Proximity labeling and identification of endogenous client proteins recruited to Y15-based artificial granules tethering a bait protein.

Protein clustering is a ubiquitous event in diverse cellular processes. Self-association of proteins triggers recruitment of downstream proteins to regulate cellular signaling. To investigate the interactions in detail, chemical biology tools to identify proteins recruited to defined assemblies are required. Here, we exploit an identification of proteins recruited in artificial granules (IPRAG) platform that combines intracellular Y15-based supramolecule construction with a proximity labeling method. We validated the IPRAG tool using Nck1 as a target bait protein. We constructed Nck1-tethering granules, labeled the recruited proteins with biotin, and analyzed them by LC-MS/MS. As a result, we successfully identified proteins that directly or indirectly interact with Nck1.

Pattern enrichment analysis for phage selection of stapled peptide ligands.

Phage display is the most widely used technique to discover de novo peptides that bind to target proteins. However, it is associated with some challenges such as compositional bias. In this study, to overcome these difficulties, we devised a 'pattern enrichment analysis.' In this method, two samples (one obtained by affinity selection, the other simply amplified without selection) are prepared, and the two sequence datasets read on next-generation sequencer are compared to find the three-residue pattern most enriched in the selected sample. This allows us to compare two sequence datasets with high coverage and facilitates the identification of peptide sequences and the key residues for binding. We also demonstrated that this approach in the combination with structured peptide libraries allowed spatial mapping of the enriched sequence patterns. Here, we prepared a phage library displaying chemically stapled helical peptides with the X1C2X3X4X5X6X7X8C9X10 sequence, where X is any amino acid. To validate our method, we performed screening against the HDM2 protein. The results showed that the hydrophobic residues (Phe, Tyr, Trp and Leu) that are key to interactions with HDM2 were clearly identified by the pattern enrichment analysis. We also performed selection targeting the SARS-CoV-2 spike RBD in the same manner. The results showed that similar patterns were enriched among the hit peptides that inhibited the protein-protein interaction.

Effects of Hydrophobic Residues on the Intracellular Self-Assembly of De Novo Designed Peptide Tags and Their Orthogonality.

Protein assemblies forming nano- to micro-sized structures underlie versatile biological events in living systems. For mimicking and engineering these protein assemblies through a bottom-up approach, self-assembling peptides (SAPs) that form nanofibril structures via ß-sheets serve as potential practical tags. Nevertheless, the development of SAP tags is still in its infancy, and insight into the relationship between peptide sequences and intracellular self-assembly is limited. In this study, we focused on hydrophobic residues in SAPs and examined the self-assembly of SAP-tagged superfolder GFPs (green fluorescent proteins) in COS-7 cells. Based on XEXK (X; hydrophobic amino acids: F, L, I, V, W, or Y) sequence units, we designed a panel of Xn peptides with different hydrophobic residues (X) and chain lengths (n). We observed that the self-assembly propensity, the size of the assemblies, the influence on protein denaturation, and the subcellular localization differed significantly depending on the hydrophobic amino acid. F9, L9, I7, and V13 peptides formed µm-scaled granules, W13 formed small oligomeric clusters in the cytoplasm, and Y15 formed assemblies in the nucleus. In addition, we investigated the orthogonality of their interaction. Strikingly, W13- and Y15-tagged proteins interacted independently and formed two distinct assemblies in cells. Herein, we have demonstrated the great opportunities for rationalizing artificial protein assemblies and orthogonal structures in an intracellular context using the designed SAPs.

A guide-tag system controlling client enrichment into Y15 peptide-based granules for an in-cell protein recruitment assay.

Self-assembling peptides (SAPs) are valuable building blocks for the fabrication of artificial supramolecules. We developed a guide-tag system that concentrates client proteins into SAP-based scaffolds in cellular environments at various enrichment levels. This system provides a tool to analyse the protein-protein interactions caused by protein clustering in cells.

