Casting metal nanowires within discrete self-assembled peptide nanotubes

Microporous Organic Materials from Hydrophobic Dipeptides

In the last few years dipeptides with two hydrophobic residues (hydrophobic dipeptides) have emerged as an unexpected source of stable microporous organic materials. Supramolecular self-assembly of the rather small building blocks is dictated by stringent demands on the hydrogen-bond formation by the peptide main chains and the aggregation of hydrophobic entities in the side chains. A systematic survey of structures derived from single-crystal X-ray diffraction studies has revealed the existence of two large classes of structures, differing in the dimensionality of the hydrogen-bonding patterns in the crystals and the nature of the channels. The present review summarizes the structural properties of the microporous dipeptides and discusses their potential applications.

Self assembly of short aromatic peptides into amyloid fibrils and related nanostructures

The formation of amyloid fibrils is the hallmark of more than twenty human disorders of unrelated etiology. In all these cases, ordered fibrillar protein assemblies with a diameter of 7-10 nm are being observed. In spite of the great clinical important of amyloid-associated diseases, the molecular recognition and self-assembly processes that lead to the formation of the fibrils are not fully understood. One direction to decipher the mechanism of amyloid formation is the use of short peptides fragments as model systems. Short peptide fragments, as short as pentapeptides, were shown to form typical amyloid assemblies in vitro that have ultrastructural, biophysical, and cytotoxic properties, as those of assemblies that are being formed by full length polypeptides. When we analyzed such short fragments, we identified the central role of aromatic moieties in the ability to aggregate into ordered nano-fibrillar structures. This notion allowed us to discover additional very short amyloidogenic peptides as well as other aromatic peptide motifs, which can form various assemblies at the nano-scale (including nanotubes, nanospheres, and macroscopic hydrogels with nano-scale order). Other practical utilization of this concept, together with novel beta breakage methods, is their use for the development of novel classes of amyloid formation inhibitors.

Ion channels and pores, made from scratch

We elaborate on the structural diversity well beyond the biological limitations that becomes accessible with synthetic ion channels and pores, and on the importance of advanced nanoarchitecture to create significant function.

Biomolecule–nanoparticle hybrids as functional units for nanobiotechnology

Biomolecule-metal or semiconductor nanoparticle (NP) hybrid systems combine the recognition and catalytic properties of biomolecules with the unique electronic and optical properties of NPs. This enables the application of the hybrid systems in developing new electronic and optical biosensors, to synthesize nanowires and nanocircuits, and to fabricate new devices. Metal NPs are employed as nano-connectors that activate redox enzymes, and they act as electrical or optical labels for biorecognition events. Similarly, semiconductor NPs act as optical probes for biorecognition processes. Double-stranded DNA or protein chains that are modified with metallic nanoclusters act as templates for the synthesis of metallic nanowires. The nanowires are used as building blocks to assemble nano-devices such as a transistor or a nanotransporter.

Self-assembly and potassium ion triggered disruption of peptide-based soft structures

This report describes formation of soft vesicular structures by a tetrapeptide and its disruption triggered by potassium ions.

Backbone-modified amylin derivatives: implications for amyloid inhibitor design and as template for self-assembling bionanomaterials

This report reviews our approach to the design, synthesis and structural/morphological analysis of backbone-modified amylin(20-29) derivatives. Depending on the position in the peptide backbone and the type of amide bond isostere/modification, the amylin(20-29) peptides behave either as inhibitors of amyloid fibril formation, which are able to retard amyloid formation of native amylin(20-29), or as templates for the formation of self-assembled supramolecular structures. Molecular fine-tuning of the hydrogen-bond accepting/donating properties allows the control over the morphology of the supramolecular aggregation motifs such as helical ribbons and tapes, ribbons progressing to closed peptide nanotubes, (twisted) lamellar sheets or amyloid fibrils.

Use of biomolecular templates for the fabrication of metal nanowires

The nano-scale spatial organization of metallic and other inorganic materials into 1D objects is a key task in nanotechnology. Nano-scale fibers and tubes are very useful templates for such organization because of their inherent 1D organization. Fibrillar biological molecules and biomolecular assemblies are excellent physical supports on which to organize the inorganic material. Furthermore, these biological assemblies can facilitate high-order organization and specific orientation of inorganic structures by their utilization of highly specific biological recognition properties. In this minireview, I will describe the use of biomolecules and biomolecular assemblies, including DNA, proteins, peptides, and even viral particles, which are excellent templates for 1D organization of inorganic materials into wires. This ranges from simple attempts at electroless deposition on inert biological templates to the advanced use of structural motifs and specific protein-DNA interactions for nano-bio-lithography as well as the fabrication of multilayer organic and inorganic composites. The potential technological applications of these hybrid biological-inorganic assemblies will be discussed.

