The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer's β-amyloid polypeptide

Tuning the mechanical properties of self-assembled mixed-peptide tubes

In this study, nano- and microscale fibrillar and tubular structures formed by mixing two aromatic peptides known to self-assemble separately, (diphenylalanine and di-D-2-napthylalanine) have been investigated. The morphology, mechanical strength and thermal stability of the tubular structures formed have been studied. The tubes are shown to consist of both peptides with some degree of nanoscale phase separation. The ability of the mixed peptides to form structures, which display variable mechanical properties dependent on the percentage composition of the peptides is presented. Such materials with tuneable properties will be required for a range of applications in nanotechnology and biotechnology.

Aliphatic peptides show similar self-assembly to amyloid core sequences, challenging the importance of aromatic interactions in amyloidosis

The self-assembly of abnormally folded proteins into amyloid fibrils is a hallmark of many debilitating diseases, from Alzheimer's and Parkinson diseases to prion-related disorders and diabetes type II. However, the fundamental mechanism of amyloid aggregation remains poorly understood. Core sequences of four to seven amino acids within natural amyloid proteins that form toxic fibrils have been used to study amyloidogenesis. We recently reported a class of systematically designed ultrasmall peptides that self-assemble in water into cross-β-type fibers. Here we compare the self-assembly of these peptides with natural core sequences. These include core segments from Alzheimer's amyloid-β, human amylin, and calcitonin. We analyzed the self-assembly process using circular dichroism, electron microscopy, X-ray diffraction, rheology, and molecular dynamics simulations. We found that the designed aliphatic peptides exhibited a similar self-assembly mechanism to several natural sequences, with formation of α-helical intermediates being a common feature. Interestingly, the self-assembly of a second core sequence from amyloid-β, containing the diphenylalanine motif, was distinctly different from all other examined sequences. The diphenylalanine-containing sequence formed β-sheet aggregates without going through the α-helical intermediate step, giving a unique fiber-diffraction pattern and simulation structure. Based on these results, we propose a simplified aliphatic model system to study amyloidosis. Our results provide vital insight into the nature of early intermediates formed and suggest that aromatic interactions are not as important in amyloid formation as previously postulated. This information is necessary for developing therapeutic drugs that inhibit and control amyloid formation.

Autonomous motors of a metal-organic framework powered by reorganization of self-assembled peptides at interfaces

A variety of microsystems have been developed that harness energy and convert it to mechanical motion. Here we have developed new autonomous biochemical motors by integrating a metal-organic framework (MOF) and self-assembling peptides. The MOF is applied as an energy-storing cell that assembles peptides inside nanoscale pores of the coordination framework. The nature of peptides enables their assemblies to be reconfigured at the water/MOF interface, and thus converted to fuel energy. Reorganization of hydrophobic peptides can create a large surface-tension gradient around the MOF that can efficiently power its translational motion. As a comparison, the velocity normalized by volume for the diphenylalanine-MOF particle is faster and the kinetic energy per unit mass of fuel is more than twice as great as that for previous gel motor systems. This demonstration opens the route towards new applications of MOFs and reconfigurable molecular self-assembly, possibly evolving into a smart autonomous motor capable of mimicking swimming bacteria and, with integrated recognition units, harvesting target chemicals.

Unzipping the role of chirality in nanoscale self-assembly of tripeptide hydrogels

Change of chirality is a useful tool to manipulate the aqueous self-assembly behaviour of uncapped, hydrophobic tripeptides. In contrast with other short peptides, these tripeptides form hydrogels at a physiological pH without the aid of organic solvents or end-capping groups (e.g. Fmoc). The novel hydrogel forming peptide (D)Leu-Phe-Phe ((D)LFF) and its epimer Leu-Phe-Phe (LFF) exemplify dramatic supramolecular effects induced by subtle changes to stereochemistry. Only the d-amino acid-containing peptide instantly forms a hydrogel in aqueous solution following a pH switch, generating long fibres (>100 μm) that entangle into a 3D network. However, unexpected nanostructures are observed for both peptides and they are particularly heterogeneous for LFF. Structural analyses using CD, FT-IR and fluorescent amyloid staining reveal anti-parallel beta-sheets for both peptides. XRD analysis also identifies key distances consistent with beta-sheet formation in both peptides, but suggests additional high molecular order and extended molecular length for (D)LFF only. Molecular modelling of the two peptides highlights the key interactions responsible for self-assembly; in particular, rapid self-assembly of (D)LFF is promoted by a phenylalanine zipper, which is not possible because of steric factors for LFF. In conclusion, this study elucidates for the first time the molecular basis for how chirality can dramatically influence supramolecular organisation in very short peptide sequences.

