Design of a dual-function peptide probe as a binder of angiotensin II and an inducer of silver nanoparticle aggregation for use in label-free colorimetric assays

Peptide array-based inhibition ELISA for evaluating antigenicity in infant formulas

With increased awareness among consumers regarding food safety and security, food allergen control has become an indispensable requirement in the food industry. Although several methods for detecting allergens in food products are available, highly sensitive techniques are required. In this study, we developed a technique named as peptide array-based inhibition enzyme-linked immunosorbent assay (ELISA), Pep-iEIA, for evaluating antigenicity and detecting cow's milk antigen in infant formula products, using a peptide array consisting of a series of overlapping peptides found in allergenic milk proteins. Pep-iEIA was used to examine five cow's milk-based infant formulas with different degrees of hydrolyzation, and the assay offered both more sensitive detection and detailed analysis of remaining antigenic peptides in allergen compared to conventional ELISA. The antigenicity level of the allergenic peptides identified using Pep-iEIA was confirmed by surface plasmon resonance assay. We believe that Pep-iEIA will be highly useful for antigenicity evaluation of dairy products consumed by infants and patients with cow's milk allergy.

Array-Based Screening of Silver Nanoparticle Mineralization Peptides

The use of biomolecules in nanomaterial synthesis has received increasing attention, because they can function as a medium to produce inorganic materials in ambient conditions. Short peptides are putative ligands that interact with metallic surfaces, as they have the potential to control the synthesis of nanoscale materials. Silver nanoparticle (AgNP) mineralization using peptides has been investigated; however, further comprehensive analysis must be carried out, because the design of peptide mediated-AgNP properties is still highly challenging. Herein, we employed an array comprising 200 spot synthesis-based peptides, which were previously isolated as gold nanoparticle (AuNP)-binding and/or mineralization peptides, and the AgNP mineralization activity of each peptide was broadly evaluated. Among 10 peptides showing the highest AgNP-synthesis activity (TOP10), nine showed the presence of EE and E[X]E (E: glutamic acid, and X: any amino acid), whereas none of these motifs were found in the WORST25 (25 peptides showing the lowest AgNP synthesis activity) peptides. The size and morphology of the particles synthesized by TOP3 peptides were dependent on their sequences. These results suggested not only that array-based techniques are effective for the peptide screening of AgNP mineralization, but also that AgNP mineralization regulated by peptides has the potential for the synthesis of AgNPs, with controlled morphology in environmentally friendly conditions.

Screening of peptide probe binding to particulate matter with a high metal content

Particulate matter (PM) is becoming an increasing health concern and there is a need to develop detection methods to keep its harmful effects in check. Generation of reactive oxygen species (ROS) by PM is often associated with metal compounds, hence our aim is to screen for a peptide probe towards improved collection and the detection of PM having a high metal content. Peptides are putative recognition molecules due to their versatility and ease of modification to enhance their binding selectivities. PM binding peptides were screened using the peptide array and different binding behaviors in terms of different spot colors (yellow, mixed and gray), indicating the different composition of bound PMs, were observed. The strongest binding peptides were identified as follows: NHVNTNYYPTLH (gray), NGYYPHSHSYHQ (mixed) and HHLHWPHHHSYT (yellow), with relative binding ratios of 125%, 144% and 136%, in comparison with WQDFGAVRSTRS, a peptide screened from a phage display in our previous study. Inductively coupled plasma mass spectrometry (ICPMS) analyses revealed that Co, Ni and Zn content in the PM bound to the HHLHWPHHHSYT peptide spot were respectively 12.5, 15.8 and 7.8 times that of the PM bound to no peptide spot, suggesting this peptide probe is applicable to collect PM with a high metal content.

Screening of bacteria-binding peptides and one-pot ZnO surface modification for bacterial cell entrapment

Short functional peptides are promising materials for use as targeting recognition probes. Toll-like receptor 4 (TLR4) plays an essential role in pathogen recognition and in activation of innate immunity. Here, the TLR4 amino acid sequence was used to screen for bacterial cell binding peptides using a peptide array. Several octamer peptides, including GRHIFWRR, demonstrated binding to Escherichia coli as well as lipopolysaccharides. Linking this peptide with the ZnO-binding peptide HKVAPR, creates a bi-functional peptide capable of one-step ZnO surface modification for bacterial cell entrapment. Ten-fold increase in entrapment of E. coli was observed using the bi-functional peptide. The screened peptides and the simple strategy for nanomaterial surface functionalization can be employed for various biotechnological applications including bacterial cell entrapment onto ZnO surfaces.

Linking the screened bacteria-binding peptide with the ZnO-binding peptide HKVAPR, created a bifunctional peptide capable of one-step simple ZnO surface modification and of bacterial cell entrapment.