Nanoparticle-enzyme hybrid systems for nanobiotechnology

Biomolecule-nanoparticle (NP) [or quantum-dot (QD)] hybrid systems combine the recognition and biocatalytic properties of biomolecules with the unique electronic, optical, and catalytic features of NPs and yield composite materials with new functionalities. The biomolecule-NP hybrid systems allow the development of new biosensors, the synthesis of metallic nanowires, and the fabrication of nanostructured patterns of metallic or magnetic NPs on surfaces. These advances in nanobiotechnology are exemplified by the development of amperometric glucose sensors by the electrical contacting of redox enzymes by means of AuNPs, and the design of an optical glucose sensor by the biocatalytic growth of AuNPs. The biocatalytic growth of metallic NPs is used to fabricate Au and Ag nanowires on surfaces. The fluorescence properties of semiconductor QDs are used to develop competitive maltose biosensors and to probe the biocatalytic functions of proteases. Similarly, semiconductor NPs, associated with electrodes, are used to photoactivate bioelectrocatalytic cascades while generating photocurrents.

Controlled patterning of aligned self-assembled peptide nanotubes

Controlling the spatial organization of objects at the nanoscale is a key challenge in enabling their technological application. Biomolecular assemblies are attractive nanostructures owing to their biocompatibility, straightforward chemical modifiability, inherent molecular recognition properties and their availability for bottom-up fabrication. Aromatic peptide nanotubes are self-assembled nanostructures with unique physical and chemical stability and remarkable mechanical rigidity. Their application in the fabrication of metallic nanowires and in the improvement of the sensitivity of electrochemical biosensors have already been demonstrated. Here we show the formation of a vertically aligned nanoforest by axial unidirectional growth of a dense array of these peptide tubes. We also achieved horizontal alignment of the tubes through noncovalent coating of the tubes with a ferrofluid and the application of an external magnetic field. Taken together, our results demonstrate the ability to form a two-dimensional dense array of nanotube assemblies with either vertical or horizontal patterns.

Integrated nanoparticle-biomolecule systems for biosensing and bioelectronics

The similar dimensions of biomolecules such as enzymes, antibodies or DNA, and metallic or semiconductor nanoparticles (NPs) enable the synthesis of biomolecule-NP hybrid systems where the unique electronic, photonic and catalytic properties of NPs are combined with the specific recognition and biocatalytic properties of biomolecules. The unique functions of biomolecule-NP hybrid systems are discussed with several examples: (i) the electrical contacting of redox enzymes with electrodes is the basis for the development of enzymatic electrodes for amperometric biosensors or biofuel cell elements. The reconstitution of the apo-glucose oxidase or apo-glucose dehydrogenase on flavin adenine dinucleotide (FAD)-functionalized Au NPs (1.4 nm) associated with electrodes, or on pyrroloquinoline quinone (PQQ)-functionalized Au NPs (1.4 nm) associated with electrodes, respectively, yields electrically contacted enzyme electrodes. The aligned, reconstituted enzymes on the electrode surfaces reveal effective electrical contacting, and the glucose oxidase and glucose dehydrogenase reveal turnover rates of 5000 and 11,800 s(-1), respectively. (ii) The photoexcitation of semiconductor nanoparticles yields fluorescence with a wavelength controlled by the size of the NPs. The fluorescence functions of semiconductor NPs are used to develop a fluorescence resonance energy transfer (FRET) assay for nucleic acids, and specifically, for analyzing telomerase activity in cancer cells. CdSe-ZnS NPs are functionalized by a primer recognized by telomerase, and this is elongated by telomerase extracted from HeLa cancer cells in the presence of dNTPs and Texas-red-functionalized dUTP. The dye integrated into the telomers allows the FRET process that is intensified as telomerization proceeds. Also, the photoexcited electron-hole pair generated in semiconductor NPs is used to generate photocurrents in a CdS-DNA hybrid system associated with an electrode. A redox-active intercalator, methylene blue, was incorporated into a CdS-duplex DNA monolayer associated with a Au electrode, and this facilitated the electron transfer between the electrode and the CdS NPs. The direction of the photocurrent was controlled by the oxidation state of the intercalator. (iii) Biocatalysts grow metallic NPs, and the absorbance of the NPs provides a means to assay the biocatalytic transformations. This is exemplified with the glucose oxidase-induced growth of Au NPs and with the tyrosinase-stimulated growth of Au NPs, in the presence of glucose or tyrosine, respectively. The biocatalytic growth of the metallic NPs is used to grow nanowires on surfaces. Glucose oxidase or alkaline phosphatase functionalized with Au NPs (1.4 nm) acted as 'biocatalytic inks' for the synthesis of metallic nanowires. The deposition of the Au NP-modified glucose oxidase, or the Au NP-modified alkaline phosphatase on Si surfaces by dip-pen nanolithography led to biocatalytic templates, that after interaction with glucose/AuCl4- or p-aminophenolphosphate/Ag+, allowed the synthesis of Au nanowires or Ag nanowires, respectively.

