Self-assembled Peptide Nanotubes Research Articles

Self-assembled peptide nanotubes (SPNTs)/SnO2 nanocomposites for high-performance NO2 sensing at room temperature

Nitrogen dioxide (NO2) is a major pollutant that poses significant risks to sustainable human life. As a result, a growing focus has been placed on the development of highly selective and sensitive gas sensors for NO2. Traditional cutting-edge non-organic NO2 gas detectors often necessitate stringent production conditions and potentially harmful materials, which are not environmentally friendly, and these shortcomings have limited their widespread practical use. To overcome these challenges, we synthesized self-assembled peptide nanotubes (SPNTs) through a molecular self-assembly process. The SPNTs were then combined with SnO2 in varying proportions to construct NO2 gas sensors. The design of this sensor ensured efficient electron transfer and leverage the extensive surface area of the SPNTs for enhanced gas adsorption and the effective dispersion of SnO2 nanoparticles. Notably, the performance of the sensor, including its sensitivity, response time, and recovery rate, along with a lower detection threshold, could be finely tuned by varying the SPNTs content. This approach illustrated the potential of bioinspired methodologies, using peptide self-assemblies, to develop integrated sensors for pollutant detection, providing a significant development in environmentally conscious sensor technology.

Direct electrochemistry of hemoglobin/peptide-carbon nanotube modified electrode for hydrogen peroxide biosensing

Mediatorless enzymatic biosensors based on direct electron transfer show promise due to their high stability and remarkable electrocatalytical performance. In this study, the direct electrochemistry of a glassy carbon electrode modified with hemoglobin (Hb) embedded in a hybrid layer of self-assembling EFK8 peptide and single-walled carbon nanotubes (SWNTs) was investigated. Electrochemical studies in 0.1 M phosphate buffer (PB) revealed that the immobilized Hb did not denature and retained its bio-catalytic activity. The resulting biosensor was used to detect and measure the hydrogen peroxide (H2O2) concentration in 0.1 M PB (pH 7.0), yielding a linear detection range from 20 to 960 µM and a detection limit of 7.54 µM (S/N = 3). The EFK8-SWNT hybrid layer shows promise as a biocompatible layer for simple non-covalent enzyme immobilization as the basis for future mediatorless enzymatic biosensors.

Peptide nanotube/hemin composite with enhanced peroxidase activity for the detection of dopamine in food and drug samples.

Inspired by natural enzymes, artificial enzymes have been widely studied due to their ease of mass production, robustness to harsh environments and high stability. In this work, a peptide nanotube/hemin composite (KL@hemin) as an artificial enzyme was prepared by immobilizing hemin onto self-assembled peptide nanotubes (PNTs). The successful loading of hemin was determined by a series of characterizations. The multiple noncovalent interactions between the PNTs and hemin endow KL@hemin with strong stability. Subsequent enzyme activity tests showed that the prepared KL@hemin exhibited enhanced peroxidase activity. Further experiments indicate that PNTs as carriers can not only protect hemin from dimerization to maintainenzyme activity but also increase the affinity of hemin to the substrate for faster binding and accelerate mass transfer, thus promoting the whole catalytic process. Coupled with a peroxidase-catalyzed chromogenic system, a colorimetric method for dopamine detection was constructed based on KL@hemin. The strategy shows high sensitivity and selectivity and has been applied to the determination of dopamine in dopamine injection and meat samples.

Molecular Dynamics Simulations of Transmembrane Cyclic Peptide Nanotubes Using Classical Force Fields, Hydrogen Mass Repartitioning, and Hydrogen Isotope Exchange Methods: A Critical Comparison

