Casting metal nanowires within discrete self-assembled peptide nanotubes

A model for the role of short self-assembled peptides in the very early stages of the origin of life

The molecular basis of the origin of life is one of the most fundamental questions in modern biology. While the "RNA world" hypothesis offers a very sensible model for the evolvement of the current biochemical networks, there is a lack of knowledge about the early steps that led to the formation of the first RNA molecules. This issue is essential as it is practically impossible that complex molecules as functional RNA oligonucleotides had evolved spontaneously. It was recently demonstrated that peptide molecules as simple as dipeptides can self-assemble into well-ordered tubular, fibrilar, and closed-cage structures. Other studies have confirmed the ability of dipeptides to act as catalysts and the capability of other peptides, as short as tripeptides, to serve as a template for nucleotide binding and orientation. Unlike complex RNA molecules, the spontaneous formation of functional short peptides in the primordial earth conditions is very likely. We suggest a novel mechanism for the origin of life that is based on the ability of short peptides to form encapsulated structures, catalyst chemical reaction, and serve as highly ordered template for the assembly of nucleotides. This model may explain the early events that led to the formation of the current biochemical machinery that combines the elaborated and coordinated interaction between nucleic acids and proteins to allow the function of living systems.

Concepts and schemes for the re-engineering of physical protein modules: generating nanodevices via targeted replacements with constrained amino acids

Physically building complex multi-molecular structures from naturally occurring biological macromolecules has aroused a great deal of interest. Here we focus on nanostructures composed of re-engineered, natural 'foldamer' building blocks. Our aim is to provide some of the underlying concepts and schemes for crafting structures utilizing such conformationally relatively stable molecular components. We describe how, via chemical biology strategies, it is further possible to chemically manipulate the foldamer building blocks toward specific shape-driven structures, which in turn could be used toward potential-designed functions. We outline the criteria in choosing candidate foldamers from the vast biological repertoire, and how to enhance their stability through selected targeted replacements by non-proteinogenic conformationally constrained amino acids. These approaches combine bioinformatics, high performance computations and mathematics with synthetic organic chemistry. The resulting artificially engineered self-organizing molecular scale structures take advantage of nature's nanobiology toolkit and at the same time improve on it, since their new targeted function differs from that optimized by evolution. The major challenge facing nanobiology is to be able to exercise fine control over the performance of these target-specific molecular machines.

Designed aromatic homo-dipeptides: formation of ordered nanostructures and potential nanotechnological applications

Molecular self-assembly offers new routes for the fabrication of novel materials at the nano-scale. Peptide-based nanostructures represent nano-objects of particular interest, as they are biocompatible, can be easily synthesized in large amounts, can be decorated with functional elements and can be used in various biological and non-biological applications. We had previously revealed the formation of highly ordered tubular structures by the diphenylalanine peptide, the core recognition motif of Alzheimer's beta-amyloid polypeptide, due to specific aromatic interactions. We further confirmed this model and demonstrated that a non-charged peptide analogue, Ac-Phe-Phe-NH2, self-assembled into similar tubular structures. We later explored other amine and carboxyl modified diphenylalanine peptide analogues and revealed that these dipeptides can form ordered tubular structures at the nanometric scale. Moreover, a very similar peptide, the diphenylglycine, self-assembled into ordered nano-spherical assemblies. Here we extend our research and explore the self-assembly of other homo-aromatic dipeptides in which their phenyl side-chains are modified with halogen atoms (di-para-fluoro-Phe, di-pentafluoro-Phe, di-para-iodo-Phe), additional phenyl groups (di-4-phenyl-Phe), or with nitro substitutions (di-para-nitro-Phe). We also probed the effect of the alteration of the phenyl groups with naphtyl groups (di-D-1-Nal and di-D-2-Nal). In all cases, well-ordered nanostructures were obtained and studied by scanning electron microscopy, transmission electron microscopy and vibrational spectroscopy. Taken together, the current work and previous ones define the homo-aromatic dipeptide as a central motif for the formation of ordered self-assembled tubular, spherical and two-dimensional structures at the nano-scale.

