Isolation of ZnO-Binding 12-mer Peptides and Determination of Their Binding Epitopes by NMR Spectroscopy

Molecular Adhesion of a Pilus-Derived Peptide Involved in Pseudomonas aeruginosa Biofilm Formation on Non-Polar ZnO-Surfaces

Bacterial colonization and biofilm formation on abiotic surfaces are initiated by the adhesion of peptides and proteins. Understanding the adhesion of such peptides and proteins at a molecular level thus represents an important step toward controlling and suppressing biofilm formation on technological and medical materials. This study investigates the molecular adhesion of a pilus-derived peptide that facilitates biofilm formation of Pseudomonas aeruginosa, a multidrug-resistant opportunistic pathogen frequently encountered in healthcare settings. Single-molecule force spectroscopy (SMFS) was performed on chemically etched ZnO11 2 ‾ 0 ${\left(11\bar{2}0\right)}$ surfaces to gather insights about peptide adsorption force and its kinetics. Metal-free click chemistry for the fabrication of peptide-terminated SMFS cantilevers was performed on amine-terminated gold cantilevers and verified by X-ray photoelectron spectroscopy (XPS) and polarization-modulated infrared reflection absorption spectroscopy (PM-IRRAS). Atomic force microscopy (AFM) and XPS analyses reveal stable topographies and surface chemistries of the substrates that are not affected by SMFS. Rupture events described by the worm-like chain model (WLC) up to 600 pN were detected for the non-polar ZnO surfaces. The dissociation barrier energy at zero force ΔG(0), the transition state distance xb and bound-unbound dissociation rate at zero force koff (0) for the single crystalline substrate indicate that coordination and hydrogen bonds dominate the peptide/surface interaction.

Functional mimicry of sea urchin biomineralization proteins with CaCO3-binding peptides selected by phage display

The intricate process of biomineralization, e.g. in sea urchins, involves the precise interplay of highly regulated mineralization proteins and the spatiotemporal coordination achieved through compartmentalization. However, the investigation of biomineralization effector molecules, e.g. proteins, is challenging, due to their very low abundance. Therefore, we investigate the functional mimicry in the bioinspired precipitation of calcium carbonate (CaCO3) with artificial peptides selected from a peptide library by phage display based on peptide-binding to calcite and aragonite, respectively. The structure-directing effects of the identified peptides were compared to those of natural protein mixes isolated from skeletal (test) structures of two sea urchin species (Arbacia lixula and Paracentrotus lividus). The calcium carbonate samples deposited in the absence or presence of peptides were analyzed with a set of complementary techniques with regard to morphology, polymorph, and nanostructural motifs. Remarkably, some of the CaCO3-binding peptides induced morphological features in calcite that appeared similar to those obtained in the presence of the natural protein mixes. Many of the peptides identified as most effective in exerting a structure-directing effect on calcium carbonate crystallization were rich in basic amino acid residues. Hence, our in vitro mineralization study further highlights the important, but often neglected, role of positively charged soluble organic matrices associated with biological and bioinspired CaCO3 deposition.

Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints

The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.

Identification of the First Sulfobetaine Hydrogel-Binding Peptides via Phage Display Assay

Using the M13 phage display, a series of 7- and 12-mer peptides which interact with new sulfobetaine hydrogels are identified. Two peptides each from the 7- and 12-mer peptide libraries bind to the new sulfobetaine hydrogels with high affinity compared to the wild-type phage lacking a dedicated hydrogel binding peptide. This is the first report of peptides binding to zwitterionic sulfobetaine hydrogels and the study therefore opens up the pathway toward new phage or peptide/hydrogel hybrids with high application potential.

Rational Design of a Bifunctional Peptide Exhibiting Lithium Titanate Oxide and Carbon Nanotube Affinities for Lithium-Ion Battery Applications

Phage display is employed as a method for identifying polypeptides that bind to lithium-ion battery materials, specifically lithium titanate oxide (LTO) and multiwalled carbon nanotubes (MWCNTs). Output/input assays are used as a quantitative measure to narrow down the strongest binding polypeptides from several peptides selected through biopanning. Negatively stained transmission electron microscopy is used to verify that a phage presenting a particular LTO or MWCNT binding peptide sequence colocalizes with the respective material. Heterologous expression allows for ample polypeptides to be grown and purified using a peptide expression vector. Isothermal titration calorimetry in conjunction with alanine scanning enables determination of the pertinent residues involved in LTO binding and yields a dissociation constant of 3.41 μM. A rationally designed bifunctional peptide exhibiting LTO and MWCNT binding domains is subsequently validated to exhibit both LTO and MWCNT affinities and is incorporated as a binding agent in LTO coin-type electrochemical cells where the bifunctional peptide demonstrates stability at high cycle rates and potential as an alternative to non-specific binding agents for aqueous slurry processing of lithium-ion battery electrodes.

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.