Self-assembled cyclic peptide nanotubes with alternating D- and L-amino acid residues in the sequence of each subunit have attracted a great deal of attention due to their potential for new nanotechnology and biomedical applications, mainly in the field of antimicrobial peptides. Molecular dynamics simulations can be used to characterize these systems with atomic resolution at different time scales, providing information that is difficult to obtain via wet lab experiments. However, the performance of classical force fields typically employed in the simulation of biomolecules has not yet been extensively tested with this kind of highly constrained peptide. Four different classical force fields (AMBER, CHARMM, OPLS, and GROMOS), using a nanotube formed by eight D,L-α-cyclic peptides inserted into a lipid bilayer as a model system, were employed here to fill this gap. Significant differences in the pseudo-cylindrical cavities formed by the nanotubes were observed, the most important being the diameter of the nanopores, the number and location of confined water molecules, and the density distribution of the solvent molecules. Furthermore, several modifications were performed on GROMOS54a7, aiming to explore acceleration strategies of the MD simulations. The hydrogen mass repartitioning (HMR) and hydrogen isotope exchange (HIE) methods were tested to slow down the fastest degrees of freedom. These approaches allowed a significant increase in the time step employed in the equation of the motion integration algorithm, from 2 fs up to 5–7 fs, with no serious changes in the structural and dynamical properties of the nanopores. Subtle differences with respect to the simulations with the unmodified force fields were observed in the concerted movements of the cyclic peptides, as well as in the lifetime of several H-bonds. All together, these results are expected to contribute to better understanding of the behavior of self-assembled cyclic peptide nanotubes, as well as to support the methods tested to speed up general MD simulations; additionally, they do provide a number of quantitative descriptors that are expected to be used as a reference to design new experiments intended to validate and complement computational studies of antimicrobial cyclic peptides.

Cryo-EM of Helical Polymers.

While the application of cryogenic electron microscopy (cryo-EM) to helical polymers in biology has a long history, due to the huge number of helical macromolecular assemblies in viruses, bacteria, archaea, and eukaryotes, the use of cryo-EM to study synthetic soft matter noncovalent polymers has been much more limited. This has mainly been due to the lack of familiarity with cryo-EM in the materials science and chemistry communities, in contrast to the fact that cryo-EM was developed as a biological technique. Nevertheless, the relatively few structures of self-assembled peptide nanotubes and ribbons solved at near-atomic resolution by cryo-EM have demonstrated that cryo-EM should be the method of choice for a structural analysis of synthetic helical filaments. In addition, cryo-EM has also demonstrated that the self-assembly of soft matter polymers has enormous potential for polymorphism, something that may be obscured by techniques such as scattering and spectroscopy. These cryo-EM structures have revealed how far we currently are from being able to predict the structure of these polymers due to their chaotic self-assembly behavior.

Modeling of Self-Assembled Peptide Nanotubes and Determination of Their Chirality Sign Based on Dipole Moment Calculations.

The chirality quantification is of great importance in structural biology, where the differences in proteins twisting can provide essentially different physiological effects. However, this aspect of the chirality is still poorly studied for helix-like supramolecular structures. In this work, a method for chirality quantification based on the calculation of scalar triple products of dipole moments is suggested. As a model structure, self-assembled nanotubes of diphenylalanine (FF) made of L- and D-enantiomers were considered. The dipole moments of FF molecules were calculated using semi-empirical quantum-chemical method PM3 and the Amber force field method. The obtained results do not depend on the used simulation and calculation method, and show that the D-FF nanotubes are twisted tighter than L-FF. Moreover, the type of chirality of the helix-like nanotube is opposite to that of the initial individual molecule that is in line with the chirality alternation rule general for different levels of hierarchical organization of molecular systems. The proposed method can be applied to study other helix-like supramolecular structures.

Transmembrane Self-Assembled Cyclic Peptide Nanotubes Based on α-Residues and Cyclic δ-Amino Acids: A Computational Study.

Self-assembling cyclic peptide nanotubes have been shown to function as synthetic, integral transmembrane channels. The combination of natural and nonnatural aminoacids in the sequence of cyclic peptides enables the control not only of their outer surface but also of the inner cavity behavior and properties, affecting, for instance, their permeability to different molecules including water and ions. Here, a thorough computational study on a new class of self-assembling peptide motifs, in which δ-aminocycloalkanecarboxylic acids are alternated with natural α-amino acids, is presented. The presence of synthetic δ-residues creates hydrophobic regions in these α,δ-SCPNs, which makes them especially attractive for their potential implementation in the design of new drug or diagnostic agent carrier systems. Using molecular dynamics simulations, the behavior of water molecules, different ions (Li+, Na+, K+, Cs+, and Ca2+), and their correspondent counter Cl− anions is extensively investigated in the nanoconfined environment. The structure and dynamics are mutually combined in a diving immersion inside these transmembrane channels to discover a fascinating submarine nanoworld where star-shaped water channels guide the passage of cations and anions therethrough.