Biofunctional supramolecular hydrogels fabricated from a short self-assembling peptide modified with bioactive sequences for the 3D culture of breast cancer MCF-7 cells.

Self-assembling peptides are a type of molecule with promise as scaffold materials for cancer cell engineering. We have reported a short self-assembling peptide, (FFiK)2, that had a symmetric structure connected via a urea bond. In this study, we functionalized (FFiK)2 by conjugation with various bioactive sequences for the 3D culture of cancer cells. Four sequences, RGDS and PHSRN derived from fibronectin and AG73 and C16 derived from laminin, were selected as bioactive sequences to promote cell adhesion, proliferation or migration. (FFiK)2, and its derivatives could co-assemble into supramolecular nanofibers displaying bioactive sequences and form hydrogels. MCF-7 cells were encapsulated in functionalized peptide hydrogels without significant cytotoxicity. Encapsulated MCF-7 cells proliferated under 3D culture conditions. MCF-7 cells proliferated with spheroid formation in hydrogels that displayed RGDS or PHSRN sequences, which will be able to be applied to drug screening targeting cancer stem cells. On the other hand, since MCF-7 cells migrated in a 3D hydrogel that displayed AG73, we could construct the metastatic model of breast cancer cells, which is helpful for the elucidation of breast cancer cells and drug screening against cancer cells under metastatic state. Therefore, functionalized (FFiK)2 hydrogels with various bioactive sequences can be used to regulate cancer cell function for tumor engineering and drug screening.

Intracellular artificial supramolecules based on de novo designed Y15 peptides.

De novo designed self-assembling peptides (SAPs) are promising building blocks of supramolecular biomaterials, which can fulfill a wide range of applications, such as scaffolds for tissue culture, three-dimensional cell culture, and vaccine adjuvants. Nevertheless, the use of SAPs in intracellular spaces has mostly been unexplored. Here, we report a self-assembling peptide, Y15 (YEYKYEYKYEYKYEY), which readily forms ß-sheet structures to facilitate bottom-up synthesis of functional protein assemblies in living cells. Superfolder green fluorescent protein (sfGFP) fused to Y15 assembles into fibrils and is observed as fluorescent puncta in mammalian cells. Y15 self-assembly is validated by fluorescence anisotropy and pull-down assays. By using the Y15 platform, we demonstrate intracellular reconstitution of Nck assembly, a Src-homology 2 and 3 domain-containing adaptor protein. The artificial clusters of Nck induce N-WASP (neural Wiskott-Aldrich syndrome protein)-mediated actin polymerization, and the functional importance of Nck domain valency and density is evaluated.

Selection of fluorescent biosensors against galectin-3 from an NBD-modified phage library displaying designed α-helical peptides.

Fluorescent biosensors are indispensable tools for molecular imaging, detection, and drug screening. Conventionally, fluorescent biosensors were constructed by incorporating fluorophores into ligands. Here, to develop ligand-independent biosensors, we demonstrated biosensor selection from a fluorophore-modified peptide phage library. In this library, the peptides were designed to form α-helical structures, and one cysteine, the probe modification site, was located at the center of four randomized residues on the same face of the helix. By conjugation with 4-nitrobenzoxadiazole (NBD), we constructed an NBD-modified phage library. We conducted selection against galectin-3 (Gal-3), a galactose-specific lectin associated with various biological events such as tumor metastasis and insulin resistance. After biopanning, we obtained NBD-modified peptides that selectively bind to Gal-3 from the library. The fluorescence intensity of the hit biosensors increased with the concentration of Gal-3, and this fluorescent response was visually observed.

Affinity Control of Monosaccharide Conjugated Peptides against Lectins with a Set of Amino Acid Substitutions on α-Helical Structures.

