Identification of Soft Matter Binding Peptide Ligands Using Phage Display

Peptide-Based Recognition Agents of Histamine: A Biopanning Approach with Enhanced Specificity

Histamine is a biogenic amine that poses a potential threat to public health due to its toxicological effects. In this study, we identified histamine-binding peptides by screening a random 12-mer peptide library, employing a novel biopanning approach that excluded histidine-binding sequences in the final round. This additional step enhanced the selectivity of the peptides and prevented interference from histidine during detection. The binding affinities of synthesized peptides to histamine were assessed using isothermal titration calorimetry (ITC). Among the identified peptides, HBF10 (SGFRDGIEDFLW) and HBF26 (IPLENQHKIYST) showed significant affinity to histamine, with Ka values of 2.56×104 (M-1) and 8.94×104 (M-1), respectively. Notably, the identified peptides did not demonstrate binding affinity towards histidine, despite its structural similarity to histamine. Subsequently, the surface plasmon resonance (SPR) sensor surface was prepared by immobilizing the peptide HBF26 to investigate the potential of the peptide as a recognition agent for histamine detection. The findings suggest that the identified peptides have an affinity to histamine specifically, showcasing their potential applications as diagnostic agents with specific targeting capabilities.

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.

Mariz B, Moreira IP, Kalafatovic D, Morais Faustino BM, Narang V, Wang T, Pappas CG, Ferreira I, Roque ACA, Ulijn RV. Discovery of phosphotyrosine-binding oligopeptides with supramolecular target selectivity

Phage-display screening on self-assembled tyrosine-phosphate ligands enables the identification of oligopeptides selective to dynamic supramolecular targets, with the lead peptide showing a preferred hairpin-like conformation and catalytic activity.

Identification of Water-Soluble Polymers through Discrimination of Multiple Optical Signals from a Single Peptide Sensor

The pollution of water environments is a worldwide concern. Not only marine pollution by plastic litter, including microplastics, but also the spillage of water-soluble synthetic polymers in wastewater have recently gained increasing attention due to their potential risks to soil and water environments. However, conventional methods to identify polymers dissolved in water are laborious and time-consuming. Here, we propose a simple approach to identify synthetic polymers dissolved in water using a peptide-based molecular sensor with a fluorophore unit. Supervised machine learning of multiple fluorescence signals from the sensor, which specifically or nonspecifically interacted with the polymers, was applied for polymer classification as a proof of principle demonstration. Aqueous solutions containing different polymers or multiple polymer species with different mixture ratios were identified successfully. We found that fluorophore-introduced biomolecular sensors have great potential to provide discriminative information regarding water-soluble polymers. Our approach based on the discrimination of multiple optical signals of water-soluble polymers from peptide-based molecular sensors through machine learning will be applicable to next-generation sensing systems for polymers in wastewater or natural environments.

Modelling peptide adsorption energies on gold surfaces with an effective implicit solvent and surface model

The interaction of proteins and peptides with inorganic surfaces is relevant in a wide array of technological applications. A rational approach to design peptides for specific surfaces would build on amino-acid and surface specific interaction models, which are difficult to characterize experimentally or by modeling. Even with such a model at hand, the large number of possible sequences and the large conformation space of peptides make comparative simulations challenging. Here we present a computational protocol, the effective implicit surface model (EISM), for efficient in silico evaluation of the binding affinity trends of peptides on parameterized surface, with a specific application to the widely studied gold surface. In EISM the peptide surface interactions are modeled with an amino-acid and surface specific implicit solvent model, which permits rapid exploration of the peptide conformational degrees of freedom. We demonstrate the parametrization of the model and compare the results with all-atom simulations and experimental results for specific peptides.

Design of peptides with strong binding affinity to poly(methyl methacrylate) resin by use of molecular simulation-based materials informatics

Peptides with strong binding affinities for poly(methyl methacrylate) (PMMA) resin were designed by use of materials informatics technology based on molecular dynamics simulation for the purpose of covering the resin surface with adhesive peptides, which were expected to result in eco-friendly and biocompatible biomaterials. From the results of binding affinity obtained with this molecular simulation, it was confirmed that experimental values could be predicted with errors <10%. By analyzing the simulation data with the response-surface method, we found that three peptides (RWWRPWW, EWWRPWR, and RWWRPWR), which consist of arginine (R), tryptophan (W), and proline (P), have strong binding affinity to the PMMA resin. These amino acids were effective because arginine and tryptophan have strong binding affinities for methoxycarbonyl groups and methyl groups, which are the main constituents of the PMMA resin, and proline stabilizes the flat zigzag structures of the peptides in water. The strong binding affinities of the three peptides were confirmed by experiments (surface plasmon resonance methods).

