Self-assembled peptide nanotubes (SPNTs)/SnO2nanocomposites for high-performance NO2sensing 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 NO2gas 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 SnO2in varying proportions to construct NO2gas 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 SnO2nanoparticles. 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.

DNA-inspired nanomaterials for enhanced endosomal escape.

To realize RNA interference (RNAi) therapeutics, it is necessary to deliver therapeutic RNAs (such as small interfering RNA or siRNA) into cell cytoplasm. A major challenge of RNAi therapeutics is the endosomal entrapment of the delivered siRNA. In this study, we developed a family of delivery vehicles called Janus base nanopieces (NPs). They are rod-shaped nanoparticles formed by bundles of Janus base nanotubes (JBNTs) with RNA cargoes incorporated inside via charge interactions. JBNTs are formed by noncovalent interactions of small molecules consisting of a base component mimicking DNA bases and an amino acid side chain. NPs presented many advantages over conventional delivery materials. NPs efficiently entered cells via macropinocytosis similar to lipid nanoparticles while presenting much better endosomal escape ability than lipid nanoparticles; NPs escaped from endosomes via a "proton sponge" effect similar to cationic polymers while presenting significant lower cytotoxicity compared to polymers and lipids due to their noncovalent structures and DNA-mimicking chemistry. In a proof-of-concept experiment, we have shown that NPs are promising candidates for antiviral delivery applications, which may be used for conditions such as COVID-19 in the future.

Polymeric Nanotubes as Drug Delivery Vectors─Comparison of Covalently and Supramolecularly Assembled Constructs.

Rod-shaped nanoparticles have been identified as promising drug delivery candidates. In this report, the in vitro cell uptake and in vivo pharmacokinetic/bio-distribution behavior of molecular bottle-brush (BB) and cyclic peptide self-assembled nanotubes were studied in the size range of 36-41 nm in length. It was found that BB possessed the longest plasma circulation time (t1\2 > 35 h), with the cyclic peptide system displaying an intermediate half-life (14.6 h), although still substantially elevated over a non-assembling linear control (2.7 h). The covalently bound BB underwent substantial distribution into the liver, whereas the cyclic peptide nanotube was able to mostly circumvent organ accumulation, highlighting the advantage of the inherent degradability of the cyclic peptide systems through their reversible aggregation of hydrogen bonding core units.

Peptide nanotube functionalized molecularly imprinted polydopamine based single-use sensor for impedimetric detection of malathion.

In the present study, a peptide nanotube functionalized polydopamine (p-Dop) based molecularly imprinted (MIP) sensor system was constructed, characterized, and studied for the impedimetric sensing of an organophosphorus pesticide, malathion (MLT). Electropolymerization in the presence of a template (MLT) was utilized as a convenient and effective strategy to generate imprinted p-Dop films on peptide nanotubes (PNTs) modified graphite electrodes (PGEs). Upon the removal of template, the adsorption of MLT on the specific cavities formed in the MIP film was tracked using electrochemical impedance spectroscopy (EIS). To attain optimal sensor response, experimental conditions, such as film thickness, analyte/functional monomer ratio, and desorption/adsorption time, were analyzed. The obtained MIP(p-Dop)-PNT-PGE sensor exhibited high sensitivity for electrochemical MLT analysis with a wide dynamic detection range of 13 pg mL-1 - 1.3 µg mL-1 and a LOD of 1.39 pg mL-1. The combination of a bio-inspired p-Dop-based MIP with the EIS technique allowed excellent sensitivity and selectivity toward MLT sensing which also yielded high recoveries in real samples. The success of this research strategy in real samples revealed its potential for various future environmental applications.

Double Orthogonal Click Reactions for the Development of Antimicrobial Peptide Nanotubes.

A new class of amphipathic cyclic peptides, which assemble in bacteria membranes to form polymeric supramolecular nanotubes giving them antimicrobial properties, is described. The method is based on the use of two orthogonal clickable transformations to incorporate different hydrophobic or hydrophilic moieties in a simple, regioselective, and divergent manner. The resulting cationic amphipathic cyclic peptides described in this article exhibit strong antimicrobial properties with a broad therapeutic window. Our studies suggest that the active form is the nanotube resulted from the parallel stacking of the cyclic peptide precursors. Several techniques, CD, FTIR, fluorescence, and STEM, among others, confirm the nanotube formation.

