Controlling multiple fluorescent signal output in cyclic peptide-based supramolecular systems

Hierarchical Assembly of Intrinsically Disordered Short Peptides

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

Cu2+-Induced self-assembly and amyloid formation of a cyclic D,L-α-peptide: structure and function

In a wide spectrum of neurodegenerative diseases, self-assembly of pathogenic proteins to cytotoxic intermediates is accelerated by the presence of metal ions such as Cu²⁺. Only low concentrations of these early transient oligomeric intermediates are present in a mixture of species during fibril formation, and hence information on the extent of structuring of these oligomers is still largely unknown. Here, we investigate dimers as the first intermediates in the Cu²⁺-driven aggregation of a cyclic D,L-α-peptide architecture. The unique structural and functional properties of this model system recapitulate the self-assembling properties of amyloidogenic proteins including β-sheet conformation and cross-interaction with pathogenic amyloids. We show that a histidine-rich cyclic D,L-α-octapeptide binds Cu²⁺ with high affinity and selectivity to generate amyloid-like cross-β-sheet structures. By taking advantage of backbone amide methylation to arrest the self-assembly at the dimeric stage, we obtain structural information and characterize the degree of local order for the dimer. We found that, while catalytic amounts of Cu²⁺ promote aggregation of the peptide to fibrillar structures, higher concentrations dose-dependently reduce fibrillization and lead to formation of spherical particles, showing self-assembly to different polymorphs. For the initial self-assembly step to the dimers, we found that Cu²⁺ is coordinated on average by two histidines, similar to self-assembled peptides, indicating that a similar binding interface is perpetuated during Cu²⁺-driven oligomerization. The dimer itself is found in heterogeneous conformations that undergo dynamic exchange, leading to the formation of different polymorphs at the initial stage of the aggregation process.

1D alignment of proteins and other nanoparticles by using reversible covalent bonds on cyclic peptide nanotubes

Peptide nanotubes deposit on mica surface can be used for the alignment of proteins thank to the use of dynamic covalent bonds that allow the incorporation of appropriate ligands on nanotube surface.

Molecular Self-Assembly and Supramolecular Chemistry of Cyclic Peptides

This Review focuses on the establishment and development of self-assemblies governed by the supramolecular interactions between cyclic peptides. The Review first describes the type of cyclic peptides able to assemble into tubular structures to form supramolecular cyclic peptide nanotubes. A range of cyclic peptides have been identified to have such properties, including α-peptides, β-peptides, α,γ-peptides, and peptides based on δ- and ε-amino acids. The Review covers the design and functionalization of these cyclic peptides and expands to a recent advance in the design and application of these materials through their conjugation to polymer chains to generate cyclic peptide-polymer conjugates nanostructures. The Review, then, concentrates on the challenges in characterizing these systems and presents an overview of the various analytical and characterization techniques used to date. This overview concludes with a critical survey of the various applications of the nanomaterials obtained from supramolecular cyclic peptide nanotubes, with a focus on biological and medical applications, ranging from ion channels and membrane insertion to antibacterial materials, anticancer drug delivery, gene delivery, and antiviral applications.

100th Anniversary of Macromolecular Science Viewpoint: User's Guide to Supramolecular Peptide-Polymer Conjugates

This Viewpoint highlights the design principles and development of peptide-based supramolecular polymers. Here we delve deep into the practicalities of synthesizing and characterizing these macromolecular structures and provide a thorough overview of the benefits and challenges that come with these systems. This Viewpoint emphasizes to beginners and experts alike the importance of understanding the fundamental behavior and self-assembly processes when designing these complex and dynamic functional materials.

Understanding complex supramolecular landscapes: non-covalent macrocyclization equilibria examined by fluorescence resonance energy transfer

As molecular self-assembled systems increase in complexity, due to a large number of participating entities and/or the establishment of multiple competing equilibria, their full understanding becomes likewise more complicated, and the use of diverse analytical techniques that can afford complementary information is required. We demonstrate in this work that resonance excitation energy transfer phenomena, measured by fluorescence spectroscopy in combination with other optical spectroscopies, can be a valuable tool to obtain supplementary thermodynamic data about complex supramolecular landscapes that other methods fail to provide. In particular, noncovalent macrocyclization processes of lipophilic dinucleosides are studied here by setting up a competition between intra- and intermolecular association processes of Watson-Crick H-bonding pairs. Multiwavelength analysis of the monomer emission changes allowed us to determine cyclotetramerization constants and to quantify chelate cooperativity, which was confirmed to be substantially larger for the G-C than for the A-U pair. Furthermore, when bithiophene-BODIPY donor-acceptor energy transfer probes are employed in these competition experiments, fluorescence and circular dichroism spectroscopy measurements in different regions of the visible spectrum additionally reveal intermolecular interactions occurring simultaneously at both sides of the macrocyclization reaction: the cyclic product, acting as a host for the competitor, and the monomer reactant, ultimately leading to macrocycle denaturation.

