Controlling the surface chemistry of graphite by engineered self-assembled peptides

Two-Dimensional Layered Nanomaterials Steering Self-Assembly of Dodecapeptides with Three Building Blocks

Self-assembly of peptides on layered nanomaterials such as graphite and MoS2 in the formation of long-range ordered two-dimensional nanocrystal patterns leading to its potential applications for biosensing and bioelectronics has attracted significant interest in nanoscience and nanotechnology. However, controlling the self-assembly of peptides on nanomaterials is still challenging due to the unclear role of nanomaterials in steering self-assembly. Here, we used the in-situ AFM technique to capture different changes of peptide coverage as well as lengthening and widening rates depending on peptide concentrations, show the distinct boundary dynamics of two stabilized peptide domains, and resolve the molecular resolution structural differences and specific orientation of peptide on both nanomaterials. Moreover, ex-situ results showed that the nanomaterial layers tuned the opposite changes of nanowire heights and densities and displayed the different water-resistance stabilities on both nanomaterials. This work provides a basis for understanding nanomaterials steering peptide self-assembly and using hybrid bionanomaterials as a scaffold, enabling for potential biosensing and bioelectronics applications.

Structural Analyses of DP-1, a Protein with the Ability To Bind Gold Nanoparticles, by Using Nuclear Magnetic Resonance Spectroscopy

Gold nanoparticles (AuNPs), consisting of metallic gold, are applied in various fields owing to their characteristic physical properties. Collimonas sp. D-25 (D-25) is a Gram-negative bacterium obtained from soil, compost, and other environmental materials in the Akita Prefecture. DP-1 is a water-soluble protein found in D-25 that binds specifically to AuNPs and retains them with high stability. This study aimed to identify the part of DP-1 that interacts with AuNPs and determine its 3D structure in solution using nuclear magnetic resonance spectroscopy. Peptide fragments obtained by trypsin digestion were examined for their AuNP-binding capacity to determine the key Au-binding domain of DP-1. A fragment consisting of 16 amino acid residues (GHAATPEQYGVVTANK) was identified as the peptide with the highest binding activity. Structural analyses of this peptide indicated that the main chain was elongated, and negatively charged residues in the side chain were exposed on the surface by incorporating AuNPs. These results suggest that DP-1 interacts with AuNPs through negatively charged residues and extended hydrophobic residues for protein-protein interactions. The structural data also provide new insights into biomimetic technologies.

Designable peptides on graphene field-effect transistors for selective detection of odor molecules

Gas sensing based on graphene field-effect transistors (GFETs) has gained broad interest due to their high sensitivity. Further progress in gas sensing with GFETs requires to detection of various odor molecules for applications in the environmental monitoring, healthcare, food, and cosmetic industries. To develop the ubiquitous odor-sensing system, establishing an artificial sense of smell with electronic devices by mimicking olfactory receptors will be key. Although the application of olfactory receptors to GFETs is straightforward for odor sensing, synthetic molecules with a similar function to olfactory receptors would be desirable to realize the robust performance of sensing. In this work, we designed three new peptides consisting of two domains: a bio-probe to the target molecules and a molecular scaffold. These peptides were rationally designed based on a motif sequence in olfactory receptors and self-assembled into a molecular thin film on GFETs. Limonene, methyl salicylate, and menthol were employed as representative odor molecules of plant flavors to demonstrate the biosensing of odor molecules. The conductivity change of GFETs against the binding to odor molecules with various concentrations and the dynamic response revealed a distinct signature of three different peptides against individual species of the target molecules. The kinetic response of each peptide exhibited characteristic time constants in the adsorption and desorption process, also supported by the principal component analysis. Our demonstration of the graphene odor sensors with the designed peptides opens a way to establish future peptide-array sensors with multi-sequence of peptide, realizing an odor sensing system with higher selectivity.

Supramolecular assembly of protein building blocks: from folding to function

Several phenomena occurring throughout the life of living things start and end with proteins. Various proteins form one complex structure to control detailed reactions. In contrast, one protein forms various structures and implements other biological phenomena depending on the situation. The basic principle that forms these hierarchical structures is protein self-assembly. A single building block is sufficient to create homogeneous structures with complex shapes, such as rings, filaments, or containers. These assemblies are widely used in biology as they enable multivalent binding, ultra-sensitive regulation, and compartmentalization. Moreover, with advances in the computational design of protein folding and protein-protein interfaces, considerable progress has recently been made in the de novo design of protein assemblies. Our review presents a description of the components of supramolecular protein assembly and their application in understanding biological phenomena to therapeutics.

