Quantitative Affinity of Genetically Engineered Repeating Polypeptides to Inorganic Surfaces

Energy Landscape of Relaxation and Interaction of an Amino Acid, Glutamine (L), on Pristine and Au/Ag/Cu-Doped TiO2 Surfaces

Studying the interaction of inorganic systems with organic ones is a highly important avenue for finding new drugs and treatment methods. Tumor cells show an increased demand for amino acids due to their rapid proliferation; thus, targeting their metabolism is becoming a potential oncological therapeutic strategy. One of the inorganic materials that show antitumor properties is titanium dioxide, while its doping was found to enhance interactions with biological systems. Thus, in this study, we investigated the energy landscape of glutamine (L), an amino acid, on pristine and doped TiO2 surfaces. We first locally optimized 2D-slab structures of pristine and Au/Ag/Cu-doped anatase (001 and 101 surfaces) and similarly optimized a single molecule of glutamine in vacuum. Next, we placed the pre-optimized glutamine molecule in various orientations and on a variety of locations onto the relaxed substrate surfaces (in vacuum) and performed ab initio relaxations of the molecule on the substrate slabs. We employed the DFT method with a GGA-PBE functional implemented in the Quantum Espresso code. Comparisons of the optimized conformations and electronic structures of the amino acid in vacuum and on the surfaces yield useful insights into various biological processes.

Biomedical applications of solid-binding peptides and proteins

Over the past decades, solid-binding peptides (SBPs) have found multiple applications in materials science. In non-covalent surface modification strategies, solid-binding peptides are a simple and versatile tool for the immobilization of biomolecules on a vast variety of solid surfaces. Especially in physiological environments, SBPs can increase the biocompatibility of hybrid materials and offer tunable properties for the display of biomolecules with minimal impact on their functionality. All these features make SBPs attractive for the manufacturing of bioinspired materials in diagnostic and therapeutic applications. In particular, biomedical applications such as drug delivery, biosensing, and regenerative therapies have benefited from the introduction of SBPs. Here, we review recent literature on the use of solid-binding peptides and solid-binding proteins in biomedical applications. We focus on applications where modulating the interactions between solid materials and biomolecules is crucial. In this review, we describe solid-binding peptides and proteins, providing background on sequence design and binding mechanism. We then discuss their application on materials relevant for biomedicine (calcium phosphates, silicates, ice crystals, metals, plastics, and graphene). Although the limited characterization of SBPs still represents a challenge for their design and widespread application, our review shows that SBP-mediated bioconjugation can be easily introduced into complex designs and on nanomaterials with very different surface chemistries.

Design of Polypeptides Self-Assembling into Antifouling Coatings: Exploiting Multivalency

We propose to exploit multivalent binding of solid-binding peptides (SBPs) for the physical attachment of antifouling polypeptide brushes on solid surfaces. Using a silica-binding peptide as a model SBP, we find that both tandem-repeated SBPs and SBPs repeated in branched architectures implemented via a multimerization domain work very well to improve the binding strength of polypeptide brushes, as compared to earlier designs with a single SBP. At the same time, for many of the designed sequences, either the solubility or the yield of recombinant production is low. For a single design, with the domain structure B-M-E, both solubility and yield of recombinant production were high. In this design, B is a silica-binding peptide, M is a highly thermostable, de novo-designed trimerization domain, and E is a hydrophilic elastin-like polypeptide. We show that the B-M-E triblock polypeptide rapidly assembles into highly stable polypeptide brushes on silica surfaces, with excellent antifouling properties against high concentrations of serum albumin. Given that SBPs attaching to a wide range of materials have been identified, the B-M-E triblock design provides a template for the development of polypeptides for coating many other materials such as metals or plastics.

Chimeric Peptide-Based Biomolecular Constructs for Versatile Nucleic Acid Biosensing

Nucleic acid biomarkers hold great potential as key indicators for the diagnosis and monitoring of diseases. Herein we design and implement bifunctional chimeric biomolecules composed of a solid-binding peptide (SBP) domain that specifically adsorbs onto solid sensor surfaces and a peptide nucleic acid (PNA) moiety that facilitates anchoring of antisense oligonucleotide (ASO) probes for the detection of nucleic acid targets. A gold-binding peptide, AuBP1, previously selected by directed evolution to specifically bind to gold, served as the basis for immobilizing nucleic acid probes onto gold substrates. Using surface plasmon resonance (SPR) spectroscopy and quartz crystal microbalance (QCM) analyses, we demonstrate the sequential biomolecular assembly of the heterofunctional solid-binding peptide-antisense oligomer (SBP-ASO) construct onto a sensor surface and the subsequent detection of DNA in an aqueous environment. The effect of steric hindrance on optimal probe assembly is observed, establishing that less packing density results in greater target capture efficacy. In addition, an adsorbed layer of chimeric solid-binding peptide-peptide nucleic acid (SBP-PNA) undergoes viscoelastic changes at the solid-liquid interface upon probe immobilization and DNA target capture, whereby the rigid biofunctional layer becomes more flexible. The dual nature of the chimeric construct is highly amenable to a variety of platforms allowing for both specific recognition and probe immobilization on the sensor surface, while the modular design of the solid-binding peptide-antisense oligonucleotide provides facile functionalization of a wide diversity of solid substrates.

