Effect of solvent on the self-assembly of dialanine and diphenylalanine peptides

Molecular simulations of peptide amphiphiles

This review describes recent progress in the area of molecular simulations of peptide assemblies, including peptide-amphiphiles and drug-amphiphiles. The ability to predict the structure and stability of peptide self-assemblies from the molecular level up is vital to the field of nanobiotechnology. Computational methods such as molecular dynamics offer the opportunity to characterize intermolecular forces between peptide-amphiphiles that are critical to the self-assembly process. Furthermore, these computational methods provide the ability to computationally probe the structure of these supramolecular assemblies at the molecular level, which is a challenge experimentally. Herein, we briefly highlight progress in the areas of all-atomistic and coarse-grained simulation studies investigating the self-assembly process of short peptides and peptide amphiphiles. We also discuss recent all-atomistic and coarse-grained simulations of the self-assembly of a drug-amphiphile into elongated filaments. Next, we discuss how these computational methods can provide further insight into the pathway of cylindrical nanofiber formation and predict their biocompatibility by studying the interaction of these peptide-amphiphile nanostructures with model cell membranes.

Diphenylalanine in tetrahydrofuran: a highly potent candidate for the development of novel nanomaterials

The peptide di-L-phenylalanine (FF) has emerged as a highly potent candidate for the development of novel nanomaterials. The unprotected peptide was dissolved in 1,1,1,3,3,3-hexafluoropropan-2-ol (HFIP) mixed with tetrahydrofuran (THF) and single crystals of the THF monosolvate, C18H20N2O3·C4H8O, were grown by slow evaporation in a `vial-in-closed-bottle' system. THF is a molecule that can only act as a hydrogen-bond acceptor. Thus, the hydrogen-bond patterns observed in the crystal structures at 100 and 299 K are different compared to that of crystals grown from water and methanol [Mason et al. (2014). ACS Nano. 8, 1243–1253].

Co-assembly of Fmoc-tripeptide and gold nanoparticles as a facile approach to immobilize nanocatalysts

AuNPs are immobilized onto peptide-based nanofibers through co-assembly Fmoc-FFX and nanoparticles, which shows favorable catalytic activity toward 4-nitrophenol.

Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly

Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical peptide self-assembly from the molecular level to the mesoscale.

Metal-induced supramolecular chirality inversion of small self-assembled molecules in solution

The first example of supramolecular chirality inversion of small self-assembled ligands in solution by complexation to metal ions is presented.

Sensitive and selective ratiometric fluorescent detection of monosaccharides in aqueous solutions at physiological pH using self-assembled peptides with different aromatic side chains

The control of disassembly of supramolecular nanostructures of the self-assembled peptides by monosaccharides was investigated for the fluorescent detection of monosaccharides in aqueous solutions.

Dynamic microfluidic control of supramolecular peptide self-assembly

The dynamic nature of supramolecular polymers has a key role in their organization. Yet, the manipulation of their dimensions and polarity remains a challenge. Here, the minimalistic diphenylalanine building block was applied to demonstrate control of nano-assemblies growth and shrinkage using microfluidics. To fine-tune differential local environments, peptide nanotubes were confined by micron-scale pillars and subjected to monomer flows of various saturation levels to control assembly and disassembly. The small-volume device allows the rapid adjustment of conditions within the system. A simplified kinetic model was applied to calculate parameters of the growth mechanism. Direct real-time microscopy analysis revealed that different peptide derivatives show unidirectional or bidirectional axial dimension variation. Atomistic simulations show that unidirectional growth is dictated by the differences in the axial ends, as observed in the crystalline order of symmetry. This work lays foundations for the rational control of nano-materials dimensions for applications in biomedicine and material science.

The organization of supramolecular peptide polymers determines their properties; however, controlling their dimensions still remains a problem. Here, Gazit et al. show the spontaneous elongation and shortening of these polymers at an individual nano-assembly level by using a microfluidic platform.