The Formation of Nematic Liquid Crystal Phases by Hen Lysozyme Amyloid Fibrils

Amyloid fibrils are a polymeric aggregate of protein. The fibrils are typically on the order of micrometers long, with widths of 10-20 nm. They are generally regarded as stiff, and nonbranching. It is well-known that similar synthetic polymers and biopolymers such as DNA and polysaccharides, have a tendency to form liquid crystalline phases when incubated under appropriate conditions. Here we show that amyloid fibrils from the protein hen lysozyme can similarly form liquid crystal phases. The most common phase observed is the nematic. Alignment can persist for several centimeters. When the fibrils are freeze-thawed to shorten them, similar phases form but at higher concentrations, confirming the importance of the aspect ratio of the fibrils. Freeze-thawed fibrils are also seen to form "tactoids", discrete liquid crystalline structures. The addition of NaCl to the solutions appears to only have a minor effect, while the effect of pH appears much more significant. We propose that the consideration of amyloid fibrils as polymer analogues should open new routes to explore in the burgeoning field of biomaterials.

Patterning amyloid peptide fibrils by AFM charge writing

Surface charge patterns generated by atomic force microscopy-based charge writing were used to pattern amyloid-like peptide fibrils on a solid substrate. Fibrils of the short peptide TTR105-115 were encapsulated inside water droplets of a water-in-perfluorocarbon oil emulsion and retained their rod morphology. They were observed to deposit selectively with a lateral resolution of approximately 1 microm onto negatively charged patterns on a polymethyl-methacrylate substrate.

Molecular alignment within beta-sheets in Abeta(14-23) fibrils: solid-state NMR experiments and theoretical predictions

We report investigations of the molecular structure of amyloid fibrils formed by residues 14-23 of the beta-amyloid peptide associated with Alzheimer's disease (Abeta(14-23)), using solid-state nuclear magnetic resonance (NMR) techniques in conjunction with electron microscopy and atomic force microscopy. The NMR measurements, which include two-dimensional proton-mediated (13)C-(13)C exchange and two-dimensional relayed proton-mediated (13)C-(13)C exchange spectra, show that Abeta(14-23) fibrils contain antiparallel beta-sheets with a registry of backbone hydrogen bonds that aligns residue 17+k of each peptide molecule with residue 22-k of neighboring molecules in the same beta-sheet. We compare these results, as well as previously reported experimental results for fibrils formed by other beta-amyloid fragments, with theoretical predictions of molecular alignment based on databases of residue-specific alignments in antiparallel beta-sheets in known protein structures. While the theoretical predictions are not in exact agreement with the experimental results, they facilitate the design of experiments by suggesting a small number of plausible alignments that are readily distinguished by solid-state NMR.

