Protein fibers as performance proteins: new technologies and applications

Proteins and peptides as biological nanowires: towards biosensing devices

The current landscape of nanotechnology is such that attention is being given to those materials that self-assemble, as a mode of "bottom-up" fabrication of nanomaterials. The field of nanotubes and nanowires has long been dominated by carbon nanotubes and inorganic materials. However in more recent years, the search for materials with desirable properties, such as self-assembly, has unsurprisingly led to the biological world, where functional nanoscale biomolecular assemblies are in abundance.Potential has been seen for a number of these assemblies to be translated into functional nanomaterials. The early days of bionanotechnology saw a lot of attention given to DNA molecules as nanowires, and proteins and peptides have now also been seen to have promise in this area. With most of the biological structures investigated having low conductivity in the native state, the use of biomolecules as templates for the formation of metallic and semiconductor nanowires has been the direction taken.This chapter will discuss the use of various biomolecules and biomolecular assemblies as nanowires, with a particular emphasis on proteins, beginning with an introduction into the field of nanotubes and nanowires. Many applications are now recognized for nanowires, but for brevity, this chapter will focus solely on their use as biosensors, using glucose sensors as a case study.

Formation of α-helical nanofibers by mixing β-structured and α-helical coiled coil peptides

The helical coiled coil is a well-studied folding motif that can be used for the design of nanometer-sized bioinspired fibrous structures with potential applications as functional materials. A two-component system of coiled coil based model peptides is investigated, which forms, under acidic conditions, uniform, hundreds of nanometers long, and ~2.6 nm thick trimeric α-helical fibers. In the absence of the other component and under the same solvent conditions, one model peptide forms β-sheet-rich amyloid fibrils and the other forms stable trimeric α-helical coiled coils, respectively. These observations reveal that the complementary interactions driving helical folding are much stronger here than those promoting the intermolecular β-sheet formation. The results of this study are important in the context of amyloid inhibition but also open up new avenues for the design of novel fibrous peptidic materials.

Silk materials--a road to sustainable high technology

This review addresses the use of silk protein as a sustainable material in optics and photonics, electronics and optoelectronic applications. These options represent additional developments for this technology platform that compound the broad utility and impact of this material for medical needs that have been recently described in the literature. The favorable properties of the material certainly make a favorable case for the use of silk, yet serve as a broad inspiration to further develop biological foundries for both the synthesis and processing of Nature's materials for technological applications.

AMYLOID: A NATURAL NANOMATERIAL

Amyloids are stable, β-sheet-rich protein/peptides aggregates with 2–15 nm diameter and few micrometers long. It is originally associated with many human diseases such as Alzheimer's, Parkinson's and prion diseases. Amyloids are resistant to enzyme degradation, temperature changes and wide ranges of pH. Although, amyloids are hard and their stiffness is comparable to steel, a constant recycling of monomer occur inside the amyloid fibrils. It grows in a nucleation dependent polymerization manner by recruiting native soluble protein and by converting them to amyloid. These extraordinary physical properties make amyloids attractive for nanotechnological applications. Some amyloid fibrils have also evolved to perform native biological functions (functional amyloid) of the host organism. Functional amyloids are present in mammals such as amyloids of pMel17 and pituitary hormones, where they help in skin pigmentation and hormone storage, respectively. Here, the progress of utilizing amyloid fibrils for nanobiotechnological applications with particular emphasis on the recent studies that amyloid could be utilized for the formulation of peptide/protein drugs depot and how secretory cells uses amyloid for hormone storage will be reviewed.