Thermal and chemical stability of diphenylalanine peptide nanotubes: implications for nanotechnological applications

The diphenylalanine peptide, the core recognition motif of the beta-amyloid polypeptide, efficiently self-assembles into discrete, well-ordered nanotubes. Here, we describe the notable thermal and chemical stability of these tubular structures both in aqueous solution and under dry conditions. Scanning and transmission electron microscopy (SEM and TEM) as well as atomic force microscopy (AFM) revealed the stability of the nanotubes in aqueous solution at temperatures above the boiling point of water upon autoclave treatment. The nanotubes preserved their secondary structure at temperatures up to 90 degrees C, as shown by circular dichroism (CD) spectra. Cold field emission gun (CFEG) high-resolution scanning electron microscope (HRSEM) and thermogravimetric analysis (TGA) of the peptide nanotubes after dry heat revealed durability at higher temperature. It was shown that the thermal stability of diphenylalanine peptide nanotubes is significantly higher than that of a nonassembling dipeptide, dialanine. In addition to thermal stability, the peptide nanotubes were chemically stable in organic solvents such as ethanol, methanol, 2-propanol, acetone, and acetonitrile, as shown by SEM analysis. Moreover, the acetone environment enabled AFM imaging of the nanotubes in solution. The significant thermal and chemical stability of the peptide nanotubes demonstrated here points toward their possible use in conventional microelectronic and microelectromechanics processes and fabrication into functional nanotechnological devices.

Networks of gold nanoparticles and bacteriophage as biological sensors and cell-targeting agents

Biological molecular assemblies are excellent models for the development of nanoengineered systems with desirable biomedical properties. Here we report an approach for fabrication of spontaneous, biologically active molecular networks consisting of bacteriophage (phage) directly assembled with gold (Au) nanoparticles (termed Au-phage). We show that when the phage are engineered so that each phage particle displays a peptide, such networks preserve the cell surface receptor binding and internalization attributes of the displayed peptide. The spontaneous organization of these targeted networks can be manipulated further by incorporation of imidazole (Au-phage-imid), which induces changes in fractal structure and near-infrared optical properties. The networks can be used as labels for enhanced fluorescence and dark-field microscopy, surface-enhanced Raman scattering detection, and near-infrared photon-to-heat conversion. Together, the physical and biological features within these targeted networks offer convenient multifunctional integration within a single entity with potential for nanotechnology-based biomedical applications.

Cyclodextrin-covered organic nanotubes derived from self-assembly of dendrons and their supramolecular transformation

The dendritic building blocks with a focal pyrene unit self-organize into vesicles in aqueous phase. The in situ inclusion of the focal pyrene units into the cavity of beta- or gamma-cyclodextrin (CD) induces self-assembled organic nanotubes with an average outer diameter of approximately 45 nm and inner diameter of 22 nm. The surface of the nanotube is covered with CD. Therefore, the functional group on the surface of the nanotube is controlled simply by modifying the functionality of CD. The removal of CD from the nanotube with poly(propylene glycol) reversibly generates vesicles. This work provides an efficient methodology not only to create an additional class of CD-covered organic nanotubes but also to exhibit reversible transformation of nanotubes and vesicles triggered by the motifs of dendron self-assembly, CD inclusion, and pseudorotaxane formation.

Cytochrome Display on Amyloid Fibrils

Protein amyloid fibrils can be functionalized by coating the core protofilament with high concentrations of proteins and enzymes. This can be done elegantly by appending a functional domain to an amyloidogenic protein monomer, then assembling the monomers into a fibril. To display an array of biologically functional porphyrins on the surface of protein fibrils, we have fused the sequence of the small, soluble cytochrome b562 to an SH3 dimer sequence that can form classical amyloid fibrils rapidly under well-defined conditions. The resulting fusion protein also forms amyloid fibrils and, in addition, binds metalloporphyrins, at half of the porphyrin binding sites as shown by UV-vis and NMR spectroscopies. Once metalloporphyrins are bound to the fibrils, the resulting holo-cytochrome domains are spectroscopically identical to the wild type cytochrome. The concentration of metalloporphyrins on a saturated fibril is estimated to be of the order of approximately 20 mM, suggesting that they could be interesting systems for applications in nanotechnology.

