Catalytic supramolecular self-assembled peptide nanostructures for ester hydrolysis

Exploring the Use of a Lipopeptide in Dipalmitoylphosphatidylcholine Monolayers for Enhanced Detection of Glyphosate in Aqueous Environments

The growing reliance on pesticides for pest management in agriculture highlights the need for new analytical methods to detect these substances in food and water. Our research introduces a SPRWG-(C18H37) lipopeptide (LP) as a functional analog of acetylcholinesterase (AChE) for glyphosate detection in environmental samples using phosphatidylcholine (PC) monolayers. This LP, containing hydrophilic amino acids linked to an 18-carbon aliphatic chain, alters lipid assembly properties, leading to a more flexible system. Changes included reduced molecular area and peak pressure in Langmuir adsorption isotherms. Small angle X-ray scattering (SAXS) and atomic force microscopy (AFM) analyses provided insights into the LP's structural organization within the membrane and its interaction with glyphosate (PNG). Structural and geometric parameters, as derived from in silico molecular dynamics simulations (MD), substantiated the impact of LP on the monolayer structure and the interaction with PNG. Notably, the presence of the LP and glyphosate increased charge transfer resistance, indicating strong adherence of the monolayer to the indium tin oxide (ITO) surface and effective pesticide interaction. A calibration curve for glyphosate concentration adjustment revealed a detection limit (LOD) of 24 nmol L-1, showcasing the high sensitivity of this electrochemical biosensor. This LOD is significantly lower than that of a similar colorimetric biosensor in aqueous media with a detection limit of approximately 0.3 μmol L-1. Such an improvement in sensitivity likely stems from adding a polar residue to the amino acid chain of the LP.

Developing Isomeric Peptides for Mimicking the Sequence-Activity Landscapes of Enzyme Evolution

Enzymes catalyze almost all material conversion processes within living organisms, yet their natural evolution remains unobserved. Short peptides, derived from proteins and featuring active sites, have emerged as promising building blocks for constructing bioactive supramolecular materials that mimic native proteins through self-assembly. Herein, we employ histidine-containing isomeric tetrapeptides KHFF, HKFF, KFHF, HFKF, FKHF, and FHKF to craft supramolecular self-assemblies, aiming to explore the sequence-activity landscapes of enzyme evolution. Our investigations reveal the profound impact of peptide sequence variations on both assembly behavior and catalytic activity as hydrolytic simulation enzymes. During self-assembly, a delicate balance of multiple intermolecular interactions, particularly hydrogen bonding and aromatic-aromatic interactions, influences nanostructure formation, yielding various morphologies (e.g., nanofibers, nanospheres, and nanodiscs). Furthermore, the analysis of the structure-activity relationship demonstrates a strong correlation between the distribution of the His active site on the nanostructures and the formation of the catalytic microenvironment. This investigation of the sequence-structure-activity paradigm reflects how natural enzymes enhance catalytic activity by adjusting the primary structure during evolution, promoting fundamental research related to enzyme evolutionary processes.

Catalytic physiological amyloids

Amyloid fibrils have been identified in many protein systems, mostly linked to progression and cytotoxicity in neurodegenerative diseases and other pathologies, but have also been observed in normal physiological systems. A growing body of work has shown that amyloid fibrils can catalyze chemical reactions. Most studies have focused on catalysis by de-novo synthetic amyloid-like peptides; however, recent studies reveal that physiological, native amyloids are catalytic as well. Here, we discuss methodologies and major experimental aspects pertaining to physiological catalytic amyloids. We highlight analyzes of kinetic parameters related to the catalytic activities of amyloid fibrils, structure-function considerations, characterization of the catalytic active sites, and deciphering of catalytic mechanisms.