The Effect of Oligomerization on A Solid-Binding Peptide Binding to Silica-Based Materials

The bifunctional linker-protein G (LPG) fusion protein comprises a peptide (linker) sequence and a truncated form of Streptococcus strain G148 protein G (protein G). The linker represents a multimeric solid-binding peptide (SBP) comprising 4 × 21-amino acid sequence repeats that display high binding affinity towards silica-based materials. In this study, several truncated derivatives were investigated to determine the effect of the SBP oligomerization on the silica binding function of LPG (for the sake of clarity, LPG will be referred from here on as 4 × LPG). Various biophysical characterization techniques were used to quantify and compare the truncated derivatives against 4 × LPG and protein G without linker (PG). The derivative containing two sequence repeats (2 × LPG) showed minimal binding to silica, while the truncated derivative with only a single sequence (1 × LPG) displayed no binding. The derivative containing three sequence repeats (3 × LPG) was able to bind to silica with a binding affinity of K_D = 53.23 ± 4.5 nM, which is 1.5 times lower than that obtained for 4 × LPG under similar experimental conditions. Circular dichroism (CD) spectroscopy and fluorescence spectroscopy studies indicated that the SBP degree of oligomerization has only a small effect on the secondary structure (the linker unravels the beginning of the protein G sequence) and chemical stability of the parent protein G. However, based on quartz crystal microbalance with dissipation monitoring (QCM-D), oligomerization is an important parameter for a strong and stable binding to silica. The replacement of three sequence repeats by a (GGGGS)₁₂ glycine-rich spacer indicated that the overall length rather than the SBP oligomerization mediated the effective binding to silica.

Elucidating the Binding Mechanism of a Novel Silica-Binding Peptide

Linker-protein G (LPG) is a bifunctional fusion protein composed of a solid-binding peptide (SBP, referred as the "linker") with high affinity to silica-based compounds and a Streptococcus protein G (PG), which binds antibodies. The binding mechanisms of LPG to silica-based materials was studied using different biophysical techniques and compared to that of PG without the linker. LPG displayed high binding affinity to a silica surface (K_D = 34.77 ± 11.8 nM), with a vertical orientation, in comparison to parent PG, which exhibited no measurable binding affinity. Incorporation of the linker in the fusion protein, LPG, had no effect on the antibody-binding function of PG, which retained its secondary structure and displayed no alteration of its chemical stability. The LPG system provided a milder, easier, and faster affinity-driven immobilization of antibodies to inorganic surfaces when compared to traditional chemical coupling techniques.

Modeling the Cooperative Adsorption of Solid-Binding Proteins on Silica: Molecular Insights from Surface Plasmon Resonance Measurements

Combinatorially selected solid-binding peptides (SBPs) provide a versatile route for synthesizing advanced materials and devices, especially when they are installed within structurally or functionally useful protein scaffolds. However, their promise has not been fully realized because we lack a predictive understanding of SBP-material interactions. Thermodynamic and kinetic binding parameters obtained by fitting quartz crystal microbalance and surface plasmon resonance (SPR) data with the Langmuir model whose assumptions are rarely satisfied provide limited information on underpinning molecular interactions. Using SPR, we show here that a technologically useful SBP called Car9 confers proteins to which is fused a sigmoidal adsorption behavior modulated by partner identity, quaternary structure, and ionic strength. We develop a two-step cooperative model that accurately captures the kinetics of silica binding and provides insights into how SBP-SBP interactions, fused scaffold, and solution conditions modulate adsorption. Because cooperative binding can be converted to Langmuir adhesion by mutagenesis, our approach offers a path to identify and to better understand and design practically useful SBPs.