Assessment of the Oral Delivery of a Myelin Basic Protein Gene Promoter with Antiapoptotic bcl-xL (pMBP-bcl-xL) DNA by Cyclic Peptide Nanotubes with Two Aspect Ratios and Its Biodistribution in the Brain and Spinal Cord.

Cyclo-(D-Trp-Tyr) peptide nanotubes (PNTs) were reported to be potential carriers for oral gene delivery in our previous study; however, the effect of the aspect ratio (AR) of these PNTs on gene delivery in vivo could affect penetration or interception in biological environments. The aim of this study was to assess the feasibility of cyclo-(D-Trp-Tyr) PNTs with two ARs as carriers for oral pMBP-bcl-xL-hRluc delivery to the spinal cord to treat spinal cord injury (SCI). We evaluated the biodistribution of oligodendrocyte (OLG)-specific myelin basic protein gene promoter-driven antiapoptotic DNA (pMBP-bcl-xL) to the brain and spinal cord delivered with cyclo-(D-Trp-Tyr) PNTs with large (L) and small (S) PNTs with two ARs. After complex formation, the length, width, and AR of the L-PNTs/DNA were 77.86 ± 3.30, 6.51 ± 0.28, and 13.75 ± 7.29 µm, respectively, and the length and width of the S-PNTs/DNA were 1.17 ± 0.52 and 0.17 ± 0.05 µm, respectively, giving an AR of 7.12 ± 3.17 as detected by scanning electron microscopy. Each of these three parameters exhibited significant differences (p < 0.05) between L-PNTs/DNA and S-PNTs/DNA. However, there were no significant differences (p > 0.05) between the L-PNTs and S-PNTs for either their DNA encapsulation efficiency (29.72 ± 14.19 and 34.31 ± 16.78%, respectively) or loading efficiency (5.15 ± 2.58 and 5.95 ± 2.91%). The results of the in vitro analysis showed that the S-PNT/DNA complexes had a significantly higher DNA release rate and DNA permeation in the duodenum than the L-PNT/DNA complexes. Using Cy5 and TM-rhodamine to individually and chemically conjugate the PNTs with plasmid DNA, we observed, using laser confocal microscopy, that the PNTs and DNA colocalized in complexes. We further confirmed the complexation between DNA and the PNTs using fluorescence resonance energy transfer (FRET). Data from an in vivo imaging system (IVIS) showed that there was no significant difference (p > 0.05) in PNT distribution between L-PNTs/DNA and S-PNTs/DNA within 4 h. However, the S-PNT/DNA group had a significantly higher DNA distribution (p < 0.05) in several organs, including the ilium, heart, lungs, spleen, kidneys, testes, brain, and spinal cord. Finally, we determined the bcl-xL protein expression levels in the brain and spinal cord regions for the L-PNT/DNA and S-PNT/DNA complex formulations. These results suggested that either L-PNTs or S-PNTs may be used as potential carriers for oral gene delivery to treat SCI.

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.

Bioinspired Multivalent Peptide Nanotubes for Sialic Acid Targeting and Imaging-Guided Treatment of Metastatic Melanoma.

Tumor metastasis is considered a major cause of cancer-related human mortalities. However, it still remains a formidable challenge in clinics. Herein, a bioinspired multivalent nanoplatform for the highly effective treatment of the metastatic melanoma is reported. The versatile nanoplatform is designed by integrating indocyanine green and a chemotherapeutic drug (7-ethyl-10-hydroxycamptothecin) into phenylboronic acid (PBA)-functionalized peptide nanotubes (termed as I/S-PPNTs). I/S-PPNTs precisely target tumor cells through multivalent interaction between PBA and overexpressed sialic acid on the tumor surface in order to achieve imaging-guided combination therapy. It is demonstrated that I/S-PPNTs are efficiently internalized by the B16-F10 melanoma cells in vitro in a PBA grafting density-dependent manner. It is further shown that I/S-PPNTs specifically accumulate and deeply penetrate into both the subcutaneous and lung metastatic B16-F10 melanoma tumors. More importantly, I/S-PPNT-mediated combination chemo- and photodynamic therapy efficiently eradicates tumor and suppresses the lung metastasis of B16-F10 melanoma in an immunocompetent C57BL/6 mouse model. The results highlight the promising potential of the multivalent peptide nanotubes for active tumor targeting and imaging-guided cancer therapy.