Probing the self-assembly mechanism of diphenylalanine-based peptide nanovesicles and nanotubes

Nanostructures, particularly those from peptide self-assemblies, have attracted great attention lately due to their potential applications in nanotemplating and nanotechnology. Recent experimental studies reported that diphenylalanine-based peptides can self-assemble into highly ordered nanostructures such as nanovesicles and nanotubes. However, the molecular mechanism of the self-organization of such well-defined nanoarchitectures remains elusive. In this study, we investigate the assembly pathway of 600 diphenylalanine (FF) peptides at different peptide concentrations by performing extensive coarse-grained molecular dynamics (MD) simulations. Based on forty 0.6-1.8 μs trajectories at 310 K starting from random configurations, we find that FF dipeptides not only spontaneously assemble into spherical vesicles and nanotubes, consistent with previous experiments, but also form new ordered nanoarchitectures, namely, planar bilayers and a rich variety of other shapes of vesicle-like structures including toroid, ellipsoid, discoid, and pot-shaped vesicles. The assembly pathways are concentration-dependent. At low peptide concentrations, the self-assembly involves the fusion of small vesicles and bilayers, whereas at high concentrations, it occurs through the formation of a bilayer first, followed by the bending and closure of the bilayer. Energetic analysis suggests that the formation of different nanostructures is a result of the delicate balance between peptide-peptide and peptide-water interactions. Our all-atom MD simulation shows that FF nanostructures are stabilized by a combination of T-shaped aromatic stacking, interpeptide head-to-tail hydrogen-bonding, and peptide-water hydrogen-bonding interactions. This study provides, for the first time to our knowledge, the self-assembly mechanism and the molecular organization of FF dipeptide nanostructures.

Supramolecular hydrogelators of N-terminated dipeptides selectively inhibit cancer cells

Consisting of N-terminated diphenylalanine, a new type of supramolecular hydrogelators forms hydrogels within a narrow pH window (pH 5.0 to 6.0) and selectively inhibits growth of HeLa cells, which provides important and useful insights for designing molecular nanofibers as potential nanomedicines.

Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly

Several short peptide sequences are known to self-assemble into supramolecular nanostructures with interesting properties. In this study, coarse-grained molecular dynamics is employed to rapidly screen all 400 dipeptide combinations and predict their ability to aggregate as a potential precursor to their self-assembly. The simulation protocol and scoring method proposed allows a rapid determination of whether a given peptide sequence is likely to aggregate (an indicator for the ability to self-assemble) under aqueous conditions. Systems that show strong aggregation tendencies in the initial screening are selected for longer simulations, which result in good agreement with the known self-assembly or aggregation of dipeptides reported in the literature. Our extended simulations of the diphenylalanine system show that the coarse-grain model is able to reproduce salient features of nanoscale systems and provide insight into the self-assembly process for this system.

Effects of water molecules on photoluminescence from hierarchical peptide nanotubes and water probing capability

Photoluminescence (PL) spectra reveal that deficiency of water molecules in the channel cores of bioinspired hierarchical diphenylalanine ( L -Phe- L -Phe, FF) peptide nanotubes (PNTs) not only modifies the bandgap of the subnanometer crystalline structure formed by the self-assembly process, but also induces a characteristic ultraviolet PL peak the position of which is linearly proportional to the number of water molecules in the PNTs. Addition or loss of water molecules gives rise to the UV PL redshift or blueshift. Density functional theory calculation also confirms that addition of water molecules to the PNTs causes splitting of the valence-band peak, which corresponds to the shift and splitting of the observed UV PL peak. Water molecules play an important role in the biological properties of FF PNTs and the results demonstrate that the PL spectra can be used to probe the number of water molecules bonded to the FF molecules.

Ultrasmall peptides self-assemble into diverse nanostructures: morphological evaluation and potential implications

In this study, we perform a morphological evaluation of the diverse nanostructures formed by varying concentration and amino acid sequence of a unique class of ultrasmall self-assembling peptides. We modified these peptides by replacing the aliphatic amino acid at the C-aliphatic terminus with different aromatic amino acids. We tracked the effect of introducing aromatic residues on self-assembly and morphology of resulting nanostructures. Whereas aliphatic peptides formed long, helical fibers that entangle into meshes and entrap >99.9% water, the modified peptides contrastingly formed short, straight fibers with a flat morphology. No helical fibers were observed for the modified peptides. For the aliphatic peptides at low concentrations, different supramolecular assemblies such as hollow nanospheres and membrane blebs were found. Since the ultrasmall peptides are made of simple, aliphatic amino acids, considered to have existed in the primordial soup, study of these supramolecular assemblies could be relevant to understanding chemical evolution leading to the origin of life on Earth. In particular, we propose a variety of potential applications in bioengineering and nanotechnology for the diverse self-assembled nanostructures.