Saccharides are well-known to play important roles in various biological events through specific interactions with target molecules such as carbohydrate-binding proteins (so-called lectins). Although characterization and identification of lectin molecules with saccharides are essential to understand biological events, they are still difficult due to weak interactions of saccharides, especially with monosaccharides. Herein, we demonstrate enhancement and control of monosaccharide affinity toward lectin proteins using chemical conjugation of monosaccharides with structurally regulated peptide and amino acid substitution. Thermodynamic analyses of the interactions by isothermal calorimetry measurements were performed to characterize the interactions between monosaccharide-conjugated peptide and the lectin molecules in detail. Conjugation with α-helical 16-mer short peptides drastically enhanced the affinity to lectins as compared with peptides with random coil structures, indicating that the α-helical peptide-based scaffold cooperatively interacted with lectins through additional interactions by suitable amino acids. Furthermore, suitable arrangement of the amino acids surrounding the monosaccharides on the α-helix afforded the conjugated peptides with varied affinities for two types of lectins. Our results indicate that the affinity of monosaccharide-conjugated peptides toward lectins is generally designable by appropriate conjugation of a simple monosaccharide with designed peptides, leading to the construction of a monosaccharide-modified peptide microarray toward high-throughput identification and/or screening of lectins in various biological events.

hDM2 protein-binding peptides screened from stapled α-helical peptide phage display libraries with different types of staple linkers.

Chemically modified peptide ligands were identified from α-helix peptide phage libraries with different types of staple linkers. The hDM2-protein was used as a representative target of protein-protein interactions to screen ligands for p53 binding sites in hDM2. Two types of staple linkers were used for the chemical modification of the peptide phage display libraries before affinity selection. The identified stapled peptides could bind to hDM2 competitively with the p53 peptide. The stapled peptide phage libraries developed in this study will improve the discovery of protein-protein interaction inhibitors through the synergistic effect of peptide units and staple linkers.

Construction of a Stapled α-Helix Peptide Library Displayed on Phage for the Screening of Galectin-3-Binding Peptide Ligands.

A stapled α-helix peptide library was designed and constructed using a chemically modified phage display system for screening stapled-peptide ligands against target proteins. The α-helix peptide library, with two cysteine residues on the opposite side of the randomized face, was modified with a rigid hydrocarbon staple linker on a phage. The stapled α-helix peptide phage library was screened against galectin-3 (Gal-3), a cancer-related galactose-binding protein. The obtained stapled peptides showed a high binding affinity (K d = 0.45 µM) despite being nonsugar ligands. The stapled modification played important roles in stabilizing the α-helical structure that contributed to the high binding affinity to Gal-3. In addition, the best stapled peptide ligands showed specific binding to Gal-3 among various carbohydrate-binding proteins. Thus, the designed α-helix peptide phage library with a constrained structure by the staple linker will advance the discovery of peptide ligands with improved specificity and affinity.

Osteoblastic differentiation on hydrogels fabricated from Ca2+-responsive self-assembling peptides functionalized with bioactive peptides.

We recently developed an amphiphilic peptide, E1Y9 (Ac-E-YEYKYEYKY-NH2), that self-assembles into nanofibers and forms a hydrogel in the presence of Ca2+ ion. Four E1Y9-derivatives (E1Y9-ALK, E1Y9-DGR, E1Y9-PRG and E1Y9-RGD) were designed as conjugates of E1Y9 with bioactive peptide sequences named as ALK (ALKRQGRTLYGF), DGR (DGRDSVAYG), PRG (PRGDSGYRGDS) and RGD (RGDS), respectively, and stimulated osteoblast cells growth as well as differentiation. In this study, E1Y9/E1Y9-derivative mixed hydrogels were constructed to serve as scaffolds for osteoblastic differentiation of MC3T3-E1 cells. E1Y9 and E1Y9-derivatives co-assembled into networked nanofibers and formed hydrogels in response to Ca2+ ion. The pre-osteoblast cell line MC3T3-E1 was cultured and differentiated on mixed hydrogels. An E1Y9/E1Y9-ALK mixed hydrogel exhibited the highest cell proliferation and differentiation activity among the peptide hydrogels. The peptide sequence ALK promoted expression of RUNX2 and osteopontin, a key transcription factor and bone tissue matrix protein, respectively, during the differentiation stage. During the later stage, localization of RUNX2 and osteopontin was regulated in the cytosol and extracellularly, respectively, indicating that the E1Y9/E1Y9-ALK mixed hydrogel controlled the differentiation of MC3T3-E1 cells. Thus, the E1Y9/E1Y9-ALK mixed hydrogel developed in this study showed potential for the culture and regulation of differentiation of osteoblast cells for bone regeneration.