Cosolvents Restrain Self-Assembly of a Fibroin-Like Peptide on Graphite

Controllable self-assembly of peptides on solid surfaces has been investigated for establishing functional bio/solid interfaces. In this work, we study the influence of organic solvents on the self-assembly of a fibroin-like peptide on a graphite surface. The peptide has been designed by mimicking fibroin proteins to have strong hydrogen bonds among peptides enabling their self-assembly. We have employed cosolvents of water and organic solvents with a wide range of dielectric constants to control peptide self-assembly on the surface. Atomic force microscopy has revealed that the peptides self-assemble into highly ordered monolayer-thick linear structures on graphite after incubation in pure water, where the coverage of peptides on the surface is more than 85%. When methanol is mixed, the peptide coverage becomes zero at a threshold concentration of 30% methanol on graphite and 25% methanol on MoS₂. The threshold concentration in ethanol, isopropanol, dimethyl sulfoxide, and acetone varies depending on the dielectric constant with restraining self-assembly of the peptides, and particularly low dielectric-constant protic solvents prevent the peptide self-assembly significantly. The observed phenomena are explained by competitive surface adsorption of the organic solvents and peptides and the solvation effect of the peptide assembly.

Keratinocyte-Specific Peptide-Based Surfaces for Hemidesmosome Upregulation and Prevention of Bacterial Colonization

Percutaneous devices like orthopedic prosthetic implants for amputees, catheters, and dental implants suffer from high infection rates. A critical aspect mediating peri-implant infection of dental implants is the lack of a structural barrier between the soft tissue and the implant surface which could impede bacteria access and colonization of exposed implant surfaces. Parafunctional soft tissue regeneration around dental implants is marked by a lack of hemidesmosome formation and thereby weakened mechanical attachment. In response to this healthcare burden, a simultaneously hemidesmosome-inducing, antimicrobial, multifunctional implant surface was engineered. A designer antimicrobial peptide, GL13K, and a laminin-derived peptide, LamLG3, were coimmobilized with two different surface fractional areas. The coimmobilized peptide surfaces showed antibiofilm activity against Streptococcus gordonii while enhancing proliferation, hemidesmosome formation, and mechanical attachment of orally derived keratinocytes. Notably, the coatings demonstrated specific activation of keratinocytes: the coatings showed no effects on gingival fibroblasts which are known to impede the quality of soft tissue attachment to dental implants. These coatings demonstrated stability and retained activity against mechanical and thermochemical challenges, suggesting their intraoral durability. Overall, these multifunctional surfaces may be able to reduce peri-implantitis rates and enhance the success rates of all percutaneous devices via strong antimicrobial activity and enhanced soft tissue attachment to implants.

Thermal Selection of Aqueous Molecular Conformations for Tailored Energetics of Peptide Assemblies at Solid Interfaces

Key to the development of functional bioinorganic soft interfaces is the predictive control over the micron-scale assembly structure and energetics of biomolecules at solid interfaces. While assembly of labile biomolecules, such as short peptides, at interfaces is a great deal affected by the shape of the molecule, biomolecular conformations are prompted by external solution conditions, involving temperature, pH, and salt concentration. In this light, one can expect that the environmental conformational selection of aqueous biomolecules could potentially allow for fine-tuning of the equilibrium assembly structure at interfaces, as well as, the binding strength and molecular mobility within these assemblies. Here, we demonstrate the energetic and structural tailoring of two-dimensional surface assemblies of graphite-binding dodecapeptides, through the thermal selection of aqueous peptide conformations. Our findings based on a scanning probe energetic analysis, supplemented by molecular dynamics modeling, show that peptide-graphite and peptide-peptide intermolecular interactions strongly depend on the thermally selected molecular conformation and that the extent of the conformational change is directly related to the observed assembled structure. Enabled by these results was the design of a peptide with predictable binding and assembled structure, thus, suggesting environmental preconditioning of peptides as a means for controlling self-assembling active bioinorganic interfaces for bioelectronic implementations such as biomolecular fuel cells and biosensors.

Biomolecular Material Recognition in Two Dimensions: Peptide Binding to Graphene, h-BN, and MoS2 Nanosheets as Unique Bioconjugates

Two-dimensional nanosheet-based materials such as graphene, hexagonal boron nitride, and MoS₂ represent intriguing structures for a variety of biological applications ranging from biosensing to nanomedicine. Recent advances have demonstrated that peptides can be identified with affinity for these three materials, thus generating a highly unique bioconjugate interfacial system. This Review focuses on recent advances in the formation of bioconjugates of these types, paying particular attention to the structure/function relationship of the peptide overlayer. This is achieved through the amino acid composition of the nanosheet binding peptides, thus allowing for precise control over the properties of the final materials. Such bioconjugate systems offer rapid advances via direct property control that remain difficult to achieve for biological applications using nonbiological approaches.