Adsorption of Collagen-like Peptides onto Gold Nanosurfaces

The molecular behavior of proteins in the presence of inorganic surfaces is of fundamental biological significance. Examples include extracellular matrix proteins interacting with gold nanoparticles and metallic implant biomaterials, such as titanium and stainless steels. Uncharged inorganic surfaces that interact strongly with the solution phase (hydrophilic surfaces) have been commonly used in disease treatments. A deep understanding of the molecular behavior of body proteins in the presence of hydrophilic surfaces is important in terms of clinical applications. However, the adsorption mechanism of proteins onto hydrophilic surfaces remains not fully understood. Here, comprehensive molecular dynamics simulations are carried out to study the molecular response of a human collagen molecule segment (CMS) to the presence of a planar gold surface (AuNS) in explicit solvent, aiming to unravel the adsorption mechanism of proteins onto hydrophilic surfaces. The results demonstrate that in the presence of AuNS, the CMS first biasedly diffuses toward AuNS, followed by anchoring to the gold surface, and finally adsorbs stepwise onto AuNS, where the protein adjusts its structure to maximize the interaction with AuNS. We conclude that adsorption of proteins onto hydrophilic surfaces adheres to three steps, namely, biased diffusion, anchoring, and stepwise adsorption accompanied by structural adaptation. The obtained adsorption mechanism provides insights into the development of inorganic surfaces for biomedical and therapeutic applications.

Interactions between Metal Oxides and Biomolecules: from Fundamental Understanding to Applications

Metallo-oxide (MO)-based bioinorganic nanocomposites promise unique structures, physicochemical properties, and novel biochemical functionalities, and within the past decade, investment in research on materials such as ZnO, TiO₂, SiO₂, and GeO₂ has significantly increased. Besides traditional approaches, the synthesis, shaping, structural patterning, and postprocessing chemical functionalization of the materials surface is inspired by strategies which mimic processes in nature. Would such materials deliver new technologies? Answering this question requires the merging of historical knowledge and current research from different fields of science. Practically, we need an effective defragmentation of the research area. From our perspective, the superficial accounting of material properties, chemistry of the surfaces, and the behavior of biomolecules next to such surfaces is a problem. This is particularly of concern when we wish to bridge between technologies in vitro and biotechnologies in vivo. Further, besides the potential practical technological efficiency and advantages such materials might exhibit, we have to consider the wider long-term implications of material stability and toxicity. In this contribution, we present a critical review of recent advances in the chemistry and engineering of MO-based biocomposites, highlighting the role of interactions at the interface and the techniques by which these can be studied. At the end of the article, we outline the challenges which hamper progress in research and extrapolate to developing and promising directions including additive manufacturing and synthetic biology that could benefit from molecular level understanding of interactions occurring between inanimate (abiotic) and living (biotic) materials.

Selection of a platinum-binding sequence in a loop of a four-helix bundle protein

Protein-metal hybrids are functional materials with various industrial applications. For example, a redox enzyme immobilized on a platinum electrode is a key component of some biofuel cells and biosensors. To create these hybrid materials, protein molecules are bound to metal surfaces. Here, we report the selection of a novel platinum-binding sequence in a loop of a four-helix bundle protein, the Lac repressor four-helix protein (LARFH), an artificial protein in which four identical α-helices are connected via three identical loops. We created a genetic library in which the Ser-Gly-Gln-Gly-Gly-Ser sequence within the first inter-helical loop of LARFH was semi-randomly mutated. The library was then subjected to selection for platinum-binding affinity by using the T7 phage display method. The majority of the selected variants contained the Tyr-Lys-Arg-Gly-Tyr-Lys (YKRGYK) sequence in their randomized segment. We characterized the platinum-binding properties of mutant LARFH by using quartz crystal microbalance analysis. Mutant LARFH seemed to interact with platinum through its loop containing the YKRGYK sequence, as judged by the estimated exclusive area occupied by a single molecule. Furthermore, a 10-residue peptide containing the YKRGYK sequence bound to platinum with reasonably high affinity and basic side chains in the peptide were crucial in mediating this interaction. In conclusion, we have identified an amino acid sequence, YKRGYK, in the loop of a helix-loop-helix motif that shows high platinum-binding affinity. This sequence could be grafted into loops of other polypeptides as an approach to immobilize proteins on platinum electrodes for use as biosensors among other applications.

Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity

Amyloids are highly ordered, hierarchal protein nanoassemblies. Functional amyloids in bacterial biofilms, such as Escherichia coli curli fibers, are formed by the polymerization of monomeric proteins secreted into the extracellular space. Curli is synthesized by living cells, is primarily composed of the major curlin subunit CsgA, and forms biological nanofibers with high aspect ratios. Here, we explore the application of curli fibers for nanotechnology by engineering curli to mediate tunable biological interfaces with inorganic materials and to controllably form gold nanoparticles and gold nanowires. Specifically, we used cell-synthesized curli fibers as templates for nucleating and growing gold nanoparticles and showed that nanoparticle size could be modulated as a function of curli fiber gold-binding affinity. Furthermore, we demonstrated that gold nanoparticles can be preseeded onto curli fibers and followed by gold enhancement to form nanowires. Using these two approaches, we created artificial cellular systems that integrate inorganic-organic materials to achieve tunable electrical conductivity. We envision that cell-synthesized amyloid nanofibers will be useful for interfacing abiotic and biotic systems to create living functional materials..