Mechanisms of amyloid fibril self-assembly and inhibition. Model short peptides as a key research tool

The formation of amyloid fibrils is associated with various human medical disorders of unrelated origin. Recent research indicates that self-assembled amyloid fibrils are also involved in physiological processes in several micro-organisms. Yet, the molecular basis for the recognition and self-assembly processes mediating the formation of such structures from their soluble protein precursors is not fully understood. Short peptide models have provided novel insight into the mechanistic issues of amyloid formation, revealing that very short peptides (as short as a tetrapeptide) contain all the necessary molecular information for forming typical amyloid fibrils. A careful analysis of short peptides has not only facilitated the identification of molecular recognition modules that promote the interaction and self-assembly of fibrils but also revealed that aromatic interactions are important in many cases of amyloid formation. The realization of the role of aromatic moieties in fibril formation is currently being used to develop novel inhibitors that can serve as therapeutic agents to treat amyloid-associated disorders.

Tuning amyloidogenic conformations through cosolvents and hydrostatic pressure: when the soft matter becomes even softer

Compact packing, burial of hydrophobic side-chains, and low free energy levels of folded conformations contribute to stability of native proteins. Essentially, the same factors are implicated in an even higher stability of mature amyloid fibrils. Although both native insulin and insulin amyloid are resistant to high pressure and influence of cosolvents, intermediate aggregation-prone conformations are susceptible to either condition. Consequently, insulin fibrillation may be tuned under hydrostatic pressure or-- through cosolvents and cosolutes-- by preferential exclusion or binding. Paradoxically, under high pressure, which generally disfavors aggregation of insulin, an alternative "low-volume" aggregation pathway, which leads to unique circular amyloid is permitted. Likewise, cosolvents are capable of preventing, or altering amyloidogenesis of insulin. As a result of cosolvent-induced perturbation, distinct conformational variants of fibrils are formed. Such variants, when used as templates for seeding daughter generations, reproduce initial folding patterns regardless of environmental biases. By the close analogy, this suggests that the "prion strains" phenomenon may mirror a generic, common feature in amyloids. The susceptibility of amyloidogenic conformations to pressure and cosolvents is likely to arise from their "frustration", as unfolding results in less-densely packed side-chains, void volumes, and exposure of hydrophobic groups. The effects of cosolvents and pressure are discussed in the context of studies on other amyloidogenic protein models, amyloid polymorphism, and "strains".

Enzymatically triggered self-assembly of poly(ethylene glycol)-attached oligopeptides into well-organized nanofibers

A unique and programmable peptide self-assembling system has been fabricated by using poly(ethylene glycol)-attached amphiphilic oligopeptide, which shows rapid self-assembly into well-organized beta-sheet nanofibers in response to an enzymatic reaction.

Direct observation of amyloid growth monitored by total internal reflection fluorescence microscopy

Most morphological investigations of amyloid fibrils have been performed with various microscopic methods. Among them, direct observation of fibril growth is possible using atomic force microscopy and fluorescence microscopy. Direct observation provides information about the rate and direction of growth at the single fibril level, which cannot be obtained from averaged ensemble measurements. In this chapter, we describe a new technique for the direct observation of amyloid fibril growth using total internal reflection fluorescence microscopy (TIRFM) combined with amyloid-specific thioflavin T (ThT) fluorescence. TIRFM has been developed to monitor single molecules by effectively reducing the background fluorescence in an evanescent field. One of the advantages of TIRFM is that one can selectively monitor fibrils lying along a glass slide, so that one can obtain the exact length of fibrils. This method was used to follow the kinetics of seed-dependent fibril growth of amyloid beta (1-40). The fibril growth was a highly cooperative process, with the fibril ends extending at a constant rate. Because ThT binding is common to all amyloid fibrils, the present method will have general applicability to the real-time analysis of amyloid fibrils.

Formation of triple helical nanofibers using self-assembling chiral benzene-1,3,5-tricarboxamides and reversal of the nanostructure's handedness using mirror image building blocks

Intertwining triple helical nanofibers with an overall handedness have been formed from self-assembling chiral benzene-1,3,5-tricarboxamides , and , whereas the achiral benzene-1,3,5-tricarboxamide upon self-association gives rise to straight nanofibers without any twist and transmission electron microscopy images of chiral compounds clearly demonstrate that the handedness of the triple helical nanofibers can be reversed by using the enantiomeric benzene-1,3,5-tricarboxamide building blocks.