Gold Nanoparticles Conjugated with Glycopeptides for Lectin Detection and Imaging on Cell Surface.

BACKGROUND: Lectins are carbohydrate binding proteins and related to various biological events and diseases including virus infection and cancer metastasis. In particular, galactose-binding lectins have attracted attention as targets for drug delivery and cancer markers. We, previously, demonstrated that sugar-modified peptides (glycopeptides) were useful ligands for the detection and characterization of lectins compared to the sugar unit alone. Gold nanoparticles (GNPs) conjugated with mannose-modified glycopeptides were useful in detection of concanavalin A, a mannose binding lectin. OBJECTIVES: The main objective of this study was to expand our glycopeptide-GNP conjugates for detection and imaging of galactose-binding lectins. METHODS: Four galactose-modified peptides (glycopeptides) were synthesized by Fmoc-based solid peptide synthesis method. Synthesized glycopeptides were conjugated with PEG-coated GNPs using thiol-maleimide chemistry. The interaction between glycopeptide-GNPs (GP/GNPs) (0.5 nM) and RCA120, a galactose binding lectin, (0.5-1000 nM) was evaluated by mesuring absorption spectra of GNPs. The inhibition experiment in the interaction between GP/GNPs (0.5 nM) and RCA120 (100 nM) was performed in the presence of 60 mM α- methyl mannose or 60 mM lactose. HepG2 and MCF7 cells were placed on 22×22 mm cover slip in 6 well cell culture plates (2×105 cells / well) and cultured overnight at 37°C under 5% CO2 condition. 1 mL of GP/GNPs (0.2 nM) were added in each well and incubated for 18 h at 37°C under 5% CO2 condition. After incubation, cells were washed twice with PBS and fixed with 4% paraformaldehyde solution. The cover slips were coated with 90% glycerol and sealed to slide glass. Dark-field images based on elastic light scattering were taken using a Nikon microscope (TieU) with an immersion dark field condenser. RESULTS: In the titration experiment of RCA120, GP/GNPs showed a decrease of absorbance according to the addition of RCA120, suggesting that the aggregation of GP/GNPs is induced through the binding to RCA120. The EC50 values of AA(Gal)/GNP, WF(Gal)/GNP, TS(Gal)/GNP and ED(Gal)/ GNP were estimated as 66.2 nM, 43.2 nM, 38.6 nM and 104.4 nM, respectively. TS(Gal)/GNP showed the lowest EC50 value among GP/GNPs. RCA120 has several binding sites for the galactose, and there are hydrophilic amino acids (Thr24, Glu26, Gln35, Asn42 and Asp44) around one of galactose binding sites. This result indicates that the hydrogen bonds between these amino acids and Thr/Ser residues of TS(Gal) contribute to the efficient aggregation of TS(Gal)/GNP. Next, inhibition experiments in the aggregation of WF(Gal)/GNP with RCA120 revealed that lactose inhibits the WF(Gal)/GNP binding with RCA120, but α-methyl mannose does not, and that WF(Gal)/GNP selectively interacts with RCA120 and forms the aggregate. Finally, a galactose binding protein on the surface of HepG2 cells was successfully visualized by using GP/GNPs as optical probes. CONCLUSION: Our results demonstrated that GP/GNPs could detect RCA120 by the selective binding and the aggregation formation. Furthermore, a galactose binding protein on the surface of HepG2 cells is successfully visualized using WF(Gal)/GNP as an optical probe. Thus, GNPs conjugated with glycopeptides will be useful probes for the selective detection and imaging of lectins.