A minimalistic cyclic ice-binding peptide from phage display

Developing molecules that emulate the properties of naturally occurring ice-binding proteins (IBPs) is a daunting challenge. Rather than relying on the (limited) existing structure-property relationships that have been established for IBPs, here we report the use of phage display for the identification of short peptide mimics of IBPs. To this end, an ice-affinity selection protocol is developed, which enables the selection of a cyclic ice-binding peptide containing just 14 amino acids. Mutational analysis identifies three residues, Asp8, Thr10 and Thr14, which are found to be essential for ice binding. Molecular dynamics simulations reveal that the side chain of Thr10 hydrophobically binds to ice revealing a potential mechanism. To demonstrate the biotechnological potential of this peptide, it is expressed as a fusion ('Ice-Tag') with mCherry and used to purify proteins directly from cell lysate.

Accessing the Next Generation of Synthetic Mussel-Glue Polymers via Mussel-Inspired Polymerization

The formation of cysteinyldopa as biogenic connectivity in proteins is used to inspire a chemical pathway toward mussel-adhesive mimics. The mussel-inspired polymerization (MIPoly) exploits the chemically diverse family of bisphenol monomers that is oxidizable with 2-iodoxybenzoic acid to give bisquinones. Those react at room temperature with dithiols in Michael-type polyadditions, which leads to polymers with thiol-catechol connectivities (TCC). A set of TCC polymers proved adhesive behavior even on challenging poly(propylene) substrates, where they compete with commercial epoxy resins in dry adhesive strength. MIPoly promises facile scale up and exhibits high modularity to tailor adhesives, as proven on a small library where one candidate showed wet adhesion on aluminum substrates in both water and sea water models.

Discovery of Surfactant-Like Peptides from a Phage-Displayed Peptide Library

Peptides with specific affinities for various materials have been identified in the past three decades and utilized in materials science and engineering. A peptide's capability to specifically interact with materials is not naturally derived but screened from a biologically constructed peptide library displayed on phages or cells. To date, due to limitations in the screening procedure, the function of screened peptides has been primarily limited to the affinity for target materials. Herein, we demonstrated the screening of surfactant-like peptides from a phage-displayed peptide library. A screened phage clone displaying a peptide showed high activity for accumulating at emulsion surfaces with certain assembled structures, resulting in stable emulsions. The surface tension for the solution of the chemically synthesized peptide decreased with increasing peptide concentration, demonstrating certain surface activity, which corresponded to the ability to decrease the surface tension of liquids (e.g., water), owing to the accumulation of molecules at the air-liquid or liquid-liquid interface. Peptides with a randomized sequence did not lower the surface tension, indicating the essential role of amino acid sequences in surface activity. Our strategy for identifying novel functional peptides from a phage-displayed peptide library can be used to expand the applicability of peptidyl materials and biosurfactants.

Affinity-based thermoresponsive fluorescence switching of proteins conjugated with a polymer-binding peptide

The affinity-based thermoresponsive fluorescence switching of proteins conjugated with a polymer-binding peptide is demonstrated. The specific affinity of the peptide and thermoresponsive structural transitions of the polymer are essential for reliable fluorescence switching behavior.

Evaluation of a peptide motif designed for protein tethering to polymer surfaces

In search for peptide motifs that allow us to efficiently tether fusion proteins onto polymer surfaces, we designed a KLKLKLKLKL (KL5) decapeptide in which basic and hydrophobic amino acids were alternately linked. By means of genetic engineering technology together with a bacterial expression system, the KL5 fusions of epidermal growth factor (EGF), basic fibroblast growth factor, and stromal cell-derived factor-1α were prepared together with their control counterparts without KL5. The adsorption experiments were performed for these fusion proteins on the surface of polystyrene, hydrophilized polystyrene, and polycaprolactone by surface plasmon resonance analysis. To understand the results of the binding assays, the structure of the fusion proteins was predicted by ab initio computer simulation and analyzed empirically by circular dichroism spectroscopy. The result of structural analyses suggested that the KL5 peptide is exposed to the outside and has a negligible effect on the structure of the protein partners. However, it was found that the efficiency of KL5 as a peptide motif greatly depends on protein partners. Our results showed that KL5 exerts most effectively its function as a peptide motif when fused to acidic proteins such as EGF. Indeed, the number of living human mesenchymal stem cells determined after 7-day culture was larger on the polystyrene and polycaprolactone surfaces with EGF tethered through the KL5 peptide than control surfaces. According to the results obtained in this study, we conclude that KL5 is useful as a peptide motif for tethering a specific class of protein partners.