Structure by design: from single proteins and their building blocks to nanostructures

Nanotechnology realizes the advantages of naturally occurring biological macromolecules and their building-block nature for design. Frequently, assembly starts with the choice of a "good" molecule that is synthetically optimized towards the desired shape. By contrast, we propose starting with a pre-specified nanostructure shape, selecting candidate protein building blocks from a library and mapping them onto the shape and, finally, testing the stability of the construct. Such a shape-based, part-assembly strategy is conceptually similar to protein design through the combinatorial assembly of building blocks. If the conformational preferences of the building blocks are retained and their interactions are favorable, the nanostructure will be stable. The richness of the conformations, shapes and chemistries of the protein building blocks suggests a broad range of potential applications; at the same time, it also highlights their complexity. In this Opinion article, we focus on the first step: validating such a strategy against experimental data.

Anion effect on the nanostructure of a metal ion binding self-assembling peptide

Effects of copper salts containing different anions (SO(4)(2)(-), Cl(-), and NO(3)(-)) on the self-assembly of a designed peptide EAK16(II)GGH with affinity for Cu(2+) have been investigated. The peptide secondary structure, self-assembled nanostructures, and surface activity were observed to depend strongly on the type of anion. Over a salt concentration range from 0.05 to 10.0 mM, SO(4)(2)(-) induced long fiber formation, whereas Cl(-) and NO(3)(-) caused short fiber formation. The fiber length increased with copper sulfate concentration, but the concentration of copper chloride and copper nitrate did not affect the peptide nanostructures significantly. Analysis by Fourier transform infrared spectroscopy (FTIR) revealed that the addition of the copper salts tended to cause the peptide conformation to change from alpha-helix/random coil to beta-sheet, the extent to which depended on the anion type. This evidence of the anion effect was also supported by surface tension measurements using the axisymmetric drop shape analysis-profile (ADSA-P) technique. An explanation for the effect of anions on the peptide self-assembly was proposed. The divalent anion SO(4)(2)(-) might serve as a bridge by electrostatically interacting with two lysine residues from different peptide molecules, promoting beta-sheet formation. The extensive beta-sheet formation may further promote peptide self-assembly into long fibers. On the other hand, monovalent anions Cl(-) and NO(3)(-) may only electrostatically interact with one charged residue of the peptide; hence, a mixed secondary structure of alpha-helix/random coil and beta-sheet was observed. This observation might explain the predominant formation of short fibers in copper chloride and copper nitrate solutions.

Molecular designer self-assembling peptides

Chemistry has generally been associated with inorganic and organic syntheses, metal-organic composites, coordinate metal chemistry, catalyses, block copolymer, coating, thin film, industrial surfactants and small-molecule drug development. That is about to change. Chemistry will also expand to the discovery and fabrication of biological and molecular materials with diverse structures, functionalities and utilities. The advent of biotechnology, nanotechnology and nanobiotechnology has accelerated this trend. Nature has selected and evolved numerous molecular architectural motifs at nanometer scale over billions of years for particular functions. These molecular nanomotifs can now be designed for new materials and nanodevices from the bottom up. Chemistry will again harness Nature's enormous power to benefit other disciplines and society. This tutorial review focuses on two self-assembling peptide systems.

Peptide-based stimuli-responsive biomaterials

This article explores recent advances in the design and engineering of materials wholly or principally constructed from peptides. We focus on materials that are able to respond to changes in their environment (pH, ionic strength, temperature, light, oxidation/reduction state, presence of small molecules or the catalytic activity of enzymes) by altering their macromolecular structure. Such peptide-based responsive biomaterials have exciting prospects for a variety of biomedical and bionanotechnology applications in drug delivery, bio-sensing and regenerative medicine.

Aggregation of small peptides studied by molecular dynamics simulations

Peptides and proteins tend to aggregate under appropriate conditions. The amyloid fibrils that are ubiquitously found among these structures are associated with major human diseases like Alzheimer's disease, type II diabetes, and various prion diseases. Lately, it has been observed that even very short peptides like tetra and pentapeptides can form ordered amyloid structures. Here, we present aggregation studies of three such small polypeptide systems, namely, the two amyloidogenic peptides DFNKF and FF, and a control (nonamyloidogenic) one, the AGAIL. The respective aggregation process is studied by all-atom Molecular Dynamics simulations, which allow to shed light on the fine details of the association and aggregation process. Our analysis suggests that naturally aggregating systems exhibit significantly diverse overall cluster shape properties and specific intermolecular interactions. Additional analysis was also performed on the previously studied NFGAIL system.