Strong Structural and Electronic Binding of Bovine Serum Albumin to ZnO via Specific Amino Acid Residues and Zinc Atoms

ZnO biointerfaces with serum albumin have attracted noticeable attention due to the increasing interest in developing ZnO-based materials for biomedical applications. ZnO surface morphology and chemistry are expected to play a critical role on the structural, optical, and electronic properties of albumin-ZnO complexes. Yet there are still large gaps in the understanding of these biological interfaces. Herein we comprehensively elucidate the interactions at such interfaces by using atomic force microscopy and nanoshaving experiments to determine roughness, thickness, and adhesion properties of BSA layers adsorbed on the most typical polar and non-polar ZnO single-crystal facets. These experiments are corroborated by force field (FF) and density-functional tight-binding (DFTB) calculations on ZnO-BSA interfaces. We show that BSA adsorbs on all the studied ZnO surfaces while interactions of BSA with ZnO are found to be considerably affected by the atomic surface structure of ZnO. BSA layers on the ( 000 1 ‾ ) surface have the highest roughness and thickness, hinting at a specific upright BSA arrangement. BSA layers on ( 10 1 ‾ 0 ) surface have the strongest binding, which is well correlated with DFTB simulations showing atomic rearrangement and bonding between specific amino acids (AAs) and ZnO. Besides the structural properties, the ZnO interaction with these AAs also controls the charge transfer and HOMO-LUMO energy positions in the BSA-ZnO complexes. This ZnO facet-specific protein binding and related structural and electronic effects can be useful for improving the design and functionality of ZnO-based materials and devices.

Peptide-based system for sensing Pb2+ and molecular logic computing

Peptides with recognition, assembly, various activities exhibit strong power and application prospects in sensing, material science, biomedicine. However, peptide-based sensing and expanding application is still at an early stage. Herein, a peptide-based sensing and logic system was developed for highly sensitive and selective detection of Pb²⁺ and implementation of logic operations. Our Pb²⁺ assay method was ultra-rapid (less than 1 min), direct, simple with detection limit of 0.75 nM. Flexibility and scalability of peptide-based solution system facilitated the execution of sensing and logic operations from simple to complex. This research will not only inspire discovery and comprehensive applications (such as sensing and assembly) of more functional peptides, but also provide more opportunities for development and design of peptide-based systems and molecular information technologies.

Investigation of Adsorption Behavior of Anticancer Drug on Zinc Oxide Nanoparticles: A Solid State NMR and Cyclic Voltammetry (CV) Analysis

The present study aims to comprehend the adsorption behavior of a set of anticancer drugs namely 5-fluorouracil (5-FU), doxorubicin and daunorubicin on ZnO nanoparticles (ZnO NPs) proposed as drug delivery systems employing solid state (ss) NMR, FTIR and Cyclic Voltammetry (CV) analysis. FTIR and ¹H MAS ssNMR data recorded for bare ZnO nanoparticle confirmed the presence of adsorbed -OH groups on the surface. ¹³C CP-MAS NMR spectra recorded for free and ZnO surface adsorbed drug samples exhibited considerable line broadening and chemical shift changes that complemented our earlier report on UV-DRS and XRD data of surface adsorption in case of 5-FU. Moreover, a remarkable enhancement of ¹³C signal intensity in case of loaded 5-FU was observed. This clearly indicated rigid nature of the drug on the surface allowing efficient transfer of ¹H polarization from the hetero nitrogen of 5-FU to ZnO to form surface hydroxyl (-OH) groups and the same has been observed in the quantum chemical calculations. To further analyze the motional dynamics of the surface adsorbed 5-FU, longitudinal relaxation times (T₁) were quantified employing Torchia method that revealed significant enhancement of ¹³C relaxation rate of adsorbed 5-FU. The enhanced rate suggested an effective role of quadrupolar contribution from ⁶⁷Zn to the ¹³C relaxation mechanism of ZnO_5-FU. The heterogeneous rate constant (k_het), average free energy of activation (∆G^≠) and point of zero charge (PZC) measured for free and drug loaded ZnO NPs samples using CV further support the SS-NMR results.

Lessons from a Challenging System: Accurate Adsorption Free Energies at the Amino Acid/ZnO Interface

We undertake steps to overcome four challenges that have hindered the understanding of ZnO/biomolecule interfaces at the atomic scale: parametrization of a classical force field, ZnO surface termination and amino acid protonation state in methanol, and convergence of enhanced sampling molecular dynamics simulations. We predict adsorption free energies for histidine, serine, cysteine, and tryptophan in remarkable agreement with experimental measurements obtained via a novel indicator-displacement assay. Adsorption is driven by direct surface/amino-acid interactions mediated by terminal hydroxyl groups and stabilized by strongly structured methanol solvation shells.

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.

A novel biofunctionalizing peptide for metallic alloy

OBJECTIVES

Improving biocompatibility of metallic alloy biomaterials has been of great interest to prevent implant associated-diseases, such as stent thrombosis. Herein a simple and efficient procedure was designed to biofunctionalize a biomaterial surface by isolating a SUS316L stainless steel binding peptide.

