Peptide Nanotubes Research Articles

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.

Construction and Piezoelectric Properties of a Single-Peptide Nanotube Composed of Cyclic β-peptides with Helical Peptides on the Side Chains.

To develop nanopiezoelectronics, it is necessary to investigate the relationship between the sizes and piezoelectric properties of the material. Peptide nanotubes (PNTs) composed of cyclic β-peptides have been studied as leading candidates for nanopiezoelectric materials. The current drawback of PNTs is aggregation to form a PNT bundle structure due to strong dipole-dipole interactions between PNTs. Here, we report the construction and piezoelectric properties of single PNTs without nonspecific aggregation by side-chain modification of helical peptides. A cyclic tri-β-peptide with a helical peptide was prepared by multiple-step liquid-phase peptide synthesis and assembled into PNTs by the vapor diffusion method. These nanotubes were characterized by polarized light microscopy and Fourier transform infrared (FTIR) spectroscopy. Additionally, atomic force microscopy (AFM) topographic images showed nanotubes with a height of 4 nm, which corresponds to the diameter of a PNT on a gold-coated mica substrate, indicating that a single PNT was prepared successfully. The converted piezoelectric response of a single PNT was determined to be 1.39 ± 0.12 pm/V. This value was consistent with that of a PNT bundle, which reveals that the piezoelectricity of PNTs is induced by deformation of their cyclic skeletons and is independent of the bundled structure. This finding not only demonstrates a new molecular design strategy to construct these smallest piezoelectric biomaterials by controlling the supramolecular hierarchical structures but also provides insights into the correlation between molecular assembly morphology and size-dependent piezoelectric properties.

Molecular Self-Assembly and Supramolecular Chemistry of Cyclic Peptides.

This Review focuses on the establishment and development of self-assemblies governed by the supramolecular interactions between cyclic peptides. The Review first describes the type of cyclic peptides able to assemble into tubular structures to form supramolecular cyclic peptide nanotubes. A range of cyclic peptides have been identified to have such properties, including α-peptides, β-peptides, α,γ-peptides, and peptides based on δ- and ε-amino acids. The Review covers the design and functionalization of these cyclic peptides and expands to a recent advance in the design and application of these materials through their conjugation to polymer chains to generate cyclic peptide–polymer conjugates nanostructures. The Review, then, concentrates on the challenges in characterizing these systems and presents an overview of the various analytical and characterization techniques used to date. This overview concludes with a critical survey of the various applications of the nanomaterials obtained from supramolecular cyclic peptide nanotubes, with a focus on biological and medical applications, ranging from ion channels and membrane insertion to antibacterial materials, anticancer drug delivery, gene delivery, and antiviral applications.

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.

SAXS/WAXS Investigation of Amyloid-β(16-22) Peptide Nanotubes.

This brief report presents an X-ray scattering investigation of self-assembled nanotubes formed by a short peptide. X-ray scattering methods enable multiscale structural elucidation of these nanotubes in solution under the same conditions involved in the self-assembly process. In particular, the dimensions of nanotubes and the crystalline organization within their walls can be determined quantitatively. This is illustrated in the case of amyloid-β(16-22) peptide nanotubes.

Attenuated total reflection-Fourier transform infrared spectroscopy: a tool to characterize antimicrobial cyclic peptide-membrane interactions.

Attenuated total reflection-Fourier transform infrared spectroscopy (ATR-FTIR) has been used for the structural characterization of peptides and their interactions with membranes. Antimicrobial peptides (AMPs) are part of our immune system and widely studied in recent years. Many linear AMPs have been studied, but their cyclization was shown to enhance the peptide's activity. We have used cyclic peptides (CPs) of an even number of alternating D- and L-α-amino acids, an emerging class of potential AMPs. These CPs can adopt a flat-ring shape that can stack into an antiparallel structure, forming intermolecular hydrogen bonds between different units, creating a tubular β-sheet structure-self-assembled cyclic peptide nanotubes (SCPNs). To get the structural information on peptides in solution and/or in contact with membranes, Amide I and II absorptions are used as they can adopt frequency and shape band characteristics that are influenced by the strength of existing hydrogen bonds between the amide CO and NH involved in secondary structures such as helix, β-sheet or aperiodic structures. The combination of polarized lens with ATR-FTIR provides an important tool to study the orientation of peptides when interacting with lipid membranes as the information can be derived on the position relative to the membrane normal. This work shows how ATR-FTIR used together with polarized light was successfully used to characterize structurally two CPs (RSKSWPgKQ and RSKSWXC10KQ) in solution and upon interaction with negatively charged membranes of DMPG, assessing the formation and orientation of tubular structures (SCPNs) that were shown to be enhanced by the presence of the lipid membrane.