Tailor-Made Functional Peptide Self-Assembling Nanostructures

Noncovalent interactions are the main driving force in the folding of proteins into a 3D functional structure. Motivated by the wish to reveal the mechanisms of the associated self-assembly processes, scientists are focusing on studying self-assembly processes of short protein segments (peptides). While this research has led to major advances in the understanding of biological and pathological process, only in recent years has the applicative potential of the resulting self-assembled peptide assemblies started to be explored. Here, major advances in the development of biomimetic supramolecular peptide assemblies as coatings, gels, and as electroactive materials, are highlighted. The guiding lines for the design of helical peptides, β strand peptides, as well as surface binding monolayer-forming peptides that can be utilized for a specific function are highlighted. Examples of their applications in diverse immerging applications in, e.g., ecology, biomedicine, and electronics, are described. Taking into account that, in addition to extraordinary design flexibility, these materials are naturally biocompatible and ecologically friendly, and their production is cost effective, the emergence of devices incorporating these biomimetic materials in the market is envisioned in the near future.

Probing nano-patterned peptide self-organisation at the aqueous graphene interface

The peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on graphite. However, under aqueous conditions neither the molecular conformations of the adsorbed peptide chains, nor the molecular-level spatial ordering of the over-layer, has been directly resolved. Here, we use advanced molecular dynamics simulations of GrBP5, and related mutant sequences, to elucidate the adsorbed structures of both the peptide and the adsorbed peptide over-layer at the aqueous graphene interface. In agreement with a previous hypothesis, we find GrBP5 binds at the aqueous graphene interface chiefly via the tyrosine-rich C-terminal region. Our simulations of the adsorbed peptide over-layers reveal that the peptide chains form an aggregate that does not evolve further into ordered patterns. Instead, we find that the inter-chain interactions are driven by hydrogen bonding and charge-charge interactions that are not sufficiently specific to support pattern formation. Overall, we suggest that the experimentally-observed over-layer pattern may be due to the drying of the sample, and may not be prevalent at the solvated interface. However, our simulations indicate sequence modifications of GrBP5 to promote over-layer ordering under aqueous conditions.

Graphene Symmetry Amplified by Designed Peptide Self-Assembly

We present a strategy for designed self-assembly of peptides into two-dimensional monolayer crystals on the surface of graphene and graphite. As predicted by computation, designed peptides assemble on the surface of graphene to form very long, parallel, in-register β-sheets, which we call β-tapes. Peptides extend perpendicularly to the long axis of each β-tape, defining its width, with hydrogen bonds running along the axis. Tapes align on the surface to create highly regular microdomains containing 4-nm pitch striations. Moreover, in agreement with calculations, the atomic structure of the underlying graphene dictates the arrangement of the β-tapes, as they orient along one of six directions defined by graphene’s sixfold symmetry. A cationic-assembled peptide surface is shown here to strongly adhere to DNA, preferentially orienting the double helix along β-tape axes. This orientational preference is well anticipated from calculations, given the underlying peptide layer structure. These studies illustrate how designed peptides can amplify the Ångstrom-level atomic symmetry of a surface onto the micrometer scale, further imparting long-range directional order onto the next level of assembly. The remarkably stable nature of these assemblies under various environmental conditions suggests applications in enzymelike catalysis, biological interfaces for cellular recognition, and two-dimensional platforms for studying DNA-peptide interactions.

Peptide engineered microcantilevers for selective chemical force microscopy and monitoring of nanoparticle capture

Engineered peptides capable of binding to silica have been used to provide contrast in chemical force microscopy and tested for their capacity to selectively capture silica nanoparticles (NPs). Gold coated atomic force microscopy (AFM) microcantilevers with integrated tips and colloidal probes were functionalized with engineered peptides through a thiol group of a terminal cysteine which was linked via a glycine trimer to a 12-mer binding sequence. The functionalized probes demonstrated a significantly increased binding force on silicon oxide areas of a gold-patterned silicon wafer, whereas plain gold probes, and those functionalized with a random permutation of the silica binding peptide motif or an all-histidine sequence displayed similar adhesion forces to gold and silicon oxide. As the functionalized probes also allowed contact mode imaging subsequently to the adhesion mapping, also the associated friction contrast was measured and found to be similar to the adhesion contrast. Furthermore, the adsorption of silica NPs onto planar gold surfaces functionalized in the same manner was observed to be selective. Notably, the surface coverage with silica NPs was found to decrease with increasing pH, implying the importance of electrostatic interactions between the peptide and the NPs. Finally, the adsorption of silica NPs was monitored via the decrease in fundamental resonance frequency of an AFM microcantilever functionalized with silica binding peptides.