RESULTS

After three rounds of phage panning procedure, 12 mer peptide (SBP-A; VQHNTKYSVVIR) was identified as SUS316L-binding peptide. The SBP-A peptide formed a stable bond to a SUS316L modified surface and was not toxic to HUVECs. The SBP-A was then used for anti-ICAM antibody modification on SUS316L to construct a vascular endothelial cell-selective surface. The constructed surface dominantly immobilized vascular endothelial cells to smooth muscle cells, demonstrating that the SBP-A enabled simple immobilization of biomolecules without disturbing their active biological function.

CONCLUSIONS

The SUS316L surface was successfully biofunctionalized using the novel isolated peptide SBP-A, showing its potential as an ideal interface molecule for stent modification. This is the first report of material binding peptide-based optimal surface functionalization to promote endothelialisation. This simple and efficient biofunctionalization procedure is expected to contribute to the development of biocompatible materials.

Platform for Screening Abiotic/Biotic Interactions Using Indicator Displacement Assays

This paper describes novel adaptations of optically sectioned planar format assays to screen compounds for their affinities to materials surfaces. The novel platform, which we name optically sectioned indicator displacement assays (O-IDA), makes use of displaceable dyes in a format adaptable to high-throughput multiwell plate technologies. We describe two approaches: the first being where the dye exhibits fluorescence in both the surface bound and unbound state and the second, where fluorescence is lost upon displacement of the dye from the surface. Half maximal inhibitory concentration (IC₅₀), binding affinity (K_i), and binding free energy (ΔG_ads) values can be extracted from the raw data. Representative biomolecules were tested for interactions with silica in an aqueous environment and ZnO(0001)-Zn and (10-10) facets in a nonaqueous environment. We provide the first experimental values for both the binding of small molecules to silica and the facet-dependent ZnO binding affinity of key amino acids associated with ZnO-specific oligopeptides. The specific data will be invaluable to those studying interactions at interfaces both experimentally and computationally. O-IDA provides a general framework for the high-throughput screening of molecule binding to materials surfaces, which has important applications in drug delivery, (bio-) catalysis, biosensing, and biomaterial engineering.

Bioprospecting solid binding polypeptides for lithium ion battery cathode materials

Biotemplating presents a promising approach to improve the performance of inorganic materials via specific control over morphology, crystal structure, and the size of particles during synthesis and assembly. Among other biotemplates, solid binding polypeptides (SBPs) isolated for the material of interest provide high binding affinity and selectivity due to distinct combinations of functional groups found in amino acids. Nanomaterials assembled and synthesized with SBPs have found widespread applications from drug delivery to catalysis and energy storage due to their improved properties. In this study, the authors describe the identification of SBPs for binding to Li-ion battery cathode materials LiCoPO₄, LiMn_1.5Ni_0.5O₄, and LiMn₂O₄, which all have potential for improvement toward their theoretical values. The binding affinity of isolated peptides was assessed via phage binding assays and confirmed with electron microscopy in order to select for potential biotemplates. The authors demonstrate ten binding peptides for each material and analyze the sequences for enrichment in specific amino acids toward each structure (olivine and spinel oxide), as well as the test for specificity of selected sequences. In further studies, the authors believe that the isolated SBPs will serve as a template for synthesis and aid in assembly of cathode materials resulting in improved electrochemical properties for Li-ion batteries.

Genetically Modified M13 Bacteriophage Nanonets for Enzyme Catalysis and Recovery

Enzyme-based biocatalysis exhibits multiple advantages over inorganic catalysts, including the biocompatibility and the unchallenged specificity of enzymes towards their substrate. The recovery and repeated use of enzymes is essential for any realistic application in biotechnology, but is not easily achieved with current strategies. For this purpose, enzymes are often immobilized on inorganic scaffolds, which could entail a reduction of the enzymes’ activity. Here, we show that immobilization to a nano-scaled biological scaffold, a nanonetwork of end-to-end cross-linked M13 bacteriophages, ensures high enzymatic activity and at the same time allows for the simple recovery of the enzymes. The bacteriophages have been genetically engineered to express AviTags at their ends, which permit biotinylation and their specific end-to-end self-assembly while allowing space on the major coat protein for enzyme coupling. We demonstrate that the phages form nanonetwork structures and that these so-called nanonets remain highly active even after re-using the nanonets multiple times in a flow-through reactor.

Phage Display in the Quest for New Selective Recognition Elements for Biosensors

Phages are bacterial viruses that have gained a significant role in biotechnology owing to their widely studied biology and many advantageous characteristics. Perhaps the best-known application of phages is phage display that refers to the expression of foreign peptides or proteins outside the phage virion as a fusion with one of the phage coat proteins. In 2018, one half of the Nobel prize in chemistry was awarded jointly to George P. Smith and Sir Gregory P. Winter "for the phage display of peptides and antibodies." The outstanding technology has evolved and developed considerably since its first description in 1985, and today phage display is commonly used in a wide variety of disciplines, including drug discovery, enzyme optimization, biomolecular interaction studies, as well as biosensor development. A cornerstone of all biosensors, regardless of the sensor platform or transduction scheme used, is a sensitive and selective bioreceptor, or a recognition element, that can provide specific binding to the target analyte. Many environmentally or pharmacologically interesting target analytes might not have naturally appropriate binding partners for biosensor development, but phage display can facilitate the production of novel receptors beyond known biomolecular interactions, or against toxic or nonimmunogenic targets, making the technology a valuable tool in the quest of new recognition elements for biosensor development.