X-Ray fiber and powder diffraction of PrP prion peptides

A conformational change from the alpha-helical, cellular form of prion to the beta-sheet, scrapie (infectious) form is the central event for prion replication. The folding mechanism underlying this conformational change has not yet been deciphered. Here, we review prion pathology and summarize X-ray fiber and powder diffraction studies on the N-terminal fragments of prion protein and on short sequences that initiate the beta-assembly for various fibrils, including poly(L-alanine) and poly(L-glutamine). We discuss how the quarter-staggered beta-sheet assembly (like in polyalanine) and polar-zipper beta-sheet formation (like in polyglutamine) may be involved in the formation of the scrapie form of prion.

Synthesis and structural investigations of N-alkylated β-peptidosulfonamide–peptide hybrids of the amyloidogenic amylin(20–29) sequence: implications of supramolecular folding for the design of peptide-based bionanomaterials

The incorporation of a single beta-aminoethane sulfonyl amide moiety in a highly amyloidogenic peptide sequence resulted in a complete loss of amyloid fibril formation. Instead, supramolecular folding morphologies were observed. Subsequent chemoselective N-alkylation of the sulfonamide resulted in amphiphilic peptide-based hydrogelators. It was found that variation of merely the alkyl chain induced a dramatic variation in aggregation motifs such as helical ribbons and tapes, ribbons progressing to closed tubes, twisted lamellar sheets and entangled/branched fibers.

The structure of nanotubes formed by diphenylalanine, the core recognition motif of Alzheimer's β-amyloid polypeptide

Alzheimer's beta-amyloid diphenylalanine motif has previously been shown to self-assemble into discrete and extraordinary stiff nanotubes; these nanotubes were initially thought to be distinct from the single crystal structure of diphenylalanine, but it is now shown that the X-ray powder diffraction pattern of the nanotubes is identical to the simulated pattern for the single crystal structure, affording a new foundation for understanding and rationalizing the properties of this remarkable organic material.

Natural Triple β‐Stranded Fibrous Folds1

A distinctive family of beta-structured folds has recently been described for fibrous proteins from viruses. Virus fibers are usually involved in specific host-cell recognition. They are asymmetric homotrimeric proteins consisting of an N-terminal virus-binding tail, a central shaft or stalk domain, and a C-terminal globular receptor-binding domain. Often they are entirely or nearly entirely composed of beta-structure. Apart from their biological relevance and possible gene therapy applications, their shape, stability, and rigidity suggest they may be useful as blueprints for biomechanical design. Folding and unfolding studies suggest their globular C-terminal domain may fold first, followed by a "zipping-up" of the shaft domains. The C-terminal domains appear to be important for registration because peptides corresponding to shaft domains alone aggregate into nonnative fibers and/or amyloid structures. C-terminal domains can be exchanged between different fibers and the resulting chimeric proteins are useful as a way to solve structures of unknown parts of the shaft domains. The following natural triple beta-stranded fibrous folds have been discovered by X-ray crystallography: the triple beta-spiral, triple beta-helix, and T4 short tail fiber fold. All have a central longitudinal hydrophobic core and extensive intermonomer polar and nonpolar interactions. Now that a reasonable body of structural and folding knowledge has been assembled about these fibrous proteins, the next challenge and opportunity is to start using this information in medical and industrial applications such as gene therapy and nanotechnology.

Annealing prion protein amyloid fibrils at high temperature results in extension of a proteinase K-resistant core

Amyloids are highly ordered, rigid beta-sheet-rich structures that appear to have minimal dynamic flexibility in individual polypeptide chains. Here, we demonstrate that substantial conformational rearrangements occur within mature amyloid fibrils produced from full-length mammalian prion protein. The rearrangement results in a substantial extension of a proteinase K-resistant core and is accompanied by an increase in the beta-sheet-rich conformation. The conformational rearrangement was induced in the presence of low concentrations of Triton X-100 either by brief exposure to 80 degrees C or, with less efficacy, by prolonged incubation at 37 degrees C at pH 7.5 and is referred to here as "annealing." Upon annealing, amyloid fibrils acquired a proteinase K-resistant core identical to that found in bovine spongiform encephalopathy-specific scrapie-associated prion protein. Annealing was also observed when amyloid fibrils were exposed to high temperatures in the absence of detergent but in the presence of brain homogenate. These findings suggest that the amyloid fibrils exist in two conformationally distinct states that are separated by a high energy barrier and that yet unknown cellular cofactors may facilitate transition of the fibrils into thermodynamically more stable state. Our studies provide new insight into the complex behavior of prion polymerization and highlight the annealing process, a previously unknown step in the evolution of amyloid structures.

