Surface-assisted assembly of an ionic-complementary peptide: controllable growth of nanofibers

Living Growth Kinetics of Polymeric Micelles on a Substrate

Living growth of micelles on the substrate is an intriguing phenomenon; however, little is known about its growth kinetics, especially from a theoretical viewpoint. Here, we examine the living growth kinetics of polymeric micelles on a hydrophobic substrate immersed in an aqueous solution. The block copolymers first assemble into short cylinder seeds anchored on the substrate. Then, the small aggregates of block copolymers in the solutions fuse onto the active ends of the anchored seeds, leading to micelle growth on the substrate. A theoretical model is proposed to interpret such living growth kinetics. It is revealed that the growth rate coefficient on the substrate is independent of the copolymer concentration and the multistep feedings; however, it is significantly affected by the surface hydrophobicity. Brownian dynamics simulations further support the proposed growth mechanism and the kinetic model. This work enriches living assembly systems and provides guidance for fabricating bioinspired surface nanostructures.

Protein and Peptide-Based Nanotechnology for Enhancing Stability, Bioactivity, and Delivery of Anthocyanins

Anthocyanin, a unique natural polyphenol, is abundant in plants and widely utilized in biomedicine, cosmetics, and the food industry due to its excellent antioxidant, anticancer, antiaging, antimicrobial, and anti-inflammatory properties. However, the degradation of anthocyanin in an extreme environment, such as alkali pH, high temperatures, and metal ions, limits its physiochemical stabilities and bioavailabilities. Encapsulation and combining anthocyanin with biomaterials could efficiently stabilize anthocyanin for protection. Promisingly, natural or artificially designed proteins and peptides with favorable stabilities, excellent biocapacity, and wide sources are potential candidates to stabilize anthocyanin. This review focuses on recent progress, strategies, and perspectives on protein and peptide for anthocyanin functionalization and delivery, i.e., formulation technologies, physicochemical stability enhancement, cellular uptake, bioavailabilities, and biological activities development. Interestingly, due to the simplicity and diversity of peptide structure, the interaction mechanisms between peptide and anthocyanin could be illustrated. This work sheds light on the mechanism of protein/peptide-anthocyanin nanoparticle construction and expands on potential applications of anthocyanin in nutrition and biomedicine.

Tailoring Peptide Self-Assembly and Formation of 2D Nanoribbons on Mica and HOPG Surface

Studying the interactions between biomolecules and material interfaces play a crucial role in the designing and synthesizing of functional bionanomaterials with tailored structure and function. Previously, a lot of studies were performed on the self-assembly of peptides in solution through internal and external stimulations, which mediated the creation of peptide nanostructures from zero-dimension to three-dimension. In this study, we demonstrate the self-assembly behavior of the GNNQQNY peptide on the surface of mica and highly oriented pyrolytic graphite through tailoring the self-assembly conditions. Various factors, such as the type of dissolvent, peptide concentration, pH value, and evaporation period on the formation of peptide nanofibers and nanoribbons with single- and bi-directional arrays are investigated. It is found that the creation of peptide nanoribbons on both mica and HOPG can be achieved effectively through adjusting and optimizing the experimental parameters. Based on the obtained results, the self-assembly and formation mechanisms of peptide nanoribbons on both material interfaces are discussed. It is expected that the findings obtained in this study will inspire the design of motif-specific peptides with high binding affinity towards materials and mediate the green synthesis of peptide-based bionanomaterials with unique function and application potential.

The effects of nanobubbles on the assembly of glucagon amyloid fibrils

Some recent studies have shown that the surface and interface play an important role in the assembly and aggregation of amyloid proteins. However, it is unclear how the gas-liquid interface affects the protein assembly at the nanometer scale although the presence of gas-liquid interfaces is very common in in vitro experiments. Nanobubbles have a large specific surface area, which provides a stage for interactions with various proteins and peptides on the nanometer scale. In this work, nanobubbles produced in solution were employed for studying the effects of the gas-liquid interface on the assembly of glucagon proteins. Atomic force microscopy (AFM) studies showed that nanobubble-treated glucagon solution formed fibrils with an apparent height of 4.02 ± 0.71 nm, in contrast to the fibrils formed with a height of 2.14 ± 0.53 nm in the control. Transmission electron microscopy (TEM) results also showed that nanobubbles promoted the assembly of glucagon to form more fibrils. Thioflavin T (ThT) fluorescence and Fourier transform infrared (FTIR) analyses indicated that the nanobubbles induced the change of the glucagon conformation to a β-sheet structure. A mechanism that explains how nanobubbles affect the assembly of glucagon amyloid fibrils was proposed based on the above-mentioned experimental results. Given the fact that there are a considerable amount of nanobubbles existing in protein solutions, our results indicate that nanobubbles should be considered for fully understanding the protein aggregation events in vitro.