Multicomponent peptide assemblies

Self-assembled peptide nanostructures have been increasingly exploited as functional materials for applications in biomedicine and energy. The emergent properties of these nanomaterials determine the applications for which they can be exploited. It has recently been appreciated that nanomaterials composed of multicomponent coassembled peptides often display unique emergent properties that have the potential to dramatically expand the functional utility of peptide-based materials. This review presents recent efforts in the development of multicomponent peptide assemblies. The discussion includes multicomponent assemblies derived from short low molecular weight peptides, peptide amphiphiles, coiled coil peptides, collagen, and β-sheet peptides. The design, structure, emergent properties, and applications for these multicomponent assemblies are presented in order to illustrate the potential of these formulations as sophisticated next-generation bio-inspired materials.

Molecular Dynamics Simulations on the Behaviors of Hydrophilic/Hydrophobic Cyclic Peptide Nanotubes at the Water/Hexane Interface

In this work, nine kinds of amino acid residues, i.e., alanine (A), leucine (L), valine (V), isoleucine (I), tryptophan (W), glutamine (Q), threonine (T), serine (S), and cysteine (C), were selected to construct seven cyclic peptide nanotubes (CPNTs) with diverse hydrophilic/hydrophobic external surfaces, which were further separately inserted at the water/hexane interface to investigate their microstructures and interfacial properties. Molecular dynamics (MD) simulations reveal that all the CPNTs except the QT- and VL-CPNTs have different degrees of tilt, fracture, and shedding at the interface. The end-CPs are more susceptible to the effect of the surroundings than the mid-CPs. The interactions of individual CP subunits with the neighborings disclose the firmness of the mid-CPs and the dissociation of the end-CPs. The results indicate that a hydrophobic CPNT is prone to stay at the interface, while a hydrophilic CPNT easily enters the water phase, resulting in many H-bonds with water. Results in this work enrich the dynamic properties of a hydrophilic/hydrophobic CPNT at the biphase interface at the atomic level.

Recent advances in controlling the internal and external properties of self-assembling cyclic peptide nanotubes and dimers

Tuning the internal and external properties of self-assembling cyclic peptide nanotubes.

Dye-conjugated complementary lipophilic nucleosides as useful probes to study association processes by fluorescence resonance energy transfer

Resonance energy transfer is used here to study the association and self-sorting events between lipophilic nucleosides in apolar aromatic solvents.

Self-assembled peptide nanomaterials for biomedical applications: promises and pitfalls

Over the last several decades, a great number of advances have been made in the area of self-assembled supramolecules for regenerative medicine. Such advances have involved the design, preparation, and characterization of brand new self-assembled peptide nanomaterials for a variety of applications. Among all biomolecules considered for self-assembly applications, peptides have attracted a great deal of attention as building blocks for bottom-up fabrication, due to their versatility, ease of manufacturing, low costs, tunable structures, and versatile properties. Herein, some of the more exciting new designs of self-assembled peptides and their associated unique features are reviewed and several promising applications of how self-assembled peptides are advancing drug delivery, tissue engineering, antibacterial therapy, and biosensor device applications are highlighted.

Rational Design of Push-Pull Fluorene Dyes: Synthesis and Structure-Photophysics Relationship

Our work surveyed experimental and theoretical investigations to construct highly emissive D-π-A (D=donor, A=acceptor) fluorenes. The synthetic routes were optimised to be concise and gram-scalable. The molecular design was first rationalised by varying the electron-withdrawing group from an aldehyde, ketotriazole or succinyl to methylenemalonitrile or benzothiadiazole. The electron-donating group was next varied from aliphatic or aromatic amines to saturated cyclic amines ranging from aziridine to azepane. Spectroscopic studies correlated with TD-DFT calculations provided the optimised structures. The selected push-pull dyes exhibited visible absorptions, significant brightness, important solvatofluorochromism, mega-Stokes shifts (>250 nm) and dramatic shifts in emission to the near-infrared. The current library includes the comprehensive characterization of 16 prospective dyes for fluorescence applications. Among them, several fluorene derivatives bearing different conjugation anchors were tested for coupling and demonstrated to preserve the photophysical responses once further bound.