Peptide Controlled Shaping of Biomineralized Tin(II) Oxide into Flower-Like Particles

The size and morphology of metal oxide particles have a large impact on the physicochemical properties of these materials, e.g., the aspect ratio of particles affects their catalytic activity. Bioinspired synthesis routes give the opportunity to control precisely the structure and aspect ratio of the metal oxide particles by bioorganic molecules, such as peptides. This study focusses on the identification of tin(II) oxide (tin monoxide, SnO) binding peptides, and their effect on the synthesis of crystalline SnO microstructures. The phage display technique was used to identify the 7-mer peptide SnBP01 (LPPWKLK), which shows a high binding affinity towards crystalline SnO. It was found that the derivatives of the SnBP01 peptide, varying in peptide length and thus in their interaction, significantly affect the aspect ratio and the size dimension of mineralized SnO particles, resulting in flower-like morphology. Furthermore, the important role of the N-terminal leucine residue in the peptide for the strong organic⁻inorganic interaction was revealed by FTIR investigations. This bioinspired approach shows a facile procedure for the detailed investigation of peptide-to-metal oxide interactions, as well as an easy method for the controlled synthesis of tin(II) oxide particles with different morphologies.

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.

Cancer cells biomineralize ionic gold into nanoparticles-microplates via secreting defense proteins with specific gold-binding peptides

Cancer cells have the capacity to synthesize nanoparticles (NPs). The detailed mechanism of this process is not very well documented. We report the mechanism of biomineralization of aqueous gold chloride into NPs and microplates in the breast-cancer cell line MCF7. Spherical gold NPs are synthesized in these cells in the presence of serum in the culture media by the reduction of HAuCl₄. In the absence of serum, the cells exhibit gold microplate formation through seed-mediate growth albeit slower reduction. The structural characteristics of the two types of NPs under different media conditions were confirmed using scanning electron microscopy (SEM); crystallinity and metallic properties were assessed with transmission electron microscopy (TEM) and x-ray photoelectron spectroscopy (XPS). Gold-reducing proteins, related to cell stress initiate the biomineralization of HAuCl₄ in cells (under serum free conditions) as confirmed by infrared (IR) spectroscopy. MCF7 cells undergo irreversible replicative senescence when exposed to a high concentration of ionic gold and conversely remain in a dormant reversible quiescent state when exposed to a low gold concentration. The latter cellular state was achievable in the presence of the rho/ROCK inhibitor Y-27632. Proteomic analysis revealed consistent expression of specific proteins under serum and serum-free conditions. A high-throughput proteomic approach to screen gold-reducing proteins and peptide sequences was utilized and validated by quartz crystal microbalance with dissipation (QCM-D).

STATEMENT OF SIGNIFICANCE

Cancer cells are known to synthesize gold nanoparticles and microstructures, which are promising for bioimaging and other therapeutic applications. However, the detailed mechanism of such biomineralization process is not well understood yet. Herein, we demonstrate that cancer cells exposed to gold ions (grown in serum/serum-free conditions) secrete shock and stress-related proteins with specific gold-binding/reducing polypeptides. Cells undergo reversible senescence and can recover normal physiology when treated with the senescence inhibitor depending on culture condition. The use of mammalian cells as microincubators for synthesis of such particles could have potential influence on their uptake and biocompatibility. This study has important implications for in-situ reduction of ionic gold to anisotropic micro-nanostructures that could be used in-vivo clinical applications and tumor photothermal therapy.

Biogenic and Synthetic Peptides with Oppositely Charged Amino Acids as Binding Sites for Mineralization

Proteins regulate diverse biological processes by the specific interaction with, e.g., nucleic acids, proteins and inorganic molecules. The generation of inorganic hybrid materials, such as shell formation in mollusks, is a protein-controlled mineralization process. Moreover, inorganic-binding peptides are attractive for the bioinspired mineralization of non-natural inorganic functional materials for technical applications. However, it is still challenging to identify mineral-binding peptide motifs from biological systems as well as for technical systems. Here, three complementary approaches were combined to analyze protein motifs consisting of alternating positively and negatively charged amino acids: (i) the screening of natural biomineralization proteins; (ii) the selection of inorganic-binding peptides derived from phage display; and (iii) the mineralization of tobacco mosaic virus (TMV)-based templates. A respective peptide motif displayed on the TMV surface had a major impact on the SiO₂ mineralization. In addition, similar motifs were found in zinc oxide- and zirconia-binding peptides indicating a general binding feature. The comparative analysis presented here raises new questions regarding whether or not there is a common design principle based on acidic and basic amino acids for peptides interacting with minerals.