Charged diphenylalanine nanotubes and controlled hierarchical self-assembly

Hexagonal hierarchical microtubular structures are produced by diphenylalanine self-assembly and the ratio of the relative humidity in the growth chamber to the diphenylalanine concentration (defined as the RH-FF ratio) determines the microtubular morphology. The hexagonal arrangement of the diphenylalanine molecules first induces the hexagonal nanotubes with opposite charges on the two ends, and the dipolar electric field on the nanotubes serves as the driving force. Side-by-side hexagonal aggregation and end-to-end arrangement ensue finally producing a hexagonal hierarchical microtubular structure. Staining experiments and the external electric field-induced parallel arrangement provide evidence of the existence of opposite charges and dipolar electric field. In this self-assembly, the different RH-FF ratios induce different contents of crystalline phases. This leads to different initial nanotube numbers finally yielding different microtubular morphologies. Our calculation based on the dipole model supports the dipole-field mechanism that leads to the different microtubular morphologies.

Creating prebiotic sanctuary: self-assembling supramolecular Peptide structures bind and stabilize RNA

Any attempt to uncover the origins of life must tackle the known 'blind watchmaker problem'. That is to demonstrate the likelihood of the emergence of a prebiotic system simple enough to be formed spontaneously and yet complex enough to allow natural selection that will lead to Darwinistic evolution. Studies of short aromatic peptides revealed their ability to self-assemble into ordered and stable structures. The unique physical and chemical characteristics of these peptide assemblies point out to their possible role in the origins of life. We have explored mechanisms by which self-assembling short peptides and RNA fragments could interact together and go through a molecular co-evolution, using diphenylalanine supramolecular assemblies as a model system. The spontaneous formation of these self-assembling peptides under prebiotic conditions, through the salt-induced peptide formation (SIPF) pathway was demonstrated. These peptide assemblies possess the ability to bind and stabilize ribonucleotides in a sequence-depended manner, thus increase their relative fitness. The formation of these peptide assemblies is dependent on the homochirality of the peptide monomers: while homochiral peptides (L-Phe-L-Phe and D-Phe-D-Phe) self-assemble rapidly in aqueous environment, heterochiral diastereoisomers (L-Phe-D-Phe and D-Phe-L-Phe) do not tend to self-assemble. This characteristic consists with the homochirality of all living matter. Finally, based on these findings, we propose a model for the role of short self-assembling peptides in the prebiotic molecular evolution and the origin of life.

De novo design of α,β-didehydrophenylalanine containing peptides: from models to applications

The de novo design of peptides and proteins has emerged as an approach for investigating protein structure and function. The success relies heavily on the ability to design relatively short peptides that can adopt stable secondary structures. To this end, substitution with α,β-dehydroamino acids, especially α,β-didehydrophenylalanine (ΔPhe or ΔF) has blossomed in manifold directions, providing a rich diversity of well-defined structural motifs. Introduction of α,β-didehydrophenylalanine induces β-bends in small and 3(10)-helices in longer peptide sequences. Most favorable conformation of ΔF residues are (φ,ψ) ∼(60°, 30°), (-60°, -30°), (-60°, 150°), and (60°, -150°). These features have been exploited in designing helix-turn-helix, helical bundle arrangements, and glycine zipper type super secondary structural motifs. The unusual capability of α,β-didehydrophenylalanine ring to form a variety of multicentered interactions (N-H…O, C-H…O, C-H…π, and N-H…π) suggests its possible exploitation for future de novo design of supramolecular structures. This work has now been extended to the de novo design of peptides with antibiotic, antifibrillization activity, etc. More recently, self-assembling properties of small dehydropeptides have been explored. This review focuses primarily on the structural and functional behavior of α,β-didehydrophenylalanine containing peptides.

Stability of diphenylalanine peptide nanotubes in solution

Over the last couple of years, self-organizing nanotubes based on the dipeptide diphenylalanine have received much attention, mainly as possible building blocks for the next generation of biosensors and as drug delivery systems. One of the main reasons for this large interest is that these peptide nanotubes are believed to be very stable both thermally and chemically. Previously, the chemical and thermal stability of self-organizing structures has been investigated after the evaporation of the solvent. However, it was recently discovered that the stability of the structures differed significantly when the tubes were in solution. It has been shown that, in solution, the peptide nanotubes can easily be dissolved in several solvents including water. It is therefore of critical importance that the stability of the nanotubes in solution and not after solvent evaporation be investigated prior to applications in which the nanotube will be submerged in liquid. The present article reports results demonstrating the instability and suggests a possible approach to a stabilization procedure, which drastically improves the stability of the formed structures. The results presented herein provide new information regarding the stability of self-organizing diphenylalanine nanotubes in solution.