One-Dimensional Colloidal Gold and Silver Nanostructures

One-dimensional (1-D) metallic nanoscale materials have long been of interest to many groups of scientists. Within the last 2 decades, great advances in the synthesis of metallic nanorods and nanowires have been made, with a variety of templating methods. More recently, bottom-up chemical syntheses of these materials have become increasingly reported in the literature. This Forum Article describes the synthesis, physical properties, and potential applications of 1-D metals, with an emphasis on silver and gold derived from studies in the authors' laboratories.

Self-assembly of Au Nanoparticle-containing Peptide Nano-rings on Surfaces

The peptide nano-rings containing Au nanoparticles inside their cavities were self-assembled on dithiol SAMs patterned as an array by AFM-based nanolithography. The peptide nano-rings were aligned as a line on these SAMs, and Au formed lines with the spacing between these nanoparticles as the peptide nano-rings functioned as spacers. This type of array fabrication will provide improved tunability in their optical properties of resulting nanoparticle-assembled arrays. In addition, optimization of the inter-particle distance of nanoparticles in the array with various spacers may allow one to design new types of photonic crystals with desired optical properties.

Stability and structure of oligomers of the Alzheimer peptide Abeta16-22: from the dimer to the 32-mer

Several neurodegenerative diseases such as Alzheimer's, Parkinson's, and Huntington's diseases are associated with amyloid fibrils formed by different polypeptides. We probe the structure and stability of oligomers of different sizes of the fragment Abeta(16-22) of the Alzheimer beta-amyloid peptide using atomic-detail molecular dynamics simulations with explicit solvent. We find that only large oligomers form a stable beta-sheet aggregate, the minimum nucleus size being of the order of 8-16 peptides. This effect is attributed to better hydrophobic contacts and a better shielding of backbone-backbone hydrogen bonds from the solvent in bigger assemblies. Moreover, the observed stability of beta-sheet aggregates with a different number of layers can be explained on the basis of their solvent-accessible surface area. Depending on the stacking interface between the sheets, we observe straight or twisted structures, which could be linked to the experimentally observed polymorphism of amyloid fibrils. To compare our 32-mer structure to experimental data, we calculate its x-ray diffraction pattern. Good agreement is found between experimentally and theoretically determined reflections, suggesting that our model indeed closely resembles the structures found in vitro.

Sequence and structure analysis of parallel beta helices: implication for constructing amyloid structural models

Increasing evidence suggests that amyloids and parallel beta helices may share similar motifs. A systemic analysis of beta helices is performed to examine their sequence and structural characteristics. Ile prefers to occur in beta strands. In contrast, Pro is disfavored, compatible with the underlying assumption in Pro-scanning mutagenesis. Cys, Asn, and Phe form significant homostacking (identical amino acid interactions). Asn is highly conserved in the high-energy, left-handed alpha-helical conformation, where it frequently forms amide stacking. Based on the observed prominent stacking of chemically similar residues in parallel beta helices, we propose that within the "cross-beta" framework, amyloids with longer peptide chains may have common structural features of in-register, parallel alignment, with the side chains forming identical amino acid ladders. The requirement of ladder formation limits the combinations of side chain interactions. Such a limit combined with environmental conditions (e.g., pH, concentration) could be a major reason for the ability of most polypeptides to form amyloids.

Fabrication of coaxial metal nanocables using a self-assembled peptide nanotube scaffold

The design and fabrication of complex nanostructures with specific geometry and composition is one of the main challenges of nanotechnology. Here we demonstrate the devise of metal-insulator-metal, trilayered, coaxial nanocables. Such coaxial geometry may give rise to useful and unique electromagnetic properties. We have fabricated these nanostructures using a scaffold of self-assembled peptide nanotubes. Gold nanoparticles were bound to the surface of peptide nanotubes via a common molecular recognition element that was included in various linker peptides. This enabled us to promote site-specific metal reduction and to create the coaxial nanostructure. Using electron microscopy, 1H NMR spectra, and energy-dispersive X-ray analysis, we monitored the different steps within the process, gaining further understanding of its mechanism.