Solid-Binding Peptides in Biomedicine

Some peptides are able to bind to inorganic materials such as silica and gold. Over the past decade, Solid-binding peptides (SBPs) have been used increasingly as molecular building blocks in nanobiotechnology. These peptides show selectivity and bind with high affinity to a diverse range of inorganic surfaces e.g. metals, metal oxides, metal compounds, magnetic materials, semiconductors, carbon materials, polymers and minerals. They can be used in applications such as protein purification and synthesis, assembly and the functionalization of nanomaterials. They offer simple and versatile bioconjugation methods that can increase biocompatibility and also direct the immobilization and orientation of nanoscale entities onto solid supports without impeding their functionality. SBPs have been employed in numerous nanobiotechnological applications such as the controlled synthesis of nanomaterials and nanostructures, formation of hybrid biomaterials, immobilization of functional proteins and improved nanomaterial biocompatibility. With advances in nanotechnology, a multitude of novel nanomaterials have been designed and synthesized for diagnostic and therapeutic applications. New approaches have been developed recently to exert a greater control over bioconjugation and eventually, over the optimal and functional display of biomolecules on the surfaces of many types of solid materials. In this chapter we describe SBPs and highlight some selected examples of their potential applications in biomedicine.

PHASTpep: Analysis Software for Discovery of Cell-Selective Peptides via Phage Display and Next-Generation Sequencing

Next-generation sequencing has enhanced the phage display process, allowing for the quantification of millions of sequences resulting from the biopanning process. In response, many valuable analysis programs focused on specificity and finding targeted motifs or consensus sequences were developed. For targeted drug delivery and molecular imaging, it is also necessary to find peptides that are selective—targeting only the cell type or tissue of interest. We present a new analysis strategy and accompanying software, PHage Analysis for Selective Targeted PEPtides (PHASTpep), which identifies highly specific and selective peptides. Using this process, we discovered and validated, both in vitro and in vivo in mice, two sequences (HTTIPKV and APPIMSV) targeted to pancreatic cancer-associated fibroblasts that escaped identification using previously existing software. Our selectivity analysis makes it possible to discover peptides that target a specific cell type and avoid other cell types, enhancing clinical translatability by circumventing complications with systemic use.

Generic Biocombinatorial Strategy to Select Tailor-Made Stabilizers for Sol-Gel Nanoparticle Synthesis

A generic route for the selection of nanoparticle stabilizers via biocombinatorial means of phage display peptide screening is presented, providing magnesium fluoride nanoparticle synthesis as example. Selected sequence-specific MgF2 binders are evaluated for their adsorption behavior. Peptide-polymer conjugates derived from the best binding peptide are used for the stabilization of MgF2 sol nanoparticles, yielding fully redispersable dry states and improoving processability significantly.

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).

Tethering of Epidermal Growth Factor (EGF) to Beta Tricalcium Phosphate (βTCP) via Fusion to a High Affinity, Multimeric βTCP-Binding Peptide: Effects on Human Multipotent Stromal Cells/Connective Tissue Progenitors

Transplantation of freshly-aspirated autologous bone marrow, together with a scaffold, is a promising clinical alternative to harvest and transplantation of autologous bone for treatment of large defects. However, survival proliferation, and osteogenic differentiation of the marrow-resident stem and progenitor cells with osteogenic potential can be limited in large defects by the inflammatory microenvironment. Previous studies using EGF tethered to synthetic polymer substrates have demonstrated that surface-tethered EGF can protect human bone marrow-derived osteogenic stem and progenitor cells from pro-death inflammatory cues and enhance their proliferation without detriment to subsequent osteogenic differentiation. The objective of this study was to identify a facile means of tethering EGF to clinically-relevant βTCP scaffolds and to demonstrate the bioactivity of EGF tethered to βTCP using stimulation of the proliferative response of human bone-marrow derived mesenchymal stem cells (hBMSC) as a phenotypic metric. We used a phage display library and panned against βTCP and composites of βTCP with a degradable polyester biomaterial, together with orthogonal blocking schemes, to identify a 12-amino acid consensus binding peptide sequence, LLADTTHHRPWT, with high affinity for βTCP. When a single copy of this βTCP-binding peptide sequence was fused to EGF via a flexible peptide tether domain and expressed recombinantly in E. coli together with a maltose-binding domain to aid purification, the resulting fusion protein exhibited modest affinity for βTCP. However, a fusion protein containing a linear concatamer containing 10 repeats of the binding motif the resulting fusion protein showed high affinity stable binding to βTCP, with only 25% of the protein released after 7 days at 37oC. The fusion protein was bioactive, as assessed by its abilities to activate kinase signaling pathways downstream of the EGF receptor when presented in soluble form, and to enhance the proliferation of hBMSC when presented in tethered form on commercial βTCP bone regeneration scaffolds.