Biologically templated assembly of hybrid semiconducting nanomesh for high performance field effect transistors and sensors

Delicately assembled composites of semiconducting nanomaterials and biological materials provide an attractive interface for emerging applications, such as chemical/biological sensors, wearable health monitoring devices, and therapeutic agent releasing devices. The nanostructure of composites as a channel and a sensing material plays a critical role in the performance of field effect transistors (FETs). Therefore, it is highly desirable to prepare elaborate composite that can allow the fabrication of high performance FETs and also provide high sensitivity and selectivity in detecting specific chemical/biological targets. In this work, we demonstrate that high performance FETs can be fabricated with a hydrodynamically assembled composite, a semiconducting nanomesh, of semiconducting single-walled carbon nanotubes (S-SWNTs) and a genetically engineered M13 phage to show strong binding affinity toward SWNTs. The semiconducting nanomesh enables a high on/off ratio (~10⁴) of FETs. We also show that the threshold voltage and the channel current of the nanomesh FETs are sensitive to the change of the M13 phage surface charge. This biological gate effect of the phage enables the detection of biologically important molecules such as dopamine and bisphenol A using nanomesh-based FETs. Our results provide a new insight for the preparation of composite material platform for highly controllable bio/electronics interfaces.

Water stability of self-assembled peptide nanostructures for sequential formation of two-dimensional interstitial patterns on layered materials

Sequential-assembly of LEY and GrBP5 peptides on a graphite surface.

Molecular-level understanding of the adsorption mechanism of a graphite-binding peptide at the water/graphite interface

The association of proteins and peptides with inorganic material has vast technological potential. An understanding of the adsorption of peptides at liquid/solid interfaces on a molecular-level is fundamental to fully realising this potential. Combining our prior work along with the statistical analysis of 100+ molecular dynamics simulations of adsorption of an experimentally identified graphite binding peptide, GrBP5, at the water/graphite interface has been used here to propose a model for the adsorption of a peptide at a liquid/solid interface. This bottom-up model splits the adsorption process into three reversible phases: biased diffusion, anchoring and lockdown. Statistical analysis highlighted the distinct roles played by regions of the peptide studied here throughout the adsorption process: the hydrophobic domain plays a significant role in the biased diffusion and anchoring phases suggesting that the initial impetus for association between the peptide and the interface may be hydrophobic in origin; aromatic residues dominate the interaction between the peptide and the surface in the adsorbed state and the polar region in the middle of the peptide affords a high conformational flexibility allowing strongly interacting residues to maximise favourable interactions with the surface. Reversible adsorption was observed here, unlike in our prior work focused on a more strongly interacting surface. However, this reversibility is unlikely to be seen once the peptide-surface interaction exceeds 10 kcal mol(-1).

Selective detection of target proteins by peptide-enabled graphene biosensor

Direct molecular detection of biomarkers is a promising approach for diagnosis and monitoring of numerous diseases, as well as a cornerstone of modern molecular medicine and drug discovery. Currently, clinical applications of biomarkers are limited by the sensitivity, complexity and low selectivity of available indirect detection methods. Electronic 1D and 2D nano-materials such as carbon nanotubes and graphene, respectively, offer unique advantages as sensing substrates for simple, fast and ultrasensitive detection of biomolecular binding. Versatile methods, however, have yet to be developed for simultaneous functionalization and passivation of the sensor surface to allow for enhanced detection and selectivity of the device. Herein, we demonstrate selective detection of a model protein against a background of serum protein using a graphene sensor functionalized via self-assembling multifunctional short peptides. The two peptides are engineered to bind to graphene and undergo co-assembly in the form of an ordered monomolecular film on the substrate. While the probe peptide displays the bioactive molecule, the passivating peptide prevents non-specific protein adsorption onto the device surface, ensuring target selectivity. In particular, we demonstrate a graphene field effect transistor (gFET) biosensor which can detect streptavidin against a background of serum bovine albumin at less than 50 ng/ml. Our nano-sensor design, allows us to restore the graphene surface and utilize each sensor in multiple experiments. The peptide-enabled gFET device has great potential to address a variety of bio-sensing problems, such as studying ligand-receptor interactions, or detection of biomarkers in a clinical setting.