Expanding the Nanoarchitectural Diversity Through Aromatic Di- and Tri-Peptide Coassembly: Nanostructures and Molecular Mechanisms

Molecular self-assembly is pivotal for the formation of ordered nanostructures, yet the structural diversity obtained by the use of a single type of building block is limited. Multicomponent coassembly, utilized to expand the architectural space, is principally based on empirical observations rather than rational design. Here we report large-scale molecular dynamics simulations of the coassembly of diphenylalanine (FF) and triphenylalanine (FFF) peptides at various mass ratios. Our simulations show that FF and FFF can co-organize into both canonical and noncanonical assemblies. Strikingly, toroid nanostructures, which were rarely observed for the extensively studied FF or FFF, are often seen in the FF-FFF coassembly simulations and later corroborated by scanning electron microscopy. Our simulations demonstrate a wide ratio-dependent variation of nanostructure morphologies including hollow and solid assemblies, much richer than those formed by each individual moiety. The hollow-solid structural transformation displays a discontinuous transition feature, and the toroids appear to be an obligatory intermediate for the structural transition. Interaction analysis reveals that the hollow-solid structural transition is mostly dominated by FF-FFF interactions, while the nanotoroid formation is determined by the competition between FF-water and FFF-water interactions. This study provides both structural and mechanistic insights into the coassembly of FF and FFF peptides, thus offering a molecular basis for the rational design of bionanomaterials utilizing peptide coassembly.

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.

Peptide self-assembly: thermodynamics and kinetics

Self-assembling systems play a significant role in physiological functions and have therefore attracted tremendous attention due to their great potential for applications in energy, biomedicine and nanotechnology. Peptides, consisting of amino acids, are among the most popular building blocks and programmable molecular motifs. Nanostructures and materials assembled using peptides exhibit important potential for green-life new technology and biomedical applications mostly because of their bio-friendliness and reversibility. The formation of these ordered nanostructures pertains to the synergistic effect of various intermolecular non-covalent interactions, including hydrogen-bonding, π-π stacking, electrostatic, hydrophobic, and van der Waals interactions. Therefore, the self-assembly process is mainly driven by thermodynamics; however, kinetics is also a critical factor in structural modulation and function integration. In this review, we focus on the influence of thermodynamic and kinetic factors on structural assembly and regulation based on different types of peptide building blocks, including aromatic dipeptides, amphiphilic peptides, polypeptides, and amyloid-relevant peptides.

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.

Molecular and mesoscale mechanism for hierarchical self-assembly of dipeptide and porphyrin light-harvesting system

Multiscale theoretical models are built to unravel the hierarchically ordered organization of dipeptide–porphyrin co-assemblies with different light-harvesting efficiencies.

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.

Understanding the self-assembly of Fmoc-phenylalanine to hydrogel formation

Hydrogels of low molecular weight molecules are important in biomedical applications. Multiple factors are responsible for hydrogel formation, but their role in governing self-assembly to hydrogel formation is poorly understood. Herein, we report the hydrogel formation of fluorenylmethyloxycarbonyl phenylalanine (FmocF) molecule. We used physical and thermal stimuli for solubilizing FmocF above the critical concentration to induce gel formation. The key role of Fmoc, Fmoc and phenylalanine covalent linkage, flexibility of phe side chain, pH, and buffer ions in self-assembly of FmocF to gel formation is described. We found that the collective action of different non-covalent interactions play a role in making FmocF hydrogel. Using powder diffraction and infrared spectroscopy, we also report a new polymorphic form of FmocF after transitioning to hydrogel. In addition, we are proposing a model for drug release from FmocF hydrogel.

Morphological Versatility in the Self-Assembly of Val-Ala and Ala-Val Dipeptides

Since the discovery of dipeptide self-assembly, diphenylalanine (Phe-Phe)-based dipeptides have been widely investigated in a variety of fields. Although various supramolecular Phe-Phe-based structures including tubes, vesicles, fibrils, sheets, necklaces, flakes, ribbons, and wires have been demonstrated by manipulating the external physical or chemical conditions applied, studies of the morphological diversity of dipeptides other than Phe-Phe are still required to understand both how these small molecules respond to external conditions such as the type of solvent and how the peptide sequence affects self-assembly and the corresponding molecular structures. In this work, we investigated the self-assembly of valine-alanine (Val-Ala) and alanine-valine (Ala-Val) dipeptides by varying the solvent medium. It was observed that Val-Ala dipeptide molecules may generate unique self-assembly-based morphologies in response to the solvent medium used. Interestingly, when Ala-Val dipeptides were utilized as a peptide source instead of Val-Ala, we observed distinct differences in the final dipeptide structures. We believe that such manipulation may not only provide us with a better understanding of the fundamentals of the dipeptide self-assembly process but also may enable us to generate novel peptide-based materials for various applications.

