied for these studies. The results obtained of a number of physical properties (interacting energies, dipole moments, polarization values) are given for various cases and analyzed in comparison with the known data. These data are necessary for analyzing the interactions of water molecules with hydrophilic parts of nanotube molecules based on FF, such as COO- and NH3 + , since they determine many properties of the structures under study. The data obtained are useful for further analysis of the possible adhesion and capture of medical molecular components by active layers of FF-based PNT, which can be designed for creating capsules for targeted delivery of pharmaceuticals and drugs on their basis.

Molecular Dynamics Simulation Study of the Self-Assembly of Phenylalanine Peptide Nanotubes

In this paper, we propose and use a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure using external force actions. A molecular dynamics manipulator (MD manipulator) is a controlled MDS type. As an example, the applicability of the developed algorithm for assembling peptide nanotubes (PNT) from linear phenylalanine (F or Phe) chains of different chirality is presented. The most adequate regimes for the formation of nanotubes of right chirality D from the initial L-F and nanotubes of left chirality L of their initial dipeptides D-F modes were determined. We use the method of a mixed (vector–scalar) product of the vectors of the sequence of dipole moments of phenylalanine molecules located along the nanotube helix to calculate the magnitude and sign of chirality of self-assembled helical phenylalanine nanotubes, which shows the validity of the proposed approach. As result, all data obtained correspond to the regularity of the chirality sign change of the molecular structures with a hierarchical complication of their organization.

Phthalocyanine-Triggered Helical Dipeptide Nanotubes with Intense Circularly Polarized Luminescence

Nanotubes with circularly polarized luminescence (CPL) are attracting much attention due to many potential applications, such as chiroptical materials, displays, and sensing. However, it remains a challenge to change the assemblies of ordinarily molecular building blocks into CPL supramolecular nanotubes. Herein, the regulation of quite common dipeptide (Fmoc-FF) assemblies into unprecedented helical nanotubes exhibiting intense CPL is reported by simply doping a few phthalocyanine (octakis(carboxyl)phthalocyaninato zinc complex (Pc)) molecules. Interestingly, altering the Fmoc-FF/Pc molar ratios over a wide range cannot change the nanotubes structures according to transmission electron microscopy (TEM) and atomic force microscope (AFM) measurements. Although molecular dynamics simulations suggest that the noncovalent interactions between Fmoc-FF and Pc are quite weak, few Pc molecules can still change the secondary structures of a large number of Fmoc-FF assemblies, which hierarchically form helical supramolecular nanotubes with long-range ordered molecular packing, leading to intense CPL signals with large luminescence dissymmetry factor (g_lum  = 0.04). Consequently, the chiral reorganization of Fmoc-FF assemblies is dependent on the coassembly between Pc molecule and Fmoc-FF supramolecular architectures. These results open the possibility for the fine-tuning of helix and supramolecular nanotubes with CPL properties by using a small number of cofactors.

Protecting Group-Directed Diversity in the Morphology of Self-Assembled Ant-Aib Dipeptides: Garland-Like Architecture and Nanovesicle Formation

The morphology and molecular organization of a set of different N-terminal protecting groups containing dipeptides were investigated. The dipeptides consisted of two rigid noncanonical amino acids, Ant and Aib (X-Ant-Aib-OMe; Ant: anthranilic acid and 2-aminobenzoic acid, Aib: 2-aminoisobutyric acid). The change of the N-terminal protecting groups (X = Boc (peptide 1), N^α-fluorenylmethoxycarbonyl (Fmoc) (peptide 2), o-NBS (peptide 3), and p-NBS (peptide 4); NBS = nitrobenzyl sulfonyl group) displayed a characteristic morphological variety. Field emission scanning electron microscopy (FE-SEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM) experiments suggested that while t-butyloxycarbonyl (Boc) and p-NBS containing peptides exhibited distinct rod-like fiber structures, Fmoc and o-NBS containing peptides displayed remarkable vesicular structures. FE-SEM and thermogravimetric analysis (TGA) suggested that peptide nanostructures demonstrated excellent thermal stability in dry conditions. Interestingly, peptides 2 and 4 exhibited a type-III N₂ gas adsorption isotherm. Fluorescence microscopy analysis revealed that nanovesicles formed by peptides 2 and 3 have drug encapsulation properties exemplified by curcumin, rhodamine B, and carboxyfluorescein. These results will help in designing peptide-based nanomaterials for diverse applications.