Preparation of Biocomposite Soft Nanoparticles Composed of Poly(Propylene Oxide) and the Polymer-Binding Peptides

The molecular recognition capability of naturally occurring biomolecules is generally expressed against biomolecules in the biological milieu. Recently, it was demonstrated that the specific interactions of biomolecules such as short peptides were applicable to artificial materials. We have developed peptides with specific affinities for synthetic polymers toward functional biocomposite polymeric materials. In this study, we demonstrated the preparation of biocomposite nanoparticles composed of poly(propylene oxide) (PPO) and PPO-binding peptides. A simple injection of a concentrated PPO solution dissolved in an organic solvent into the peptide solution under sonication resulted in the formation of nanospherical structures. Morphological observation indicated characteristic softness and high applicability as a molecular carrier of the biocomposite nanoparticles. Structural characterization of PPO and the PPO-binding peptide revealed the structural conformability of these molecules to interact specifically with each other. Our findings expand the potential applicability of polymer-binding peptides for the future construction of biomedical materials composed of peptides and various polymers.

Affinity-Based Functionalization of Biomedically Utilized Micelles Composed of Triblock Copolymers through Polymer-Binding Peptides

Polymeric micelles and vesicles that are self-assembled from amphiphilic block copolymers are frequently used in biomedical applications. Poly(ethylene oxide) (PEO)-poly(propylene oxide) (PPO)-PEO, so-called Pluronic, is a Food and Drug Administration approved triblock copolymer utilized in biomedical applications. However, the control of drug loading and surface functionalization of micelles remain challenging due to structural limitations. In this study, Pluronic micelles with various structures were rationally functionalized via the PPO-binding peptide, which was previously identified using a biologically constructed peptide library displayed on filamentous phages. The interactions between the peptide and Pluronic micelles were characterized in detail based on fluorescence changes in an extrinsic fluorescence dye, and a sufficient PPO chain length of Pluronic was essential for the interactions. Furthermore, enzymatic degradation of the model substrate-conjugated peptide loaded into Pluronic micelles showed stable loading of the peptide. Importantly, the exposure level of the conjugated molecules to the peptide was dependent on the PEO chain length of Pluronic, suggesting controllable functionalization of polymeric micelles. Anticancer drug-conjugated peptide-loaded Pluronic micelles with suitable polymeric structures were applied in a cell culture assay. The anticancer efficacy of the loaded drugs can be controlled by the molecular design of the binding peptide and polymers. These results demonstrate that an affinity-based functionalization strategy may facilitate polymeric micelles for various biomedical applications.

Selection of Peptides that Associate with Dye-Conjugated Solid Surfaces in a pH-Dependent Manner Using cDNA Display

Peptides that recognize artificial materials including synthetic polymers and small molecules are drawing attention in the fields of biotechnology and chemical biology. In particular, reversible peptide aptamers that associate with the target molecules only under specific conditions are interesting. In this work, peptide aptamers that recognize a phenolphthalein derivative (PhP: a pH-sensitive organic dye) immobilized on a solid surface in a pH-dependent manner were selected using an in vitro display method (cDNA display). Considering the hydrophobic and aromatic nature of PhP, we prepared a biased DNA library (3A library) that encodes more aromatic amino acids than the standard random codon and performed seven rounds of selection from >10¹⁰ peptide species. The selected peptides including LVFLIWWM (LV59) associated with PhP-modified solid support (sepharose resin and magnetic beads) in neutral buffer but readily dissociated under basic conditions where PhP undergoes large structural change from lactone to quinoid, which is accompanied by increase of hydrophilicity and anionic charge. Control experiments suggested that LV59 recognized both phenol and lactone moieties, and the association under neutral pH is mainly driven by π-stacking and hydrophobic interaction between the peptide and PhP. Notably, however, total hydrophobicity and number of aromatic rings did not completely explain the affinity, and sequence specificity was observed to some extent. After further optimization, this interaction pair would be practically useful for protein purification.

Experimental and theoretical tools to elucidate the binding mechanisms of solid-binding peptides

The interactions between biomolecules and solid surfaces play an important role in designing new materials and applications which mimic nature. Recently, solid-binding peptides (SBPs) have emerged as potential molecular building blocks in nanobiotechnology. SBPs exhibit high selectivity and binding affinity towards a wide range of inorganic and organic materials. Although these peptides have been widely used in various applications, there is a need to understand the interaction mechanism between the peptide and its material substrate, which is challenging both experimentally and theoretically. This review describes the main characterisation techniques currently available to study SBP-surface interactions and their contribution to gain a better insight for designing new peptides for tailored binding.

