Peptide Nanotubes Research Articles

Flexing Piezoelectric Diphenylalanine–Plasmonic Metal Nanocomposites to Increase SERS Signal Strength

Piezoelectric quasi-1D peptide nanotubes and plasmonic metal nanoparticles are combined to create a flexible and self-energized surface-enhanced Raman spectroscopy (SERS) substrate that strengthens SERS signal intensities by over an order of magnitude compared to an unflexed substrate. The platform is used to sense bovine serum albumin, lysozyme, glucose, and adenine. Finite-element electromagnetic modeling indicates that the signal enhancement results from piezoelectric-induced charge, which is mechanically activated via substrate bending. The results presented here open the possibility of using peptide nanotubes on conformal substrates for in situ SERS detection.

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.

Piezoelectric properties reflecting nanostructures of tetrathiafulvalene and chloranil complexes using cyclic peptide nanotube scaffolds

AbstractTetrathiafulvalene (TTF) and chloranil were introduced at the side chains of different cyclic tripeptides, which were self‐assembled into peptide nanotubes (PNTs). PNTs were used as scaffolds for alignment of the charge‐transfer complexes between TTF and chloranil, and they were prepared via two methods, one is that mixing a PNT comprising only TTF with a PNT comprising only chloranil (method 1), and the other is that one pot mixing of cyclic tripeptides with TTF and cyclic tripeptides with chloranil to be self‐assembled into PNTs (method 2). These PNTs naturally associated to form PNT bundles. The surface potentials of the PNT bundles became larger for the PNTs carrying charge‐transfer complexes along the PNT (method 2) than those between PNTs (method 1). This bundle of PNT carrying charge‐transfer complexes along the PNT (method 2) showed a hysteresis response in the piezoelectric force curve with varying bias voltages according to piezoelectric force microscope measurements.

Energy harvesting with peptide nanotube–graphene oxide flexible substrates prepared with electric field and wettability assisted self-assembly

Piezoelectric diphenylalanine peptide nanotubes (PNTs) have recently been demonstrated in energy harvesting applications, typically based on vertically aligned PNTs that generate charge when pressed. In this work, we use a wettability difference and an applied electric field to align PNTs and PNT-based composites on flexible substrates. Open-circuit voltages and short-circuit currents exceeding 6 V and 60 nA, respectively, are achieved by bending the substrate, opening up the use of horizontally aligned PNTs as flexible energy harvesting substrates.

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.

The effects of amino acid sequence and solvent polarity on the self-assembling of cyclic peptide nanotubes and molecular channel formation inside the lipid bilayer

In this article, the effects of amino acid sequence and solvent polarity on the self-assembling process of cyclic peptides (CPs) were investigated by employing molecular dynamic (MD) simulations and quantum chemistry calculations. As a result, CP dimers are not stable in water, because of hydrogen bond (H-bond) lost between the CP units, while chloroform increases the stability of the CP dimers. MM-PBSA and MM-GBSA calculations confirmed that solvent polarity has an important effect on the stability of the CP dimers. Dynamical behavior of the cyclic peptide nanotubes (CPNTs) in chloroform indicates that CPNTs composed of leucine and phenylalanine are better molecular containers than that of isoleucine. At the next step, the ability of these CPNTs in molecular channel formation inside a fully hydrated DMPC (dimyristoylphosphatidylcholine) bilayer was investigated during 50 ns MD simulations. The obtained results show that only CPNT composed of isoleucine can form a molecular channel inside the DMPC membrane because isoleucine has a greater hydrophobicity than leucine and phenylalanine. This property increases the interactions between the CPNT and lipid residues, which elevates the stability of the CPNT inside the DMPC bilayer. Quantum chemistry calculations and non-covalent interactions analysis indicate that the solvent changes the stability and dynamical behavior of the CPNTs through the change in the H-bond strength. Finally, according to the different analyses, it can be concluded that the amino acid sequence in the CP units has an important role in designing specific nanostructures.

Pharmaceutical Formulation and Characterization of Dipeptide Nanotubes for Drug Delivery Applications.

Peptide nanotubes are promising materials for a variety of biomedical applications with ultrashort (≤7 amino acids) forms providing particular promise for clinical translation. The manufacture of peptide nanotubes has, however, been associated with toxic organic solvents restricting clinical use. The purpose of this work is to formulate dipeptide nanotubes using mild techniques easily translated to industrial upscale and to characterize their physiochemical and biological properties. Phenylalanine-phenylalanine variants can be successfully formulated using distilled water as demonstrated here. Formulations are homogenous in shape (tubular), with apparent size (50-260 nm) and a zeta potential of up to +30 mV. L-(H2 N-FF-COOH), and D-enantiomers (H2 N-ff-COOH) demonstrate no toxicity against glioblastoma cells and are explored for ability to deliver a model hydrophilic molecule, sodium fluorescein, at pH 5.5 (tumor) and 7.4 (physiological). Peptide nanotubes loaded with >85% sodium fluorescein, demonstrate burst release characteristics, fitting the Weibull model of drug release. This research provides important data contributing to the pharmaceutical formulation of peptide nanotubes as drug delivery platforms for hydrophilic drugs.