Inhibition of amyloid fibril formation by polyphenols: structural similarity and aromatic interactions as a common inhibition mechanism

The formation of well-ordered fibrillar protein deposits is common to a large group of amyloid-associated disorders. This group consists of several major human diseases such as Alzheimer's disease, Parkinson's disease, prion diseases, and type II diabetes. Currently, there is no approved therapeutic agent directed towards the formation of fibrillar assemblies, which have been recently shown to have a key role in the cytotoxic nature of amyloidogenic proteins. One important approach in the development of therapeutic agents is the use of small molecules that specifically and efficiently inhibit the aggregation process. Several small polyphenol molecules have been demonstrated to remarkably inhibit the formation of fibrillar assemblies in vitro and their associated cytotoxicity. Yet, the inhibition mechanism was mostly attributed to the antioxidative properties of these polyphenol compounds. Based on several observations demonstrating that polyphenols are capable of inhibiting amyloid fibril formation in vitro, regardless of oxidative conditions, and in view of their structural similarities we suggest an additional mechanism of action. This mechanism is assuming structural constraints and specific aromatic interactions, which direct polyphenol inhibitors to the amyloidogenic core. This proposed mechanism is highly relevant for future de novo inhibitors' design as therapeutic agents for the treatment of amyloid-associated diseases.

Preparation of Highly Conductive, Self-Assembled Gold/Polyaniline Nanocables and Polyaniline Nanotubes

One-dimensional gold/polyaniline (Au/PANI-CSA) coaxial nanocables with an average diameter of 50-60 nm and lengths of more than 1 mum were successfully synthesized by reacting aniline monomer with chlorauric acid (HAuCl(4)) through a self-assembly process in the presence of D-camphor-10-sulfonic acid (CSA), which acts as both a dopant and surfactant. It was found that the formation probability and the size of the Au/PANI-CSA nanocables depends on the molar ratio of aniline to HAuCl(4) and the concentration of CSA, respectively. A synergistic growth mechanism was proposed to interpret the formation of the Au/PANI-CSA nanocables. The directly measured conductivity of a single gold/polyaniline nanocable was found to be high (approximately 77.2 S cm(-1)). Hollow PANI-CSA nanotubes, with an average diameter of 50-60 nm, were also obtained successfully by dissolving the Au nanowire core of the Au/PANI-CSA nanocables.

Atomic layer deposition on biological macromolecules: metal oxide coating of tobacco mosaic virus and ferritin

Decoration of nanoparticles, in particular biomolecules, gathered high attention in recent years.(1-7) Of special interest is the potential use of biomolecules as templates for the fabrication of semiconducting or metallic nanostructures.(1-7,26) In this work we show the application of atomic layer deposition, a gas-phase thin film deposition process, to biological macromolecules, which are frequently used as templates in nanoscale science, and the possibility to fabricate metal oxide nanotubes and thin films with embedded biomolecules.(1-13).

Ammonium lithocholate nanotubes: stability and copper metallization

Ammonium lithocholate nanotubes (NHLC) have been prepared in alkaline ammonia solutions and exhibited remarkable monodisperse cross-sectional dimensions (external diameter = 52 nm) as shown by cryo-transmission electron microscopy measurements. A classical electroless metallic replication method was used with a single poly(ethylene-imine) PEI layer coating the negatively charged NHLC nanotubes. Short copper rods (external diameter ∼ 80 nm) were observed by scanning electron microscopy that corresponded to the original organic templates. The results obtained in acidic conditions are analyzed in terms of the lifetime of the self-assembled structures and formation of bundles of tubes. Dynamic light scattering measurements and optical observations show that the system in the presence of controlled amounts of hydrochloric acid is stable enough to account for a metallic replication in acidic conditions. An average apparent diffusion coefficient of the organic NHLC assemblies is extracted (∼ 9.8 × 10 nm s) in homogeneous suspensions where bundles have been dispersed by the acidic additions.

Direct Observation of the Release of Phenylalanine from Diphenylalanine Nanotubes

The core recognition motif of the amyloidogenic beta-amyloid polypeptide is a dipeptide of phenylalanine. This dipeptide readily self-assembles to form discrete, hollow nanotubes with high persistence lengths. The simplicity of the nanotube formation, combined with ideal physical properties, make these nanotubes highly desirable for a range of applications in bionanotechnology. To fully realize the potential of such structures, it is first necessary to gain a comprehensive understanding of their chemical and physical properties. Previously, the thermal stability of these nanotubes has been investigated by electron microscopy. Here, we further our understanding of the structural stability of the nanotubes upon dry-heating using the atomic force microscope (AFM), and for the first time identify their degradation product utilizing time-of-flight secondary-ion mass spectrometry. We show that the nanotubes are stable at temperatures up to 100 degrees C, but on heating to higher temperatures begin to lose their structural integrity with an apparent collapse in tubular structure. With further increases in temperature up to and above 150 degrees C, there is a degradation of the structure of the nanotubes through the release of phenylalanine building blocks. The breakdown of structure is observed in samples that are either imaged at elevated temperatures or imaged following cooling, suggesting that once phenylalanine is lost from the nanotubes they are susceptible to mechanical deformation by the imaging AFM probe. This temperature-induced plasticity may provide novel properties for these peptide nanotubes, including possible applications as scaffolds and drug delivery devices.