Biofabrication with Chitosan

The traditional motivation for integrating biological components into microfabricated devices has been to create biosensors that meld the molecular recognition capabilities of biology with the signal processing capabilities of electronic devices. However, a different motivation is emerging; biological components are being explored to radically change how fabrication is achieved at the micro- and nanoscales. Here we review biofabrication, the use of biological materials for fabrication, and focus on three specific biofabrication approaches: directed assembly, where localized external stimuli are employed to guide assembly; enzymatic assembly, where selective biocatalysts are enlisted to build macromolecular structure; and self-assembly, where information internal to the biological material guides its own assembly. Also reviewed are recent results with the aminopolysaccharide chitosan, a material that offers a combination of properties uniquely suited for biofabrication. In particular, chitosan can be directed to assemble in response to locally applied electrical signals, and the chitosan backbone provides sites that can be employed for the assembly of proteins, nucleic acids, and virus particles.

Room-Temperature Wurtzite ZnS Nanocrystal Growth on Zn Finger-like Peptide Nanotubes by Controlling Their Unfolding Peptide Structures

ZnS nanocrystal, a class of wide-gap semiconductors, has shown interesting optical, electrical, and optoelectric properties via quantum confinement. For those applications, phase controls of ZnS nanocrystals and nanowires were critical to tune their physical properties to the appropriate ones. The wurtzite ZnS nanocrystal growth at room temperature is the useful fabrication; however, the most stable ZnS structure in nanoscale is the zinc blende (cubic) structure, and scientists have just begun exploring the room-temperature synthesis of the wurtzite (hexagonal) structure of ZnS nanocrystals. In this report, we applied the Zn finger-like peptides as templates to control the phase of ZnS nanocrystals to the wurtzite structure at room temperature. The peptide nanotubes, consisting of a 20 amino acids (VAL-CYS-ALA-THR-CYS-GLU-GLN-ILE-ALA-ASP-SER-GLN-HIS-ARG-SER-HIS-ARG-GLN-MET-VAL, M1 peptide) synthesized based on the peptide motif of the Influenza Virus Matrix Protein M1, could grow the wurtzite ZnS nanocrystals on the nanotube templates in solution. In the M1 protein, the unfolding process of the helical peptide motif via pH change creates a linker region between N- and C-terminated helical domains that contains a Zn finger-like Cys2His2 motif. Because the higher pH increases the uptake of Zn ions in the Cys2His2 motif of the M1 peptide by unfolding more helical domains, the pH change can essentially control the size and the number of the nucleation sites in the M1 peptides to grow ZnS nanocrystals with desired phases. Here we optimized the nucleation sites in the M1 peptides by unfolding them via pH change to obtain highly monodisperse and crystalline wurtzite ZnS nanocrystals on the template nanotubes at room temperature. This type of peptide-induced biomineralization technique will provide a clean and reproducible method to produce semiconductor nanotubes due to its efficient nanocrystal formation, and the band gaps of resulting nanotubes can also be tuned simply by phase control of ZnS nanocrystal coatings via the optimization of the unfolding peptide structures.

Integrated nanoparticle-biomolecule hybrid systems: synthesis, properties, and applications

Nanomaterials, such as metal or semiconductor nanoparticles and nanorods, exhibit similar dimensions to those of biomolecules, such as proteins (enzymes, antigens, antibodies) or DNA. The integration of nanoparticles, which exhibit unique electronic, photonic, and catalytic properties, with biomaterials, which display unique recognition, catalytic, and inhibition properties, yields novel hybrid nanobiomaterials of synergetic properties and functions. This review describes recent advances in the synthesis of biomolecule-nanoparticle/nanorod hybrid systems and the application of such assemblies in the generation of 2D and 3D ordered structures in solutions and on surfaces. Particular emphasis is directed to the use of biomolecule-nanoparticle (metallic or semiconductive) assemblies for bioanalytical applications and for the fabrication of bioelectronic devices.

