Self-Assembly of Cyclo-diphenylalanine Peptides in Vacuum

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

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

Halogen Interaction Effects on Chiral Self-Assemblies on Cyclodipeptide Scaffolds Across Hierarchy

How halogenation affects protein or peptide folding and self-assembly hierarchically? This study tries to answer this question by using the halogen bonding mediated self-assemblies on cyclodipeptide scaffolds. Single-functionalized cyclodipeptides (Cyclo-GX) based on para-halogenated phenylalanine in the solid state form homochiral helical nanotubes via consecutive X···O bonds (X = Cl, Br, and I) independent of halogen kinds. In contrast, double-functionalized cyclodipeptides (Cyclo-XX) feature versatile self-assembly architectures depending on the para-substituents (X = H, F, Cl, Br, and I), affording nanotubular, lamellar, and triple helical nanotubular architectures. Cyclo-BrBr exclusively adopts intramolecular Type-IV X···X interaction that alters the molecular folding and packing, which also gives rise to opposite chirality at molecular folding (secondary structure), stacking (tertiary structure), and self-assembled nanohelices (quarternary structure) at macroscopic scale. It unveils how halogenation impacts on the self-assembly and chirality at hierarchical levels in specific peptides. Clusteroluminescence is found for the cyclodipeptides, achieving high quantum yield up to 71%, whereby circularly polarized luminescence is realized with tunable handedness by controlling halogen substituents.

Self-Assembly of Phenylalanine-Leucine, Leucine-Phenylalanine, and Cyclo(-leucine-phenylalanine) Dipeptides through Simulations and Experiments

For over two decades, peptide self-assembly has been the focus of attention and a great source of inspiration for biomedical and nanotechnological applications. The resulting peptide nanostructures and their properties are closely related to the information encoded within each peptide building block, their sequence, and their modes of self-organization. In this work. we assess the behavior and differences between the self-association of the aromatic-aliphatic Phe-Leu dipeptide compared to its retro-sequence Leu-Phe and cyclic Cyclo(-Leu-Phe) counterparts, using a combination of simulation and experimental methods. Detailed all-atom molecular dynamics (MD) simulations offer a quantitative prediction at the molecular level of the conformational, dynamical and structural properties of the peptides' self-assembly, while field emission scanning electron microscopy (FESEM) experiments allow microscopic observation of the self-assembled end-structures. The complementarity and qualitative agreement between the two methods not only highlights the differences between the self-assembly propensity of cyclic and linear retro-sequence peptides but also sheds light on underlying mechanisms of self-organization. The self-assembling propensity was found to follow the order: Cyclo(-Leu-Phe) > Leu-Phe > Phe-Leu.

Triboelectric Generator Based on Oriented Self-Assembled Peptide Microbelts

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

Structural Properties of Phenylalanine-Based Dimers Revealed Using IR Action Spectroscopy

Peptide segments with phenylalanine residues are commonly found in proteins that are related to neurodegenerative diseases. However, the self-assembly of phenylalanine-based peptides can be also functional. Peptides containing phenylalanine residues with different side caps, composition, and chemical alteration can form different types of nanostructures that find many applications in technology and medicine. Various studies have been performed in order to explain the remarkable stability of the resulting nanostructures. Here, we study the early stages of self-assembly of two phenylalanine derived peptides in the gas phase using IR action spectroscopy. Our focus lies on the identification of the key intra- and intermolecular interactions that govern the formation of the dimers. The far-IR region allowed us to distinguish between structural families and to assign the 2-(2-amino-2-phenylacetamido)-2-phenylacetic acid (PhgPhg) dimer to a very symmetric structure with two intermolecular hydrogen bonds and its aromatic rings folded away from the backbone. By comparison with the phenylalanine-based peptide cyclic L-phenylalanyl-L-phenylalanine (cyclo-FF), we found that the linear FF dimer likely adopts a less ordered structure. However, when one more phenylalanine residue is added (FFF), a more structurally organized dimer is formed with several intermolecular hydrogen bonds.