The Josephin domain determines the morphological and mechanical properties of ataxin-3 fibrils

Fibrillar aggregation of the protein ataxin-3 is linked to the inherited neurodegenerative disorder Spinocerebellar ataxia type 3, a member of the polyQ expansion disease family. We previously reported that aggregation and stability of the nonpathological form of ataxin-3, carrying an unexpanded polyQ tract, are modulated by its N-terminal Josephin domain. It was also shown that expanded ataxin-3 aggregates via a two-stage mechanism initially involving Josephin self-association, followed by a polyQ-dependent step. Despite this recent progress, however, the exact mechanism of ataxin-3 fibrilization remains elusive. Here, we have used electron microscopy, atomic force microscopy, and other biophysical techniques to characterize the morphological and mechanical properties of nonexpanded ataxin-3 fibrils. By comparing aggregates of ataxin-3 and of the isolated Josephin domain, we show that the two proteins self-assemble into fibrils with markedly similar features over the temperature range 37-50°C. Estimates of persistence length and Young's modulus of the fibrils reveal a great flexibility. Our data indicate that, under physiological conditions, during early aggregation Josephin retains a nativelike secondary structure but loses its enzymatic activity. The results suggest a key role of Josephin in ataxin-3 fibrillar aggregation.

Structural and mechanical properties of TTR105-115 amyloid fibrils from compression experiments

Amyloid fibrils, originally associated with neurodegenerative diseases, are now recognized to have interesting mechanical properties. By using synchrotron x-ray diffraction at high pressure in a diamond anvil cell we determined the bulk modulus of TTR105-115 amyloid fibrils in water and in silicone oil to be 2.6 and 8.1 GPa, respectively. The compression characteristics of the fibrils are quite different in the two media, revealing the presence of cavities along the axis of the fibrils, but not between the β-sheets, which are separated by a dry interface as in a steric zipper motif. Our results emphasize the importance of peptide packing in determining the structural and mechanical properties of amyloid fibrils.

Metal-driven viscoelastic wormlike micelle in anionic/zwitterionic surfactant systems and template-directed synthesis of dendritic silver nanostructures

In this work, metal ion-induced viscoelastic wormlike micelles in anionic/zwitterionic surfactant solutions (sodium dodecylsulfate/tetradecyldimethylammoniumpropanesulfonate, SDS/TPS) are reported. Steady and dynamic rheology and cryogenic transmission electron microscopy (cryo-TEM) are employed to characterize wormlike micelles in the SDS/TPS/Ca(NO(3))(2) system. Moreover, the surfactant mixing ratio and surfactant tail length are varied to reveal the factors that influence wormlike micelle growth and solution viscoelasticity. A series of metal ions such as Na(+), Mg(2+), Zn(2+), and Al(3+) are proven to promote viscoelastic wormlike micelle formation in the SDS/TPS system. The metal-containing wormlike micelles are expected to be good candidates for directing the synthesis of inorganic nanomaterials. In this article, dendritic silver nanostructures have been prepared in the surfactant wormlike micelle by in situ UV irradiation for the first time.

Bioinspired peptide nanotubes: deposition technology, basic physics and nanotechnology applications

Synthetic peptide monomers can self-assemble into PNM such as nanotubes, nanospheres, hydrogels, etc. which represent a novel class of nanomaterials. Molecular recognition processes lead to the formation of supramolecular PNM ensembles containing crystalline building blocks. Such low-dimensional highly ordered regions create a new physical situation and provide unique physical properties based on electron-hole QC phenomena. In the case of asymmetrical crystalline structure, basic physical phenomena such as linear electro-optic, piezoelectric, and nonlinear optical effects, described by tensors of the odd rank, should be explored. Some of the PNM crystalline structures permit the existence of spontaneous electrical polarization and observation of ferroelectricity. The PNM crystalline arrangement creates highly porous nanotubes when various residues are packed into structural network with specific wettability and electrochemical properties. We report in this review on a wide research of PNM intrinsic physical properties, their electronic and optical properties related to QC effect, unique SHG, piezoelectricity and ferroelectric spontaneous polarization observed in PNT due to their asymmetric structure. We also describe PNM wettability phenomenon based on their nanoporous structure and its influence on electrochemical properties in PNM. The new bottom-up large scale technology of PNT physical vapor deposition and patterning combined with found physical effects at nanoscale, developed by us, opens the avenue for emerging nanotechnology applications of PNM in novel fields of nanophotonics, nanopiezotronics and energy storage devices.