MD Simulations on the Transport Behaviors of Mixed Na+ and Li+ in a Transmembrane Cyclic Peptide Nanotube under an Electric Field.

Due to its inherently stronger hydration, Li+ faces a higher dehydration energy than Na+ at the entrance of the 8×(WL)4/POPE-CPNT. Present MD simulations show that it can enter the channel from a NaCl/LiCl solution only under an electric field stronger than 0.3 V nm-1, while Na+ is easier to move into the channel, which is well elucidated by two cations' PMF profiles. The cation-Ow radial distribution functions, the electrostatic interactions with water, and the orientations of neighboring water all refer to a more compact solvation structure and stronger hydration of Li+. Regardless of whether there is an external electric field, Na+ mainly appears in an α-plane zone, while Li+ does so in a midplane region. The increase in the electric field strength significantly accelerates the cations' axial diffusions, shortening the residence times of two cations in the channel. Furthermore, it makes channel water tend to take positive dipole states.

Piezoelectric property of bundled peptide nanotubes stapled by bis-cyclic-ß-peptide.

Cyclic tetra-ß-peptides (CP4s) and a bis-CP4 were synthesized to prepare peptide nanotubes (PNTs) by molecular stacking of cyclic peptides. The addition of bis-CP4 to the PNT preparation afforded PNT bundles increasing the direct and converse piezoelectiric coefficients, which is ascribable to bis-CP4 stapling PNTs into the parallel alignment of PNT dipoles.

Competitive double-switched self-assembled cyclic peptide nanotubes: a dual internal and external control.

"Intelligent" materials based on synthetic small molecules that become functional only under specific conditions provide new opportunities for developing regulated systems aimed at a large number of applications. For instance, biologically active supramolecular entities that are sensitive to environmental conditions, such as the presence of bacterial membranes, are extremely interesting in biomedicine. In this work, we have designed and investigated, using molecular dynamics simulations, a doubly modulable nanotube formed by the self-assembly of cyclic peptides sensitive to both the presence of a lipid membrane and the pH of the aqueous media. The cyclic peptides were designed to self-assemble into peptide nanotubes in the presence of a lipid bilayer and at low pH values. Under these conditions, the residual side chains point outside the cyclic peptides, being exposed to the lipid bilayer, and the inner groups (carboxylic acids) are protonated, thus allowing the permeation of water and preventing that of ions. Higher pH values are expected to create carboxylate groups at the lumen of the peptides, leading to the disassembly of the nanotube, the attraction and translocation of ions towards the hydrophobic core of the bilayer, and eventually killing the target malignant cells. Our results suggest that by introducing a second switch in a membrane sensitive system, it is possible to modulate its interaction with the lipid bilayer. This opens the door to new strategies for the preparation of antimicrobial peptides that interact at the membrane level.

Peptide Nanotube Encapsulated Enzyme Biosensor for Vapor Phase Detection of Malathion, an Organophosphorus Compound.

This study explores the use of a butyrylcholinesterase (BChE)-based, reversible reaction biosensor using screen-printed electrodes (SPEs) having a smaller working surface area than the single-use electrodes previously studied. Previous research demonstrated the prospective application of a single-use biosensor fabricated with an acetylcholinesterase (AChE) enzyme encapsulated in peptide nanotubes (PNTs) and enhanced with horseradish peroxidase (HRP) to detect organophosphorus compounds (OPCs) in aqueous and gas phases. In the current study, potential improvements to the biosensor are investigated. BChE-based biosensors were fabricated using PNTs, HRP, and Nafion in combination to increase the reactive surface area, enhance sensitivity, and maintain enzyme stability. Cyclic voltammetry (CV) was used along with the new modified sensor to measure malathion concentration in the gas phase. The results show that a BChE-based biosensor could reliably measure gas phase malathion concentrations between 6-25 ppbv by CV with the extent of inhibition linearly proportional to the malathion concentration (R2 = 0.941). This research demonstrated that fabricated BChE-based biosensors could be stored without cold storage requirement for up to six weeks with minimal performance degradation. Moreover, the sensor electrodes were each reused several times, and were still useable at the conclusion of the research. This research demonstrates the potential of fabricating a reusable, inexpensive biosensor that is capable of OPC detection with high sensitivity and a low detection limit without a long-term cold storage requirement.

Two one-dimensional arrays of naphthyl and anthryl groups along peptide nanotubes prepared from cyclic peptides comprising α- and ß-amino acids.