Specific Decoration of a Discrete Bismuth Oxido Cluster by Selected Peptides towards the Design of Metal Tags

Metal tags find application in a multitude of biomedical systems and the combination with laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) offers an opportunity for multiplexing. To lay the foundation for an increase of the signal intensities in such processes, we herein present a general approach for efficient functionalization of a well-defined metal oxido cluster [Bi₆ O₄ (OH)₄ (SO₃ CF₃ )₆ (CH₃ CN)₆ ]⋅2 CH₃ CN (1), which can be realized by selecting 7mer peptide sequences via combinatorial means from large one-bead one-compound peptide libraries. Selective cluster-binding peptide sequences (CBS) for 1 were discriminated from non-binders by treatment with H₂ S gas to form the reduction product Bi₂ S₃ , clearly visible to the naked eye. Interactions were further confirmed by NMR experiments. Extension of a binding peptide with a maleimide linker (Mal) introduces the possibility to covalently attach thiol-bearing moieties such as biological probes and for their analysis the presence of the cluster instead of mononuclear entities should lead to an increase of signal intensities in LA-ICP-MS measurements. To prove this, CBS-Mal was covalently bound onto thiol-presenting glass substrates, which then captured 1 effectively, so that LA-ICP-MS measurements demonstrated drastic signal amplification compared to single lanthanide tags.

Bioinspired structural transition of synthetic polymers through biomolecular ligand binding

The bioinspired structural transition of thermoresponsive poly(N-isopropylacrylamide) was demonstrated by specific ligand binding of artificially evolved peptides to the polymer.

Selective Peptide-Mediated Enhanced Deposition of Polymer Fragrance Delivery Systems on Human Hair

The deposition of fragrance delivery systems onto human hair from a shampoo formulation is a challenging task, as the primary function of shampoo is to cleanse the hair by removing primarily hydrophobic moieties. In this work, to tackle this challenge, phage-display-identified peptides that can bind to human hair under shampooing conditions are first identified and subsequently used to enhance the deposition of model fragrance delivery systems. These delivery systems are based on either poly(N-(2-hydroxypropyl)methacrylamide) (PHPMA) copolymers as a representative for polymeric profragrances or polyurethane/polyurea-type core-shell microcapsules as a model physical fragrance carrier. The incorporation of a hair-binding peptide enhanced the deposition of PHPMA copolymers by a factor of 3.5-5.0 depending on the extent of peptide incorporation, whereas 10 wt % surface functionalization of microcapsules with the peptide led to a 20-fold increase in their deposition. In a final experiment, treatment of the hair samples under realistic application conditions with the peptide-functionalized microcapsules resulted in an increase in fragrance release from the hair surfaces.

Orientation and Incorporation of Photosystem I in Bioelectronics Devices Enabled by Phage Display

Interfacing proteins with electrode surfaces is important for the field of bioelectronics. Here, a general concept based on phage display is presented to evolve small peptide binders for immobilizing and orienting large protein complexes on semiconducting substrates. Employing this method, photosystem I is incorporated into solid-state biophotovoltaic cells.

Enzyme-Triggered Antifouling Coatings: Switching Bioconjugate Adsorption via Proteolytically Cleavable Interfering Domains

Protease activable antifouling coatings based on peptide-poly(ethylene glycol) conjugates are shown. The material-specific adsorption of a bioconjugate is temporarily suppressed by extending a titanium binding sequence with a proteolytically cleavable epitope and a suitable interfering domain. The adsorption of the PEG-peptide conjugates onto titanium substrates can be regained by cleaving the interfering domain with Tobacco Etch Virus protease. This activates peptide-mediated PEGylation of titanium surfaces and results in coatings that are stable against dilution and suppress nonreversible adsorption of blood protein models. Effects of branched and linear peptidic binding domains on coating stability and antifouling properties are elucidated.

Affinity-based release of polymer-binding peptides from hydrogels with the target segments of peptides

Peptides with affinities for the target segments of polymer hydrogels were identified by phage display methods and exhibited affinity-based release capability from the hydrogels. The sustained anticancer effects of the drug-conjugated peptides were also demonstrated by their release from the hydrogels.

Affinity-based thermoresponsive precipitation of proteins modified with polymer-binding peptides

A model protein (i.e., human serum albumin) chemically modified with a 12-mer peptide with an affinity for the meso diad sequence of poly(N-isopropylacrylamide) (PNIPAM) was successfully precipitated with PNIPAM above the lower critical solution temperature of PNIPAM.