Protein-mediated hydroxyapatite composite layer formation on nanotubular titania

Realising controllable interactions at the bio-nanomaterial interfaces are vital in developing next-generation engineered implant materials. Titanium-based implants are key materials in biomedical engineering due to excellent bulk mechanical properties and biocompatibilities. Advanced bio-interfaces resolving nanostructured modulated surfaces that allow manipulation with the biological molecules is one of the keys to enhance favourable interactions with the surrounding biological species. Here, we developed a protein-mediated hydroxyapatite composite layer on nanotubular titania surface. Green fluorescence protein, engineered to contain hydroxyapatite binding peptides (GFPuv-HABP), was co-deposited with the hydroxyapatite precursors onto the titania nanotubes that are formed by anodisation. Ordered titanium dioxide nanotubular surfaces were coated with hydroxyapatite at physiological pH and temperature using simulated body fluid and pulsed electrochemical cathodisation. The hydroxyapatite deposit interdigitated into the nanotubes, producing a metal oxide-mineral composite. The engineered GFPuv-HABP protein was then self-assembled on the hydroxyapatite, forming a bio-modulated interface. Additionally, the engineered proteins were co-deposited with the precursor ions of hydroxyapatite mineral on the nanotubular titania plate. Bio-mediated assembly resulted in formation of a hybrid composite as an integrated interface on the nanotubular surface. Biomolecular assisted fabrication of hybrid composite interface on metal oxide substrate offers wide range of opportunities to design novel interfaces.

Engineering of the function of diamond-like carbon binding peptides through structural design

The use of phage display to select material-specific peptides provides a general route towards modification and functionalization of surfaces and interfaces. However, a rational structural engineering of the peptides for optimal affinity is typically not feasible because of insufficient structure-function understanding. Here, we investigate the influence of multivalency of diamond-like carbon (DLC) binding peptides on binding characteristics. We show that facile linking of peptides together using different lengths of spacers and multivalency leads to a tuning of affinity and kinetics. Notably, increased length of spacers in divalent systems led to significantly increased affinities. Making multimers influenced also kinetic aspects of surface competition. Additionally, the multivalent peptides were applied as surface functionalization components for a colloidal form of DLC. The work suggests the use of a set of linking systems to screen parameters for functional optimization of selected material-specific peptides.

Engineered peptides for nanohybrid assemblies

Inspired by biological material synthesis, synthetic biomineralization peptides have been screened through a laboratory evolution using biocombinatorial techniques. In this study, using the fine examples in nature, silica binding peptides and gold binding peptides were fused together to form a hybrid peptide. We designed fusion peptides with different gold binding and silica binding parts. First, we have tested the binding capability of the fusion peptides using quartz crystal microbalance on gold surface and silica surface. Second, S1G1 hybrid peptide enabled assembly of gold nanoparticles on a silica surface was achieved. Finally, nanomaterial synthesis ability of the S1G1 peptide was presented by the formation of a silica film on a gold surface. In this study, we are presenting a hybrid peptide tool for nanohybrid assembly as a promising route for nanotechnology applications.

Molecular-level understanding of protein adsorption at the interface between water and a strongly interacting uncharged solid surface

Although protein adsorption on solids is of immense relevance, experimental limitations mean there is still a remarkable lack of understanding of the adsorption mechanism, particularly at a molecular level. By subjecting 240+ molecular dynamics simulations of two peptide/water/solid surface systems to statistical analysis, a generalized molecular level mechanism for peptide adsorption has been identified for uncharged surfaces that interact strongly with the solution phase. This mechanism is composed of three phases: (1) biased diffusion of the peptide from the bulk phase toward the surface; (2) anchoring of the peptide to the water/solid interface via interaction of a hydrophilic group with the water adjacent to the surface or a strongly interacting hydrophobic group with the surface; and (3) lockdown of the peptide on the surface via a slow, stepwise and largely sequential adsorption of its residues, which we term 'statistical zippering'. The adsorption mechanism is dictated by the existence of water layers adjacent to the solid and orientational ordering therein. By extending the solid into the solution by ~8 Å and endowing it with a charged character, the water layers ensure the peptide feels the effect of the solid at a range well beyond the dispersion force that arises from it, thus inducing biased diffusion from afar. The charging of the interface also facilitates anchoring of the peptide near the surface via one of its hydrophilic groups, allowing it time it would otherwise not have to rearrange and lockdown. Finally, the slowness of the lockdown process is dictated by the need for the peptide groups to replace adjacent tightly bound interfacial water.