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.

Diphenylalanine self assembly: novel ion mobility methods showing the essential role of water

The mechanism and driving forces behind the formation of diphenylalanine (FF) nanotubes have attracted much attention in the past decades. The hollow structure of the nanotubes suggests a role for water during the self-assembly process. Here, we use novel ion-mobility mass spectrometry methods to probe the early oligomers formed by diphenylalanine peptides. Interestingly, water-bound oligomers are observed in nano-electrospray ionization (ESI) mass spectra in the absence of bulk solvent. In addition, ligated water clusters transit the ion mobility cell but (often) dissociate before detection. These water molecules are shown to be essential for the formation of diphenylalanine oligomers larger than the dimer. The ligated water molecules exist in the solvent free environment either as neutral water or as protonated water clusters, depending on the composition of solvent from which they are sprayed. Water adduction helps stabilize conformers that are otherwise energetically unstable ultimately leading to the assembly of FF nanotubes.

Single water solvation dynamics in the 4-aminobenzonitrile–water cluster cation revealed by picosecond time-resolved infrared spectroscopy

The excess energy of photoionization can control the time scale of single water solvent orientation dynamics from picoseconds to infinitely long trapping in a local minimum.

Supramolecular self-assembly of 14-helical nanorods with tunable linear and dendritic hierarchical morphologies

Varying the solvent offers a simple way to control superstructure polymorphism of a tri-β³-peptide-based supramolecular system.

Expanding the solvent chemical space for self-assembly of dipeptide nanostructures

Nanostructures composed of short, noncyclic peptides represent a growing field of research in nanotechnology due to their ease of production, often remarkable material properties, and biocompatibility. Such structures have so far been almost exclusively obtained through self-assembly from aqueous solution, and their morphologies are determined by the interactions between building blocks as well as interactions between building blocks and water. Using the diphenylalanine system, we demonstrate here that, in order to achieve structural and morphological control, a change in the solvent environment represents a simple and convenient alternative strategy to the chemical modification of the building blocks. Diphenylalanine (FF) is a dipeptide capable of self-assembly in aqueous solution into needle-like hollow micro- and nanocrystals with continuous nanoscale channels that possess advantageous properties such as high stiffness and piezoelectricity and have so emerged as attractive candidates for functional nanomaterials. We investigate systematically the solubility of diphenylalanine in a range of organic solvents and probe the role of the solvent in the kinetics of self-assembly and the structures of the final materials. Finally, we report the crystal structure of the FF peptide in microcrystalline form grown from MeOH solution at 1 Å resolution and discuss the structural changes relative to the conventional materials self-assembled in aqueous solution. These findings provide a significant expansion of the structures and morphologies that are accessible through FF self-assembly for existing and future nanotechnological applications of this peptide. Solvent mediation of molecular recognition and self-association processes represents an important route to the design of new supramolecular architectures deriving their functionality from the nanoscale ordering of their components.

Enhanced solid-state electron transport via tryptophan containing peptide networks

The electrical conductivity via peptide networks was measured using conductive probe atomic force microscopy, where the tryptophan-containing peptide network (composed of Phe-Trp dipeptides) exhibited a superior (5 fold) conductivity in comparison to an all phenylalanine network (composed of Phe-Phe dipeptides). These results are in line with previous spectroscopic measurements exploring intramolecular electron transfer in proteins. Bias-scaling factors (instead of the more commonly used transition voltage spectroscopy method) were calculated for the two peptide networks. These calculations showed substantial differences between the two peptide networks, suggesting different electron transport characteristics. While the factor for the tryptophan-containing network is similar to conjugated molecules with a low electron-tunneling barrier, the one for the all phenylalanine network can be ascribed as an 'intermediate' factor between conjugated and saturated molecules.

Self-assembly of a tripeptide into a functional coating that resists fouling

A short peptide (tripeptide) self-assembles into a supramolecular functional coating with antifouling activity. This coating can be useful in applications where the adsorption of proteins, bacteria and other organisms should be avoided.