Discovery of 12-mer peptides that bind to wood lignin

Lignin, an abundant terrestrial polymer, is the only large-volume renewable feedstock composed of an aromatic skeleton. Lignin has been used mostly as an energy source during paper production; however, recent interest in replacing fossil fuels with renewable resources has highlighted its potential value in providing aromatic chemicals. Highly selective degradation of lignin is pivotal for industrial production of paper, biofuels, chemicals, and materials. However, few studies have examined natural and synthetic molecular components recognizing the heterogeneous aromatic polymer. Here, we report the first identification of lignin-binding peptides possessing characteristic sequences using a phage display technique. The consensus sequence HFPSP was found in several lignin-binding peptides, and the outer amino acid sequence affected the binding affinity of the peptides. Substitution of phenylalanine7 with Ile in the lignin-binding peptide C416 (HFPSPIFQRHSH) decreased the affinity of the peptide for softwood lignin without changing its affinity for hardwood lignin, indicating that C416 recognised structural differences between the lignins. Circular dichroism spectroscopy demonstrated that this peptide adopted a highly flexible random coil structure, allowing key residues to be appropriately arranged in relation to the binding site in lignin. These results provide a useful platform for designing synthetic and biological catalysts selectively bind to lignin.

Development and characterization of antibody reagents for detecting nanoparticles

The increasing use of nanoparticles (NPs) in technological applications and in commercial products has escalated environmental health and safety concerns. The detection of NPs in the environment and in biological systems is challenged by limitations associated with commonly used analytical techniques. In this paper we report on the development and characterization of NP binding antibodies, termed NProbes. Phage display methodology was used to discover antibodies that bind NPs dispersed in solution. We present a proof-of-concept for the generation of NProbes and their use for detecting quantum dots and titanium dioxide NPs in vitro and in an ex vivo human skin model. Continued development and refinement of NProbes to detect NPs that vary in composition, shape, size, and surface coating will comprise a powerful tool kit that can be used to advance nanotechnology research particularly in the nanotoxicology and nanotherapeutics fields.

Effects of crystallographic facet-specific peptide adsorption along single ZnO nanorods on the characteristic fluorescence intensification on nanorod ends (FINE) phenomenon

The precise effect of crystallographically discriminating biomolecular adsorption on the fluorescence intensification profiles of individual zinc oxide nanorod (ZnO NR) platforms was elucidated in this study by employing peptide binding epitopes biased towards particular ZnO crystal surfaces and isolating the peptides on given crystalline facets of ZnO NRs. Subsequently, the fluorescence emission profiles of the preferentially bound peptide cases on the basal versus prismic planes of ZnO NRs were carefully evaluated both experimentally and via computer simulations. The phenomenon of fluorescence intensification on NR ends (FINE) was persistently observed on the individual ZnO NR platforms, regardless of the location of the bound peptides. In contrast to the consistent occurrence of FINE, the degree and magnitude of FINE were largely influenced by the discriminatory peptide adsorption to different ZnO NR facets. The temporal stability of the fluorescence signal was also greatly affected by the selectively located peptides on the ZnO NR crystal when spatially resolved on different NR facets. Similarities and differences in the spatial and temporal fluorescence signal of the crystalline NR facet-specific versus -nonspecific biomolecular adsorption events were then compared. To further illuminate the basis of our experimental findings, we also performed finite-difference-time-domain (FDTD) calculations and examined the different degrees of FINE by modelling the biased peptide adsorption cases. Our multifaceted efforts, providing combined insight into the spatial and temporal characteristics of the biomolecular fluorescence signal characteristically governed by the biomolecular location on the specific NR facets, will be valuable for novel applications and accurate signal interpretation of ZnO NR-based biosensors in many rapidly growing, highly miniaturized biodetection configurations.

Low-Index ZnO Crystal Plane-Specific Binding Behavior of Whole Immunoglobulin G Proteins

Crystallographic surface-resolved examination of protein-ZnO interactions can greatly enhance the fundamental understanding of protein adsorption on these technologically important solid surfaces which, in turn, will be tremendously valuable for the emerging applications of ZnO-based biomaterials and biosensors. We examine experimentally and via computer simulations the intriguing differences in the adsorption preferences and binding behavior of whole immunoglobulin G (IgG) proteins to various, low-index ZnO crystal surfaces at the individual biomolecule level. By performing direct atomic force microscopy imaging, we determine that IgG predominantly binds to the ZnO plane of (101̅0) relative to the other three low-index planes of (0001), (0001̅), and (112̅0). This phenomenon is highly unusual, particularly considering the fact that the average binding energy of amino acids (AAs) on the ZnO (0001) facet is higher than that on the (101̅0) plane. In conjunction with combined Monte Carlo-molecular dynamics simulations, we further explain the possible origins of our unusual experimental findings with critical factors such as the specific spatial locations of strongly binding AAs in the protein and their spatial distributions on the exterior surface of the protein.