Array-Based Rational Design of Short Peptide Probe-Derived from an Anti-TNT Monoclonal Antibody

Complementarity-determining regions (CDRs) are sites on the variable chains of antibodies responsible for binding to specific antigens. In this study, a short peptide probe for recognition of 2,4,6-trinitrotoluene (TNT), was identified by testing sequences derived from the CDRs of an anti-TNT monoclonal antibody. The major TNT-binding site in this antibody was identified in the heavy chain CDR3 by antigen docking simulation and confirmed by an immunoassay using a spot-synthesis based peptide array comprising amino acid sequences of six CDRs in the variable region. A peptide derived from heavy chain CDR3 (RGYSSFIYWF) bound to TNT with a dissociation constant of 1.3 μM measured by surface plasmon resonance. Substitution of selected amino acids with basic residues increased TNT binding while substitution with acidic amino acids decreased affinity, an isoleucine to arginine change showed the greatest improvement of 1.8-fold. The ability to create simple peptide binders of volatile organic compounds from sequence information provided by the immune system in the creation of an immune response will be beneficial for sensor developments in the future.

Surface plasmon resonance based spectrophotometric determination of medicinally important thiol compounds using unmodified silver nanoparticles

The determination of thiol based biological molecules and drugs, such as cysteine (Cys) (I), α-lipoic acid (II), and sodium 2-sulfanylethane sulphonate (Mesna (III)) in human plasma are becoming progressively more important due to the growing body of knowledge about their essential role in numerous biological pathways. Herein we demonstrate a sensitive colorimetric sensor for the determination of medicinally important thiol drugs based on aggregation of the citrate capped silver nanoparticles (Ag NPs). This approach exploited the high affinity of thiols towards the Ag NPs surface which could tempt replacement of the citrate shell by the thiolate shell of target molecules, resulting in aggregation of the NPs through intermolecular electrostatic interaction or hydrogen-bonding. Because of aggregation, the plasmon band at around 400nm decreases gradually, along with the appearance of a new band connoting a red shift. The calibration curves are derived from the intensity ratios of A₅₃₀/A₄₀₀, which display a linear relation in the range of 1μM-150μM, 5μM-200μM and 10μM-130μM, respectively. The obtained detection limits (3σ) were found to be 1.5μM, 5.6μM and 10.2μM for compound I-III, respectively. The proposed method has been successfully applied for the detection of thiol compounds in real samples.

Array-based functional peptide screening and characterization of gold nanoparticle synthesis

Based on inorganic material production through biomineralization in organisms, the use of biological molecules in nanomaterial production has received increasing attention as a vehicle to synthesize inorganic materials with selected properties in ambient conditions. Among various biological molecules that interact with metallic surfaces, short peptides are putative ligand molecules as they exhibit potential to control the synthesis of nanoscale materials with tailored functions. Herein, using a spot synthesis-based peptide array, the gold nanoparticle (AuNP) binding activities of approximately 1800 peptides were evaluated and revealed various activities ranging from positive (high-affinity binding peptides) to negative (weak- or null-affinity binding peptides). Among 50 peptides showing the highest AuNP binding activity, 46 sequences showed the presence of tryptophan-based motifs including W[X_n]W, H[X_n]W, and W[X_n]H (W: tryptophan, X: any amino acid, n: 1-8 amino acid residues), whereas none of these motifs was found in the WORST50 peptides. Notably, three peptides showing the highest binding affinities possessed bi-functionality in AuNP binding and Au(III) reduction in solution and on solid surfaces. In addition, the characterization of truncated peptide derivatives revealed unique peptide motifs for their function expressions that also supported the importance of tryptophan-based motifs for peptide-AuNP binding. These findings open the door for peptide-mediated precise regulation of AuNP synthesis in ambient condition and for site dependent controlled AuNP integration onto nanotechnological devices.

STATEMENT OF SIGNIFICANCE

The development of a technique for functionally regulated nanosized material production in ambient condition is broadly required according to the expansion of nanomaterial based applications. Short peptides, which bind to metallic surfaces, have great potential for the technique development, but the realization remains a difficult challenge due to the lack of metal binding peptide varieties. Herein, approximately 1800 peptides with the gold nanoparticle (AuNP) binding activity are reported and characterized. Furthermore, by three highest binding peptides, the expression of bi-functionality in AuNP binding and Au(III) reduction was serendipitously discovered in solution and on solid surfaces. These findings will be attributed to new technique development of functional nanoparticle synthesis in mild condition, and for site-dependent AuNP integration in various nanotechnological devices.

A plasmonic colorimetric strategy for visual miRNA detection based on hybridization chain reaction

In this work, a novel colorimetric strategy for miRNA analysis is proposed based on hybridization chain reaction (HCR)-mediated localized surface plasmon resonance (LSPR) variation of silver nanoparticles (AgNPs). miRNA in the sample to be tested is able to release HCR initiator from a solid interface to AgNPs colloid system by toehold exchange-mediated strand displacement, which then triggers the consumption of fuel strands with single-stranded tails for HCR. The final produced long nicked double-stranded DNA loses the ability to protect AgNPs from salt-induced aggregation. The stability variation of the colloid system can then be monitored by recording corresponding UV-vis spectrum and initial miRNA level is thus determined. This sensing system involves only four DNA strands which is quite simple. The practical utility is confirmed to be excellent by employing different biological samples.

A molecular peptide beacon for IgG detection

A molecular peptide beacon was designed for fluorescence detection of IgG in a homogeneous assay.