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

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

Solid-state synthesis of cyclo LD-diphenylalanine: A chiral phase built from achiral subunits

The solid-state structure of LL/DD or LD/DL diphenylalanine diluted in KBr pellets is studied by infrared (IR) absorption and vibrational circular dichroism (VCD) spectroscopy. The structure depends on the absolute configuration of the residues. The natural LL diphenylalanine exists as a mixture of neutral and zwitterionic structures, depending on the humidity of the sample, while mostly the zwitterion is observed for LD diphenylalanine whatever the experimental conditions. The system undergoes spontaneous cyclization upon heating at 125°C, resulting to the formation of a diketopiperazine (DKP) dipeptide as the only product. The reaction is faster for LD than for LL diphenylalanine. As expected, LL and DD diphenylalanine react to form the LL and DD enantiomers of cyclo diphenylalanine. Interestingly, the DKP dipeptides formed from the LD or DL diphenylalanine show unexpected optical activity, with opposite VCD spectra for the products formed from the LD and DL reagents. This is explained in terms of chirality synchronization between the monomers within the crystal, which retain the symmetry of the reagent, resulting to the formation of a new chiral phase made from transiently chiral molecules.

Assembly modes of hexaphenylalanine variants as function of the charge states of their terminal ends

The ability of peptides to self-assemble represents a valuable tool for the development of biomaterials of biotechnological and/or biomedical interest. Diphenylalanine homodimer (FF) and its analogues are among the most promising systems in this field. The longest Phe-based building block hitherto characterized is pentaphenylalanine (F5). We studied the aggregation propensity and the structural/morphological features of assemblies of zwitterionic hexaphenylalanine H+-F6-O- and of three variants characterized by different charged states of the terminal ends (Ac-F6-Amide, H+-F6-Amide and Ac-F6-O-). As previously observed for PEGylated hexaphenylalanine (PEG8-F6), all F6 variants show a strong tendency to form β-rich assemblies in which the structural motif is constituted by antiparallel β-strands in the cross-β framework. Extensive replica exchange molecular dynamics simulations carried out on a pairs of F6 peptides indicate that the antiparallel β-structure of the final assemblies is likely dictated by the preferred association modes of the individual chains in the very early stages of the aggregation process. Our data suggest that even very small F6 peptides are properly pre-organized and prone to the build-up of the final assembly.

Guiding principles for peptide nanotechnology through directed discovery

Life's diverse molecular functions are largely based on only a small number of highly conserved building blocks - the twenty canonical amino acids. These building blocks are chemically simple, but when they are organized in three-dimensional structures of tremendous complexity, new properties emerge. This review explores recent efforts in the directed discovery of functional nanoscale systems and materials based on these same amino acids, but that are not guided by copying or editing biological systems. The review summarises insights obtained using three complementary approaches of searching the sequence space to explore sequence-structure relationships for assembly, reactivity and complexation, namely: (i) strategic editing of short peptide sequences; (ii) computational approaches to predicting and comparing assembly behaviours; (iii) dynamic peptide libraries that explore the free energy landscape. These approaches give rise to guiding principles on controlling order/disorder, complexation and reactivity by peptide sequence design.

The effect of carbohydrate structures on the hydrogelation ability and morphology of self-assembled structures of peptide-carbohydrate conjugates in water

We describe the construction of peptide-carbohydrate conjugates, namely glycopeptides, capable of self-assembling in water. We found that disaccharide structures (epimer or glycosidic-bond geometry) appended to the glycopeptides have a noticeable effect on the hydrogel formation ability as well as the morphology of the self-assembled structures. The soft materials consisting of self-assembled structures with carbohydrates on their surface and various types of morphologies might be useful as matrices to investigate the function of carbohydrates in biological events.

Diphenylalanine-Based Microribbons for Piezoelectric Applications via Inkjet Printing

Peptide-based nanostructures are very promising for nanotechnological applications because of their excellent self-assembly properties, biological and chemical flexibility, and unique multifunctional performance. However, one of the limiting factors for the integration of peptide assemblies into functional devices is poor control of their alignment and other geometrical parameters required for device fabrication. In this work, we report a novel method for the controlled deposition of one of the representative self-assembled peptides-diphenylalanine (FF)-using a commercial inkjet printer. The initial FF solution, which has been shown to readily self-assemble into different structures such as nano- and microtubes and microrods, was modified to be used as an efficient ink for the printing of aligned FF-based structures. Furthermore, during the development of the suitable ink, we were able to produce a novel type of FF conformation with high piezoelectric response and excellent stability. By using this method, ribbonlike microcrystals based on FF could be formed and precisely patterned on different surfaces. Possible mechanisms of structure formation and piezoelectric effect in printed microribbons are discussed along with the possible applications.