Label-free impedimetric miRNA-192 genosensor platform using graphene oxide decorated peptide nanotubes composite

Here, we report on the preparation of a sensor platform that implies diphenylalanine based self-assembled peptide nanotubes (PNTs) with graphene oxide (GO) on pencil graphite electrodes (PGEs) and its evaluation for quantification of diabetic nephropathy and cancer-related microRNA-192. The PNT-GO structures were characterized and used to functionalize PGE for biosensor construction. The measured impedance was utilized for the first time as the signal to evaluate the hybridization between miRNA-192 and its corresponding ss-DNA probe owing to the features of PNT-GO. PNT-GO/PGE showed high sensitivity for electrochemical miRNA-192 analysis with a very wide dynamic detection range of 10 fM–1.0 nM and a low sensing limit of 8 fM. Evaluation of the developed impedimetric biosensor in peripheral serum samples revealed its potential for future clinical applications and diverse biomedical applications without the aid for extraction, sample pretreatment or amplification steps.

Multiscale Structural Elucidation of Peptide Nanotubes by X-Ray Scattering Methods.

This mini-review presents the structural investigations of the self-assembled peptide nanotubes using X-ray scattering techniques. As compared to electron microscopy, scattering methods enable studies of nanotubes in solution under the appropriate physicochemical conditions and probe their formation mechanism. In addition, a combination of X-ray scattering methods allow the elucidation of structural organization from the molecular scale to the dimension of nanotubes.

Effect of Water Models on Transmembrane Self-Assembled Cyclic Peptide Nanotubes.

Self-assembling cyclic peptide nanotubes can form nanopores when they are inserted in lipid bilayers, acting as ion and/or water permeable channels. In order to improve the versatility of these systems, it is possible to specifically design cyclic peptides with a combination of natural and non-natural amino acids, enabling the control of the nature of the inner cavity of the channels. Here, the behavior of two types of self-assembling peptide motifs, alternating α-amino acids with γ- or δ-aminocycloalkanecarboxylic acids, is studied via molecular dynamics (MD) simulations. The behavior of water molecules in nanopores is expected to affect the properties of these channels and therefore merits detailed examination. A number of water models commonly used in MD simulations have been validated by how well they reproduce bulk water properties. However, it is less clear how these water models behave in the nanoconfined condition inside a channel. The behavior of four different water models—TIP3P, TIP4P, TIP4P/2005, and OPC—are evaluated in MD simulations of self-assembled cyclic peptide nanotubes of distinct composition and diameter. The dynamic behavior of the water molecules and ions in these designed artificial channels depends subtly on the water model used. TIP3P water molecules move faster than those of TIP4P, TIP4P/2005, and OPC. This demeanor is clearly observed in the filling of the nanotube, in water diffusion within the pore, and in the number and stability of hydrogen bonds of the peptides with water. It was also shown that the water model influences the simulated ion flux through the nanotubes, with TIP3P producing the greatest ion flux. Additionally, the two more recent models, TIP4P/2005 and OPC, which are known to reproduce the experimental self-diffusion coefficient of bulk water quite well, exhibit very similar results under the nanoconfined conditions studied here. Because none of these models have been parametrized specifically for waters confined in peptide nanotubes, this study provides a point of reference for further validation.

Cross α-Helical Nanotubes: Mining the Designability Landscape for Filamentous Peptide Nanomaterials

The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the creation of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within these cross-α nanotubes. The structure of these resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to native protein filaments such as flagella and pili.

Structural analysis of cross \u03b1-helical nanotubes provides insight into the designability of filamentous peptide nanomaterials

The exquisite structure-function correlations observed in filamentous protein assemblies provide a paradigm for the design of synthetic peptide-based nanomaterials. However, the plasticity of quaternary structure in sequence-space and the lability of helical symmetry present significant challenges to the de novo design and structural analysis of such filaments. Here, we describe a rational approach to design self-assembling peptide nanotubes based on controlling lateral interactions between protofilaments having an unusual cross-α supramolecular architecture. Near-atomic resolution cryo-EM structural analysis of seven designed nanotubes provides insight into the designability of interfaces within these synthetic peptide assemblies and identifies a non-native structural interaction based on a pair of arginine residues. This arginine clasp motif can robustly mediate cohesive interactions between protofilaments within the cross-α nanotubes. The structure of the resultant assemblies can be controlled through the sequence and length of the peptide subunits, which generates synthetic peptide filaments of similar dimensions to flagella and pili.

