Efficient Water Self-Diffusion in Diphenylalanine Peptide Nanotubes

New Insight into the Structural Nature of Diphenylalanine Nanotube through Comparison with Amyloid Assemblies

Diphenylalanine (FF) nanotubes are a star material in the field of peptide self-assembly and have demonstrated numerous intriguing applications. Due to its resemblance to amyloid assembly, the FF nanotube is widely regarded as a simplified mimic of amyloids. Yet, whether FF nanotube truly possesses amyloid structure remains an open question. To better understand the structural nature of FF nanotube, we herein performed a comparative structural investigation between FF nanotube and typical amyloid systems by Aβ1-40, Aβ1-42, Aβ16-22, Aβ13-23, α-synuclein, and lysozyme using Fourier transform infrared spectroscopy. Through this comparative investigation, we obtained clear evidence to support that the FF nanotube does not possess a β-sheet structure, a key structural characteristic of amyloid assembly, thus revealing the non-amyloid structural nature of the FF nanotube. At last, in light of our new finding, we further discussed the unique self-assembly behaviors of FF during nanotube formation and the implications of our work for FF nanotube related applications.

Structure and Dynamics of Confined Water Inside Diphenylalanine Peptide Nanotubes

Diphenylalanine (FF) peptides exhibit a unique ability to self-assemble into nanotubes with confined water molecules playing pivotal roles in their structure and function. This study investigates the structure and dynamics of diphenylalanine peptide nanotubes (FFPNTs) using all-atom molecular dynamics (MD) and grand canonical Monte Carlo combined with MD (GCMC/MD) simulations with both the CHARMM additive and Drude polarizable force fields. The occupancy and dynamics of confined water molecules were also examined. It was found that less than 2 confined water molecules per FF help stabilize the FFPNTs on the x-y plane. Analyses of the kinetics of confined water molecules revealed distinctive transport behaviors for bound and free water, and their respective diffusion coefficients were compared. Our results validate the importance of polarizable force field models in studying peptide nanotubes and provide insights into our understanding of nanoconfined water.

Helical-Like Assembly of Nateglinide as Coating for Oral Delivery of Insulin and Their Synergistic Prevention of Diabetes Mellitus

Oral delivery of antidiabetic active components promises to free millions of people from daily suffering who require routine injections. However, oral insulin (Ins) and other short-acting compounds such as nateglinide (NG) in harsh gastrointestinal tract still face great challenging, including low bioavailability, and rapid elimination. In this study, inspired by the self-assembly of phenylalanine-based peptides in nature, it is showed that NG a small phenylalanine derivative, assembles into left-handed helical nanofibers in the presence of Ca2+ . These helical NG nanofibers functioned as a coating layer on the surface of Ca2+ -linked alginate (Alg) microgels for the effective encapsulation of Ins. As expected, the sustained release and prolonged circulation of Ins and NG from the Ins-loading Alg/NG microgels (Ins@Alg/NG) in the intestinal tract synergistically maintain a relatively normal blood glucose level in streptozotocin-induced diabetic mice after oral administration of Ins@Alg/NG. This further confirms that Ins@Alg/NG ameliorated Ins resistance mainly through activating Insreceptor substrate 1 (IRS1), protein kinase B (AKT), and AMP-activated protein kinase (AMPK), as well as by repressing glycogen synthase kinase-3β (GSK-3β). The strategy of using the assembly of NG as a coating achieves the oral delivery of insulin and showcases a potential for the treatment of diabetes.

Aromatic Zipper Topology Dictates Water-Responsive Actuation in Phenylalanine-Based Crystals

Water-responsive (WR) materials that reversibly deform in response to relative humidity (RH) changes are gaining increasing interest for their potential in energy harvesting and soft robotics applications. Despite progress, there are significant gaps in the understanding of how supramolecular structure underpins the reconfiguration and performance of WR materials. Here, three crystals are compared based on the amino acid phenylalanine (F) that contain water channels and F packing domains that are either layered (F), continuously connected (phenylalanyl-phenylalanine, FF), or isolated (histidyl-tyrosyl-phenylalanine, HYF). Hydration-induced reconfiguration is analyzed through changes in hydrogen-bond interactions and aromatic zipper topology. F crystals show the greatest WR deformation (WR energy density of 19.8 MJ m^-3 ) followed by HYF (6.5 MJ m^-3 ), while FF exhibits no observable response. The difference in water-responsiveness strongly correlates to the deformability of aromatic regions, with FF crystals being too stiff to deform, whereas HYF is too soft to efficiently transfer water tension to external loads.  These findings reveal aromatic topology design rules for WR crystals and provide insight into general mechanisms of high-performance WR actuation. Moreover, the best-performing crystal, F emerges as an efficient WR material for applications at scale and low cost.

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.