Simultaneous study of exciton diffusion/dissociation and charge transport in a donor-acceptor bilayer: pentacene on a C60 -terminated self-assembled monolayer

In-situ photoinduced threshold voltage measurement is a sensitive probe for exploring charge transport and exciton diffusion simultaneously, the main determinants of the power conversion efficiency in organic photovoltaic devices. The exciton diffusion length in a pentacene film deposited onto a C60 -terminated self-assembled monolayer is measured. The methodology and analysis presented here can be applied in the design and engineering of electron/donor acceptor interfaces for photovoltaic devices..

Nanoscale dynamics and protein adhesivity of alkylamine self-assembled monolayers on graphene

Atomic-scale molecular dynamics computer simulations are used to probe the structure, dynamics, and energetics of alkylamine self-assembled monolayer (SAM) films on graphene and to model the formation of molecular bilayers and protein complexes on the films. Routes toward the development and exploitation of functionalized graphene structures are detailed here, and we show that the SAM architecture can be tailored for use in emerging applications (e.g., electrically stimulated nerve fiber growth via the targeted binding of specific cell surface peptide sequences on the functionalized graphene scaffold). The simulations quantify the changes in film physisorption on graphene and the alkyl chain packing efficiency as the film surface is made more polar by changing the terminal groups from methyl (-CH3) to amine (-NH2) to hydroxyl (-OH). The mode of molecule packing dictates the orientation and spacing between terminal groups on the surface of the SAM, which determines the way in which successive layers build up on the surface, whether via the formation of bilayers of the molecule or the immobilization of other (macro)molecules (e.g., proteins) on the SAM. The simulations show the formation of ordered, stable assemblies of monolayers and bilayers of decylamine-based molecules on graphene. These films can serve as protein adsorption platforms, with a hydrophobin protein showing strong and selective adsorption by binding via its hydrophobic patch to methyl-terminated films and binding to amine-terminated films using its more hydrophilic surface regions. Design rules obtained from modeling the atomic-scale structure of the films and interfaces may provide input into experiments for the rational design of assemblies in which the electronic, physicochemical, and mechanical properties of the substrate, film, and protein layer can be tuned to provide the desired functionality.

Concise review: carbon nanotechnology: perspectives in stem cell research

Carbon nanotechnology has developed rapidly during the last decade, and carbon allotropes, especially graphene and carbon nanotubes, have already found a wide variety of applications in industry, high-tech fields, biomedicine, and basic science. Electroconductive nanomaterials have attracted great attention from tissue engineers in the design of remotely controlled cell-substrate interfaces. Carbon nanoconstructs are also under extensive investigation by clinical scientists as potential agents in anticancer therapies. Despite the recent progress in human pluripotent stem cell research, only a few attempts to use carbon nanotechnology in the stem cell field have been reported. However, acquired experience with and knowledge of carbon nanomaterials may be efficiently used in the development of future personalized medicine and in tissue engineering.

Low-temperature aluminum reduction of graphene oxide, electrical properties, surface wettability, and energy storage applications

Low-temperature aluminum (Al) reduction is first introduced to reduce graphene oxide (GO) at 100-200 °C in a two-zone furnace. The melted Al metal exhibits an excellent deoxygen ability to produce well-crystallized reduced graphene oxide (RGO) papers with a low O/C ratio of 0.058 (Al-RGO), compared with 0.201 in the thermally reduced one (T-RGO). The Al-RGO papers possess outstanding mechanical flexibility and extremely high electrical conductivities (sheet resistance R(s) ~ 1.75 Ω/sq), compared with 20.12 Ω/sq of T-RGO. More interestingly, very nice hydrophobic nature (90.5°) was observed, significantly superior to the reported chemically or thermally reduced papers. These enhanced properties are attributed to the low oxygen content in the RGO papers. During the aluminum reduction, highly active H atoms from H(2)O reacted with melted Al promise an efficient oxygen removal. This method was also applicable to reduce graphene oxide foams, which were used in the GO/SA (stearic acid) composite as a highly thermally conductive reservoir to hold the phase change material for thermal energy storage. The Al-reduced RGO/SnS(2) composites were further used in an anode material of lithium ion batteries possessing a higher specific capacity. Overall, low-temperature Al reduction is an effective method to prepare highly conductive RGO papers and related composites for flexible energy conversion and storage device applications.