Effect of Terminal Modifications on the Adsorption and Assembly of hIAPP(20-29)

The assembly of peptides and proteins into nanoscale amyloid fibrils via formation of intermolecular β-sheets not only plays an important role in the development of degenerative diseases but also represents a promising approach for the synthesis of functional nanomaterials. In many biological and technological settings, peptide assembly occurs in the presence of organic and inorganic interfaces with different physicochemical properties. In an attempt to dissect the relative contributions of the different molecular interactions governing amyloid assembly at interfaces, we here present a systematic study of the effects of terminal modifications on the adsorption and assembly of the human islet amyloid polypeptide fragment hIAPP(20-29) at organic self-assembled monolayers (SAMs) presenting different functional groups (cationic, anionic, polar, or hydrophobic). Using a selection of complementary in situ and ex situ analytical techniques, we find that even this well-defined and comparatively simple model system is governed by a rather complex interplay of electrostatic interactions, hydrophobic interactions, and hydrogen bonding, resulting in a plethora of observations and dependencies, some of which are rather counterintuitive. In particular, our results demonstrate that terminal modifications can have tremendous effects on peptide adsorption and assembly dynamics, as well as aggregate morphology and molecular structure. The effects exerted by the terminal modifications can furthermore be modulated in nontrivial ways by the physicochemical properties of the SAM surface. Therefore, terminal modifications are an important factor to consider when conducting and comparing peptide adsorption and aggregation studies and may represent an additional parameter for guiding the assembly of peptide-based nanomaterials.

Surface-assisted assembly of a histidine-rich lipidated peptide for simultaneous exfoliation of graphite and functionalization of graphene nanosheets

Biological molecules have promising potential to exfoliate graphite and produce biocompatible graphene nano-materials for biomedical applications. Here, a systematic design of a histidine-rich lipidated peptide sequence is presented that simultaneously exfoliates graphite flakes and functionalizes the resulting graphene nanosheets (∼150 nm lateral size) with long-term dispersion stability in aqueous solution (>8 months). The details of peptide/peptide and peptide/graphite interactions are probed using various microscopy, spectroscopy and molecular dynamics simulation methods. The results show that histidine and stearic acid interact with the graphite surface through π-π stacking and hydrophobic forces, respectively. Surface-assisted assembly of peptide molecules is then initiated via hydrogen bonds between deprotonated histidine segments, and a textured peptide nano-structure is formed. The work of adhesion between the peptide and graphite is found to be high enough to promote exfoliation of graphite flakes through layer-by-layer peeling of graphene nanosheets. The positively charged arginine in the peptide is exposed outward, and is responsible for the stable dispersion. The peptide molecules are sufficiently small, presenting the possibility to insert into and increase the spacing between the graphitic layers for enhanced exfoliation. The peptide-functionalized graphene nanosheets not only show great biocompatibility with cells in vitro, but also enhance cancer drug uptake by the cells.

Surface-Mediated Supramolecular Self-Assembly of Protein, Peptide, and Nucleoside Derivatives: From Surface Design to the Underlying Mechanism and Tailored Functions

Among the many parameters that have been explored to exercise control over self-assembly processes, the influence of surface properties on self-assembly has been recognized as important but has received considerably less attention than other factors. This is particularly true for biomolecule-derived self-assembling molecules such as protein, peptide, and nucleobase derivatives. Because of their relevance to biomaterial and drug delivery applications, interest in these materials is increasing. As the formation of supramolecular structures from these biomolecule derivatives inevitably brings them into contact with the surfaces of surrounding materials, understanding and controlling the impact of the properties of these surfaces on the self-assembly process are important. In this feature article, we present an overview of the different surface parameters that have been used and studied for the direction of the self-assembly of protein, peptide, and nucleoside-based molecules. The current mechanistic understanding of these processes will be discussed, and potential applications of surface-mediated self-assembly will be outlined.

Effects of nanobubbles on peptide self-assembly

It is believed that the aggregation of amyloid proteins or peptides is promoted by the presence of an air-water interface, and substantial evidence suggests that the characteristics of the air-water interface play critical roles in foam-induced protein aggregation during foam fractionation. However, the effects of the air-water interface on the self-assembly of amyloid-like peptides have not yet been elucidated clearly at the nanometer scale. In this work, air nanobubbles produced in water solution were employed for studying interfacial effects on the self-assembly of a model amyloid peptide termed P11. An atomic force microscopy study showed that the air nanobubbles induced the formation of peptide fibrils with a 9-13 nm helix structure in the P11 solution. Thioflavin T fluorescence and circular dichroism spectroscopic analysis indicated that the nanobubbles induced the change of the peptide conformation to a β-sheet structure. Based on these observations, we have proposed a mechanism to explain how the nanobubbles affect the self-assembly of the P11 peptide at the nanometer scale. Since air nanobubbles are present in water solutions in addition to an air-water interface in normal experiments in vitro, our results indicate that nanobubbles must be taken into account to achieve a complete understanding of protein aggregation events.

Self-Assembly, Dynamics, and Polymorphism of hIAPP(20-29) Aggregates at Solid-Liquid Interfaces

The misfolding and subsequent assembly of proteins and peptides into insoluble amyloid structures play important roles in the development of numerous diseases. The dynamics of self-assembly and the morphology of the resulting aggregates critically depend on various environmental factors and especially on the presence of interfaces. Here, we show in detail how the presence of surfaces with different physicochemical properties influences the assembly dynamics and especially the aggregate morphology of hIAPP(20-29), an amyloidogenic fragment of the peptide hormone human islet amyloid polypeptide (hIAPP), which is involved in the development of type 2 diabetes. Time-lapse atomic force microscopy is employed to study the assembly dynamics of hIAPP(20-29) and the morphology of the resulting aggregates in bulk solution as well as at hydrophilic and hydrophobic model surfaces. We find that the presence of hydrophilic mica surfaces promotes fibrillation when compared with the assembly in bulk solution and results in a more pronounced polymorphism. Three fibrillar species are found to coexist on the mica surface, that is, straight, coiled, and ribbon-like fibrils, whereas only the straight and coiled fibrils are observed in bulk solution after comparable incubation times. In addition, the straight and coiled fibrils assembled at the mica surface have significantly different dimensions compared with those assembled in bulk solution. The three fibrillar species found on the mica surface most likely form independently by lateral association of arbitrary numbers of protofibrils with about 2 nm height. On hydrophobic hydrocarbon surfaces, fibrillation is retarded but not completely suppressed, in contrast to previous observations for full-length hIAPP(1-37). Our results show that peptide-surface interactions may induce diverse, peptide-specific alterations of amyloid assembly dynamics and fibrillar polymorphism. They may therefore contribute to a deeper understanding of the molecular processes that govern amyloid aggregation at different surfaces.