Assembly pathway of a designed alpha-helical protein fiber

Interest in the design of peptide-based fibrous materials is growing because it opens possibilities to explore fundamental aspects of peptide self-assembly and to exploit the resulting structures--for example, as scaffolds for tissue engineering. Here we investigate the assembly pathway of self-assembling fibers, a rationally designed alpha-helical coiled-coil system comprising two peptides that assemble on mixing. The dimensions spanned by the peptides and final structures (nanometers to micrometers), and the timescale over which folding and assembly occur (seconds to hours), necessitate a multi-technique approach employing spectroscopy, analytical ultracentrifugation, electron and light microscopy, and protein design to produce a physical model. We show that fibers form via a nucleation and growth mechanism. The two peptides combine rapidly (in less than seconds) to form sticky ended, partly helical heterodimers. A lag phase follows, on the order of tens of minutes, and is concentration-dependent. The critical nucleus comprises six to eight partially folded dimers. Growth is then linear in dimers, and subsequent fiber growth occurs in hours through both elongation and thickening. At later times (several hours), fibers grow predominantly through elongation. This kinetic, biomolecular description of the folding-and-assembly process allows the self-assembling fiber system to be manipulated and controlled, which we demonstrate through seeding experiments to obtain different distributions of fiber lengths. This study and the resulting mechanism we propose provide a potential route to achieving temporal control of functional fibers with future applications in biotechnology and nanoscale science and technology.

About the albumin structure in solution and related electro-spinnability issues

In this work, we study the relationship between the shape and form of bovine serum albumin (BSA) protein in different solutions and their ability to form electrospun nanofibers. Small-angle X-ray scattering (SAXS) of the BSA in a water environment, in a 2,2,2-trifluoroethanol (TFE) environment, and in a TFE/beta-mercaptoethanol (beta-ME) environment demonstrated an unfolding pathway; folded, partially unfolded and unfolded states of the protein, respectively. The scattering plot of BSA in water is characterized by a strong peak, thereby describing a solution of densely packaged globules. The scattering of BSA in TFE is attributed to a chain with compact folded-domains along its length, where the scattering of BSA in a mixture of TFE and beta-ME suggests that the protein molecule adopts a freely coiled conformation in this solution. The zeta potential for both solutions of BSA in TFE was found to have an almost zero net charge, while the BSA solution in the water was highly negatively charged. This unfolding between three conformational states was correlated with the changes in electro-spinnability. Results show that the unfolded BSA is the only spinnable solution, producing long and continuous fibers with good mechanical stability.

Building fibrous biomaterials from alpha-helical and collagen-like coiled-coil peptides

Over the decade and a half, interest has soared in the development of peptide-based biomaterials and their potential applications in biotechnology. This review outlines the advances during this time in the construction of biomaterials based on the alpha-helical coiled-coil and collagen-like peptides. These structures and the resulting designs are distinct from the more commonly used beta-structured peptides, which often lead to hydrogels comprising amyloid-like fibrils. The review covers basic design rules for these helical assemblies, and the various fibrous biomaterials that can be accomplished with them, which include rigid structures with straight, branched, or networked structures, decorated and functionalized systems, and most recently flexible fibers and entangled hydrogel networks. This plethora of alpha-helix-based biomaterials, together with more recent collagen-like assemblies, that are emerging from various laboratories complement those developed using beta-structured peptides, and open exciting new avenues for biomaterials research and potential new application areas.

Role of polyalanine domains in beta-sheet formation in spider silk block copolymers

Genetically engineered spider silk-like block copolymers were studied to determine the influence of polyalanine domain size on secondary structure. The role of polyalanine block distribution on beta-sheet formation was explored using FT-IR and WAXS. The number of polyalanine blocks had a direct effect on the formation of crystalline beta-sheets, reflected in the change in crystallinity index as the blocks of polyalanines increased. WAXS analysis confirmed the crystalline nature of the sample with the largest number of polyalanine blocks. This approach provides a platform for further exploration of the role of specific amino acid chemistries in regulating the assembly of beta-sheet secondary structures, leading to options to regulate material properties through manipulation of this key component in spider silks.