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.

A Novel Copper-Binding Peptide That Self-Assembles Into a Transparent Antibacterial and Antiviral Coating

The health, economy, and quality of life all over the world are greatly affected by bacterial infections and viral outbreaks. Bacterial cells and viruses, such as influenza, can spread through contaminated surfaces and fomites. Therefore, a possible way to fight these pathogens is to utilize antibacterial and antiviral coatings, which reduce their numbers on contaminated surfaces. Here, we present a novel short peptide that can self-assemble, adhere to various surfaces, and bind different metal ions such as copper, which provides the surface with antibacterial and antiviral properties. For these functions, the peptide incorporates the amino acid 3,4-dihydroxyphenylalanine (DOPA), which provides the peptide with adhesive capabilities; a diphenylalanine motif that induces the self-assembly of the peptide; the metal-binding hexahistidine sequence. Our results demonstrate that the coating, which releases monovalent cuprous ions and hydrogen peroxide, provides the surfaces with significant antibacterial and antiviral properties. Additionally, the coating remains transparent, which is favorable for many objects and especially for display screens.

Supramolecular Structures Generated via Self-Assembly of a Cell Penetrating Tetrapeptide Facilitate Intracellular Delivery of a Pro-apoptotic Chemotherapeutic Drug

Development of drug carriers, which can chaperone xenobiotics directly to their site of action, is an essential step for the advancement of precision medicine. Cationic nanoparticles can be used as a drug delivery platform for various agents including chemotherapeutics, oligonucleotides, and antibodies. Self-assembly of short peptides facilitates the formation of well-defined nanostructures suitable for drug delivery, and varying the polarity of the self-assembly medium changes the nature of noncovalent interactions in such a way as to generate numerous unique nanostructures. Here, we have synthesized an ultrashort cell-penetrating tetrapeptide (sequence Lys-Val-Ala-Val), with Lys as a cationic amino acid, and studied the self-assembly property of the BOC-protected (L1) and -deprotected (L2) analogues. Spherical assemblies obtained from L1/L2 in a 1:1 aqueous ethanol system have the ability to encapsulate small molecules and successfully enter into cells, thus representing them as potential candidates for intracellular drug delivery. To verify the efficacy of these peptides in the facilitation of drug efficacy, we generated encapsulated versions of the chemotherapeutic drug doxorubicin (Dox). L1- and L2-encapsulated Dox (Dox-L1 and Dox-L2), similar to the unencapsulated drug, induced upregulation of regulator of G protein signaling 6 (RGS6) and Gβ5, the critical mediators of ATM/p53-dependent apoptosis in Dox-treated cancer cells. Further, Dox-L1/L2 damaged DNA, triggered oxidative stress and mitochondrial dysfunction, compromised cell viability, and induced apoptosis. The ability of Dox-L1 to mediate cell death could be ameliorated via knockdown of either RGS6 or Gβ5, comparable to the results obtained with the unencapsulated drug. These data provide an important proof of principle, identifying L1/L2 as drug delivery matrices.

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.

Systematic Method for the Exploration, Representation, and Classification of the Diphenylalanine Solvatomorphic Space

An understanding of the conditions that govern the self-assembly process of peptides is a fundamental step toward the design of new nanostructures that possess interesting properties. In this work, we first synthesize and explore extensively diphenylalanine (FF) self-assembling crystals formed in different solvents (i.e., solvatomorphs) using polarized optical microscopy and transmission electron microscopy. Then, we develop a numerical method that allows an unambiguous classification of the solvatomorphs through a K-means automatic clustering method. In addition, we generate a two-dimensional (2D) representation of the solvatomorphic space together with the clustering results via a principal component analysis (PCA). The classification is based on structural similarities of solvatomorphs as revealed by the analysis of their respective infrared spectra. Among the 20 samples considered, 4 clear clusters are extracted within which the compounds show very similar crystalline structures. The information extracted allows us to assign many of the peaks that appear in the complex IR spectra of the samples considered. The implementation of the overall procedure we propose, i.e., "GAULOIS" and "REFRACT-R", is transferable to other types of spectra and paves the way for a systematic, fast, and accurate classification method applicable to various types of experimental spectroscopic data.