Peptides derived from α-lactalbumin membrane binding helices oligomerize in presence of lipids and disrupt bilayers

Helix A and -C of α-lactalbumin, a loosely folded amphitropic protein, perturb lipid monolayers by the formation of amyloid pore-like structures. To investigate whether these helices are able to disrupt fully formed bilayers, we designed peptides comprised of Helix A and -C, and investigated their membrane-perturbing properties. The peptides, designated A-Cage-C and A-Lnk-C, were prepared with tryptophan sites in the helical and the spacer segments in order to monitor which part were involved in membrane association under given conditions. The peptides associate with and disrupt negatively charged bilayers in a pH-dependent manner and α-helical tendencies increased upon membrane association. Both helices and the spacer segment were involved in membrane binding in the case of A-Lnk-C, and there are indications that the two helixes act in synergy to affect the membrane. However, the helices and the spacer segment could not intercalate when present as A-Cage-C at neutral conditions. At acidic pH, both helices could intercalate, but not the central spacer segment. AFM performed on bilayers under aqueous conditions revealed oligomers formed by the peptides. The presence of bilayers and acidic pHs were both drivers for the formation of these, suggestive of models for peptide oligomerization where segments of the peptide are stacked in an electrostatically favorable manner by the surface. Of the two peptides, A-Lnk-C was the more prolific oligomerizer, and also formed amyloid-fibril like structures at acidic pH and elevated concentrations. Our results suggest the peptides perturb membranes not through pore-like structures, but possibly by a thinning mechanism.

Superhydrophobic Surfaces Boost Fibril Self-Assembly of Amyloid β Peptides

Amyloid β (Aβ) peptides are the main constituents of Alzheimer's amyloid plaques in the brain. Here we report how the unique microfluidic flows exerted by droplets sitting on superhydrophobic surfaces can influence the aggregation mechanisms of several Aβ fragments by boosting their fibril self-assembly. Aβ(25-35), Aβ(1-40), and Aβ(12-28) were dried both on flat hydrophilic surfaces (contact angle (CA) = 37.3°) and on nanostructured superhydrophobic ones (CA = 175.8°). By embedding nanoroughened surfaces on top of highly X-ray transparent Si3N4 membranes, it was possible to probe the solid residues by raster-scan synchrotron radiation X-ray microdiffraction (μXRD). As compared to residues obtained on flat Si3N4 membranes, a general enhancement of fibrillar material was detected for all Aβ fragments dried on superhydrophobic surfaces, with a particular emphasis on the shorter ones. Indeed, both Aβ(25-35) and Aβ(12-28) showed a marked crystalline cross-β phase with varying fiber textures. The homogeneous evaporation rate provided by these nanostructured supports, and the possibility to use transparent membranes, can open a wide range of in situ X-ray and spectroscopic characterizations of amyloidal peptides involved in neurodegenerative diseases and for the fabrication of amyloid-based nanodevices.

Surface Modification of Poly(dimethylsiloxane) Using Ionic Complementary Peptides to Minimize Nonspecific Protein Adsorption

Poly(dimethylsiloxane) (PDMS) has become a widely used material for microfluidic and biological applications. However, PDMS has unacceptably high levels of nonspecific protein adsorption, which significantly lowers the performance of PDMS-based microfluidic chips. Most existing methods to reduce protein fouling of PDMS are to make the surface more hydrophilic by surface oxidization, polymer grafting, and physisorbed coatings. These methods suffer from the relatively short-term stability, the multistep complex treatment procedure, or the insufficient adsorption reduction. Herein, we developed a novel and facile modification method based on self-assembled peptides with well-tailored amino acid composition and sequence, which can also interact strongly with the PDMS surface in the same way as proteins, for suppressing the nonspecific protein fouling and improving the biocompatibility of PDMS-based microfluidic chips. We first demonstrated that an ionic complementary peptide, EAR16-II with a sequence of [(Ala-Glu-Ala-Glu-Ala-Arg-Ala-Arg)2], can readily self-assemble into an amphipathic film predominantly composed of tightly packed β-sheets on the native hydrophobic and plasma-oxidized hydrophilic PDMS surfaces upon low concentrations of carbohydrates. The self-assembled EAR16-II amphipathic film exposed its hydrophobic side to the solution and thus rendered the PDMS surface hydrophobic with water contact angles (WCAs) of around 110.0°. However, the self-assembled EAR16-II amphipathic film exhibited excellent protein-repelling and blood compatibility properties comparable to or better than those obtained with previously reported methods. A schematic model has been proposed to explain the interactions of EAR16-II with the PDMS surface and the antifouling capability of EAR16-II coatings at a molecular level. The current work will pave the way to the development of novel coating materials to address the nonspecific protein adsorption on PDMS, thereby broadening the potential uses of PDMS-based microfluidic chips in complex biological analysis.