Nanomechanical properties of supramolecular self-assembled whiskers determined by AFM force mapping

In this Letter, we investigate the nanomechanical properties of self-assembled 1,3,5-benzenetrisamide whiskers with atomic force microscopy (AFM) bending experiments. We use force mapping to acquire spatially resolved force measurements over the full length of a whisker segment spanning a channel of a structured glass substrate. This allows validation of the experimental boundary conditions directly from the AFM data and a reliable determination of Young's modulus. The presented technique can be generalized for the mechanical characterization of other one-dimensional materials.

Silk-inspired polymers and proteins

The biocompatibility and biodegradability of natural silk fibres and the benign conditions under which they (with impressive mechanical properties) are produced represent a biomimetic ideal. This ideal has inspired people in both academia and industry to prepare silk-mimetic polymers and proteins by chemical and/or biotechnological means. In the present paper, we aim to give an overview of the design principles of such silk-inspired polymers/proteins, their processing into various materials morphologies, their mechanical and biological properties, and, finally, their technical and biomedical applications.

An evolutionarily conserved family of virion tail needles related to bacteriophage P22 gp26: correlation between structural stability and length of the alpha-helical trimeric coiled coil

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution. All gp26-like factors contain an elongated alpha-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 A. gp26 tail needles display a high level of structural stability in solution, with T(m) (temperature of melting) between 85 and 95 degrees C. To determine how the structural stability of these phage fibers correlates with the length of the alpha-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the alpha-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the alpha-helical core.

Mimicking biopolymers on a molecular scale: nano(bio)technology based on engineered proteins

Proteins are ubiquitous biopolymers that adopt distinct three-dimensional structures and fulfil a multitude of elementary functions in organisms. Recent systematic studies in molecular biology and biotechnology have improved the understanding of basic functional and architectural principles of proteins, making them attractive candidates as concept generators for technological development in material science, particularly in biomedicine and nano(bio)technology. This paper highlights the potential of molecular biomimetics in mimicking high-performance proteins and provides concepts for applications in four case studies, i.e. spider silk, antifreeze proteins, blue mussel adhesive proteins and viral ion channels.

Molecular design of performance proteins with repetitive sequences: recombinant flagelliform spider silk as basis for biomaterials

Most performance proteins responsible for the mechanical stability of cells and organisms reveal highly repetitive sequences. Mimicking such performance proteins is of high interest for the design of nanostructured biomaterials. In this article, flagelliform silk is exemplary introduced to describe a general principle for designing genes of repetitive performance proteins for recombinant expression in Escherichia coli . In the first step, repeating amino acid sequence motifs are reversely transcripted into DNA cassettes, which can in a second step be seamlessly ligated, yielding a designed gene. Recombinant expression thereof leads to proteins mimicking the natural ones. The recombinant proteins can be assembled into nanostructured materials in a controlled manner, allowing their use in several applications.

The elaborate structure of spider silk: structure and function of a natural high performance fiber

Biomaterials, having evolved over millions of years, often exceed man-made materials in their properties. Spider silk is one outstanding fibrous biomaterial which consists almost entirely of large proteins. Silk fibers have tensile strengths comparable to steel and some silks are nearly as elastic as rubber on a weight to weight basis. In combining these two properties, silks reveal a toughness that is two to three times that of synthetic fibers like Nylon or Kevlar. Spider silk is also antimicrobial, hypoallergenic and completely biodegradable. This article focuses on the structure-function relationship of the characterized highly repetitive spider silk spidroins and their conformational conversion from solution into fibers. Such knowedge is of crucial importance to understanding the intrinsic properties of spider silk and to get insight into the sophisticated assembly processes of silk proteins. This review further outlines recent progress in recombinant production of spider silk proteins and their assembly into distinct polymer materials as a basis for novel products.