Molecular dynamics simulations of Alzheimer's beta-amyloid protofilaments

Filamentous amyloid aggregates are central to the pathology of Alzheimer's disease. We use all-atom molecular dynamics (MD) simulations with explicit solvent and multiple force fields to probe the structural stability and the conformational dynamics of several models of Alzheimer's beta-amyloid fibril structures, for both wild-type and mutated amino acid sequences. The structural models are based on recent solid state NMR data. In these models, the peptides form in-register parallel beta-sheets along the fibril axis, with dimers of two U-shaped peptides located in layers normal to the fibril axis. Four different topologies are explored for stacking the beta-strand regions against each other to form a hydrophobic core. Our MD results suggest that all four NMR-based models are structurally stable, and we find good agreement with dihedral angles estimated from solid-state NMR experiments. Asp23 and Lys28 form buried salt-bridges, resulting in an alternating arrangement of the negatively and positively charged residues along the fibril axis that is reminiscent of a one-dimensional ionic crystal. Interior water molecules are solvating the buried salt-bridges. Based on data from NMR measurements and MD simulations of short amyloid fibrils, we constructed structural models of long fibrils. Calculated X-ray fiber diffraction patterns show the characteristics of packed beta-sheets seen in experiments, and suggest new experiments that could discriminate between various fibril topologies.

Peptide-Based Nanotubes and Their Applications in Bionanotechnology

In nature, biological nanomaterials are synthesized under ambient conditions in a natural microscopic-sized laboratory, such as a cell. Biological molecules, such as peptides and proteins, undergo self-assembly processes in vivo and in vitro, and these monomers are assembled into various nanometer-scale structures at room temperature and atmospheric pressure. The self-assembled peptide nanostructures can be further organized to form nanowires, nanotubes, and nanoparticles via their molecular-recognition functions. The application of molecular self-assemblies of synthetic peptides as nanometer-scale building blocks in devices is robust, practical, and affordable due to their advantages of reproducibility, large-scale production ability, monodispersity, and simpler experimental methods. It is also beneficial that smart functionalities can be added at desired positions in peptide nanotubes through well-established chemical and peptide syntheses. These features of peptide-based nanotubes are the driving force for investigating and developing peptide nanotube assemblies for biological and non-biological applications.

The Formation of Escherichia coli Curli Amyloid Fibrils is Mediated by Prion-like Peptide Repeats

Amyloid fibril formation is the hallmark of major human maladies including Alzheimer's disease, type II diabetes, and prion diseases. Prion-like phenomena were also observed in yeast. Although not evolutionarily related, one similarity between the animal PrP and the yeast Sup35 prion proteins is the occurrence of short peptide repeats that are assumed to play a key role in the assembly of the amyloid structures. It was recently demonstrated that typical amyloid fibril formation is associated with biofilm formation by Escherichia coli. Here, we note the functional and structural similarity between oligopeptide repeats of the major curli protein and those of animal and yeast prions. We demonstrate that synthetic peptides corresponding to the repeats form fibrillar structures. Furthermore, conjugation of beta-breaker elements to the prion-like repeat significantly inhibits amyloid formation and cell invasion of curli-expressing bacteria. This implies a functional role of the repeat in the self-assembly of the fibrils. Since mammal prion, yeast prion, and curli protein are evolutionarily distinct, the conserved peptide repeats most likely define an optimized self-association motif that was independently evolved by diverse systems.

In Situ Depositing Silver Nanoclusters on Silk Fibroin Fibers Supports by a Novel Biotemplate Redox Technique at Room Temperature

Evolvement of bioinspired approaches for the construction of well-ordered nanostructures is a crucial intersection of branches of materials science and biotechnology. In this paper, floriated clusters of silver nanocrystallites, which consist of polycrystalline grains about 5 nm in diameter, have been successfully prepared on silk fibroin fibers (SFFs) through an in situ biotemplate redox approach at room temperature. The reductive amino acid tyrosine of SFFs mainly provided both reduction and location functions under alkaline conditions and could reduce Ag(I) ions to Ag(0). Finally, stable silver nanoclusters were generated on SFF substrates. The morphologies of silver nanoclusters were mostly attributed to the concentration of silver nitrate solution as well as special configurations and structures of silk fibroin macromolecules. A possible mechanism was explored intensively for tyrosine-residue-based silver nanocrystal formation.