Supramolecular Hydrolase Mimics in Equilibrium and Kinetically Trapped States

The folding of proteins into intricate three-dimensional structures to achieve biological functions, such as catalysis, is governed by both kinetic and thermodynamic controls. The quest to design artificial enzymes using minimalist peptides seeks to emulate supramolecular structures existing in a catalytically active state. Drawing inspiration from the nuanced process of protein folding, our study explores the enzyme-like activity of amphiphilic peptide nanosystems in both equilibrium and non-equilibrium states, featuring the formation of supramolecular nanofibrils and nanosheets. In contrast to thermodynamically stable nanosheets, the kinetically trapped nanofibrils exhibit dynamic characteristics (e.g., rapid molecular exchange and relatively weak intermolecular packing), resulting in a higher hydrolase-mimicking activity. We emphasize that a supramolecular microenvironment characterized by an optimal local polarity, microviscosity, and β-sheet hydrogen bonding is conducive to both substrate binding and ester bond hydrolysis. Our work underscores the pivotal role of both thermodynamic and kinetic control in impacting biomimetic catalysis and sheds a light on the development of artificial enzymes.

Catechol-Amyloid Interactions

This review introduces multifaceted mutual interactions between molecules containing a catechol moiety and aggregation-prone proteins. The complex relationships between these two molecular species have previously been elucidated primarily in a unidirectional manner, as demonstrated in cases involving the development of catechol-based inhibitors for amyloid aggregation and the elucidation of the role of functional amyloid fibers in melanin biosynthesis. This review aims to consolidate scattered clues pertaining to catechol-based amyloid inhibitors, functional amyloid scaffold of melanin biosynthesis, and chemically designed peptide fibers for providing chemical insights into the role of the local three-dimensional orientation of functional groups in manifesting such interactions. These orientations may play crucial, yet undiscovered, roles in various supramolecular structures.

Supramolecular peptide nanotubes as artificial enzymes for catalysing ester hydrolysis

Peptide-based artificial enzymes are attracting significant interest because of their remarkable resemblance in both composition and structure to native enzymes. Herein, we report the construction of histidine-containing cyclic peptide-based supramolecular polymeric nanotubes to function as artificial enzymes for ester hydrolysis. The optimized catalyst shows a ca. 70-fold increase in reaction rate compared to the un-catalysed reaction when using 4-nitrophenyl acetate as a model substrate. Furthermore, the amphiphilic nature of the supramolecular catalysts enables an enhanced catalytic activity towards hydrophobic substrates. By incorporating an internal hydrophobic region within the self-assembled polymeric nanotube, we achieve a 55.4-fold acceleration in hydrolysis rate towards a more hydrophobic substrate, 4-nitrophenyl butyrate. This study introduces supramolecular peptide nanotubes as an innovative class of supramolecular scaffolds for fabricating artificial enzymes with better structural and chemical stability, catalysing not only ester hydrolysis, but also a broader spectrum of catalytic reactions.

Lipopeptides as tools in catalysis, supramolecular, materials and medicinal chemistry

Lipopeptides are amphiphilic peptides in which an aliphatic chain is attached to either the C or N terminus of peptides. Their self-assembly - into micelles, vesicles, nanotubes, fibres or nanobelts - leads to applications in nanotechnology, catalysis or medicinal chemistry. Self-organization of lipopeptides is dependent on both the length of the lipid tail and the amino acid sequence, in which the chirality of the peptide sequence can be transmitted into the supramolecular species. This Review describes the use of lipopeptides to design synthetic advanced dynamic supramolecular systems, nanostructured materials or self-responsive delivery systems in the area of medical biotechnology. We examine the influence of external stimuli, the ability of lipopeptide-derived structures to adapt over time and their application as medicinal agents with antibacterial, antifungal, antiviral or anticancer activities. Finally, we discuss the catalytic efficiency of lipopeptides, with the aim of building minimal synthetic enzymes, and recent efforts to incorporate metals into lipopeptide assemblies.

