Discovery of catalytic peptides for inorganic nanocrystal synthesis by a combinatorial phage display approach

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.

Evolving a Peptide: Library Platforms and Diversification Strategies

Peptides are widely used in pharmaceutical industry as active pharmaceutical ingredients, versatile tools in drug discovery, and for drug delivery. They find themselves at the crossroads of small molecules and proteins, possessing favorable tissue penetration and the capability to engage into specific and high-affinity interactions with endogenous receptors. One of the commonly employed approaches in peptide discovery and design is to screen combinatorial libraries, comprising a myriad of peptide variants of either chemical or biological origin. In this review, we focus mainly on recombinant peptide libraries, discussing different platforms for their display or expression, and various diversification strategies for library design. We take a look at well-established technologies as well as new developments and future directions.

Design of Catalytic Peptides and Proteins Through Rational and Combinatorial Approaches

This review focuses on recent progress in noncomputational methods to introduce catalytic function into proteins, peptides, and peptide assemblies. We discuss various approaches to creating catalytic activity and classification of noncomputational methods into rational and combinatorial classes. The section on rational design covers recent progress in the development of short peptides and oligomeric peptide assemblies for various natural and unnatural reactions. The section on combinatorial design describes recent advances in the discovery of catalytic peptides. We present the future prospects of these and other new approaches in a broader context, including implications for functional material design.

Biomimetic Crystallization of MnFe2O4 Mediated by Peptide-Catalyzed Esterification at Low Temperature

Enzymes are some of the most efficient catalysts in nature. If small catalytic peptides mimic enzymes, there is potential for broad applications from catalysis for new material synthesis to drug development, due to the ease of molecular design. Recently a hydrogel-based combinatory phage display library was developed and protease-mimicking peptides were identified. Here we advanced the previous discovery to apply one of these catalytic peptides for the synthesis of bimetal oxide nanocrystals through the catalytic ester-elimination pathway. Conventional bimetal oxide crystallization usually requires high temperatures above several hundred °C; however, this catalytic peptide could grow superparamagnetic MnFe2O4 nanocrystals at 4°C. Superconducting quantum interference device (SQUID) analysis revealed that MnFe2O4 nano-crystals grown by the catalytic peptide exhibit superpara-magnetism. This study demonstrates the usefulness of protease-mimicking catalytic peptides in the field of material synthesis.

Molecular Self-Assembly Strategy for Generating Catalytic Hybrid Polypeptides

Recently, catalytic peptides were introduced that mimicked protease activities and showed promising selectivity of products even in organic solvents where protease cannot perform well. However, their catalytic efficiency was extremely low compared to natural enzyme counterparts presumably due to the lack of stable tertiary fold. We hypothesized that assembling these peptides along with simple hydrophobic pockets, mimicking enzyme active sites, could enhance the catalytic activity. Here we fused the sequence of catalytic peptide CP4, capable of protease and esterase-like activities, into a short amyloidogenic peptide fragment of Aβ. When the fused CP4-Aβ construct assembled into antiparallel β-sheets and amyloid fibrils, a 4.0-fold increase in the hydrolysis rate of p-nitrophenyl acetate (p-NPA) compared to neat CP4 peptide was observed. The enhanced catalytic activity of CP4-Aβ assembly could be explained both by pre-organization of a catalytically competent Ser-His-acid triad and hydrophobic stabilization of a bound substrate between the triad and p-NPA, indicating that a design strategy for self-assembled peptides is important to accomplish the desired functionality.

Screening of Oligopeptides that Recognize Inorganic Crystalline Facets of Metal Nanoparticles

Peptides that possess specific affinity to distinct crystal facets have been reported previously. However, their adsorption behavior in terms of the crystal sizes and shapes is less exploited. Herein, we isolate several phage clones that show the strong affinity to {100} of Pd at a neutral pH from the M13 phage library, and among them the phages that have shape selectivity to the cubic structure are identified by eliminating ones that bind randomly shaped Pd nanoparticles (NPs). Since Pd nanocube-binding phages are eluted by lowering pH values in the biopanning process, the selected phages (and their binding peptides displayed on protein pIII) can be released from Pd surfaces through pH changes. We used this feature to modulate the capping density of selected peptides on NPs. For example, when less peptides are capped on Pd nanocubes by lowering the pH values, the shape of the nanocubes is deformed and some evolve into a concave shape, indicating that Pd atoms are released from the less protected {100} facet selectively due to the higher surface energy. This type of crystalline facet-recognizing peptides can be applied for smart capping agents that not only bind target crystalline planes, but also modify their coverage on the specific surfaces with pH changes. The peptide-capping agents could be useful to fabricate NPs with characteristic shapes through etching and adsorption of atoms on specific crystalline planes of seed nanocrystals.

Discovery of catalytic phages by biocatalytic self-assembly

Discovery of new catalysts for demanding aqueous reactions is challenging. Here, we describe methodology for selection of catalytic phages by taking advantage of localized assembly of the product of the catalytic reaction that is screened for. A phage display library covering 10(9) unique dodecapeptide sequences is incubated with nonassembling precursors. Phages which are able to catalyze formation of the self-assembling reaction product (via amide condensation) acquire an aggregate of reaction product, enabling separation by centrifugation. The thus selected phages can be amplified by infection of Escherichia coli. These phages are shown to catalyze amide condensation and hydrolysis. Kinetic analysis shows a minor role for substrate binding. The approach enables discovery and mass-production of biocatalytic phages.