Competition between surface adsorption and folding of fibril-forming polypeptides

Self-assembly of polypeptides into fibrillar structures can be initiated by planar surfaces that interact favorably with certain residues. Using a coarse-grained model, we systematically studied the folding and adsorption behavior of a β-roll forming polypeptide. We find that there are two different folding pathways depending on the temperature: (i) at low temperature, the polypeptide folds in solution into a β-roll before adsorbing onto the attractive surface; (ii) at higher temperature, the polypeptide first adsorbs in a disordered state and folds while on the surface. The folding temperature increases with increasing attraction as the folded β-roll is stabilized by the surface. Surprisingly, further increasing the attraction lowers the folding temperature again, as strong attraction also stabilizes the adsorbed disordered state, which competes with folding of the polypeptide. Our results suggest that to enhance the folding, one should use a weakly attractive surface. They also explain the recent experimental observation of the nonmonotonic effect of charge on the fibril formation on an oppositely charged surface [C. Charbonneau et al., ACS Nano 8, 2328 (2014)].

Concentration-dependent and surface-assisted self-assembly properties of a bioactive estrogen receptor α-derived peptide

We have synthesized a 17-mer peptide (ERα17p) that is issued from the hinge region of the estrogen receptor α and which activates the proliferation of breast carcinoma cells in steroid-deprived conditions. In the present paper, we show that at a concentration of ~50 μM, it rapidly forms amyloid-like fibrils with the assistance of electrostatic interactions and that at higher concentrations, it spontaneously forms a hydrogel. By using biophysical, spectral and rheological techniques, we have explored the structural, biophysical and mechanical characteristics of ERα17p with respect to fibril formation and gelation.

Kinetic signature of fractal-like filament networks formed by orientational linear epitaxy

We study a broad class of epitaxial assembly of filament networks on lattice surfaces. Over time, a scale-free behavior emerges with a 2.5-3 power-law exponent in filament length distribution. Partitioning between the power-law and exponential behaviors in a network can be used to find the stage and kinetic parameters of the assembly process. To analyze real-world networks, we develop a computer program that measures the network architecture in experimental images. Application to triaxial networks of collagen fibrils shows quantitative agreement with our model. Our unifying approach can be used for characterizing and controlling the network formation that is observed across biological and nonbiological systems.

pH-dependent self-assembly of EAK16 peptides in the presence of a hydrophobic surface: coarse-grained molecular dynamics simulation

Self-assembly behavior of the three types of ionic peptide, EAK16, is studied in the presence of a hydrophobic surface using coarse-grained molecular dynamics simulations at three pH ranges of the solution. It is found that the peptide chains of all the three types assemble on the hydrophobic surface. EAK16-I and EAK16-II peptides assemble into ribbon-like structures, regardless of the value of pH. EAK16-IV peptide chains, however, assemble into ribbon-like structures at low and high pH ranges and form disc-shaped assemblies on the hydrophobic surface at the isoelectric point, pH = 7. Strong intra-chain electrostatic interactions in the case of EAK16-IV peptide play the main role in dependence of its self-assembly behavior on pH and the different morphology of its assembly relative to those of the two other types. Kinetics of growth of the assemblies on the hydrophobic surface is also studied.

Subtle charge balance controls surface-nucleated self-assembly of designed biopolymers

We report the surface-nucleated self-assembly into fibrils of a biosynthetic amino acid polymer synthesized by the yeast Pichia pastoris. This polymer has a block-like architecture, with a central silk-like block labeled SH, responsible for the self-assembly into fibrils, and two collagen-like random coil end blocks (C) that colloidally stabilize the fibers in aqueous solution. The silk-like block contains histidine residues (pKa≈6) that are positively charged in the low pH region, which hinders self-assembly. In aqueous solution, CSHC self-assembles into fibers above a pH-dependent critical nucleation concentration Ccb. Below Ccb, where no self-assembly occurs in solution, fibril formation can be induced by a negatively charged surface (silica) in the pH range of 3.5-7. The density of the fibers at the surface and their length are controlled by a subtle balance in charge between the protein polymer and the silica surface, which is evidenced from the dependence on pH. With increasing number density of the fibers at the surface, their average length decreases. The results can be explained on the basis of a nucleation-and-growth mechanism: the surface density of fibers depends on the rate of nucleation, while their growth rate is limited by transport of proteins from solution. Screening of the charges on the surface and histidine units by adding NaCl influences the nucleation-and-growth process in a complicated fashion: at low pH, the growth is improved, while at high pH, the nucleation is limited. Under conditions where nucleation in the bulk solution is not possible, growth of the surface-nucleated fibers into the solution--away from the surface--can still occur.

Direct observation of amyloid nucleation under nanomechanical stretching

Self-assembly of amyloid nanofiber is associated with both functional biological and pathological processes such as those in neurodegenerative diseases. Despite intensive studies, the stochastic nature of the process has made it difficult to elucidate a molecular mechanism for the key amyloid nucleation event. Here we investigated nucleation of the silk-elastin-like peptide (SELP) amyloid using time-lapse lateral force microscopy (LFM). By repeated scanning of a single line on a SELP-coated mica surface, we observed a sudden stepwise height increase. This corresponds to nucleation of an amyloid fiber, which subsequently grew perpendicular to the scanning direction. The lateral force profiles followed either a worm-like chain model or an exponential function, suggesting that the atomic force microscopy (AFM) tip stretches a single or multiple SELP molecules along the scanning direction. The probability of nucleation correlated with the maximum stretching force and extension, implying that stretching of SELP molecules is a key molecular event for amyloid nucleation. The mechanically induced nucleation allows for positional and directional control of amyloid assembly in vitro, which we demonstrate by generating single nanofibers at predetermined nucleation sites.