Self-assembling α,γ-cyclic peptides that generate cavities with tunable properties

The design and synthesis of β-sheet-based self-assembling cyclic peptides with tunable cavities is described. The incorporation of a γ-amino acid with a hydroxyl group at C2 allows the incorporation of different groups that modify the internal properties of the resulting dimeric ensemble. These dimers can entrap different guests depending on the properties of the group at C2. The guest defines the geometry of the resulting aggregate.

Fluorescence emission of pyrene in surfactant solutions

The systematic description of the complex photophysical behaviour of pyrene in surfactant solutions in combination with a quantitative model for the surfactant concentrations reproduces with high accuracy the steady-state and the time resolved fluorescence intensity of pyrene in surfactant solutions near the cmc, both in the monomer and in the excimer emission bands. We present concise model equations that can be used for the analysis of the pyrene fluorescence intensity in order to estimate fundamental parameters of the pyrene-surfactant system, such as the binding equilibrium constant K of pyrene to a given surfactant micelle, the rate constant of excimer formation in micelles, and the equilibrium constant of pyrene-surfactant quenching. The values of the binding equilibrium constant K(TX100)=3300·10³ M⁻¹ and K(SDS)=190·10³ M⁻¹ for Triton X-100 (TX100) and SDS micelles, respectively, show that the partition of pyrene between bulk water and micelles cannot be ignored, even at relatively high surfactant concentrations above the cmc. We apply the model to the determination of the cmc from the pyrene fluorescence intensity, especially from the intensity ratio at two vibronic bands in the monomer emission or from the ratio of excimer to monomer emission intensity. We relate the finite width of the transition region below and above the cmc with the observed changes in the pyrene fluorescence in this region.

Self-Sorting of cyclic peptide homodimers into a heterodimeric assembly featuring an efficient photoinduced intramolecular electron-transfer process

We describe the thermodynamic characterisation of the self-sorting process experienced by two homodimers assembled by hydrogen-bonding interactions through their cyclopeptide scaffolds and decorated with Zn-porphyrin and fullerene units into a heterodimeric assembly that contains one electron-donor (Zn–porphyrin) and one electron-acceptor group (fullerene). The fluorescence of the Zn-porphyrin unit is strongly quenched upon heterodimer formation. This phenomenon is demonstrated to be the result of an efficient photoinduced electron-transfer (PET) process occurring between the Zn-porphyrin and the fullerene units of the heterodimeric system. The recombination lifetime of the charge-separated state of the heterodimer complex is in the order of 180 ns. In solution, both homo- and heterodimers are present as a mixture of three regioisomers: two staggered and one eclipsed. At the concentration used for this study, the high stability constant determined for the heterodimer suggests that the eclipsed conformer is the main component in solution. The application of the bound-state scenario allowed us to calculate that the heterodimer exists mainly as the eclipsed regioisomer (75-90 %). The attractive interaction that exists between the donor and acceptor chromophores in the heterodimeric assembly favours their arrangement in close contact. This is confirmed by the presence of charge-transfer bands centred at 720 nm in the absorption spectrum of the heterodimer. PET occurs in approximately 75% of the chromophores after excitation of both Zn-porphyrin and fullerene chromophores. Conversely, analogous systems, reported previously, decorated with extended tetrathiafulvalene and fullerene units showed a PET process in a significantly reduced extent (33%). We conclude that the strength (stability constant (K) x effective molarity (EM)) of the intramolecular interaction established between the two chromophores in the Zn-porphyrin/fullerene cyclopeptide-based heterodimers controls the regioisomeric distribution and regulates the high extent to which the PET process takes place in this system.

Peptide nanotubes

The self-assembly of different classes of peptide, including cyclic peptides, amyloid peptides and surfactant-like peptides into nanotube structures is reviewed. The modes of self-assembly are discussed. Additionally, applications in bionanotechnology and synthetic materials science are summarized.

Fluorescent environment-sensitive dyes as reporters of biomolecular interactions

Monitoring biomolecular interactions is a fundamental issue in biosensing, with numerous applications ranging from biological research to clinical diagnostics. Fluorescent dyes capable of changing their color and brightness in response to changes of their environment properties, the so-called environment-sensitive dyes, have recently emerged as reporters of these interactions. The most well established of these are dyes that undergo excited-state charge transfer showing red shift of their single emission band with increase in the solvent polarity. The other promising class are dyes of the 3-hydroxychromone family that undergo excited-state intramolecular proton transfer and show solvent-sensitive dual emission. Examples of existing solvatochromic dyes and their biosensing applications are given, with particular focus on the 3-hydroxychromones. It is shown that solvatochromic dyes are powerful tools for monitoring conformation changes of proteins and their interactions with nucleic acids, proteins, and lipid membranes.