Langmuir monolayers of the long-chain alkyl derivatives of a nucleoside analogue and the formation of self-assembled nanoparticles

The long-chain alkyl derivatives of a nucleoside analogue-acyclovir were prepared in the paper. One is stearyl-glycero-succinyl-acyclovir (SGSA) with a single 18-carbon length (C18) alkyl chain. Another is dioctadecyl-aspartate-succinyl-acyclovir (DASA) with double C18 alkyl chains. They were prepared by the esterification of succinyl-acyclovir with the lipids, and sodium salts of them were also prepared. Guanine moieties and alkyl moieties bring the derivatives intermolecular hydrogen bonding and hydrophobic interaction in water separately. The forces are influenced by the number of alkyl chains and the charged state, and determine the solubility and the self-assembly behavior of the derivatives. The double alkyl-chain derivatives (DASA and DASA-Na) formed rigid Langmuir monolayers on air/water surface, while the single alkyl chain derivatives (SGSA and SGSA-Na) did not. However, cholesterol (Chol) could assist SGSA to form rigid monolayers through inserting into the alkyl chains of SGSA to mimic the second alkyl chain. SGSA self-aggregates in water were prepared by the injection method with tetrahydrofuran as solvent. Cuboid-like shape and nanoscale size demonstrated that SGSA self-aggregates were self-assembled nanoparticles. Shape, particle size, zeta potential and phase transition of the nanoparticles were characterized. And they showed an average size of 83.2 nm, a negative surface charge of -31.3-mV zeta potential and a gel-liquid crystalline phase transition of 50.38 degrees C. The formation mechanism of self-assembled nanoparticles was analyzed. Hydrophobic interaction of alkyl chains improves SGSA molecules to form bilayers, and then cuboid-like nanoparticles were obtained by layer-by-layer aggregation based on inter-bilayers hydrogen bonding. However, the charged guanine moieties make SGSA-Na lose the function of hydrogen bonding so that SGSA-Na only forms vesicles in water based on hydrophobic interaction. Strong hydrophobicity and wide-open rigid double alkyl chains of DASA and DASA-Na restrict self-assembly in water media, and no homogeneous suspensions were obtained. Therefore, the molecular self-assembly behavior of the long-chain alkyl derivatives of nucleoside analogues on water surface or in water media is determined by the number of alkyl chains and the charged state.

Microfabrication of Three-Dimensional Bioelectronic Architectures

The functionality and structural diversity of biological macromolecules has motivated efforts to exploit proteins and DNA as templates for synthesis of electronic architectures. Although such materials offer promise for numerous applications in the fabrication of cellular interfaces, biosensors, and nanoelectronics, identification of techniques for positioning and ordering bioelectronic components into useful patterns capable of sophisticated function has presented a major challenge. Here, we describe the fabrication of electronic materials using biomolecular scaffolds that can be constructed with precisely defined topographies. In this approach, a tightly focused pulsed laser beam capable of promoting protein photo-cross-linking in specified femtoliter volume elements is scanned within a protein solution, creating biomolecular matrices that either remain in integral contact with a support surface or extend as free-standing structures through solution, tethered at their ends. Once fabricated, specific protein scaffolds can be selectively metallized via targeted deposition and growth of metal nanoparticles, yielding high-conductivity bioelectronic materials. This aqueous fabrication strategy opens new opportunities for creating electronic materials in chemically sensitive environments and may offer a general approach for creating microscopically defined inorganic landscapes.

Protein fibers as performance proteins: new technologies and applications

Protein fibers are fundamental building blocks of life playing an essential role in motility, elasticity, scaffolding, stabilization and the protection of cells, tissues and organisms. Despite nearly a century of research into the assembly mechanisms and structures of fibrous proteins, only limited information is still available. Within the past decade, however, insights have been provided into how some fibrous proteins assemble and how they function in biology. In addition, efforts are increasingly being made to employ protein fibers as performance molecules in man-made medical and technical applications.

Programmable assembly of nanoarchitectures using genetically engineered viruses

Biological systems possess inherent molecular recognition and self-assembly capabilities and are attractive templates for constructing complex material structures with molecular precision. Here we report the assembly of various nanoachitectures including nanoparticle arrays, hetero-nanoparticle architectures, and nanowires utilizing highly engineered M13 bacteriophage as templates. The genome of M13 phage can be rationally engineered to produce viral particles with distinct substrate-specific peptides expressed on the filamentous capsid and the ends, providing a generic template for programmable assembly of complex nanostructures. Phage clones with gold-binding motifs on the capsid and streptavidin-binding motifs at one end are created and used to assemble Au and CdSe nanocrytals into ordered one-dimensional arrays and more complex geometries. Initial studies show such nanoparticle arrays can further function as templates to nucleate highly conductive nanowires that are important for addressing/interconnecting individual nanostructures.