A radish seed antifungal peptide with a high amyloid fibril-forming propensity

The amyloid fibril-forming ability of two closely related antifungal and antimicrobial peptides derived from plant defensin proteins has been investigated. As assessed by sequence analysis, thioflavin T binding, transmission electron microscopy, atomic force microscopy and X-ray fiber diffraction, a 19 amino acid fragment from the C-terminal region of Raphanus sativus antifungal protein, known as RsAFP-19, is highly amyloidogenic. Further, its fibrillar morphology can be altered by externally controlled conditions. Freezing and thawing led to amyloid fibril formation which was accompanied by loss of RsAFP-19 antifungal activity. A second, closely related antifungal peptide displayed no fibril-forming capacity. It is concluded that while fibril formation is not associated with the antifungal properties of these peptides, the peptide RsAFP-19 is of potential use as a controllable, highly amyloidogenic small peptide for investigating the structure of amyloid fibrils and their mechanism of formation.

The amyloid-cell membrane system. The interplay between the biophysical features of oligomers/fibrils and cell membrane defines amyloid toxicity

Amyloid cytotoxicity, structure and polymorphisms are themes of increasing importance. Present knowledge considers any peptide/protein able to undergo misfolding and aggregation generating intrinsically cytotoxic amyloids. It also describes growth and structure of amyloid fibrils and their possible disassembly, whereas reduced information is available on oligomer structure. Recent research has highlighted the importance of the environmental conditions as determinants of the amyloid polymorphisms and cytotoxicity. Another body of evidence describes chemical or biological surfaces as key sites of protein misfolding and aggregation or of interaction with amyloids and the resulting biochemical modifications inducing cell functional/viability impairment. In particular, the membrane lipid composition appears to modulate cell response to toxic amyloids, thus contributing to explain the variable vulnerability to the same amyloids of different cell types. Finally, a recent view describes amyloid toxicity as an emerging property dependent on a complex interplay between the biophysical features of early aggregates and the interacting cell membranes taken as a whole system.

Hierarchical ordering of amyloid fibrils on the mica surface

The aggregation of amyloid peptides into ordered fibrils is closely associated with many neurodegenerative diseases. The surfaces of cell membranes and biomolecules are believed to play important roles in modulation of peptide aggregation under physiological conditions. Experimental studies of fibrillogenesis at the molecular level in vivo, however, are inherently challenging, and the molecular mechanisms of how surface affects the structure and ordering of amyloid fibrils still remain elusive. Herein we have investigated the aggregation behavior of insulin peptides within water films adsorbed on the mica surface. AFM measurements revealed that the structure and orientation of fibrils were significantly affected by the mica lattice and the peptide concentration. At low peptide concentration (~0.05 mg mL(-1)), there appeared a single layer of short and well oriented fibrils with a mean height of 1.6 nm. With an increase of concentration to a range of 0.2-2.0 mg mL(-1), a different type of fibrils with a mean height of 3.8 nm was present. Interestingly, when the concentration was above 2.0 mg mL(-1), the thicker fibrils exhibited two-dimensional liquid-crystal-like ordering probably caused by the combination of entropic and electrostatic forces. These results could help us gain better insight into the effects of the substrate on amyloid fibrillation.

Hydrophobic interaction drives surface-assisted epitaxial assembly of amyloid-like peptides

The molecular mechanism of epitaxial fibril formation has been investigated for GAV-9 (NH(3)(+)-VGGAVVAGV-CONH(2)), an amyloid-like peptide extracted from a consensus sequence of amyloidogenic proteins, which assembles with very different morphologies, "upright" on mica and "flat" on the highly oriented pyrolytic graphite (HOPG). Our all-atom molecular dynamics simulations reveal that the strong electrostatic interaction induces the "upright" conformation on mica, whereas the hydrophobic interaction favors the "flat" conformation on HOPG. We also show that the epitaxial pattern on mica is ensured by the lattice matching between the anisotropic binding sites of the basal substrate and the molecular dimension of GAV-9, accompanied with a long-range order of well-defined β-strands. Furthermore, the binding free energy surfaces indicate that the longitudinal assembly growth is predominantly driven by the hydrophobic interaction along the longer crystallographic unit cell direction of mica. These findings provide a molecular basis for the surface-assisted molecular assembly, which might also be useful for the design of de novo nanodevices.

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.

Molecular mechanism of surface-assisted epitaxial self-assembly of amyloid-like peptides

A surprising "upright" fibrilar conformation (with a height of ~2.6 nm) was observed with in situ atomic force microscopy (AFM) for an amyloid-like peptide (NH(2)-VGGAVVAV-COHN(2)) on mica surface, which is very different from its "flat" conformation (with a much smaller height of ~0.9 nm) on the HOPG surface. Our all-atom molecular dynamics (MD) simulations reveal that it is the strong electrostatic interactions between the N-terminus of the peptide and the mica surface that result in an upright conformation and a highly ordered β-stranded structure on mica, with a height of 2.5 ± 0.1 nm, consistent with the AFM experiment. Similarly, our MD simulations show that the same peptides adopt a flat conformation on HOPG surfaces due to the favorable hydrophobic interactions with HOPG. Our simulations also indicate that epitaxial patterns found in mica are preferentially controlled by anisotropic binding sites commensurate with the inherent crystallographic unit cell of the basal substrate.