Solvent-dependent formation kinetics of L,L-diphenylalanine micro/nanotubes

Investigating the molecular mechanism underlying the aggregation process of amyloid fibers is of great importance both for its implications in several degenerative diseases and for the design of new materials based on self-assembly. In particular, micro/nanotubes of L,L-diphenylalanine have been investigated as a model of amyloid plaques in Alzheimer's disease and also for their broad range of physical properties, e.g., good thermo- and mechanical stability, semiconductivity, piezoelectricity and optical properties. It has been reported that the assembly/disassembly dynamics of L,L-diphenylalanine crystals is influenced by the solvent composition being triggered by evaporation of solvents. In fact the solvatomorphism of this peptide-based nanomaterial is complex and rich attracting great attention. Here we investigated the growing kinetics of the micro/nanotubes of L,L-diphenylalanine in samples prepared with toluene, ethanol, and acetic acid solvents by time-resolved Raman spectroscopy. Our results indicated that the self-assembly in this case competes with the water evaporation process contrary to what is reported by samples prepared with widely used solvent 1,1,1,3,3,3-hexafluoro-2-propanol. We note that exclusively tubular structures (being hollow for the toluene solvent case) were observed. Interestingly our results support the fact that for acetic acid, ethanol, and toluene the micro/nanotube formation process is autocatalytic instead of being nucleation-dominating as reported for samples prepared using solvent 1,1,1,3,3,3-hexafluoro-2-propanol.

Unidirectional diphenylalanine nanotubes for dynamically guiding neurite outgrowth

Neural networks have been culturedin vitroto investigate brain functions and diseases, clinical treatments for brain damage, and device development. However, it remains challenging to form complex neural network structures with desired orientations and connectionsin vitro. Here, we introduce a dynamic strategy by using diphenylalanine (FF) nanotubes for controlling physical patterns on a substrate to regulate neurite-growth orientation in cultivating neural networks. Parallel FF nanotube patterns guide neurons to develop neurites through the unidirectional FF nanotubes while restricting their polarization direction. Subsequently, the FF nanotubes disassemble and the restriction of neurites disappear, and secondary neurite development of the neural network occurs in other direction. Experiments were conducted that use the hippocampal neurons, and the results demonstrated that the cultured neural networks by using the proposed dynamic approach can form a significant cross-connected structure with substantially more lateral neural connections than static substrates. The proposed dynamic approach for neurite outgrowing enables the construction of oriented innervation and cross-connected neural networksin vitroand may explore the way for the bio-fabrication of highly complex structures in tissue engineering.

Perineuronal nets restrict transport near the neuron surface: A coarse-grained molecular dynamics study

Perineuronal nets (PNNs) are mesh-like extracellular matrix structures that wrap around certain neurons in the central nervous system. They are hypothesized to stabilize memories in the brain and act as a barrier between cell and extracellular space. As a means to study the impact of PNNs on diffusion, the nets were approximated by negatively charged polymer brushes and simulated by coarse-grained molecular dynamics. Diffusion constants of single neutral and single charged particles were obtained in directions parallel and perpendicular to the brush substrate. The results for the neutral particle were compared to different theories of diffusion in a heuristic manner. Diffusion was found to be considerably reduced for brush spacings smaller than 10 nm, with a pronounced anisotropy for dense brushes. The exact dynamics of the chains was found to have a negligible impact on particle diffusion. The resistance of the brush proved small compared to typical values of the membrane resistance of a neuron, indicating that PNNs likely contribute little to the total resistance of an enwrapped neuron.

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.

Self-Assembly and Gelation Study of Dipeptide Isomers with Norvaline and Phenylalanine

Dipeptides have emerged as attractive building blocks for supramolecular materials thanks to their low-cost, inherent biocompatibility, ease of preparation, and environmental friendliness as they do not persist in the environment. In particular, hydrophobic amino acids are ideal candidates for self-assembly in polar and green solvents, as a certain level of hydrophobicity is required to favor their aggregation and reduce the peptide solubility. In this work, we analyzed the ability to self-assemble and the gel of dipeptides based on the amino acids norvaline (Nva) and phenylalanine (Phe), studying all their combinations and not yielding to enantiomers, which display the same physicochemical properties, and hence the same self-assembly behavior in achiral environments as those studied herein. A single-crystal X-ray diffraction of all the compounds revealed fine details over their molecular packing and non-covalent interactions.

Surfactant-Assisted Assembly of Dipeptide Forming a Broom-like Structure

Understanding the influence of surfactants on the assembly of peptides has a considerable practical motivation. In this paper, we systematically study the anionic surfactant-assisted assembly of diphenylalanine (FF). FF forms broom-like structures in a concentration of sodium cholate (NaC) around the CMC, and assembles into linear and unidirectional rods in the presence of low and high surfactant concentrations. FF’s improved hydrogen bonding and controlled assembly rates are appropriate for other anionic surfactants. At this stage, the use of FF as the simplest protein consequence can be helpful in the investigation of further protein–surfactant interactions.