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.

Modeling and physical properties of diphenylalanine peptide nanotubes containing water molecules

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

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.

Electrochemical sensors using conducting polymer/noble metal nanoparticle nanocomposites for the detection of various analytes: a review

Conducting polymer/noble metal nanoparticle (CP/NMNP) composites have made a history of sorts since its inception in the field of electrochemical research, which resulted to be an impetus for scientists to indulge and explore the opportunities it can unleash. This review throws light on the synergic effects and the enhancement in the electrocatalytic activity on dispersing noble metal particles on conducting polymers. This review aids the readers to analyse the electrochemical sensing efficiency of CP/NMNP composites, and provides a platform for the researchers to engineer and develop CP/NMNP composite materials for electrochemical sensing. This work also draws the attention of the readers to the application of NMNP (Ag, Au, Pt, Pd, Ir, and Ru) dispersed on CPs [polyaniline (PANI), polypyrrole (PPy) and poly(3,4-ethylenedioxythiophene) (PEDOT)] and their composites with other materials like carbon nanotubes (CNTs), graphene, zeolites, and peptide nanotubes (PNTs) for sensing of various analytes. This review draws the attention of the readers to the application of NMNP (Ag, Au, Pt, Pd, Ir and Ru) dispersed on CPs (polyaniline (PANI), polypyrrole (PPy) and poly(3,4-ethylenedioxythiophene) (PEDOT)) and their composites with other materials like carbon nanotubes (CNTs), graphene, zeolites, and peptide nanotubes (PNTs) for sensing of various analytes.

Structural dynamics of peptide nanotube and their conformational implication investigation by molecular modeling, molecular mechanics and molecular dynamics

Nanotubes are introduced into lipid bilayer resulting from the self-assembly of cyclic peptides formed by six a-amino acids. The insertion of peptide nanotubes into lipid bilayers modulates the cell wall's permeability qualities and thus confers potential bacteriocidal capacity. Relation of a peptide nanotube developed by cyclic hexapeptides, cyclo (KKLWLW) subunits, organized in an anti parallel; β-sheet like network joined in a hydrated dipalmitoylphosphatidylcholine bilayer surface was investigated using Schrodinger software in a molecular dynamics trajectory of 4-ns. Peptide nanotubes that results from the self-assembly of cyclic peptides having alternated D-L-a-amino acids, via an intermolecular hydrogen bond network, give a wide variety of biologically important structural and functional capabilities.

Alpha helical surfactant-like peptides self-assemble into pH-dependent nanostructures.

A designed surfactant-like peptide is shown, using a combination of cryogenic-transmission electron microscopy and small-angle X-ray scattering, to have remarkable pH-dependent self-assembly properties. Peptide Arg3-Leu12 (R3L12) forms a network of peptide nanotubes at pH 9 and below. These are associated with α-helical conformation in a "cross-α" nanotube structure, in which peptide dimers lie perpendicular to the nanotube axis, with arginine coated inner and outer nanotube walls. In contrast, this peptide forms decorated vesicular aggregates at higher pH values, close to the pKa of the arginine residues. These structures are associated with a loss of α-helical order as detected through X-ray scattering, circular dichroism and FTIR spectroscopy, the latter technique also revealing a loss of ordering of leucine side chains. This suggests a proposed model for the decorated or patchy vesicular structures that comprises disordered peptide as the matrix of the membrane, with small domains of ordered peptide dimers forming the minority domains. We ascribe this to a lipid-raft like phase separation process, due to conformational disordering of the leucine hydrophobic chains. The observation of the self-assembly of a simple surfactant-like peptide into these types of nanostructure is remarkable, and peptide R3L12 shows unique pH-dependent morphological and conformational behaviour, with the potential for a range of future applications.