Diethylene glycol functionalized self-assembling peptide nanofibers and their hydrophobic drug delivery potential

Self-assembling peptide nanofibers have emerged as important nanobiomaterials, with such applications as delivery of therapeutic agents and vaccines, nanofabrication and biomineralization, tissue engineering and regenerative medicine. Recently a new class of self-assembling peptides has been introduced, which takes into consideration amino acid pairing (AAP) strategies in the peptide sequence design. Even though these peptides have shown promising potential in the design of novel functional biomaterials, they have a propensity to initiate uncontrollable aggregation and be degraded by proteolytic enzymes. These present the most significant challenge in advancing self-assembling peptides for in vitro and in vivo applications. Functionalizing biomaterials with polyethylene glycol (PEG) has been shown to surmount such problems. Here the results of conjugating diethylene glycol (DEG), a short segment of PEG, to one of the AAP peptides, AAP8, with eight amino acids in sequence, are reported. The results indicate that incorporation of DEG into the peptide sequence modulates fiber self-assembly through creating more aligned and uniform nanostructures. This is associated with increasing solubility, stability, and secondary structure β-sheet content of the peptide. The DEG conjugate of AAP8 also shows reduced cellular cytotoxicity. Functionalization of AAP8 improves the capability of the peptide to stabilize and deliver a hydrophobic anticancer compound, ellipticine, in aqueous solution, consequently inducing greater cytotoxicity to lung carcinoma cells over a relatively long time, compared with non-functionalized AAP8. The presented functionalized peptide and its drug delivery application indicate a potentially useful design strategy for novel self-assembling peptide biomaterials for biotechnology and nanomedicine.

Dispersion of multiwalled carbon nanotubes in water using ionic-complementary peptides

We demonstrate the noncovalent modification of multiwalled carbon nanotubes (MWNTs) immersed in aqueous solution using the ionic-complementary peptide EFK16-II. This modification presumably arises through the interaction between the hydrophobic side of the EFK16-II and MWNT sidewalls and orients hydrophilic functional groups toward the solution phase and enables them to form highly stable dispersions in water. This stability can be attributed to the electrostatic repulsion between self-assembled peptides on the MWNTs. This repulsion as determined by ζ potential measurements increases as the pH diverges from the isoelectric point of ~6.7 for EFK16-II. This trend is confirmed by dynamic light scattering measurements of the suspensions showing a decrease in their particle size as the ζ potential increases. These EFK16-II-MWNT suspensions have been used to modify mica surfaces. Atomic force microscopy and scanning electron microscopy images show that this leads to a uniform distribution of individual modified MWNTs on the mica surfaces. Transmission electron microscopy reveals images of well-dispersed fibers with dimensions similar to those of individual MWNTs. Tissue culture plates previously contacted with EFK16-II-modified MWNTs have been shown to have enough biocompatibility for growth and attachment of cells. The biocompatibility and enhanced electrical conductivity that should result from the modification with these EFK16-II-MWNT suspensions opens up their use in a number of potential biomedical applications such as the design of bioelectrode interfaces and fabrication of biosensors with high sensitivity.

Nanoscopic and photonic ultrastructural characterization of two distinct insulin amyloid states

Two different conformational isoforms or amyloid strains of insulin with different cytotoxic capacity have been described previously. Herein these filamentous and fibrillar amyloid states of insulin were investigated using biophysical and spectroscopic techniques in combination with luminescent conjugated oligothiophenes (LCO). This new class of fluorescent probes has a well defined molecular structure with a distinct number of thiophene units that can adopt different dihedral angles depending on its binding site to an amyloid structure. Based on data from surface charge, hydrophobicity, fluorescence spectroscopy and imaging, along with atomic force microscopy (AFM), we deduce the ultrastructure and fluorescent properties of LCO stained insulin fibrils and filaments. Combined total internal reflection fluorescence microscopy (TIRFM) and AFM revealed rigid linear fibrous assemblies of fibrils whereas filaments showed a short curvilinear morphology which assemble into cloudy deposits. All studied LCOs bound to the filaments afforded more blue-shifted excitation and emission spectra in contrast to those corresponding to the fibril indicating a different LCO binding site, which was also supported by less efficient hydrophobic probe binding. Taken together, the multi-tool approach used here indicates the power of ultrastructure identification applying AFM together with LCO fluorescence interrogation, including TIRFM, to resolve structural differences between amyloid states.

Effect of surfaces on amyloid fibril formation

Using atomic force microscopy (AFM) we investigated the interaction of amyloid beta (Aβ) peptide with chemically modified surfaces in order to better understand the mechanism of amyloid toxicity, which involves interaction of amyloid with cell membrane surfaces. We compared the structure and density of Aβ fibrils on positively and negatively charged as well as hydrophobic chemically-modified surfaces at physiologically relevant conditions. We report that due to the complex distribution of charge and hydrophobicity amyloid oligomers bind to all types of surfaces investigated (CH₃, COOH, and NH₂) although the charge and hydrophobicity of surfaces affected the structure and size of amyloid deposits as well as surface coverage. Hydrophobic surfaces promote formation of spherical amorphous clusters, while charged surfaces promote protofibril formation. We used the nonlinear Poisson-Boltzmann equation (PBE) approach to analyze the electrostatic interactions of amyloid monomers and oligomers with modified surfaces to complement our AFM data.

