Chiral peculiar properties of self-organization of diphenylalanine peptide nanotubes: Modeling of structure and properties

The structure and properties of diphenylalanine peptide nanotubes based on phenylalanine were investigated by various molecular modeling methods. The main approaches were semi-empirical quantum-chemical methods (PM3 and AM1), and molecular mechanical ones. Both the model structures and the structures extracted from their experimental crystallographic databases obtained by X-ray methods were examined. A comparison of optimized model structures and structures obtained by naturally-occurring self-assembly showed their important differences depending on D- and L-chirality. In both the cases, the effect of chirality on the results of self-assembly of diphenylalanine peptide nanotubes was established: peptide nanotubes based on the D-diphenylalanine (D-FF) has high condensation energy E 0 in transverse direction and forms thicker and shorter peptide nanotubes bundles, than that based on L-diphenylalanine (L-FF). A topological difference was established: model peptide nanotubes were optimized into structures consisting of rings, while naturally self-assembled peptide nanotubes consisted of helical coils. The latter were different for the original L-FF and D-FF. They formed helix structures in which the chirality sign changes as the level of the macromolecule hierarchy raises. Total energy of the optimal distances between two units are deeper for L-FF (-1.014 eV) then for D-FF (-0.607 eV) for ring models, while for helix coil are approximately the same and have for L-FF (-6.18 eV) and for D-FF (-6.22 eV) by PM3 method; for molecular mechanical methods energy changes are of the order of 2-3 eV for both the cases. A topological transition between a ring and a helix coil of peptide nanotube structures is discussed: self-assembled natural helix structures are more stable and favourable, they have lower energy in optimal configuration as compared with ring models by a value of the order of 1 eV for molecular mechanical methods and 5 eV for PM3 method. © 2019 Mathematical Biology and Bioinformatics.Part of this work was developed as part of the CICECO-Aveiro Materials Institute project, POCI-01-0145-FEDER-007679 funded from Fundação para a Ciência e a Tecnologia (FCT) Ref. UID/CTM/50011/2013, and funded from national funds through FCT/MEC, and co-funded by FEDER in accordance with the PT2020 Partnership Agreement. P.Z. thanks the project FCT PTDC/QEQ-QAN/6373/2014. S.K. thanks the project FCT PTDC/CTM-CTM/31679/2017

Effect of Solvent on the Self-Assembly of Dialanine and Diphenylalanine Peptides

Diphenylalanine (FF) is a very common peptide with many potential applications, both biological and technological, due to a large number of different nanostructures which it attains. The current work concerns a detailed study of the self assembled structures of FF in two different solvents, an aqueous (H2O) and an organic (CH3OH) through simulations and experiments. Detailed atomistic Molecular Dynamics (MD) simulations of FF in both solvents have been performed, using an explicit solvent model. The self assembling propensity of FF in water is obvious while in methanol a very weak self assembling propensity is observed. We studied and compared structural properties of FF in the two different solvents and a comparison with a system of dialanine (AA) in the corresponding solvents was also performed. In addition, temperature dependence studies were carried out. Finally, the simulation predictions were compared to new experimental data, which were produced in the framework of the present work. A very good qualitative agreement between simulation and experimental observations was found

Self-Assembled Short Peptide Nanostructures: ‘’Dipeptides’’

Dipeptides are short peptide molecules formed by the peptide bond between two amino acids, and they play significant roles in various biological processes (such as protein synthesis, nutrient absorption, cellular signaling, immune response). Short peptides have a prominent place in the design of self-assembling materials. In particular, dipeptides have gained considerable attention in the field of biotechnology as a type of self-organizing nanostructure due to their low cost, simplicity of synthesis, biocompatibility, and tunability of functionality. However, there is limited knowledge about peptide and protein-based nanostructures in the literature. Therefore, more information is needed on dipeptide nanostructures, especially in terms of their potential applications for biomedical purposes. This review focuses on dipeptide nanostructures, particularly their potential uses in biomedical applications, and provides a broader perspective on the advantages, challenges, synthesis, interactions, and applications of these nanostructures

Graphene & Graphene Oxide and amyloid peptide binding and its implications in Alzheimer’s disease

Alzheimer’s disease is a neurodegenerative disease caused by the incorrect cleaving of the transmembrane Amyloid Precursor Protein into the neurotoxic Aβ40 and Aβ42 fragments2. These fragments are soluble oligomers with a random coil conformation that can impair synapses or neurotransmission; they may also aggregate into parallel and antiparallel beta sheets to form amyloid plaques, which can block or distort signaling between neuronal pathways7. Aβ fibrils self-assemble into parallel and antiparallel beta sheets on hydrophobic graphite, but not on hydrophilic mica5,6. Aβ fibrils also assemble on graphene, which irreversibly captures fibrils3, suggesting grapheme might have a role in the study of Alzheimer’s amyloid plaque. These studies characterize binding between amyloid beta peptide fibrils and graphene using Raman spectroscopy, scanning electron microscopy (SEM), and circular dichroism (CD). The goal is to provide evidence that graphene can attract free floating Aβ fibrils and Aβ plaque. Both studies currently use diphenylalanine peptide, a self-assembling model peptide for Aβ fibrils

Graphene and amyloid peptide binding and its implications in Alzheimer's disease

A poster discussing the relation of graphene and amyloid peptide binding to Alzheimer's disease

Piezoelectricity in Self-Assembled Peptides: A New Way towards Electricity Generation at Nanoscale

Self-assembled nanostructured peptides are of great interest nowadays due to their biocompatibility and an array of outstanding functional properties. Among them, strong piezoelectricity combined with low dielectric constant is beneficial for high voltage and power generation at the nanoscale. This Chapter is an overview of the piezoelectric phenomena in self-assembled peptides including effects of the growth conditions, self-assembly, and measurement techniques on their functional response as well as the origin of strong piezoelectricity in this material. The current status of electrical energy harvesting in self-assembled peptides useful for biomedical applications along with the challenges and perspectives for using these piezoelectric biomaterials will be discussed. This Chapter is expected to provide a guidance towards future design and application of novel functional self-assembled materials based on nanostructured peptides