Generation of Multishell Magnetic Hybrid Nanoparticles by Encapsulation of Genetically Engineered and Fluorescent Bacterial Magnetosomes with ZnO and SiO2

Magnetic nanoparticles (MNPs) have great potential in biomedical applications, but the chemical synthesis of size-controlled and functionalized core-shell MNPs remain challenging. Magnetosomes produced by the magnetotactic bacterium Magnetospirillum gryphiswaldense are naturally uniform and chemically pure magnetite MNPs with superior magnetic characteristics. Here, additional functionalities are made possible by the incorporation of biomolecules on the magnetosome surface; the magnetosome system is then chemically encapsulated with an inorganic coating. The novel multishell nanoparticles consist of the magnetosome core-which includes the magnetite crystal, the magnetosome membrane, and additional moieties, such as the enhanced green fluorescent protein (EGFP) and peptides-and an outer shell, comprising either silica or zinc oxide. Coating the functionalized magnetosomes with silica improves their colloidal stability and preserves the EGFP fluorescence in the presence of proteases and detergents. In addition, the surface charge of magnetosomes can be adjusted by varying the coating. This method will be useful for the versatile generation of new, multifunctional, multishell, and magnetic hybrid nanomaterials with potential applications in various biotechnological fields.

Peptide-equipped tobacco mosaic virus templates for selective and controllable biomineral deposition

The coating of regular-shaped, readily available nanorod biotemplates with inorganic compounds has attracted increasing interest during recent years. The goal is an effective, bioinspired fabrication of fiber-reinforced composites and robust, miniaturized technical devices. Major challenges in the synthesis of applicable mineralized nanorods lie in selectivity and adjustability of the inorganic material deposited on the biological, rod-shaped backbones, with respect to thickness and surface profile of the resulting coating, as well as the avoidance of aggregation into extended superstructures. Nanotubular tobacco mosaic virus (TMV) templates have proved particularly suitable towards this goal: Their multivalent protein coating can be modified by high-surface-density conjugation of peptides, inducing and governing silica deposition from precursor solutions in vitro. In this study, TMV has been equipped with mineralization-directing peptides designed to yield silica coatings in a reliable and predictable manner via precipitation from tetraethoxysilane (TEOS) precursors. Three peptide groups were compared regarding their influence on silica polymerization: (i) two peptide variants with alternating basic and acidic residues, i.e. lysine-aspartic acid (KD) x motifs expected to act as charge-relay systems promoting TEOS hydrolysis and silica polymerization; (ii) a tetrahistidine-exposing polypeptide (CA4H4) known to induce silicification due to the positive charge of its clustered imidazole side chains; and (iii) two peptides with high ZnO binding affinity. Differential effects on the mineralization of the TMV surface were demonstrated, where a (KD) x charge-relay peptide (designed in this study) led to the most reproducible and selective silica deposition. A homogenous coating of the biotemplate and tight control of shell thickness were achieved.

Thermodynamic Study of Interactions Between ZnO and ZnO Binding Peptides Using Isothermal Titration Calorimetry

While material-specific peptide binding sequences have been identified using a combination of combinatorial methods and computational modeling tools, a deep molecular level understanding of the fundamental principles through which these interactions occur and in some instances modify the morphology of inorganic materials is far from being fully realized. Understanding the thermodynamic changes that occur during peptide-inorganic interactions and correlating these to structural modifications of the inorganic materials could be the key to achieving and mastering control over material formation processes. This study is a detailed investigation applying isothermal titration calorimetry (ITC) to directly probe thermodynamic changes that occur during interaction of ZnO binding peptides (ZnO-BPs) and ZnO. The ZnO-BPs used are reported sequences G-12 (GLHVMHKVAPPR), GT-16 (GLHVMHKVAPPR-GGGC), and alanine mutants of G-12 (G-12A6, G-12A11, and G-12A12) whose interaction with ZnO during solution synthesis studies have been extensively investigated. The interactions of the ZnO-BPs with ZnO yielded biphasic isotherms comprising both an endothermic and an exothermic event. Qualitative differences were observed in the isothermal profiles of the different peptides and ZnO particles studied. Measured ΔG values were between -6 and -8.5 kcal/mol, and high adsorption affinity values indicated the occurrence of favorable ZnO-BP-ZnO interactions. ITC has great potential in its use to understand peptide-inorganic interactions, and with continued development, the knowledge gained may be instrumental for simplification of selection processes of organic molecules for the advancement of material synthesis and design.

Generation of luminescence in biomineralized zirconia by zirconia-binding peptides

Current materials research is inspired from biomineralization processes, where proteins control the formation of inorganic materials under soft reaction conditions.

Peptide-directed crystal growth modification in the formation of ZnO

ZnO-binding peptides, differing only by Met or Cys at position 5 modify the mechanism of ZnO crystal growth.