Dynamic self-assembly of supramolecular catalysts from precision macromolecules

We show the emergence of strong catalytic activity at low concentrations in dynamic libraries of complementary sequence-defined oligomeric chains comprising pendant functional catalytic groups and terminal recognition units. In solution, the dynamic constitutional library created from pairs of such complementary oligomers comprises free oligomers, self-assembled di(oligomeric) macrocycles, and a virtually infinite collection of linear poly(oligomeric) chains. We demonstrate, on an exemplary catalytic system requiring the cooperation of no less than five chemical groups, that supramolecular di(oligomeric) macrocycles exhibit a catalytic turnover frequency ca. 20 times larger than the whole collection of linear poly(oligomers) and free chains. Molecular dynamics simulations and network analysis indicate that self-assembled supramolecular di(oligomeric) macrocycles are stabilized by different interactions, among which chain end pairing. We mathematically model the catalytic properties of such complex dynamic libraries with a small set of physically relevant parameters, which provides guidelines for the synthesis of oligomers capable to self-assemble into functionally-active supramolecular macrocycles over a larger range of concentrations.

Esterase Sequence Composition Patterns for the Identification of Catalytic Triad Microenvironment Motifs

Ester hydrolysis is of wide biomedical interest, spanning from the green synthesis of pharmaceuticals to biomaterials' development. Existing peptide-based catalysts exhibit low catalytic efficiency compared to natural enzymes, due to the conformational heterogeneity of peptides. Moreover, there is lack of understanding of the correlation between the primary sequence and catalytic function. For this purpose, we statistically analyzed 22 EC 3.1 hydrolases with known catalytic triads, characterized by unique and well-defined mechanisms. The aim was to identify patterns at the sequence level that will better inform the creation of short peptides containing important information for catalysis, based on the catalytic triad, oxyanion holes and the triad residues microenvironments. Moreover, fragmentation schemes of the primary sequence of selected enzymes alongside the study of their amino acid frequencies, composition, and physicochemical properties are proposed. The results showed highly conserved catalytic sites with distinct positional patterns and chemical microenvironments that favor catalysis and revealed variations in catalytic site composition that could be useful for the design of minimalistic catalysts.

Supramolecular enzyme-mimicking catalysts self-assembled from peptides

Natural enzymes catalyze biochemical transformations in superior catalytic efficiency and remarkable substrate specificity. The excellent catalytic repertoire of enzymes is attributed to the sophisticated chemical structures of their active sites, as a result of billions-of-years natural evolution. However, large-scale practical applications of natural enzymes are restricted due to their poor stability, difficulty in modification, and high costs of production. One viable solution is to fabricate supramolecular catalysts with enzyme-mimetic active sites. In this review, we introduce the principles and strategies of designing peptide-based artificial enzymes which display catalytic activities similar to those of natural enzymes, such as aldolases, laccases, peroxidases, and hydrolases (mainly the esterases and phosphatases). We also discuss some multifunctional enzyme-mimicking systems which are capable of catalyzing orthogonal or cascade reactions. We highlight the relationship between structures of enzyme-like active sites and the catalytic properties, as well as the significance of these studies from an evolutionary point of view.

Microfluidic-driven ultrafast self-assembly of a dipeptide into stimuli-responsive 0D, 1D, and 2D nanostructures and as hydrolase mimic

Numerous peptides have been utilized to explore the efficacy of their self-assembly to produce nanostructures to mimic the self-organization capability of biomolecules in nature. Self-assembled nanostructures have significant applicability for a range of diverse applications. While the ability to create self-assembled functional materials has greatly improved, the self-assembly process, which results in ordered 0D, 1D, and 2D nanostructures, is still time-consuming. Moreover, in situ structural transformation from one self-assembled structure to another with different dimensions presents an additional challenge. Therefore, in this report, we demonstrate self-assembly in an ultrafast fashion to access four different nanostructures, namely, twisted bundle (TB), nanoparticle (NP), nanofiber (NF), and nanosheet (NS), from a simple dipeptide with the aid of simple microfluidic reactors by applying different stimuli. Additionally, an integrated microfluidic system enabled rapid structural switchover between two types in an ultrashort period of time. It is interesting to note that the formation of the twisted bundle (TB) morphology enabled the formation of an extended entangled network, which resulted in the formation of a hydrogel (1 w/v%). In addition, the nanostructures obtained using the ultrafast self-assembly process were investigated to study their hydrolase enzyme activity mimicking performance against a model substrate (p-NPA) reaction. Intriguingly, we found that our nanostructures were suitably well ordered, and when taking molecular mass into consideration, showed improved catalytic efficiency as compared to the native enzymes.