Signal Enhancement Strategies for Refractive Index-Sensitive Nanobiosensor.

BACKGROUND: Direct bio-monitoring essentially involves optical means since photon has insignificant effects over biomolecules. Over the years, laser induced surface Plasmon resonance method with various modifications as well as versatile localized Plasmon excited by incoherent light have facilitated in recording many nanobiological activities. Yet, monitoring interactions of small molecules including drugs requires signal amplification and improvement on signal-to-noise ratio. OBJECTIVES: This paper focused on how the refractive index based nanobio-sensoring gold platform can produce more efficient, adaptable and more practical detection techniques to observe molecular interactions at high degree of sensitivity. It discusses surface chemistry approach, optimisation of the refractive index of gold platform and manipulation of gold geometry augmenting signal quality. METHODS: In a normal-incidence reflectivity, r0 can be calculated using the Fresnel equation. Particularly at λ = 470 nm the ratio of r / r0 showed significant amplitude reduction mainly stemmed from the imaginary part of the Au refractive index. Hence, the fraction of reduction, Δr = 1 - r / r0. Experimentally, in a common reference frame reflectivity of a bare gold surface, R0 is compared with the reflectivity of gold surface in the presence of biolayer, R. The reduction rate (%) of reflectivity, ΔR = 1 - R / R0 is denoted as the AR signal. The method therefore enables quantitative measurement of the surface-bound protein by converting ΔR to the thickness, d, and subsequently the protein mass. We discussed four strategies to improve the AR signal by changing the effective refractive index of the biosensing platform. They are; a) Thickness optimisation of Au thin layer, b) Au / Ag bimetallic layer, c) composing alloy or Au composite, and d) Au thinlayer with nano or micro holes. RESULTS: As the result we successfully 'move' the refractive index, ε of the AR platform (gold only) to ε = -0.948 + 3.455i, a higher sensitivity platform. This was done by composing Au-Ag2O composite with ratio = 1:1. The results were compared to the potential sensitivity improvement of the AR substrate using other that could be done by further tailoring the ε advanced method. CONCLUSION: We suggested four strategies in order to realize this purpose. It is apparent that sensitivity has been improved through Au/Ag bimetallic layer or Au-Ag2O composite thin layer, This study is an important step towards fabrication of sensitive surface for detection of biomolecular interactions.

Screening for concanavalin A binders from a mannose-modified α-helix peptide phage library.

Mannose-modified lectin-binding peptides were obtained from an α-helical-designed peptide phage library. Concanavalin A (ConA) was used as a representative target protein for the lectin family. The identified glycopeptides could selectively bind to ConA with micromolar affinity. With these results, the methodologies described in this study will enhance the selection of saccharide-modified ligands through the synergistic effects of sugar and peptide units, with better specificity and affinity towards lectin proteins.

Fluorescent and luminescent fusion proteins for analyses of amyloid beta peptide aggregation.

The amyloid beta (Aß) peptide is regarded as a causative agent of Alzheimer's disease. In this study, fluorescent and luminescent fusion proteins were constructed to analyze Aß aggregation. A system was developed to monitor changes in luminescence that provides information about Aß aggregation. In the presence of monomeric Aß, the fusion protein exhibits higher luminescence intensity, and the luminescence intensity is diminished after aggregation of the fusion protein and Aß. In contrast, the fluorescence is sustained in the presence of Aß. In the absence of Aß, the fusion protein self-aggregates, and its luminescence and fluorescence are quenched, thus decreasing the background fluorescence and enhancing the detection of Aß inside and outside the cells. The ratio of the luminescence intensity to the fluorescence intensity would allow the aggregation degrees of Aß to be distinguished. This study would be a promising method for analyzing the aggregation state of a particular amyloid protein/peptide (monomer, oligomer, or fibril), as well as the distribution of the amyloid protein/peptide within and at the cell surface, by using a single fusion protein. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.

Cell differentiation on disk- and string-shaped hydrogels fabricated from Ca(2+) -responsive self-assembling peptides.