A novel cyclic hexapeptide composed of l-α-naphthylalanine, d-α-anthrylalanine, and four ß-alanines (CP6) is synthesized and its molecular assembly into peptide nanotubes (PNTs) and the electronic properties arising from one-dimensional arrays of aromatic groups along the PNTs were investigated. CP6 with a combination of l- and d-α-amino acids is designed to self-assemble into PNTs with them stacking on top of each other under the constraint of maximizing the number of intermolecular hydrogen bonds between the cyclic peptides. Upon PNT formation, the respective side chains of l- and d-α-amino acids are aligned in line along the PNTs. The topological arrangement of the anthryl groups being in close proximity in the CP6 PNT is supported by higher photo-excited energy transfer, appearance of the induced Cotton effects, and the promoted photo-dimerization reaction upon PNT formation. AFM observations reveal that PNT bundles with diameters 5-15 nm are dielectric microcrystals having a piezoelectric coefficient of 2-6 pC N-1. Kelvin force microscopy observations show the generation of surface potentials over 100 mV owing to the one-dimensional array of the anthryl groups along PNTs. Incorporation of α-amino acids with opposite chirality into cyclic ß-peptides is therefore an effective molecular design for the nano-architecture of PNTs displaying one-dimensional arrays of chromophores along PNTs.

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines.

Extended adaptive biasing force (eABF), a collective variable (CV)-based importance-sampling algorithm, has proven to be very robust and efficient compared with the original ABF algorithm. Its implementation in Colvars, a software addition to molecular dynamics (MD) engines, is, however, currently limited to NAMD and LAMMPS. To broaden the scope of eABF and its variants, like its generalized form (egABF), and make them available to other MD engines, e.g., GROMACS, AMBER, CP2K, and openMM, we present a PLUMED-based implementation, called extended-Lagrangian free energy calculation (ELF). This implementation can be used as a stand-alone gradient estimator for other CV-based sampling algorithms, such as temperature-accelerated MD (TAMD) and extended-Lagrangian metadynamics (MtD). ELF provides the end user with a convenient framework to help select the best-suited importance-sampling algorithm for a given application without any commitment to a particular MD engine.

Fusion and fission of molecular assemblies of amphiphilic polypeptides generating small vesicles from nanotubes.

Three amphiphilic block polypeptides, (sarcosine)m -b-(l- or d-Leu-Aib)n (L16, D16, D14), having different helical chain lengths or helicity are synthesized. A mixture of L16, D16, and D14 generates vesicles of diameters more than ca. 130 nm by injecting the ethanol solution into water and heating at 90°C for 1 h. On the other hand, when nanotubes composed of L16 and D14 having ca. 50 nm diameter are mixed with nanosheets composed of D16, smaller and homogeneous vesicles of ca. 60 nm diameter are obtained with the heat treatment. The time lapse TEM image analysis of the mixtures revealed some transient structures of nanotubes sticking a nanosheet or a vesicle at the open end of nanotubes. The precise size control of vesicles is therefore attainable by using nanotubes as a structural template regulating the size of vesicles near to the nanotube diameter upon the membrane fission processes.

Shear Alignment of Bola-Amphiphilic Arginine-Coated Peptide Nanotubes.

The bola-amphiphilic arginine-capped peptide RFL4RF self-assembles into nanotubes in aqueous solution. The nanostructure and rheology are probed by in situ simultaneous rheology/small-angle scattering experiments including rheo-SAXS, rheo-SANS, and rheo-GISANS (SAXS: small-angle X-ray scattering, SANS: small-angle neutron scattering, GISANS: grazing incidence small-angle neutron scattering). Nematic alignment of peptide nanotubes under shear is observed at sufficiently high shear rates under steady shear in either Couette or cone-and-plate geometry. The extent of alignment increases with shear rate. A shear plateau is observed in a flow curve measured in the Couette geometry, indicating the presence of shear banding above the shear rate at which significant orientation is observed (0.1-1 s-1). The orientation under shear is transient and is lost as soon as shear is stopped. GISANS shows that alignment at the surface of a cone-and-plate cell develops at sufficiently high shear rates, very similar to that observed in the bulk using the Couette geometry. A small isotope effect (comparing H2O/D2O solvents) is noted in the CD spectra indicating increased interpeptide hydrogen bonding in D2O, although this does not influence nanotube self-assembly. These results provide new insights into the controlled alignment of peptide nanotubes for future applications.