Nanoarchitectonics of Fullerene Based Enzyme Mimics for Osteogenic Induction of Stem Cells

Enzyme mimicry is a topic of considerable interest in the development of multifunctional biomimetic materials. Mimicking enzyme activity is a major challenge in biomaterials research, and artificial analogs that simultaneously recapitulate the catalytic and metabolic activity of native enzymes are considered to be the ultimate goal of this field. This consensus may be challenged by self-assembling multifunctional nanostructures to develop close-to-fidelity enzyme mimics. Here, we present the ability of fullerene nanostructures decorated with active units to form enzyme-like materials that can mimic phosphatases in a metal-free manner. These nanostructures self-assemble into nanoclusters forming multiple random active sites that can cleave both phosphomonoesters and phosphodiesters while being more specific for the phosphomonoesters. Moreover, they are reusable and show an increase in catalytic activity over multiple cycles similar to their natural counterparts. In addition to having enzyme-like catalytic properties, these nanocatalysts imitate the biological functions of their natural analogs by inducing biomineralization and osteoinduction in preosteoblast and mesenchymal stem cells in vitro studies. This article is protected by copyright. All rights reserved.

Minimalist De Novo Design of an Artificial Enzyme

We employed a reductionist approach in designing the first heterochiral tripeptide that forms a robust heterogeneous short peptide catalyst similar to the "histidine brace" active site of lytic polysaccharide monooxygenases. The histidine brace is a conserved divalent copper ion-binding motif that comprises two histidine side chains and an amino group to create the T-shaped 3N geometry at the reaction center. The geometry parameters, including a large twist angle (73°) between the two imidazole rings of the model complex, are identical to those of native lytic polysaccharide monooxygenases (72.61°). The complex was synthesized and characterized as a structural and functional mimic of the histidine brace. UV-vis, vis-circular dichroism, Raman, and electron paramagnetic resonance spectroscopic analyses suggest a distorted square-pyramidal geometry with a 3N coordination at pH 7. Solution- and solid-state NMR results further confirm the 3N coordination in the copper center of the complex. The complex is pH-dependent and could catalyze the oxidation of benzyl alcohol in water to benzaldehyde with yields up to 82% in 3 h at pH 7 and above at 40 °C. The catalyst achieved 100% selectivity for benzaldehyde compared to conventional copper catalysis. The design of such a minimalist building block for functional soft materials with a pH switch can be a stepping stone in addressing needs for a cleaner and sustainable future catalyst.

Supramolecular assemblies of histidine-containing peptides with switchable hydrolase and peroxidase activities through Cu(II) binding and co-assembling

Modulating enzyme activities or functionalities is one of the primary features of biological systems, which is, however, a great challenge for artificial enzyme systems. In this work, we designed and synthesized a series of self-assembling peptides from histidine and other amino acids (Asp, Ser, Lys or Arg), which exist in the active site of natural enzymes. These peptides could undergo a conformational transition from random coils to β-sheet structures under physiological conditions and formed self-assembled nanotubes with obvious hydrolase activities. After incorporation of transition metal ions such as Cu²⁺, these peptides could coordinate with Cu²⁺ ions, switch molecular conformations, and self-assemble into hybrid nanomaterials with altered morphologies and peroxidase-like activities. This work illustrates a facile approach for constructing artificial enzymes from self-assembling peptides with histidine residues whose catalytic functions could be modulated by incorporation of Cu²⁺ ions.