Компьютерное моделирование и численные исследования пептидных нанотрубок на основе дифенилаланина

The work is devoted to computer studies of the structural and physical properties of such self-organizing structures as peptide nanotubes based on diphenylanine dipeptide with different initial isomers of the left and right chiralities of these dipeptides. The structures under study are considered both with empty anhydrous and with internal cavities filled with water molecules. Molecular models of both ring and helix structures are investigated, which are consistent with the known experimental data. To study the effect of nano-sized clusters of water molecules embedded in the inner hydrophilic cavity on the properties of nanotubes (including the changes in their dipole moments and polarizations), as well as the changes in the structure and properties of water clusters themselves (their dipole moments and polarizations), the surfaces of internal cavities of nanotubes and outer surfaces of water cluster structures for both types of chirality are analyzed. Including using a specially developed method of visual differential analysis of structural features of (bio)macromolecular structures. The obtained results of calculations of a number of physical properties (polarization values, etc.) are given for various cases and analyzed in comparison with the known data. These data are necessary for analyzing the interactions of water molecules with hydrophilic parts of nanotube molecules based on diphenylalanine, such as COO&lt;sup&gt;-&lt;/sup&gt; and NH&lt;sub&gt;3&lt;/sub&gt;&lt;sup&gt;+&lt;/sup&gt;, since they determine many properties of the structures under study. A number of the obtained data are planned to be used for further analysis of the possible adhesion and capture of certain medical molecular agents (components) by active layers of diphenylalanine-based nanotubes, which can be useful for creating capsules for targeted delivery of pharmaceuticals and drugs on their basis.

Efficient Artificial Light-Harvesting System Based on Supramolecular Peptide Nanotubes in Water.

Artificial light-harvesting systems in aqueous media which mimic nature are of significant importance; however, they are often restrained by the solubility and the undesired aggregation-caused quenching effect of the hydrophobic chromophores. Here, we report a generalized strategy toward the construction of efficient artificial light-harvesting systems based on supramolecular peptide nanotubes in water. By molecularly aligning the hydrophobic chromophores along the nanotubes in a slipped manner, an artificial light-harvesting system with a two-step sequential Förster resonance energy transfer process is successfully fabricated, showing an energy transfer efficiency up to 95% and a remarkably high fluorescence quantum yield of 30%, along with high stability. Furthermore, the spectral emission could be continuously tuned from blue through green to orange, as well as outputted as a white light continuum with a fluorescence quantum yield of 29.9%. Our findings provide a versatile approach of designing efficient artificial light-harvesting systems and constructing highly emissive organic materials in aqueous media.

Structural and dynamical properties of water in surfactant-like peptide-based nanotubes: Effect of pore size, tube length and charge

Atomistic molecular dynamics simulations were carried out to study the structural and dynamical properties of water molecules around pre-assembled surfactant-like peptide (SLP) nanotubes in aqueous media. These SLPs can be thought as a class of biocompatible and biodegradable surfactants for biomedical applications. Nanotube-like structures were considered where glycine and lysine (G6K) are taken as the constituents for the composition of the SLPs. The nanotubes considered were of different dimensions; such as 18 × 15 (number of peptides on the circumference x number of peptides layers), 18 × 12 and 16 × 12 for both charged and neutral analogues. The charged composition consists of protonated nitrogen in the lysine subunit and chlorine/bromine as counter ions. It is found that the neutral SLPs have less hydrated inner core consisting of more tetrahedral water compared to their charged analogues. The hydrogen bond lifetime of water-water and water-peptide molecules increases in the inner pore and found to be maximum for charged 16 × 12 system. Outside the pore, charged analogue of 18 × 15 have more water-water hydrogen bond lifetime compared to all other systems. However, protein-water hydrogen bond lifetime was found to be more for neutral analogues outside the pore due to more probable interactions of SLPs with water molecules.

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.

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.