Self-assembled peptide nanotubes are uniquely rigid bioinspired supramolecular structures

We recently presented a novel class of self-assembled diphenylalanine-based peptide nanotubes. Here, for the first time, we present their mechanical properties, which we directly measured through indentation type experiments using atomic force microscopy. We find that the averaged point stiffness of the nanotubes is 160 N/m, and that they have a correspondingly high Young's modulus of approximately 19 GPa, as calculated by finite element analysis. This high value places these peptide nanotubes among the stiffest biological materials presently known, making them attractive building blocks for the design and assembly of biocompatible nanodevices.

Hierarchical self-assembly of a coiled-coil peptide into fractal structure

Here we report the hierarchical self-assembly of a cross-linkable coiled-coil peptide containing an internal cysteine. Atomic force microscopy (AFM) experiments revealed the fractal structure of the assemblies, and molecular simulations showed that the peptides cross-linked to form clusters of coiled-coils, which further assembled to form globules of tens of nanometers in diameter. Such hierarchical organization was modulated by pH or thiol-reducing agent. Exploitation of the fractal structures through chemical methods may be valuable for the fabrication of materials spanning multiple length scales.

Dynamic reassembly of peptide RADA16 nanofiber scaffold

Nanofiber structures of some peptides and proteins as biological materials have been studied extensively, but their molecular mechanism of self-assembly and reassembly still remains unclear. We report here the reassembly of an ionic self-complementary peptide RADARADARADARADA (RADA16-I) that forms a well defined nanofiber scaffold. The 16-residue peptide forms stable beta-sheet structure and undergoes molecular self-assembly into nanofibers and eventually a scaffold hydrogel consisting of >99.5% water. In this study, the nanofiber scaffold was sonicated into smaller fragments. Circular dichroism, atomic force microscopy, and rheology were used to follow the kinetics of the reassembly. These sonicated fragments not only quickly reassemble into nanofibers that were indistinguishable from the original material, but their reassembly also correlated with the rheological analyses showing an increase of scaffold rigidity as a function of nanofiber length. The disassembly and reassembly processes were repeated four times and, each time, the reassembly reached the original length. We proposed a plausible sliding diffusion model to interpret the reassembly involving complementary nanofiber cohesive ends. This reassembly process is important for fabrication of new scaffolds for 3D cell culture, tissue repair, and regenerative medicine.

Redox-Induced Synthesis and Encapsulation of Metal Nanoparticles in Shell-Cross-Linked Organometallic Nanotubes

A new approach to encapsulate silver nanoparticles inside block copolymer nanotubes is reported and involves an in situ redox reaction between a polyferrocenylsilane (PFS) inner wall and silver ions. Partial preoxidation of the PFS domains was found to be a key step for the efficient formation of one-dimensional arrays of silver nanoparticles confined within the nanotubes.

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder

Recent evidence suggests that amyloidogenic oligomers may be the toxic species in cell cultures. Thus, it is crucial to understand their structure and oligomerization mechanism in atomistic detail. By employing tens of fast central processing units and an advanced phase-space sampling algorithm, parallel-tempering molecular dynamics, we have explored the energy landscape of amyloidogenic peptide oligomerization in explicit water. A pentapeptide, DFNKF, derived from human calcitonin and its mutant, DFAKF, was simulated with a total simulation time of approximately 500 ns. The detailed oligomerization process of a DFNKF parallel beta-sheet formation at 300 K has been characterized. The assembly of a parallel beta-sheet from the amorphous state mainly occurs via a "bottleneck" channel where the interstrand Asn-Asn stacking is the major interaction. The interactions of Asn-Asn stacking include both backbone and side-chain hydrogen bonds. The Asn-Asn interactions work like "glue" by sticking the DFNKF strands together and assist the "on-pathway" oligomerization. The Asn-Asn stacking observed here is similar to the Asn ladder commonly found in globular beta-helix proteins. A control run shows that when Asn is mutated to Ala, the stability and population of the DFAKF parallel beta-sheet is decreased. Furthermore, our in vitro mutagenesis experiments show that the ability of DFAKF peptides to form amyloid fibrils is significantly reduced, in agreement with the simulations. Knowledge of the energy landscape of oligomerization may provide hints for rational drug design, preventing amyloid-associated diseases.