Peptide Optical waveguides.

Small-scale optical devices, designed and fabricated onto one dielectric substrate, create integrated optical chip like their microelectronic analogues. These photonic circuits, based on diverse physical phenomena such as light-matter interaction, propagation of electromagnetic waves in a thin dielectric material, nonlinear and electro-optical effects, allow transmission, distribution, modulation, and processing of optical signals in optical communication systems, chemical and biological sensors, and more. The key component of these optical circuits providing both optical processing and photonic interconnections is light waveguides. Optical confinement and transmitting of the optical waves inside the waveguide material are possible due to the higher refractive index of the waveguides in comparison with their surroundings. In this work, we propose a novel field of bionanophotonics based on a new concept of optical waveguiding in synthetic elongated peptide nanostructures composed of ordered peptide dipole biomolecules. New technology of controllable deposition of peptide optical waveguiding structures by nanofountain pen technique is developed. Experimental studies of refractive index, optical transparency, and linear and nonlinear waveguiding in out-of-plane and in-plane diphenylalanine peptide nanotubes have been conducted. Optical waveguiding phenomena in peptide structures are simulated by the finite difference time domain method. The advantages of this new class of bio-optical waveguides are high refractive index contrast, wide spectral range of optical transparency, large optical nonlinearity, and electro-optical effect, making them promising for new applications in integrated multifunctional photonic circuits. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Probing nonlinear optical coefficients in self-assembled peptide nanotubes.

Self-assembled l,l-diphenylalanine (FF) peptide micro/nanotubes represent a class of biomimetic materials with a non-centrosymmetric crystal structure and strong piezoelectricity. The peptide nanotubes synthesized by a liquid phase method yield tube lengths in the hundreds of micron range, inner diameters in the few hundred nanometer range, and outer diameters in the 5-15 µm range. Second harmonic generation (SHG) polarimetry from individual self-assembled FF nanotubes is used to obtain the nonlinear (NLO) optical coefficients as a function of the tube diameter and thermal treatment. The ratio of the shear to the longitudinal component (d15/d33) of the NLO coefficient increases with the diameter of the tubes. One of the transverse components of the nonlinear coefficient is found to be negative, and its magnitude with respect to the longitudinal component increases with the tube diameter. Thermal treatment of individual FF tubes has a similar effect upon increasing the diameter of the tubes in SHG polarimetry. Concurrent Raman scattering measurements from individual FF tubes show a distinct change in the low frequency (100 cm-1) region with the diameter of the tubes reflecting subtle effects of water.

Design of Asymmetric Peptide Bilayer Membranes.

Energetic insights emerging from the structural characterization of peptide cross-ß assemblies have enabled the design and construction of robust asymmetric bilayer peptide membranes. Two peptides differing only in their N-terminal residue, phosphotyrosine vs lysine, coassemble as stacks of antiparallel ß-sheets with precisely patterned charged lattices stabilizing the bilayer leaflet interface. Either homogeneous or mixed leaflet composition is possible, and both create nanotubes with dense negative external and positive internal solvent exposed surfaces. Cross-seeding peptide solutions with a preassembled peptide nanotube seed leads to domains of different leaflet architecture within single nanotubes. Architectural control over these cross-ß assemblies, both across the bilayer membrane and along the nanotube length, provides access to highly ordered asymmetric membranes for the further construction of functional mesoscale assemblies.

Electronic properties of tetrathiafulvalene-modified cyclic-ß-peptide nanotube.

Cyclic tri-ß-peptide having tetrathiafulvalene (TTF) at the side chain was synthesized to prepare a peptide nanotube aligning TTF side chains along the nanotube. The polarized light microscopic observations revealed crystallization of the cyclic peptide by the vapor diffusion method. Fourier-transform infrared and electron diffraction measurements of the crystals clarified formation of homogeneous hydrogen bonds making a columnar structure with a layer spacing of 4.9 Å. Electronic measurements of the peptide crystals on a gold mica substrate were carried out by the current sensing AFM. The current-voltage curves showed a rectification behavior, whose profile was consistent with a metal and p-type semiconductor junction. The p-type property is supported by the first principle calculations, which showed the HOMO orbital delocalizing fully over the plane of the TTF ring with the energy level of -5.1 eV. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 275-282, 2016.