Self-assembling A6K peptide nanotubes as a mercaptoundecahydrododecaborate (BSH) delivery system for boron neutron capture therapy (BNCT)

Boron neutron capture therapy (BNCT) is a tumor selective therapy, the effectiveness of which depends on sufficient 10B delivery to and accumulation in tumors. In this study, we used self-assembling A6K peptide nanotubes as boron carriers and prepared new boron agents by simple mixing of A6K and BSH. BSH has been used to treat malignant glioma patients in clinical trials and its drug safety and availability have been confirmed; however, its contribution to BNCT efficacy is low. A6K nanotube delivery improved two major limitations of BSH, including absence of intracellular transduction and non-specific drug delivery to tumor tissue. Varying the A6K peptide and BSH mixture ratio produced materials with different morphologies—determined by electron microscopy—and intracellular transduction efficiencies. We investigated the A6K/BSH 1:10 mixture ratio and found high intracellular boron uptake with no toxicity. Microscopy observation showed intracellular localization of A6K/BSH in the perinuclear region and endosome in human glioma cells. The intracellular boron concentration using A6K/BSH was almost 10 times higher than that of BSH. The systematic administration of A6K/BSH via mouse tail vein showed tumor specific accumulation in a mouse brain tumor model with immunohistochemistry and pharmacokinetic study. Neutron irradiation of glioma cells treated with A6K/BSH showed the inhibition of cell proliferation in a colony formation assay. Boron delivery using A6K peptide provides a unique and simple strategy for next generation BNCT drugs.

Molecular modeling and computational study of the chiral-dependent structures and properties of the self-assembling diphenylalanine peptide nanotubes, containing water molecules.

DFT (VASP) and semi-empirical (HyperChem) calculations for the L- and D-chiral diphenylalanine (L-FF and D-FF) nanotube (PNT) structures, empty and filled with water/ice clusters, are presented and analyzed. The results obtained show that after optimization, the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like-cluster obtained after optimization inside L-FF and D-FF PNT and total L-FF and D-FF PNT with embedded water/ice cluster are discussed.

Structures and Properties of the Self-Assembling Diphenylalanine Peptide Nanotubes Containing Water Molecules: Modeling and Data Analysis.

The structures and properties of the diphenylalanine (FF) peptide nanotubes (PNTs), both L-chiral and D-chiral (L-FF and D-FF) and empty and filled with water/ice clusters, are presented and analyzed. DFT (VASP) and semi-empirical calculations (HyperChem) to study these structural and physical properties of PNTs (including ferroelectric) were used. The results obtained show that after optimization the dipole moment and polarization of both chiral type L-FF and D-FF PNT and embedded water/ice cluster are enhanced; the water/ice cluster acquire the helix-like structure similar as L-FF and D-FF PNT. Ferroelectric properties of tubular water/ice helix-like cluster, obtained after optimization inside L-FF and D-FF PNT, as well of the total L-FF and D-FF PNT with embedded water/ice cluster, are discussed.

Membrane targeting antimicrobial cyclic peptide nanotubes – an experimental and computational study

The search of new antibiotics, particularly with new mechanisms of action, is nowadays a very important public health issue, due to the worldwide increase of resistant pathogens. Within this effort, much research has been done on antimicrobial peptides, because having the membrane as a target, they represent a new antibiotic paradigm. Among these, cyclic peptides (CPs) made of sequences of D- and L-amino acids have emerged as a new class of potential antimicrobial peptides, due to their expected higher resistance to protease degradation. These CPs are planar structures that can form Self-assembled Cyclic Peptide Nanotubes (SCPNs), in particular in the presence of lipid membranes. Aiming at understanding their mechanism of action, we used biophysical experimental techniques (DSC and ATR-FTIR) together with Coarse-grained molecular dynamics (CG-MD) simulations, to characterize the interaction of these CPs with model membranes of different electrostatic charges’ contents. DSC results revealed that the CPs show a strong interaction with negatively charged membranes, with differences in the strength of interactions depending on peptide and on membrane charge content, at odds with no or mild interactions with zwitterionic membranes. ATR-FTIR suggested that the peptides self-assemble at the membrane surface, adopting mainly a β-structure. The experiments with polarized light showed that in most cases they lie parallel to the membrane surface, but other forms and orientations are also apparent, depending on peptide structure and lipid:peptide ratio. The nanotube formation and orientation, as well as the dependence on membrane charge were also confirmed by the CG-MD simulations. These provide detail on the position and interactions, in agreement with the experimental results. Based on the findings reported here, we could proceed to the design and synthesis of a second-generation CPs, based on CP2 (soluble peptide), with increased activity and reduced toxicity.