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.

The influences of driving forces on behaviors of Na+ and H2O in cyclic octa-peptide nanotube: investigated by steered molecular dynamics

The behaviors of Na+ and H2O in cyclic peptide nanotube (CPN) under different conditions are important for their applications. In this study, a series of driving forces has been applied to Na+ and H2O constrained in the self-assembled nanotube of {cyclo[(-D-Ala-L-Ala)4-]}10, to understand the influence on the transport properties and behaviors of Na+ and H2O using steered molecular dynamics (SMD). The results show that H2O need less driving force (0.4 kcal mol−1 Å−1) to migrate in the nanotube than that of Na+ (2.3 kcal mol−1 Å−1). Under the same driving force, the transport speed of H2O is about 135 times faster than that of Na+. The instantaneous velocity curves reveal that water adopts a kind of irregular hopping transport mode which does not change with the driving force, while Na+ transports in an obvious hopping mode changing with driving force in three different types. Particularly, the instantaneous velocity curves of Na+ under the driving force of 3.2–5.2 kcal mol−1 Å are roughly similar to the pulse signal, which is of great significance to the treatment of human diseases and the detection of electrolytes. The transport resistance mainly comes from electrostatic interaction. Results in this work show that cyclic octa-peptide nanotubes have excellent performance sensitive to external driving forces and are good potential materials for drug design, biosensors, ion transmembrane transport and ion probe for the detection of Na+ in organisms.

One-pot synthesized gold nanoparticle-peptide nanotube modified disposable sensor for impedimetric recognition of miRNA 410

In the presented study, gold nanoparticle assembled peptide nanotube (AuNP-PNT) modified graphite sensor system was offered for the first time for the impedimetric analysis of a potential prostate cancer biomarker, circulating miRNA 410, which is secreted by prostate cancer cells and is released into peripheral blood system. The proposed disposable sensor platform was easily constructed through one-pot synthesized nanocomposite modification with physical adsorption. AuNP-PNT nanocomposite and sensor surface features were identified with physicochemical, microscopic and electrochemical methods. The parameters which affect the sensor performance such as nanocomposite adsorption, probe DNA immobilization and hybridization process time-temperature were investigated and optimized. High sensitivity and low detection limit were established as 3.90 fM with a wide linear range from 10 fM to 300 pM for the impedimetric recognition of miRNA 410 based on the hybridization process. Selectivity experiment results proved that the developed surface captured the target miRNA with good base discrimination ability. Furthermore, the fabricated disposable sensor system was successfully applied in peripheral serum with good recovery. The proposed sensor system with its outstanding features such as cheapness, easiness, time effectiveness and sensitivity can be applied as a new sensor surface for the electrochemical detection of important analytes.

A molecular dynamics investigation on transporting mechanism of glucose through a cyclic peptide nanotube

Cyclic peptide nanotubes (CPNTs) are open-ended, hollow, and tubular structures that are made of several cyclic peptide rings. These structures can act as a transmembrane channel and transport ions or small molecules. In this work, we studied the stability of a cyclic peptide nanotube 8 × [(Trp-D-Leu)4-Gln-D-Leu] into a fully hydrated membrane composed of DPPC/POPC/POPS/cholesterol and also the transport mechanism of β-D-glucose through this nanotube was investigated. Our findings revealed that the CPNT was stable in the lipid bilayer during the simulation time and non-bonded interactions, especially hydrogen bonding have an important role to form a stable CPNT in the membrane. The glucose jumps from a Cα-region into the mid-Cα region and spends more time in this region because of its more desirable interactions with water molecules and the CPNT. In the transport pathway, non-bonded interactions between glucose, water molecules and the CPNT facilitate the transport of the glucose through the CPNT. The collaboration of hydrogen bonds, electrostatic and van der Waals interactions change the pulling force and lead to transport glucose through the CPNT. Potential of mean force (PMF) calculations revealed that the glucose has a minimum value of binding free energy and maximum configurational entropy in MPR regions. These findings can be used to design more CPNTs with different goals such as drug delivery. Communicated by Ramaswamy H. Sarma

Spatially Controlled Supramolecular Polymerization of Peptide Nanotubes by Microfluidics.

Despite the importance of spatially resolved self-assembly for molecular machines, the spatial control of supramolecular polymerization with synthetic monomers had not been experimentally established. Now, a microfluidic-regulated tandem process of supramolecular polymerization and droplet encapsulation is used to control the position of self-assembled microfibrillar bundles of cyclic peptide nanotubes in water droplets. This method allows the precise preferential localization of fibers either at the interface or into the core of the droplets. UV absorbance, circular dichroism and fluorescence microscopy indicated that the microfluidic control of the stimuli (changes in pH or ionic strength) can be employed to adjust the packing degree and the spatial position of microfibrillar bundles of cyclic peptide nanotubes. Additionally, this spatially organized supramolecular polymerization of peptide nanotubes was applied in the assembly of highly ordered two-dimensional droplet networks.