Controlling the Physical Dimensions of Peptide Nanotubes by Supramolecular Polymer Coassembly

Molecular self-assembly of peptides into ordered nanotubes is highly important for various technological applications. Very short peptide building blocks, as short as dipeptides, can form assemblies with unique mechanical, optical, piezoelectric, and semiconductive properties. Yet, the control over nanotube length in solution has remained challenging, due to the inherent sequential self-assembly mechanism. Here, in line with polymer chemistry paradigms, we applied a supramolecular polymer coassembly methodology to modulate peptide nanotube elongation. Utilizing this approach, we achieved a narrow, controllable nanotube length distribution by adjusting the molecular ratio of the diphenylalanine assembly unit and its end-capped analogue. Kinetic analysis suggested a slower coassembly organization process as compared to the self-assembly dynamics of each of the building blocks separately. This is consistent with a hierarchal arrangement of the peptide moieties within the coassemblies. Mass spectrometry analysis demonstrated the bimolecular composition of the coassembled nanostructures. Moreover, the peptide nanotubes' length distribution, as determined by electron microscopy, was shown to fit a fragmentation kinetics model. Our results reveal a simple and efficient mechanism for the control of nanotube sizes through the coassembly of peptide entities at various ratios, allowing for the desired end-product formation. This dynamic size control offers tools for molecular engineering at the nanoscale exploiting the advantages of molecular coassembly.

Morphology and Pattern Control of Diphenylalanine Self-Assembly via Evaporative Dewetting

Self-assembled peptide nanostructures have unique physical and biological properties and promising applications in electrical devices and functional molecular recognition. Although solution-based peptide molecules can self-assemble into different morphologies, it is challenging to control the self-assembly process. Herein, controllable self-assembly of diphenylalanine (FF) in an evaporative dewetting solution is reported. The fluid mechanical dimensionless numbers, namely Rayleigh, Marangoni, and capillary numbers, are introduced to control the interaction between the solution and FF molecules in the self-assembly process. The difference in the film thickness reflects the effects of Rayleigh and Marangoni convection, and the water vapor flow rate reveals the role of viscous fingering in the emergence of aligned FF flakes. By employing dewetting, various FF self-assembled patterns, like concentric and spokelike, and morphologies, like strips and hexagonal tubes/rods, can be produced, and there are no significant lattice structural changes in the FF nanostructures.

Functional architectures based on self-assembly of bio-inspired dipeptides: Structure modulation and its photoelectronic applications

Getting inspiration from nature and further developing functional architectures provides an effective way to design innovative materials and systems. Among bio-inspired materials, dipeptides and its self-assembled architectures with functionalities have recently been the subject of intensive studies. However, there is still a great challenge to explore its applications likely due to the lack of effective adaptation of their self-assembled structures as well as a lack of understanding of the self-assembly mechanisms. In this context, taking diphenylalanine (FF, a core recognition motif for molecular self-assembly of the Alzheimer's β-amyloid polypeptides) as a model of bio-inspired dipeptides, recent strategies on modulation of dipeptide-based architectures were introduced with regard to both covalent (architectures modulation by coupling functional groups) and non-covalent ways (controlled architectures by different assembly pathways). Then, applications are highlighted in some newly emerging fields of innovative photoelectronic devices and materials, such as artificial photosynthetic systems for renewable solar energy storage and renewable optical waveguiding materials for optoelectronic devices. At last, the challenges and future perspectives of these bio-inspired dipeptides are also addressed.

The physical properties of supramolecular peptide assemblies: from building block association to technological applications

Bio-inspired nano-materials can be formed by the ordered assembly of elementary building blocks using recognition modules and structural elements. Among the biological sources, peptides and proteins are of special interest due to their role as major structural elements in all living systems, ranging from bacteria to humans in a continuum of magnitudes, from the nano-scale to the macro-scale. Peptides, as short as dipeptides, contain all the molecular information needed to form well-ordered structures at the nano-scale. Here, in light of the significant advancements in the field of peptide nanostructures in the last few years, we provide an updated overview of this subject. The use of these nanostructures was indeed recently demonstrated in various fields including the design of molecular motors based on nanostructure complexation with a metal-organic framework, the delivery of therapeutic agents, the development of energy storage devices and the fabrication of piezoelectric-based sensors.