Amyloid as a depot for the formulation of long-acting drugs

Amyloids are highly organized protein aggregates that are associated with both neurodegenerative diseases such as Alzheimer disease and benign functions like skin pigmentation. Amyloids self-polymerize in a nucleation-dependent manner by recruiting their soluble protein/peptide counterpart and are stable against harsh physical, chemical, and biochemical conditions. These extraordinary properties make amyloids attractive for applications in nanotechnology. Here, we suggest the use of amyloids in the formulation of long-acting drugs. It is our rationale that amyloids have the properties required of a long-acting drug because they are stable depots that guarantee a controlled release of the active peptide drug from the amyloid termini. This concept is tested with a family of short- and long-acting analogs of gonadotropin-releasing hormone (GnRH), and it is shown that amyloids thereof can act as a source for the sustained release of biologically active peptides.

Amyloids are highly organized protein aggregates that are associated with both neurodegenerative diseases such as Alzheimer disease and benign functions such as skin pigmentation. Amyloids self-polymerize by recruiting their soluble protein counterpart and remain stable against harsh physical, chemical, and biochemical conditions. These extraordinary properties make amyloids attractive for applications in nanotechnology. Here, we suggest the use of amyloids in the formulation of long-acting drugs, which are active over extended periods of days and weeks. Long-acting drugs have been designed to increase patient comfort, convenience, dosage accuracy, and assurance of patient compliance for drugs that have a low oral bioavailability. It is our rationale that amyloids have the properties required of a long-acting drug because they are stable depots that guarantee a controlled release of the active peptide drug from the amyloid termini. This concept is tested with a family of short- and long-acting analogs of gonadotropin-releasing hormone, and it is shown that amyloids thereof can act as a source for the sustained release of biologically active peptides.

Amyloids have the properties required of a long-acting drug because they are stable depots that guarantee a controlled release of the active peptide drug from the amyloid termini.

Assembly mechanism of recombinant spider silk proteins

Spider silk threads are formed by the irreversible aggregation of silk proteins in a spinning duct with dimensions of only a few micrometers. Here, we present a microfluidic device in which engineered and recombinantly produced spider dragline silk proteins eADF3 (engineered Araneus diadematus fibroin) and eADF4 are assembled into fibers. Our approach allows the direct observation and identification of the essential parameters of dragline silk assembly. Changes in ionic conditions and pH result in aggregation of the two proteins. Assembly of eADF3 fibers was induced only in the presence of an elongational flow component. Strikingly, eADF4 formed fibers only in combination with eADF3. On the basis of these results, we propose a model for dragline silk aggregation and early steps of fiber assembly in the microscopic regime.

Production of renewable polymers from crop plants

Plants produce a range of biopolymers for purposes such as maintenance of structural integrity, carbon storage, and defense against pathogens and desiccation. Several of these natural polymers are used by humans as food and materials, and increasingly as an energy carrier. In this review, we focus on plant biopolymers that are used as materials in bulk applications, such as plastics and elastomers, in the context of depleting resources and climate change, and consider technical and scientific bottlenecks in the production of novel or improved materials in transgenic or alternative crop plants. The biopolymers discussed are natural rubber and several polymers that are not naturally produced in plants, such as polyhydroxyalkanoates, fibrous proteins and poly-amino acids. In addition, monomers or precursors for the chemical synthesis of biopolymers, such as 4-hydroxybenzoate, itaconic acid, fructose and sorbitol, are discussed briefly.