Fabrication of Protein-Conjugated Silver Sulfide Nanorods in the Bovine Serum Albumin Solution

Highly ordered silver sulfide nanorods conjugated with the Bovine Serum Albumin (BSA) protein have been successfully achieved at ambient temperature. Such a process is very simple and controllable, directly using silver nitrate and thioacetamide (TAA) as the reactants in the aqueous solution of BSA. The products have been characterized by XRD, HRTEM-SAED, SEM-EDS, TG-DTA, FT-IR, and CD spectroscopy. The results of the research show that the as-prepared Ag2S nanorods are monodispersed with sizes about 40 nm in diameter and 220 nm in length, and exhibit a high degree of crystallinity and good photoluminescence. Furthermore, an interesting mechanism is discussed for the formation of the Ag2S nanorods.

Self-Assembly of Amylin(20–29) Amide-Bond Derivatives into Helical Ribbons and Peptide Nanotubes rather than Fibrils

Uncontrolled aggregation of proteins or polypeptides can be detrimental for normal cellular processes in healthy organisms. Proteins or polypeptides that form these amyloid deposits differ in their primary sequence but share a common structural motif: the (anti)parallel beta sheet. A well-accepted approach for interfering with beta-sheet formation is the design of soluble beta-sheet peptides to disrupt the hydrogen-bonding network; this ultimately leads to the disassembly of the aggregates or fibrils. Here, we describe the synthesis, spectroscopic analysis, and aggregation behavior, imaged by electron microscopy, of several backbone-modified amylin(20-29) derivatives. It was found that these amylin derivatives were not able to form fibrils and to some extent were able to inhibit fibril growth of native amylin(20-29). However, two of the amylin peptides were able to form large supramolecular assemblies, like helical ribbons and peptide nanotubes, in which beta-sheet formation was clearly absent. This was quite unexpected since these peptides have been designed as soluble beta-sheet breakers for disrupting the characteristic hydrogen-bonding network of (anti)parallel beta sheets. The increased hydrophobicity and the presence of essential amino acid side chains in the newly designed amylin(20-29) derivatives were found to be the driving force for self-assembly into helical ribbons and peptide nanotubes. This example of controlled and desired peptide aggregation may be a strong impetus for research on bionanomaterials in which special shapes and assemblies are the focus of interest.

Designing a nanotube using naturally occurring protein building blocks

Here our goal is to carry out nanotube design using naturally occurring protein building blocks. Inspection of the protein structural database reveals the richness of the conformations of proteins, their parts, and their chemistry. Given target functional protein nanotube geometry, our strategy involves scanning a library of candidate building blocks, combinatorially assembling them into the shape and testing its stability. Since self-assembly takes place on time scales not affordable for computations, here we propose a strategy for the very first step in protein nanotube design: we map the candidate building blocks onto a planar sheet and wrap the sheet around a cylinder with the target dimensions. We provide examples of three nanotubes, two peptide and one protein, in atomistic model detail for which there are experimental data. The nanotube models can be used to verify a nanostructure observed by low-resolution experiments, and to study the mechanism of tube formation.

Enzyme-triggered self-assembly of peptide hydrogels via reversed hydrolysis

We demonstrate that proteases can be used to selectively trigger the self-assembly of peptide hydrogels via reversed hydrolysis.

Structural and mechanical study of a self-assembling protein nanotube

We report a structural characterization of self-assembling nanostructures. Using atomic force microscopy (AFM), we discovered that partially hydrolyzed alpha-lactalbumin organizes in a 10-start helix forming tubes with diameters of only 21 nm. We probed the mechanical strength of these nanotubes by locally indenting them with an AFM tip. To extract the material properties of the nanotubes, we modeled the experiment using finite element methods. Our study shows that artificial helical protein self-assembly can yield very stable, strong structures that can function either as a model system for artificial self-assembly or as a nanostructure with potential for practical applications.