Spatially Controlled Supramolecular Polymerization of Peptide Nanotubes by Microfluidics

AbstractDespite the importance of spatially resolved self‐assembly for molecular machines, the spatial control of supramolecular polymerization with synthetic monomers had not been experimentally established. Now, a microfluidic‐regulated tandem process of supramolecular polymerization and droplet encapsulation is used to control the position of self‐assembled microfibrillar bundles of cyclic peptide nanotubes in water droplets. This method allows the precise preferential localization of fibers either at the interface or into the core of the droplets. UV absorbance, circular dichroism and fluorescence microscopy indicated that the microfluidic control of the stimuli (changes in pH or ionic strength) can be employed to adjust the packing degree and the spatial position of microfibrillar bundles of cyclic peptide nanotubes. Additionally, this spatially organized supramolecular polymerization of peptide nanotubes was applied in the assembly of highly ordered two‐dimensional droplet networks.

Engineering pH-responsive switching of donor-π-acceptor chromophore alignments along a peptide nanotube scaffold.

A cyclic tri-β-peptide cyclo(β-Ala-β-Ala-β-Lys) having diethylaminonaphthalimide at the β-Lys side chain (CP3Npi) self-assembled into a peptide nanotube in a solution of HFIP and water. CD spectra of the CP3Npi nanotubes show a negative Cotton effect at 441 nm and a positive Cotton effect at 393 nm, indicating that D–π–A naphthalimide chromophores are aligned in a left-handed chiral way along the nanotube. The CP3Npi nanotubes bear positive charges under acidic conditions retaining the nanotube structure but pH-responsive switching of D–π–A naphthalimide alignments along the nanotube between a left-handed chiral and random arrangement was observed. The peptide nanotube is a stable scaffold for attaining pH-responsive alignment switching of side-chain chromophores.

Peptide nanotubes self-assembled from leucine-rich alpha helical surfactant-like peptides.

The designed arginine-rich surfactant-like peptide R3L12 (arginine3-leucine12) is shown to form a remarkable diversity of self-assembled nanostructures in aqueous solution, depending on pH, including nanotubes, mesh-like tubular networks in three-dimensions and square planar arrays in two-dimensions. These structures are built from α-helical antiparallel coiled-coil peptide dimers arranged perpendicular to the nanotube axis, in a "cross-α" nanotube structure. The aggregation behavior is rationalized based on the effects of dimensionality, and the balance of hydrophobic and electrostatic interactions. The nanotube and nanomesh structures display arginine at high density on their surfaces, which may be valuable for future applications.

Hypothesis: daptomycin permeabilizes membranes by forming self assembled nanotubes

Daptomycin is the only lipopeptide antibiotic that is widely used in clinical practice. It was discovered by Eli Lilly and then studied and commercialized by Cubist Pharmaceuticals in 2003. Although this antibiotic has been used for 17 years, the debate over its mechanism of action is ongoing. In this paper, we discuss the different hypotheses on the mode of action of this antibiotic with a primary focus on the bacterial membrane permeabilization as the main mechanism of action. By comparing the experimental data on the oligomerization of daptomycin in membranes with properties of self-assembling cyclic peptides, we conclude that the structure of daptomycin oligomer should resemble the structures of peptide nanotubes that serve as ion channels in membranes.

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.

Peptide Nanotube-Templated Biomineralization of Cu2-x S Nanoparticles for Combination Treatment of Metastatic Tumor.

1D peptide nanostructures (i.e., peptide nanotubes, PNTs) exhibit tunable chemo-physical properties and functions such as improved tissue adhesion, increased cellular uptake, and elongated blood circulation. In this study, the application of PNTs as a desirable 1D template for biomineralization of Cu2-x S nanoparticles (Cu2-x S NPs, x = 1-2) is reported. Monodisperse Cu2-x S NPs are uniformly coated on the peptide nanotubes owing to the specific high binding affinity of Cu ions to the imidazole groups exposed on the surface of nanotubes. The Cu2-x S NP-coated PNTs are further covalently grafted with an oxaliplatin prodrug (Pt-CuS-PNTs) to construct a versatile nanoplatform for combination cancer therapy. Upon 808 nm laser illumination, the nanoplatform induces significant hyperthermia effect and elicits reactive oxygen species generation through electron transfer and Fenton-like reaction. It is demonstrated that the versatile nanoplatform dramatically inhibits tumor growth and lung metastasis of melanoma in a B16-F10 melanoma tumor-bearing mouse model by combined photo- and chemotherapy. This study highlights the ability of PNTs for biomineralization of metal ions and the promising potential of such nanoplatforms for cancer treatment.