Hierarchical, interface-induced self-assembly of diphenylalanine: formation of peptide nanofibers and microvesicles

To gain insight into the hierarchical self-assembly of peptides and the surface effect on assembly formation, an aromatic peptide of diphenylalanine (FF) was used in this study as the model peptide. We found that the diphenylalanine peptide could self-assemble into a core-branched nanostructure through non-covalent interactions in aqueous solution. The pre-assemblies further assembled into nanofibers and microvesicles on the glass surface and microporous membrane, respectively, showing a significant dependence on surface characteristics. The structural and morphological differences between nanofibers and microvesicles were investigated directly using several spectroscopy and microscopy techniques. Our results revealed a hierarchical and interface-induced assembly behavior of diphenylalanine peptide. The novel strategy based on the surface effect allows one to controllably fabricate various peptide-based nanostructures.

Surface self-assembly of N-fluorenyl-9-methoxycarbonyl diphenylalanine on silica wafer

N-Fluorenyl-9-methoxycarbonyl diphenylalanine (Fmoc-FF-OH) was chemically immobilized to the surface of silica wafer as the "seed". When immersing this peptide attached silica wafer into the dipeptide aqueous solution, the occurrence of a pH triggered surface self-assembly resulted in the formation of peptide nanorods on the surface of silica wafer. This surface self-assembly exhibited a dependence on the concentration of the dipeptide aqueous solution. It was proposed that the self-assembly of this dipeptide on the surface of silica wafer was similar to that in aqueous solution. In comparison with the conventional physical adsorption on the substrates, the chemically attached self-assembled nanorods exhibited much improved adsorption capacity on the substrate surface.

Influence of hydrophobicity on the surface-catalyzed assembly of the islet amyloid polypeptide

The islet amyloid polypeptide (IAPP) is a hormonal factor secreted by the β-cells in the pancreas. Aggregation of misfolded IAPP molecules and subsequent assembly of amyloid nanofibrils are critical for the development of type 2 diabetes mellitus. In the physiological environment, amyloid aggregation is affected by the presence of interfaces such as cell membranes. The physicochemical properties of the interface dictates the interaction of the peptide with the surface, i.e., electrostatic and hydrophobic interactions on hydrophilic and hydrophobic surfaces, respectively. We have studied the influence of hydrophobicity on the surface-catalyzed assembly of IAPP on ultrasmooth hydrocarbon films grown on ion-beam-modified mica surfaces by atomic force microscopy. The contact angle θ of these surfaces can be tuned continuously in the range from ≤20° to ∼90° by aging the samples without significant changes of the chemical composition or the topography of the surface. On hydrophilic surfaces with a θ of ∼20°, electrostatic interactions induce the assembly of IAPP nanofibrils, whereas aggregation of large (∼2.6 nm) oligomers is observed at hydrophobic surfaces with a θ of ∼90°. At intermediate contact angles, the interplay between electrostatic and hydrophobic substrate interactions dictates the pathway of aggregation with fibrillation getting continuously delayed when the contact angle is increased. In addition, the morphology of the formed protofibrils and mature fibrils at intermediate contact angles differs from those observed at more hydrophilic surfaces. These results might contribute to the understanding of the surface-catalyzed assembly of different amyloid aggregates and may also have implications for the technologically relevant controlled synthesis of amyloid nanofibrils of desired morphology.

Nanomechanical stimulus accelerates and directs the self-assembly of silk-elastin-like nanofibers

One-dimensional nanostructures are ideal building blocks for functional nanoscale assembly. Peptide-based nanofibers have great potential in building smart hierarchical structures due to their tunable structures at the single residue level and their ability to reconfigure themselves in response to environmental stimuli. We observed that pre-adsorbed silk-elastin-based protein polymers self-assemble into nanofibers through conformational changes on a mica substrate. Furthermore, we demonstrate that the rate of self-assembly was significantly enhanced by applying a nanomechanical stimulus using atomic force microscopy. The orientation of the newly grown nanofibers was mostly perpendicular to the scanning direction, implying that the new fiber assembly was locally activated with directional control. Our method provides a novel way to prepare nanofiber patterned substrates using a bottom-up approach.

Mechanical manipulation assisted self-assembly to achieve defect repair and guided epitaxial growth of individual peptide nanofilaments

We have succeeded in the production of defect-free and spatially organized individual one-dimensional peptide nanofilaments by real-time control of the self-assembly process on a solid substrate. Using a unique mechanical manipulation method based on atomic force microscopy, we are able to introduce mechanical stimuli to generate active ends at designated positions on an existing peptide nanofilament previously formed. By doing so, defects in the filament were removed, and self-repairing occurred when the active ends extended along the direction of the supporting lattice, resulting in the closure of the broken filament. Furthermore, new active ends of the nanofilaments can be specifically generated to guide the self-assembly of new filaments at designated positions with selected orientations. The mechanism of defect repair and guided epitaxial growth is also discussed.