Assembly of a Phenylalanine Nanotube by the use of Molecular Dynamics Manipulator

Studies of the processes of self-organization and self-assembly of various complexly organized (including spiral) structures based on amino acids intensively carried out in recent years. Various methods of molecular modeling, including molecular dynamics (MD) methods, are developed. In this paper, we propose a new approach for a relatively simple technique for conducting MD simulation (MDS) of various molecular nanostructures, determining the trajectory of the MD run and forming the final structure: a molecular dynamic manipulator (MD manipulator). It is an imitation of the operation of an existing or imaginary device or structure by applying force to the existing initial structure in order to obtain a new final structure, having the same chemical composition, but with a different geometry (topology). The PUMA-CUDA software package was applied as the main MD modeling program, which uses the physics of the PUMA software package, developed by the laboratory headed by N.K. Balabaev. Using this MDS tool, you can investigate the formation of helical structures from a linear sequence of any amino acids variation. As an example, the applicability of the developed algorithm for assembling nanotubes from linear phenylalanine (Phe) chains of different chirality (left L-Phe and right D-Phe) is considered by including additional force effects in the molecular dynamics simulation program for these structures. During the MD run, the applied actions, which are the same for the left and right helices of the formed nanotubes, lead the system to an α-helix structure. The work was carried out in an interactive mode using a number of additional programs, incl. trajectory analyzer program MD (TAMD). As a result, the modes that are most adequate for the formation of nanotubes of the right chirality D from the initial L-Phe monomer and nanotubes of the left chirality L from the D-Phe amino acid monomer were determined. The results obtained were compared with data from other works on modeling similar nanotubes of different chirality and experimental data. These are fully in line with the law of change in sign of chirality of molecular structures with complication of their hierarchical level of organization. The molecular animation of the assembly of a left-chiral nanotube from D-monomers is freely available at: http://lmd.impb.ru/Supplementary/PHE.avi.

Self-Templated, Enantioselective Assembly of an Amyloid-like Dipeptide into Multifunctional Hierarchical Helical Arrays

Chiral self-assembly of peptides has attracted great interest owing to their promising applications in biomedicine, chemistry, and materials science. However, compared with the rich knowledge about their chiral self-assembly at the molecular or nanoscale, the formation of long-range-ordered hierarchical helical arrays (HHAs) from simple peptides remains a formidable challenge. Herein, we report the self-templated assembly of an amyloid-like dipeptide into long-range-ordered HHAs by their spontaneous fibrillization and hierarchical helical assembly within a confined film. The chiral interactions between the peptide and diamines result in geometry frustration and the phase transition of self-assembling peptide films from achiral spherulite structures into chiral HHAs. By changing the chirality and enantioselective interactions, we can control the phase behavior, handedness, and chiroptics of the self-assembled HHAs precisely. Moreover, the redox activity of the HHAs allows the in situ decoration of nanoparticles with high catalytic activity. These results provide insights into the chiral self-assembly of peptides and the fabrication of highly ordered materials with complex architectures and promising applications in chiroptics and catalysis.

Self-Assembly of Ferrocenyl Phenylalanine into Nanohelical Arrays via Kinetic Control

The spontaneous alignment of self-assembled chiral nanostructures at macroscopic scales is appealing because of their unique structural features and physicochemical properties. Here we present the construction of highly ordered bioorganometallic nanohelical arrays on the basis of the hierarchical chiral self-assembly of the simple ferrocenyl l-phenylalanine (Fc-l-F). The formation of nanohelical arrays is under kinetic control, which can be controlled by changing the growth time and the vapor temperature. The chiral nanoarrays can generate circularly polarized luminescence by the incorporation of fluorescent dyes. Moreover, due to the redox activity of the Fc moiety, the nanohelical arrays show enhanced electrical capacity compared with previously reported peptide nanomaterials. The results shed light on the highly ordered chiral self-assembled nanomaterials, which have potential applications in fields of optics, sensing, and energy storage.