Evaluating protocols and analytical methods for peptide adsorption experiments

This paper evaluates analytical techniques that are relevant for performing reliable quantitative analysis of peptide adsorption on surfaces. Two salient problems are addressed: determining the solution concentrations of model GG-X-GG, X5, and X10 oligopeptides (G = glycine, X = a natural amino acid), and quantitative analysis of these peptides following adsorption on surfaces. To establish a uniform methodology for measuring peptide concentrations in water across the entire GG-X-GG and X n series, three methods were assessed: UV spectroscopy of peptides having a C-terminal tyrosine, the bicinchoninic acid (BCA) protein assay, and amino acid (AA) analysis. Due to shortcomings or caveats associated with each of the different methods, none were effective at measuring concentrations across the entire range of representative model peptides. In general, reliable measurements were within 30% of the nominal concentration based on the weight of as-received lyophilized peptide. In quantitative analysis of model peptides adsorbed on surfaces, X-ray photoelectron spectroscopy (XPS) data for a series of lysine-based peptides (GGKGG, K5, and K10) on Au substrates, and for controls incubated in buffer in the absence of peptides, suggested a significant presence of aliphatic carbon species. Detailed analysis indicated that this carbonaceous contamination adsorbed from the atmosphere after the peptide deposition. The inferred adventitious nature of the observed aliphatic carbon was supported by control experiments in which substrates were sputter-cleaned by Ar(+) ions under ultra-high vacuum (UHV) then re-exposed to ambient air. In contrast to carbon contamination, no adventitious nitrogen species were detected on the controls; therefore, the relative surface densities of irreversibly-adsorbed peptides were calculated by normalizing the N/Au ratios by the average number of nitrogen atoms per residue.

Enhancing in vitro selection techniques to assist the discovery, understanding and use of inorganic binding peptides

Reflecting the increasing interest in combinatorial approaches, peptide phage display has seen an unprecedented expansion in a wide range of research areas. Its application to the discovery and analysis of metal binding peptides has opened up new research directions and largely contributed to the nanotechnology field. The rationale behind the need to identify such peptides varies depending on the final aim of the research and its application. Therefore, the possibility to modify the selection technique according to the different requirements would allow for a more systematic approach to be adopted and would ultimately provide substantial benefits. Although the standard panning method can be virtually applied to any target, its use for the identification of metal binding peptides does not provide the characteristics and the flexibility required for an efficient and tailored selection. Here we report on the development of a new panning method that can contribute to a faster, versatile and more informative analysis. Through the use of rolling-circle amplification, polymerase reaction and wild type phage, we have converted the standard selection technique into a more dynamic process in which adjustments can be evaluated and made consistently with the need of the experiment. The successfulness of the improved method is demonstrated in a number of panning experiments with different inorganic targets. The modifications applied to each selection are described and comparisons between the results obtained are made in order to extensively assess and evaluate the impact of the new process. The importance of tailoring the screening method to the specific objectives of a study is also considered. New binder sequences for the materials included in the investigation are identified; their sequences and distinctive characteristics are reported and their ability to act as templates for the nucleation of inorganic material is demonstrated and discussed.

Biological response on a titanium implant-grade surface functionalized with modular peptides

Titanium (Ti) and its alloys are among the most successful implantable materials for dental and orthopedic applications. The combination of excellent mechanical and corrosion resistance properties makes them highly desirable as endosseous implants that can withstand a demanding biomechanical environment. Yet, the success of the implant depends on its osteointegration, which is modulated by the biological reactions occurring at the interface of the implant. A recent development for improving biological responses on the Ti-implant surface has been the realization that bifunctional peptides can impart material binding specificity not only because of their molecular recognition of the inorganic material surface, but also through their self-assembly and ease of biological conjugation properties. To assess peptide-based functionalization on bioactivity, the present authors generated a set of peptides for implant-grade Ti, using cell surface display methods. Out of 60 unique peptides selected by this method, two of the strongest titanium binding peptides, TiBP1 and TiBP2, were further characterized for molecular structure and adsorption properties. These two peptides demonstrated unique, but similar molecular conformations different from that of a weak binder peptide, TiBP60. Adsorption measurements on a Ti surface revealed that their disassociation constants were 15-fold less than TiBP60. Their flexible and modular use in biological surface functionalization were demonstrated by conjugating them with an integrin recognizing peptide motif, RGDS. The functionalization of the Ti surface by the selected peptides significantly enhanced the bioactivity of osteoblast and fibroblast cells on implant-grade materials.