Biological applications of peptides nanotubes: an overview

Recently, self-assemblies of peptide nanotubes (PNTs) have appeared as one of the most interesting nanostructures to be explored in the field of nanotechnology. These smart assemblies can have diverse applications, such as in the design of nanoreactors, sensors, electronics, and stimulus-responsive materials. Recent publications indicate that PNT synthesis and production are under extensive study. However, a more detailed safety and nanotoxicology evaluation of these materials is still necessary. This is of paramount importance since interesting and novel biomedical applications based on the use of PNTs, including the development of smart nanodevices and drug delivery systems, are under way. To this end, the aim of this mini-review is to discuss the recent biomedical applications of PNTs and, it hopes, to be a source of inspiration for researchers in different areas of expertise related to nanotechnology.

Theoretical characterization of the dynamical behavior and transport properties of alpha,gamma-peptide nanotubes in solution

We present here a molecular dynamics study on a promising class of peptide nanotubes with a partially hydrophobic inner cavity and an easy chemical functionalization of the lumen of the cylindrical structure. The structural and dynamical behavior of the nanotube in water, methanol, and chloroform has been analyzed using state of the art theoretical methods. The nanotube structure is always well preserved, but solvent-dependent dynamic alterations are evident. Such dynamic effects are surprisingly more severe in the most viscous solvent (water), as a consequence of the competition in polar solvents between intra- and intermolecular hydrogen bonds. Stiffness analysis from the collected trajectories helped us to characterize the equilibrium deformability of the nanotube, while steered dynamics simulations were used to determine the magnitude of free energy associated with nanotube growth. Analysis of the carrier and permeation properties of the compounds reveals surprising properties: (i) permeability for the most polar solvent (water), (ii) carrier properties for the most apolar solvent (chloroform), and (iii) neither good permeation nor carrier properties for the intermediate solvent in polarity (methanol). Results reported here constitute the most extensive characterization of these nanotubes presented to date and open many intriguing questions on their stability, dynamics, and transport/carrier properties.

Towards functional bionanomaterials based on self-assembling cyclic peptide nanotubes

In recent years, considerable effort has been devoted to the preparation of artificial nanotubular materials. One of the most successful approaches for the construction of noncovalently bonded nanotube entities is the self-assembly of cyclic polypeptides in stacks that are stabilized by hydrogen bonds. This tutorial review covers the history and current situation for synthetic organic nanostructures obtained from self-assembling cyclic peptides. In particular, we describe the evolution to cyclic peptides that not only allow the modification of the outer surface but also the inner cavity by paying special attention to peptide rings that contain cyclic gamma-amino acids. In this respect, we describe the synthesis, properties and application of a new class of homo- and heterodimeric supramolecular assemblies that are precursors of cyclic alpha,gamma-peptide nanotubes.

Artificial beta-sheets: chemical models of beta-sheets

Chemical models provide tools with which to simplify and study complicated biological systems. Forces and chemical processes that govern the structure, function, and interactions of a biomacromolecule can be explored with a simple, easy-to-study synthetic molecule. Chemical models of beta-sheet structures have helped to elucidate the factors influencing protein structures and functions. Chemical models that mimic beta-sheet quaternary structure and interactions are emerging as valuable tools with which to better understand and control protein recognition and protein aggregation.

Investigation of structures and properties of cyclic peptide nanotubes by experiment and molecular dynamics

In order to investigate the structures and properties of cyclic peptide nanotubes of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-], cyclo[(-D: -Phe-L: -Ala)( n = 4)-] was synthesized and self-assembled to nanotubes, and its structure and morphology of the nanotube were characterized by mass spectrometry (MS), fourier transform infrared spectroscopy (FT-IR) and scanning electron microscopy (SEM). On the basis of these experimental results, the structures of cyclo[(-D: -Phe-L: -Ala)( n = 3,4,5,6)-] were characterized by molecular dynamics. In addition, the motion behaviors of H(2)O molecules in nanotubes were investigated by molecular dynamics using a COMPASS force field. Experimental results show that cyclo[(-D: -Phe-L: -Ala)( n = 4)-] peptides self-assemble into nanotube bundles. Molecular modeling results indicate that cyclic peptide nanotubes with n = 3, 4, 5 and 6 are very stable; these nanotubes have internal diameters of 5.9 A, 8.1 A, 10.8 A and 13.1 A and outer diameters of 18.2 A, 21.7 A, 23.4 A and 25.9 A respectively. Modeling results demonstrate that H(2)O molecules move in cooperation in single nanotube and they diffuse in one dimension, but they did not diffuse unilaterally due to the antiparallel ring stacking arrangement.