Bioinspired peptide nanotubes: deposition technology, basic physics and nanotechnology applications

Synthetic peptide monomers can self-assemble into PNM such as nanotubes, nanospheres, hydrogels, etc. which represent a novel class of nanomaterials. Molecular recognition processes lead to the formation of supramolecular PNM ensembles containing crystalline building blocks. Such low-dimensional highly ordered regions create a new physical situation and provide unique physical properties based on electron-hole QC phenomena. In the case of asymmetrical crystalline structure, basic physical phenomena such as linear electro-optic, piezoelectric, and nonlinear optical effects, described by tensors of the odd rank, should be explored. Some of the PNM crystalline structures permit the existence of spontaneous electrical polarization and observation of ferroelectricity. The PNM crystalline arrangement creates highly porous nanotubes when various residues are packed into structural network with specific wettability and electrochemical properties. We report in this review on a wide research of PNM intrinsic physical properties, their electronic and optical properties related to QC effect, unique SHG, piezoelectricity and ferroelectric spontaneous polarization observed in PNT due to their asymmetric structure. We also describe PNM wettability phenomenon based on their nanoporous structure and its influence on electrochemical properties in PNM. The new bottom-up large scale technology of PNT physical vapor deposition and patterning combined with found physical effects at nanoscale, developed by us, opens the avenue for emerging nanotechnology applications of PNM in novel fields of nanophotonics, nanopiezotronics and energy storage devices.

Ion-pair induced self-assembly in aqueous solvents

The intriguing advantages of supramolecular chemistry and particularly the application of self-assembly for the construction of defined nanostructures from small, preferably synthetically easily accessible molecules has become a promising area of modern chemistry in the last years. However, the main focus of early work was based on H-bond induced self-assembly which is limited to nonpolar organic solvents. In the past years the field started to shift more and more towards obtaining self-assembling architectures in polar solvents and even water. This tutorial review will discuss some representative examples for self-assembling systems in polar solvents in order to illustrate the different concepts and strategies that can be used. We will also briefly discuss the special properties of water as the ultimate protic solvent from the perspective of a supramolecular chemist to elucidate the challenges that this solvent still poses even today to obtain specific self-assembled nanostructures.

Solvent-induced structural transition of self-assembled dipeptide: from organogels to microcrystals

Organogels that are self-assembled from simple peptide molecules are an interesting class of nano- and mesoscale soft matter with simplicity and functionality. Investigating the precise roles of the organic solvents and their effects on stabilization of the formed organogel is an important topic for the development of low-molecular-weight gelators. We report the structural transition of an organogel self-assembled from a single dipeptide building block, diphenylalanine (L-Phe-L-Phe, FF), in toluene into a flower-like microcrystal merely by introducing ethanol as a co-solvent; this provides deeper insights into the phase transition between mesostable gels and thermodynamically stable microcrystals. Multiple characterization techniques were used to reveal the transitions. The results indicate that there are different molecular-packing modes formed in the gels and in the microcrystals. Further studies show that the co-solvent, ethanol, which has a higher polarity than toluene, might be involved in the formation of hydrogen bonds during molecular self-assembly of the dipeptide in mixed solvents, thus leading to the transition of organogels into microcrystals. The structural transformation modulated by the co-solvent might have a potential implication in controllable molecular self-assembly.

Hydrogelation and self-assembly of Fmoc-tripeptides: unexpected influence of sequence on self-assembled fibril structure, and hydrogel modulus and anisotropy

The self-assembly and hydrogelation properties of two Fmoc-tripeptides [Fmoc = N-(fluorenyl-9-methoxycarbonyl)] are investigated, in borate buffer and other basic solutions. A remarkable difference in self-assembly properties is observed comparing Fmoc-VLK(Boc) with Fmoc-K(Boc)LV, both containing K protected by N(epsilon)-tert-butyloxycarbonate (Boc). In borate buffer, the former peptide forms highly anisotropic fibrils which show local alignment, and the hydrogels show flow-aligning properties. In contrast, Fmoc-K(Boc)LV forms highly branched fibrils that produce isotropic hydrogels with a much higher modulus (G' > 10(4) Pa), and lower concentration for hydrogel formation. The distinct self-assembled structures are ascribed to conformational differences, as revealed by secondary structure probes (CD, FTIR, Raman spectroscopy) and X-ray diffraction. Fmoc-VLK(Boc) forms well-defined beta-sheets with a cross-beta X-ray diffraction pattern, whereas Fmoc-KLV(Boc) forms unoriented assemblies with multiple stacked sheets. Interchange of the K and V residues when inverting the tripeptide sequence thus leads to substantial differences in self-assembled structures, suggesting a promising approach to control hydrogel properties.