Biocompatible silicon surfaces through orthogonal click chemistries and a high affinity silicon oxide binding peptide

Multifunctionality is gaining more and more importance in the field of improved biomaterials. Especially peptides feature a broad chemical variability and are versatile mediators between inorganic surfaces and living cells. Here, we synthesized a unique peptide that binds to SiO(2) with nM affinity. We equipped the peptide with the bioactive integrin binding c[RGDfK]-ligand and a fluorescent probe by stepwise Diels-Alder reaction with inverse electron demand and copper(I) catalyzed azide-alkyne cycloaddition. For the first time, we report the generation of a multifunctional peptide by combining these innovative coupling reactions. The resulting peptide displayed an outstanding binding to silicon oxide and induced a significant increase in cell spreading and cell viability of osteoblasts on the oxidized silicon surface.

Clues for biomimetics from natural composite materials

Bio-inspired material systems are derived from different living organisms such as plants, arthropods, mammals and marine organisms. These biomaterial systems from nature are always present in the form of composites, with molecular-scale interactions optimized to direct functional features. With interest in replacing synthetic materials with natural materials due to biocompatibility, sustainability and green chemistry issues, it is important to understand the molecular structure and chemistry of the raw component materials to also learn from their natural engineering, interfaces and interactions leading to durable and highly functional material architectures. This review will focus on applications of biomaterials in single material forms, as well as biomimetic composites inspired by natural organizational features. Examples of different natural composite systems will be described, followed by implementation of the principles underlying their composite organization into artificial bio-inspired systems for materials with new functional features for future medicine.

Techniques for Molecular Imaging Probe Design

Molecular imaging allows clinicians to visualize disease-specific molecules, thereby providing relevant information in the diagnosis and treatment of patients. With advances in genomics and proteomics and underlying mechanisms of disease pathology, the number of targets identified has significantly outpaced the number of developed molecular imaging probes. There has been a concerted effort to bridge this gap with multidisciplinary efforts in chemistry, proteomics, physics, material science, and biology—all essential to progress in molecular imaging probe development. In this review, we discuss target selection, screening techniques, and probe optimization with the aim of developing clinically relevant molecularly targeted imaging agents.

Adsorption of homopolypeptides on gold investigated using atomistic molecular dynamics

We investigate the role of dynamics on adsorption of peptides to gold surfaces using all-atom molecular dynamics simulations in explicit solvent. We choose six homopolypeptides [Ala(10), Ser(10), Thr(10), Arg(10), Lys(10), and Gln(10)], for which experimental surface coverages are not correlated with amino acid level affinities for gold, with the idea that dynamic properties may also play a role. To assess dynamics we determine both conformational movement and flexibility of the peptide within a given conformation. Low conformational movement indicates stability of a given conformation and leads to less adsorption than homopolypeptides with faster conformational movement. Likewise, low flexibility within a given conformation also leads to less adsorption. Neither amino acid affinities nor dynamic considerations alone predict surface coverage; rather both quantities must be considered in peptide adsorption to gold surfaces.

Assembly kinetics of nanocrystals via peptide hybridization

The assembly kinetics of colloidal semiconductor quantum dots (QDs) on solid inorganic surfaces is of fundamental importance for implementation of their solid-state devices. Herein an inorganic binding peptide, silica binding QBP1, was utilized for the self-assembly of nanocrystal quantum dots on silica surface as a smart molecular linker. The QD binding kinetics was studied comparatively in three different cases: first, QD adsorption with no functionalization of substrate or QD surface; second, QD adsorption on QBP1-modified surface; and, finally, adsorption of QBP1-functionalized QD on silica surface. The surface modification of QDs with QBP1 enabled 79.3-fold enhancement in QD binding affinity, while modification of a silica surface with QBP1 led to only 3.3-fold enhancement. The fluorescence microscopy images also supported a coherent assembly with correspondingly increased binding affinity. Decoration of QDs with inorganic peptides was shown to increase the amount of surface-bound QDs dramatically compared to the conventional methods. These results offer new opportunities for the assembly of QDs on solid surfaces for future device applications.

Peptide-mediated constructs of quantum dot nanocomposites for enzymatic control of nonradiative energy transfer

A bottom-up approach for constructing colloidal semiconductor quantum dot (QDot) nanocomposites that facilitate nonradiative Förster-type resonance energy transfer (FRET) using polyelectrolyte peptides was proposed and realized. The electrostatic interaction of these polypeptides with altering chain lengths was probed for thermodynamic, structural, and morphological aspects. The resulting nanocomposite film was successfully cut with the protease by digesting the biomimetic peptide layer upon which the QDot assembly was constructed. The ability to control photoluminescence decay lifetime was demonstrated by proteolytic enzyme activity, opening up new possibilities for biosensor applications.