Structure–charge relationship – the case of hematite (001)

We present a multidisciplinary study on the hematite (001)–aqueous solution interface, in particular the relationship between surface structure (studiedviasurface diffraction in a humid atmosphere) and the macroscopic charging (studiedviasurface- and zeta-potential measurements in electrolyte solutions as a function of pH). Upon aging in water changes in the surface structure are observed, that are accompanied by drastic changes in the zeta-potential. Surprisingly the surface potential is not accordingly affected. We interpret our results by increasing hydration of the surface with time and enhanced reactivity of singly-coordinated hydroxyl groups that cause the isoelectric point of the surface to shift to values that are reminiscent of those typically reported for hematite particles. In its initial stages after preparation the hematite surface is very flat and only weakly hydrated. Our model links the entailing weak water structure with the observed low isoelectric point reminiscent of hydrophobic surfaces. The absence of an aging effect on the surface potentialvs.pH curves is interpreted as domination of the surface potential by the doubly coordinated hydroxyls, which are present on both surfaces.

A rational biomimetic approach to structure defect generation in colloidal nanocrystals

Controlling the morphology of nanocrystals (NCs) is of paramount importance for both fundamental studies and practical applications. The morphology of NCs is determined by the seed structure and the following facet growth. While means for directing facet formation in NC growth have been extensively studied, rational strategies for the production of NCs bearing structure defects in seeds have been much less explored. Here, we report mechanistic investigations of high density twin formation induced by specific peptides in platinum (Pt) NC growth, on the basis of which we derive principles that can serve as guidelines for the rational design of molecular surfactants to introduce high yield twinning in noble metal NC syntheses. Two synergistic factors are identified in producing twinned Pt NCs with the peptide: (1) the altered reduction kinetics and crystal growth pathway as a result of the complex formation between the histidine residue on the peptide and Pt ions, and (2) the preferential stabilization of {111} planes upon the formation of twinned seeds. We further apply the discovered principles to the design of small organic molecules bearing similar binding motifs as ligands/surfactants to create single and multiple twinned Pd and Rh NCs. Our studies demonstrate the rich information derived from biomimetic synthesis and the broad applicability of biomimetic principles to NC synthesis for diverse property tailoring.

On the limited recognition of inorganic surfaces by short peptides compared with antibodies

The vast potential applications of biomolecules that bind inorganic surfaces led mostly to the isolation of short peptides that target selectively specific materials. The demonstrated differential affinity toward certain surfaces created the impression that the recognition capacity of short peptides may match that of rigid biomolecules. In the following, we challenge this view by comparing the capacity of antibody molecules to discriminate between the (100) and (111A) facets of a gallium arsenide semiconductor crystal with the capacity of short peptides to do the same. Applying selection from several peptide and single chain phage display libraries, we find a number of antibody molecules that bind preferentially a given crystal facet but fail to isolate, in dozens of attempts, a single peptide capable of such recognition. The experiments underscore the importance of rigidity to the recognition of inorganic flat targets and therefore set limitations on potential applications of short peptides in biomimetics.

Biomimetic magnetite formation: from biocombinatorial approaches to mineralization effects

Biological materials typically display complex morphologies and hierarchical architectures, properties that are hardly matched by synthetic materials. Understanding the biological control of mineral properties will enable the development of new synthetic approaches toward biomimetic functional materials. Here, we combine biocombinatorial approaches with a proteome homology search and in vitro mineralization assays to assess the role of biological determinants in biomimetic magnetite mineralization. Our results suggest that the identified proteins and biomimetic polypeptides influence nucleation in vitro. Even though the in vivo role cannot be directly determined from our experiments, we can rationalize the following design principles: proteins, larger complexes, or membrane components that promote nucleation in vivo are likely to expose positively charged residues to a negatively charged crystal surface. In turn, components with acidic (negatively charged) functionality are nucleation inhibitors, which stabilize an amorphous structure through the coordination of iron.

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.

Selection of peptides binding to metallic borides by screening M13 phage display libraries

Background

Metal borides are a class of inorganic solids that is much less known and investigated than for example metal oxides or intermetallics. At the same time it is a highly versatile and interesting class of compounds in terms of physical and chemical properties, like semiconductivity, ferromagnetism, or catalytic activity. This makes these substances attractive for the generation of new materials. Very little is known about the interaction between organic materials and borides. To generate nanostructured and composite materials which consist of metal borides and organic modifiers it is necessary to develop new synthetic strategies. Phage peptide display libraries are commonly used to select peptides that bind specifically to metals, metal oxides, and semiconductors. Further, these binding peptides can serve as templates to control the nucleation and growth of inorganic nanoparticles. Additionally, the combination of two different binding motifs into a single bifunctional phage could be useful for the generation of new composite materials.

Results

In this study, we have identified a unique set of sequences that bind to amorphous and crystalline nickel boride (Ni₃B) nanoparticles, from a random peptide library using the phage display technique. Using this technique, strong binders were identified that are selective for nickel boride. Sequence analysis of the peptides revealed that the sequences exhibit similar, yet subtle different patterns of amino acid usage. Although a predominant binding motif was not observed, certain charged amino acids emerged as essential in specific binding to both substrates. The 7-mer peptide sequence LGFREKE, isolated on amorphous Ni₃B emerged as the best binder for both substrates. Fluorescence microscopy and atomic force microscopy confirmed the specific binding affinity of LGFREKE expressing phage to amorphous and crystalline Ni₃B nanoparticles.