We recently developed a self-assembling peptide, E1Y9, that self-assembles into nanofibers and forms a hydrogel in the presence of Ca(2+) . E1Y9 derivatives conjugated with functional peptide sequences derived from extracellular matrices (ECMs) reportedly self-assemble into peptide nanofibers that enhance cell adhesion and differentiation. In this study, E1Y9/E1Y9-IKVAV-mixed hydrogels were constructed to serve as artificial ECMs that promote cell differentiation. E1Y9 and E1Y9-IKVAV co-assembled into networked nanofibers, and hydrogels with disk and string shapes were formed in response to Ca(2+) treatment. The neuronal differentiation of PC12 cells was facilitated on hydrogels of both shapes that contained the IKVAV motifs. Moreover, long neurites extended along the long axis of the string-shaped gel, suggesting that the structure of hydrogels of this shape can affect cellular orientation. Thus, E1Y9 hydrogels can potentially be used as artificial ECMs with desirable bioactivities and shapes that could be useful in tissue engineering applications. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 476-483, 2016.

Anomalous Reflection of Gold: A Novel Platform for Biochips.

The importance of protein detection system for protein functions analyses in recent post-genomic era is rising with the emergence of label-free protein detection methods. We are focusing on a simple and practical label-free optical-detection method called anomalous reflection (AR) of gold. When a molecular layer forms on the gold surface, significant reduction in reflectivity can be observed at wavelengths of 400-500 nm. This allows the detection of molecular interactions by monitoring changes in reflectivity. In this chapter, we describe the AR method with three different application platforms: (1) gold, (2) gold containing alloy/composite (AuAg2O), and (3) metal-insulator-metal (MIM) thin layers. The AuAg2O composite and MIM are implemented as important concepts for signal enhancement process for the AR technique. Moreover, the observed molecular adsorption and activity is aided by a three-dimensional surface geometry, performed using poly(amidoamine) or PAMAM dendrimer modification. The described system is suitable to be used as a platform for high-throughput detection system in a chip format.

A Cell Microarray Format: A Peptide Release System Using a Photo-Cleavable Linker for Cell Toxicity and Cell Uptake Analysis.

There has been increasing interest in the potential use of microarray technologies to perform systematic and high-throughput cell-based assays. We are currently focused on developing more practical array formats and detection methods that will enable researchers to conduct more detailed analyses in cell microarray studies. In this chapter, we describe the construction of a novel peptide-array format system for analyzing cellular toxicity and cellular uptake. In this system, a peptide is immobilized at the bottom of a conventional 96-well plate using a photo-cleavable linker. The peptide can then be released from the bottom by irradiating the desired wells with UV light, thus allowing the cytotoxicity or cellular uptake of the peptide to be monitored. This system will facilitate the realization of high-throughput cell arrays for cellomics analyses and cell-based phenotypic drug screens.

Dihydrofolate reductase inhibitory peptides screened from a structured designed ß-loop peptide library displayed on phage.

Enzyme inhibitory peptides with a loop structure stabilized using an antiparallel ß-sheet scaffold (ß-loop peptide) were obtained from a designed peptide phage library. Human dihydrofolate reductase (hDHFR) was used as the target enzyme. The obtained ß-loop peptides were competitive inhibitors of hDHFR with micromolar inhibition constants and dissociation constants.

Label and Label-Free Detection Techniques for Protein Microarrays.

Protein microarray technology has gone through numerous innovative developments in recent decades. In this review, we focus on the development of protein detection methods embedded in the technology. Early microarrays utilized useful chromophores and versatile biochemical techniques dominated by high-throughput illumination. Recently, the realization of label-free techniques has been greatly advanced by the combination of knowledge in material sciences, computational design and nanofabrication. These rapidly advancing techniques aim to provide data without the intervention of label molecules. Here, we present a brief overview of this remarkable innovation from the perspectives of label and label-free techniques in transducing nano­biological events.