DNA libraries for the construction of phage libraries: statistical and structural requirements and synthetic methods

Peptide-based molecular probes identified by bacteriophage (phage) display technology expand the peptide repertoire for in vivo diagnosis and therapy of cancer. Numerous peptides that bind cancer-associated antigens have been discovered by panning phage libraries. However, until now only few of the peptides selected by phage display have entered clinical applications. The success of phage derived peptides essentially depends on the quality of the library screened. This review summarizes the methods to achieve highly homogenous libraries that cover a maximal sequence space. Biochemical and chemical strategies for the synthesis of DNA libraries and the techniques for their integration into the viral genome are discussed in detail. A focus is set on the methods that enable the exclusion of disturbing sequences. In addition, the parameters that define the variability, the minimal numbers of copies per library and the use of alternating panning cycles to avoid the loss of selected hits are evaluated.

Material binding peptides for nanotechnology

Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.

Biological identification of peptides that specifically bind to poly(phenylene vinylene) surfaces: recognition of the branched or linear structure of the conjugated polymer

Peptides that bind to poly(phenylene vinylene) (PPV) were identified by the phage display method. Aromatic amino acids were enriched in these peptide sequences, suggesting that a π-π interaction is the key interaction between the peptides and PPV. The surface plasmon resonance (SPR) experiments using chemically synthesized peptides demonstrated that the Hyp01 peptide, with the sequence His-Thr-Asp-Trp-Arg-Leu-Gly-Thr-Trp-His-His-Ser, showed an affinity constant (7.7 × 10(5) M(-1)) for the target, hyperbranched PPV (hypPPV) film. This value is 15-fold greater than its affinity for linear PPV (linPPV). In contrast, the peptide screened for linPPV (Lin01) showed the reverse specificity for linPPV. These results suggested that the Hyp01 and Lin01 peptides selectively recognized the linear or branched structure of PPVs. The Ala-scanning experiment, circular dichroism (CD) spectrometry, and molecular modeling of the Hyp01 peptide indicated that adequate location of two Trp residues by forming the polyproline type II (P(II)) helical conformation allowed the peptide to specifically interact with hypPPV.

Biological surface effects of metallic nanomaterials for applications in assembly and catalysis

Recent experimental evidence has suggested that bioinspired techniques represent promising avenues toward the production of functional nanomaterials that possess a high degree of activity. These materials are prepared under synthetically simple and efficient conditions, thus making them attractive alternatives to many traditional methods that employ hazardous and harsh conditions. Many biomimetic methods employ peptide and amino acid binding events on the surfaces of nanostructures to generate materials that are stable in solution. The basis of both the stability and activity of these materials is likely to be controlled by the biotic/abiotic interface, which is mediated by the bioligand binding process. Unfortunately, most readily available techniques are unable to be used to study this intrinsic process; however, very recent studies have begun to shed light on this important event. In this feature article, an overview of the understanding of peptide and amino acid binding events to nanomaterials and how these motifs can be exploited for activities in nanoparticle assembly and catalytic reactivity is discussed. From both 2D surface studies and computational modeling analyses, different biomolecule binding characteristics have been elucidated. These results indicate that the amino acid sequence and peptide secondary structure play important roles in the binding capability. Furthermore, these studies suggest that the peptides are able to form specific patterns and motifs once bound to the nanoparticle surface. This attribute could affect the nanoparticle electronics and can play a significant role in their activities to generate functional materials. From these binding motifs, the ability of reagents to interact with the metallic surface is possible, thus affecting many of the properties of these materials.

Staphylococcus aureus resistance on titanium coated with multivalent PEGylated-peptides

Bacterial infections can have adverse effects on the efficacy, lifetime and safety of an implanted device and are the second most commonly attributed cause of orthopedic implant failure. We have previously shown the assembly of PEGylated titanium-binding peptides (TBPs) on Ti to obtain a bacteriophobic surface coating that can effectively resist protein adsorption and Staphylococcus aureus (S. aureus) adhesion. In the present study, we examine the effect of multiple TBP repeats on coating performance in vitro. Mono, di, and tetravalent peptides were synthesized and assessed for binding affinity and serum stability. PEGylated analogs were prepared and evaluated for their effect on S. aureus attachment and biofilm formation. Coating performance improved with the number of TBP repeats, with the tetravalent coating, TBP(4)-PEG, showing the best performance in all assays. In particular, TBP(4)-PEG forms a serum-resistant surface coating capable of preventing S. aureus colonization and subsequent biofilm formation. These results further support the role that multivalency can play in the development of improved surface coatings with enhanced stabilities and efficacy for in vivo clinical use.