Tyrosine Derivative of Aminoacid Produced Bio Inspired Nanotubes and NanovesiclesSynthesis and Characterization

3,5-bis(trifluoromethyl)benzylamine derivative of tyrosine single aminoacids have produced self-assembled peptide nanotubes and nanovesicles (BTTPNTs) depending on the concentration of the monomer study through optical and microscopic analysis. DFT simulations were carried out for a system of BTTPNTs and nanovesicles which also experimentally characterized by high resolution transmission electron microscopy (HR-TEM) and ultraviolet-visible (UV-Vis) absorbance. These results are used to examine the morphologies, size of the nanostructure and study its recognition of aminoacid motif is discussed. However, the length of the nanotubes gets larger with the increases of concentration. UV-Vis spectra clearly showed slight decrease in the intensity in absorption after the formation of nanotubes and nanovesicles. Theoretical calculations indicate that H-bonding is the key factor in making ring while other interactions including Van der Walls force, π–π stacking plays role to making self-assembled nanotubes and vesicles.

Energy behaviour of Doxorubicin interacting with peptide nanotubes

Self-assembling cyclic peptide nanotubes are widely investigated in many scientific fields due to many of their properties; controllable sizes, stable, and simple formation. In this research, the cyclic peptide nanotubes are modelled as the carriers to interact with a drug molecule. On employing the Lennard-Jones function and the continuous approximation, the energy value of the system can be evaluated. The main outcome of this research is a mathematical expression describing the relation of energy, radii of drug and peptide and the spacing between peptide units. We find that the drug is most stable when it is in the spacing between subunits of the peptide nanotubes. We also consider the energy behaviour of an offset drug inside three different sizes of the cyclic peptide nanotubes. We predict that the drug can be encapsulated inside the peptide nanotube when the difference of their radii is around 3 A.

Self-Assembled Peptide Nanotube Films with High Proton Conductivity

Design flexibility and modularity have emerged as powerful tools in the development of functional self-assembled peptide nanostructures. In particular, the tendency of peptides to form fibrils and nanotubes has motivated the investigation of electron and, more recently, proton transport in their fibrous films. In this study, we present a detailed characterization by impedance spectroscopy of films of self-assembled cyclic octa-d,l-α-peptide self-assembled nanotubes with amine side chains that promote proton transport. We show that the conductivity of the peptide nanotube film, which is in the range of 0.3 mS cm-1, is within the same order of magnitude as that of ultrathin films of Nafion, a benchmark proton conducting polymer. In addition, we show that while slow diffusion processes at the interface are present for both films, additional interface effects occur in the peptide nanotube films at the same rate as their bulk proton transport effects, further limiting charge transport at the interface. Overall, our studies demonstrate the great potential of using peptides as building blocks for the preparation of bioinspired supramolecular proton conducting polymers with improved conductivity with respect to that of natural systems.

Enhanced piezoresponse and nonlinear optical properties of fluorinated self-assembled peptide nanotubes

Self-assembled L,L-diphenylalanine (FF) nanostructures offer an attractive platform for photonics and nonlinear optics. The nonlinear optical (NLO) coefficients of FF nanotubes depend on the diameter of the tube [S. Khanra et al. Phys. Chem. Chem. Phys. 19(4), 3084–3093 (2017)]. To further enhance the NLO properties of FF, we search for structural modifications. Here, we report on the synthesis of fluorinated FF dipeptides by replacing one ortho-hydrogen atom in each of the phenyl groups of FF by a fluorine atom. Density-functional theoretical calculations yield insights into minimum energy conformers of fluorinated FF (Fl-FF). Fl-FF self-assembles akin to FF into micron-length tubes. The effects of fluorination are evaluated on the piezoelectric response and nonlinear optical properties. The piezoelectric d15 coefficient of Fl-FF is found to be more than 10 times higher than that of FF nanotubes, and the intensity of second harmonic generation (SHG) polarimetry from individual Fl-FF nanotubes is more than 20 times that of individual FF nanotubes. Furthermore, we obtain SHG images to compare the intensities of FF and Fl-FF tubes. This work demonstrates the potential of fluorine substitution in other self-assembled biomimetic peptides for enhancing nonlinear optical response and piezoelectricity.