Conclusions

This study is, to our knowledge, the first to identify peptides that bind specifically to amorphous and to crystalline Ni₃B nanoparticles. We think that the identified strong binding sequences described here could potentially serve for the utilisation of M13 phage as a viable alternative to other methods to create tailor-made boride composite materials or new catalytic surfaces by a biologically driven nano-assembly synthesis and structuring.

Identification of binding peptides on calcium silicate hydrate: a novel view on cement additives

Phage display experiments on industrially important calcium silicate hydrates (C-S-H), the main hydration product of ordinary Portland cement, suggest fundamentally different specific binding motifs compared to hitherto existing commercial cement additives. According to that, a strong and specific adsorbing additive on C-S-H should have three features which are a negative charge, H-bond formers (especially amide functions) and a hydrophobic part.

Controlling mixed-protein adsorption layers on colloidal alumina particles by tailoring carboxyl and hydroxyl surface group densities

We show that different ratios of bovine serum albumin (BSA) and lysozyme (LSZ) can be achieved in a mixed protein adsorption layer by tailoring the amounts of carboxyl (-COOH) and aluminum hydroxyl (AlOH) groups on colloidal alumina particles (d50 ≈ 180 nm). The particles are surface-functionalized with -COOH groups, and the resultant surface chemistry, including the remaining AlOH groups, is characterized and quantified using elemental analysis, ζ potential measurements, acid-base titration, IR spectroscopy, electron microscopy, nitrogen adsorption, and dynamic light scattering. BSA and LSZ are subsequently added to the particle suspensions, and protein adsorption is monitored by in situ ζ potential measurements while being quantified by UV spectroscopy and gel electrophoresis. A comparison of single-component and sequential protein adsorption reveals that BSA and LSZ have specific adsorption sites: BSA adsorbs primarily via AlOH groups, whereas LSZ adsorbs only via -COOH groups (1-2 -COOH groups on the particle surface is enough to bind one LSZ molecule). Tailoring such groups on the particle surface allows control of the composition of a mixed BSA and LSZ adsorption layer. The results provide further insight into how particle surface chemistry affects the composition of protein adsorption layers on colloidal particles and is valuable for the design of such particles for biotechnological and biomedical applications.

Genetically engineered peptides for inorganics: study of an unconstrained bacterial display technology and bulk aluminum alloy

The first-ever peptide biomaterial discovery using an unconstrained engineered bacterial display technology is reported. Using this approach, we have developed genetically engineered peptide binders for a bulk aluminum alloy and use molecular dynamics simulation of peptide conformational fluctuations to demonstrate sequence-dependent, structure-function relationships for metal and metal oxide interactions.

Probing the interaction of individual amino acids with inorganic surfaces using atomic force spectroscopy

This article describes single-molecule force spectroscopy measurements of the interaction between individual amino acid residues and inorganic surfaces in an aqueous solution. In each measurement, there is an amino acid residue, lysine, glutamate, phenylalanine, leucine, or glutamine, and each represents a class of amino acids (positively or negatively charged, aromatic, nonpolar, and polar). Force-distance curves measured the interaction of the individual amino acid bound to a silicon atomic force microscope (AFM) tip with a silcon substrate, cut from a single-crystal wafer, or mica. Using this method, we were able to measure low adhesion forces (below 300 pN) and could clearly determine the strength of interactions between the individual amino acid residues and the inorganic substrate. In addition, we observed how changes in the pH and ionic strength of the solution affected the adsorption of the residues to the substrates. Our results pinpoint the important role of hydrophobic interactions among the amino acids and the substrate, where hydrophobic phenylalanine exhibited the strongest adhesion to a silicon substrate. Additionally, electrostatic interactions also contributed to the adsorption of amino acid residues to inorganic substrates. A change in the pH or ionic strength values of the buffer altered the strength of interactions among the amino acids and the substrate. We concluded that the interplay between the hydrophobic forces and electrostatic interactions will determine the strength of adsorption among the amino acids and the surface. Overall, these results contribute to our understanding of the interaction at the organic-inorganic interface. These results may have implications for our perception of the specificity of peptide binding to inorganic surfaces. Consequently, it would possibly lead to a better design of composite materials and devices.

Development of an oligopeptide functionalized surface plasmon resonance biosensor for online detection of glyphosate

We report a surface plasmon resonance (SPR) biosensor for online detection of glyphosate. The surface of the sensing element is decorated with an oligopeptide, TPFDLRPSSDTR, which is identified by using phage display library. This oligopeptide shows high binding specificity for glyphosate (KD = 8.6 μM), probably because of the presence of R and D in the oligopeptide. To detect glyphosate in buffer solution, an SPR gold sensor chip is modified by using the oligopeptide with a surface density of 0.6 1/nm(2). The sensitivity of this oligopeptide-functionalized SPR biosensor is 1.02 RU/μM whereas the limit of detection (LOD) is 0.58 μM. This oligopeptide functionalized SPR biosensor also shows good specificity against other analytes such as glycine, thiacloprid, and imidacloprid.