The kinetics of aggregation of poly-glutamic acid based polypeptides

The aggregation of two negatively-charged polypeptides, poly-L-glutamic acid (PE) and a copolymer of poly-glutamic acid and poly-alanine (PEA), has been studied at different peptide and salt concentrations and solution pH conditions. The kinetics of aggregation were based on Thioflavin T (ThT) fluorescence measurements. The observed lag phase shortened and the aggregation was faster as the pH approached the polypeptides' isoelectric points. While the initial polypeptide structures of PE and PEA appeared identical as determined from circular dichroism spectroscopy, the final aggregate morphology differed; PE assumed large twisted lamellar structures and the PEA formed typical amyloid-like fibrils, although both contained extensive beta-sheet structure. Differences in aggregation behavior were observed for the two polypeptides as a function of salt concentration; aggregation progressed more slowly for PE and more quickly for PEA with increasing salt concentration. Several models of aggregation kinetics were fit to the data. No model yielded consistent rate constants or a critical nucleus size. A modified nucleated polymerization model was developed based on that of Powers and Powers [E.T. Powers, D.L. Powers, The kinetics of nucleated polymerizations at high concentrations: Amyloid fibril formation near and above the "supercritical concentration", Biophys. J. 91 (2006) 122-132], which incorporated the ability of oligomeric species to interact. This provided a best fit to the experimental data.

Synthesis, nano-scale assembly, and in vivo anti-thrombotic activity of novel short peptides containing L-Arg and L-Asp or L-Glu

Two tripeptides H-Asp(Arg)-Arg (3a) and H-Glu(Arg)-Arg (3b), four pentapeptides H-Asp(Arg-Asp)-Arg-Asp (6a), H-Glu(Arg-Asp)-Arg-Asp (6b), H-Asp(Asp- Arg)-Asp-Arg (10a), and H-Glu(Asp-Arg)-Asp-Arg (10b), and their Cu(II)-peptide complexes Cu(II)-Asp(Arg)-Arg [3a-Cu(II)], Cu(II)-Glu(Arg)-Arg [3b-Cu(II)], Cu(II)-Asp(Arg-Asp)-Arg-Asp [6a-Cu(II)], Cu(II)-Glu(Arg-Asp)-Arg-Asp [6b-Cu(II)], Cu(II)-Asp(Asp-Arg)-Asp-Arg [10a-Cu(II)], and Cu(II)-Glu(Asp-Arg)-Asp-Arg [10b-Cu(II)] were designed and synthesized. Their self-assembling properties and in vivo anti-thrombotic activities were investigated. In normal saline (NS), the Cu(II)-peptide complexes assembled into stable nano-particles surrounded by negative charges (-4.102 to -9.825mV), with diameters ranging from 212.1+/-4.0 to 632.4+/-36.7nm. TEM analysis exhibited that the compounds remained as nano-globes in the solid state, with diameters ranging from 15 to 20nm. In an in vivo anti-thrombotic assay, peptides (3,6,10)a,b at 5micromol/kg reduced the thrombus weights of a rat model by 15-40%. Aspirin, a widely used anti-thrombotic drug, achieved comparable activity in this model system at a dosage of ca. 110micromol/kg. The required dosage of Cu(II)-peptide complexes [(3,6,10)a,b]-Cu(II), which assemble into stable nano-particles, was significantly reduced to 0.05micromol/kg. Therefore, the anti-thrombotic activity of the nano-particles [(3,6,10)a,b]-Cu(II) increased dramatically by 100-fold over that of the corresponding peptides.

Peptide and protein building blocks for synthetic biology: from programming biomolecules to self-organized biomolecular systems

There are several approaches to creating synthetic-biological systems. Here, we describe a molecular-design approach. First, we lay out a possible synthetic-biology space, which we define with a plot of complexity of components versus divergence from nature. In this scheme, there are basic units, which range from natural amino acids to totally synthetic small molecules. These are linked together to form programmable tectons, for example, amphipathic alpha-helices. In turn, tectons can interact to give self-assembled units, which can combine and organize further to produce functional assemblies and systems. To illustrate one path through this vast landscape, we focus on protein engineering and design. We describe how, for certain protein-folding motifs, polypeptide chains can be instructed to fold. These folds can be combined to give structured complexes, and function can be incorporated through computational design. Finally, we describe how protein-based systems may be encapsulated to control and investigate their functions.