Rapid self-assembly of oligo(o-phenylenediamine) into one-dimensional structures through a facile reprecipitation route

The self-assembly of oligo(o-phenylenediamine) (OPD) into 1-D nanostructures on a macroscopic length scale was found when they were transferred from N-methyl pyrrolidone to deionized water. Field emission scanning electron microscopy and confocal fluorescence microscopy were used to investigate the morphology of the precipitates. Results showed that large amounts of OPD 1-D supertructures could be obtained through the simple reprecipitation route, and the length of the fibers could be tuned from microscale to macroscale by adjusting the ratio of two solvents. X-ray diffraction patterns and UV-vis spectra revealed that pi-pi interactions between OPD molecules that facilitated the formation of 1-D structures became predominant when they were transferred from a good solvent to a bad one. Accordingly, a possible formation mechanism was proposed.

Molecular dynamics simulation of the aggregation of the core-recognition motif of the islet amyloid polypeptide in explicit water

The formation of amyloid fibrils is associated with major human diseases. Nevertheless, the molecular mechanism that directs the nucleation of these fibrils is not fully understood. Here, we used molecular dynamics simulations to study the initial self-assembly stages of the NH2-NFGAIL-COOH peptide, the core-recognition motif of the type II diabetes associated islet amyloid polypeptide. The simulations were performed using multiple replicas of the monomers in explicit water, in a confined box starting from a random distribution of the peptides at T = 300 K and T = 340 K. At both temperatures the formation of unique clusters was observed after a few nanoseconds. Structural analysis of the clusters clearly suggested the formation of "flat" ellipsoid-shaped clusters through a preferred locally parallel alignment of the peptides. The unique assembly is facilitated by a preference for an extended conformation of the peptides and by intermolecular aromatic interactions. Taken together, our results may provide a description of the molecular recognition determinants involved in fibril formation, in terms of the atomic detailed structure of nascent aggregates. These observations may yield information on new ways to control this process for either materials development or drug design.

Structure of core domain of fibril-forming PHF/Tau fragments

Short peptide sequences within the microtubule binding domain of the protein Tau are proposed to be core nucleation sites for formation of amyloid fibrils displaying the paired helical filament (PHF) morphology characteristic of neurofibrillary tangles. To study the structure of these proposed nucleation sites, we analyzed the x-ray diffraction patterns from the assemblies formed by a variety of PHF/tau-related peptide constructs containing the motifs VQIINK (PHF6*) in the second repeat and VQIVYK (PHF6) in the third repeat of tau. Peptides included: tripeptide acetyl-VYK-amide (AcVYK), tetrapeptide acetyl-IVYK-amide (AcPHF4), hexapeptide acetyl-VQIVYK-amide (AcPHF6), and acetyl-GKVQIINKLDLSNVQKDNIKHGSVQIVYKPVDLSKVT-amide (AcTR4). All diffraction patterns showed reflections at spacings of 4.7 A, 3.8 A, and approximately 8-10 A, which are characteristic of an orthogonal unit cell of beta-sheets having dimensions a=9.4 A, b=6.6 A, and c=approximately 8-10 A (where a, b, and c are the lattice constants in the H-bonding, chain, and intersheet directions). The sharp 4.7 A reflections indicate that the beta-crystallites are likely to be elongated along the H-bonding direction and in a cross-beta conformation. The assembly of the AcTR4 peptide, which contains both the PHF6 and PHF6* motifs, consisted of twisted sheets, as indicated by a unique fanning of the diffuse equatorial scattering and meridional accentuation of the (210) reflection at 3.8 A spacing. The diffraction data for AcVYK, AcPHF4, and AcPHF6 all were consistent with approximately 50 A-wide tubular assemblies having double-walls, where beta-strands constitute the walls. In this structure, the peptides are H-bonded together in the fiber direction, and the intersheet direction is radial. The positive-charged lysine residues face the aqueous medium, and tyrosine-tyrosine aromatic interactions stabilize the intersheet (double-wall) layers. This particular contact, which may be involved in PHF fibril formation, is proposed here as a possible aromatic target for anti-tauopathy drugs.