Interaction of an ionic complementary peptide with a hydrophobic graphite surface

Protein adsorption on a surface plays an important role in biomaterial science and medicine. It is strongly related to the interaction between the protein residues and the surface. Here we report all-atom molecular dynamics simulations of the adsorption of an ionic complementary peptide, EAK16-II, to the hydrophobic highly ordered pyrolytic graphite surface. We find that, the hydrophobic interaction is the main force to govern the adsorption, and the peptide interchain electrostatic interaction affects the adsorption rate. Under neutral pH condition, the interchain electrostatic attraction facilitates the adsorption, whereas under acidic and basic conditions, because of the protonation and deprotonation of glutamic acid and lysine residues, respectively, the resulting electrostatic repulsion slows down the adsorption. We also found that under basic condition, during the adsorption peptide Chain II will be up against a choice to adsorb to the surface through the hydrophobic interaction or to form a temporary hydrophobic core with the deposited peptide Chain I. These results provide a basis for understanding some of the fundamental interactions governing peptide adsorption on the surface, which can shed new light on novel applications, such as the design of implant devices and drug delivery materials.

Structural selection of ionic-complementary peptides with electrostatic interactions

The structures of the peptides and their assembly are largely modulated by the environment. To discover the physical principles governing the structural modulations of peptides by the environment would be useful for many applications. As the typical examples, the structures of three kinds of ionic-complementary EAK16-family peptides under various environmental conditions are studied with simulations in this work. A model with intermediate resolution is used, in which both the backbone hydrogen bonds and electrostatic interactions are explicitly considered. The thermodynamics of these peptides (including the free energy and heat capacity) are described for various strengths of the electrostatic interactions which reflect the variation of environment. With these results, the phase diagrams of these peptides related to the temperature and the strength of electrostatic interactions are presented and compared. Based on the differences in the phase structures of the peptide, the different aggregation behaviors are explained based on the monomeric structural features of the peptides. Through the analysis on the stability of various secondary structures of these peptides, it is demonstrated that the charge pattern is the basic reason of the different responses of the EAK16-family peptides to the environmental changes. These results provide some examples and insights for the principles of structural selection by environment and may be helpful for further analysis and designs of peptide systems.

Improved enzyme immobilization on an ionic-complementary peptide-modified electrode for biomolecular sensing

An ionic-complementary peptide, EFK16-II, was used to modify a highly ordered pyrolytic graphite (HOPG) electrode surface. The nanofiber structure of the self-assembling peptide on the electrode surface was characterized by atomic force microscopy (AFM). Attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) spectra showed that, upon addition of 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC), EFK16-II molecules tend to be cross-linked among themselves. Cross-linking of the peptide diminishes the number of carboxyl groups available for immobilizing a sensing enzyme, which is glucose oxidase (GOx) in the present case. A simple method based on premixing of the carbodiimide and GOx was developed; it inhibited peptide cross-linking and significantly improved enzyme immobilization. Biosensors constructed in this way showed increased overall signal intensity and a much higher sensitivity at 4.94 mA M(-1) cm(-2), a 6-fold increase compared to the previously reported peptide-modified electrodes. The results presented here demonstrate significant potential for ionic-complementary peptides for constructing electrochemical biosensors.

Surface Induced nanofiber growth by self-assembly of a silk-elastin-like protein polymer

Many synthetic and natural peptides are known to self-assemble to form various nanostructures. During the self-assembling process, environmental conditions such as salt concentration, pH, temperature, and surface characteristics play a critical role by influencing intermolecular interactions, and hence the process of self-assembly. Here we studied the self-assembly of a genetically engineered protein polymer composed of silk-like and elastin-like repeats on a mica surface. Silk-elastin-like protein polymers (SELPs) consist of tandem repeats of Gly-Ala-Gly-Ala-Gly-Ser from Bombyx mori (silkworm) and Gly-Val-Gly-Val-Pro from mammalian elastin. At a very low polymer concentration of 1 mug/mL, SELPs self-assembled into nanofibrous structures on a mica surface. Examination using atomic force microscopy (AFM) and dynamic light scattering techniques showed that SELPs self-assembled into nanofibers in the presence of the mica surface but not in the bulk state. Ionic strength had a significant influence on nanofiber growth, indicating the importance of electrostatic interactions between the polymer and the mica surface. At low ionic strength, the kinetics of nanofiber growth showed that the mica surface effectively removed a lag phase by providing nucleating sites, facilitating nanofiber self-assembly of SELPs. Furthermore, self-assembly on additional substrates such as silicon and a hydrophobic pyrolytic carbon surface revealed that the charged hydrophilic surface provides the optimal surface to facilitate self-assembly of SELPs.

Ionic-complementary peptide matrix for enzyme immobilization and biomolecular sensing

A novel electrochemical biosensing platform is described using biocompatible, self-assembled ionic-complementary peptide nanofibers. The compatibility of a graphite electrode modified by these peptide nanofibers with enzymes is demonstrated using a model enzyme glucose oxidase (GOx). A glucose biosensor has been successfully fabricated by incorporating this enzyme into the modified electrode. From measurement of its electrode response and sensitivity, this nanofiber-modified electrode shows promise as an enzyme-based biosensor. The findings presented here demonstrate excellent potential of the use of ionic-complementary peptides to modify electrode surfaces for biomolecular sensing and diagnostics.

A survey of bioengineering research in Canada-2007

Research activity in bioengineering at Canadian universities has been surveyed. Details were provided by chemical engineering departments in response to a common request for information on activities by individual researchers and for key publications. The information provided has been grouped by topics within the broad theme of "Bioengineering," and contributions from individual departments have been summarized within these topics. Although many aspects of bioengineering research are being pursued in Canada, it would appear as though environmental biotechnology, biomaterials, and tissue/cell culture are the most active areas under investigation.