Systems chemistry of peptide-assemblies for biochemical transformations

During the billions of years of the evolutionary journey, primitive polymers, involved in proto metabolic pathways with low catalytic activity, played critical roles in the emergence of modern enzymes with remarkable substrate specificity. The precise positioning of amino acid residues and the complex orchestrated interplay in the binding pockets of evolved enzymes promote covalent and non-covalent interactions to foster a diverse set of complex catalytic transformations. Recent efforts to emulate the structural and functional information of extant enzymes by minimal peptide based assemblies have attempted to provide a holistic approach that could help in discerning the prebiotic origins of catalytically active binding pockets of advanced proteins. In addition to the impressive sets of advanced biochemical transformations, catalytic promiscuity and cascade catalysis by such small molecule based dynamic systems can foreshadow the ancestral catalytic processes required for the onset of protometabolism. Looking beyond minimal systems that work close to equilibrium, catalytic systems and compartments under non-equilibrium conditions utilizing simple prebiotically relevant precursors have attempted to shed light on how bioenergetics played an essential role in chemical emergence of complex behaviour. Herein, we map out these recent works and progress where diverse sets of complex enzymatic transformations were demonstrated by utilizing minimal peptide based self-assembled systems. Further, we have attempted to cover the examples of peptide assemblies that could feature promiscuous activity and promote complex multistep cascade reaction networks. The review also covers a few recent examples of minimal transient catalytic assemblies under non-equilibrium conditions. This review attempts to provide a broad perspective for potentially programming functionality via rational selection of amino acid sequences leading towards minimal catalytic systems that resemble the traits of contemporary enzymes.

Catalytic, theoretical, and biological investigation of an enzyme mimic model

Artificial catalyst studies were always stayed at the kinetics investigation level, in this work bioactivity of designed catalyst were shown by the induction of biomineralization of the cells, indicating the possible use of enzyme mimics for biological applications. The development of artificial enzymes is a continuous quest for the development of tailored catalysts with improved activity and stability. Understanding the catalytic mechanism is a replaceable step for catalytic studies and artificial enzyme mimics provide an alternative way for catalysis and a better understanding of catalytic pathways at the same time. Here we designed an artificial catalyst model by decorating peptide nanofibers with a covalently conjugated catalytic triad sequence. Owing to the self-assembling nature of the peptide amphiphiles, multiple action units can be presented on the surface for enhanced catalytic performance. The designed catalyst has shown an enzyme-like kinetics profile with a significant substrate affinity. The cooperative action in between catalytic triad amino acids has shown improved catalytic activity in comparison to only the histidine-containing control group. Histidine is an irreplaceable contributor to catalytic action and this is an additional reason for control group selection. This new method based on the self-assembly of covalently conjugated action units offers a new platform for enzyme investigations and their further applications. Artificial catalyst studies always stayed at the kinetics investigation level, in this work bioactivity of the designed catalyst was shown by the induction of biomineralization of the cells, indicating the possible use of enzyme mimics for biological applications.

Fullerene-Based Mimics of Biocatalysts Show Remarkable Activity and Modularity

The design of catalysts with greater control over catalytic activity and stability is a major challenge with substantial impact on fundamental chemistry and industrial applications. Due to their unparalleled diversity, selectivity, and efficiency, enzymes are promising models for next-generation catalysts, and considerable efforts have been devoted to incorporating the principles of their mechanisms of action into artificial systems. We report a heretofore undocumented catalyst design that introduces fullerenes to the field of biocatalysis, which we refer to as fullerene nanocatalysts, and that emulates enzymatic active sites through multifunctional self-assembled nanostructures. As a proof-of-concept, we mimicked the reactivity of hydrolases using fullerene nanocatalysts functionalized with the basic components of the parent enzyme with remarkable activity. Owing to the versatile amino acid-based functionalization repertoire of fullerene nanocatalysts, these next-generation carbon/biomolecule hybrids have potential to mimic the activity of other families of enzymes and, therefore, offer new perspectives for the design of biocompatible, high-efficiency artificial nanocatalysts.

Peptide-Based Supramolecular Systems Chemistry

Peptide-based supramolecular systems chemistry seeks to mimic the ability of life forms to use conserved sets of building blocks and chemical reactions to achieve a bewildering array of functions. Building on the design principles for short peptide-based nanomaterials with properties, such as self-assembly, recognition, catalysis, and actuation, are increasingly available. Peptide-based supramolecular systems chemistry is starting to address the far greater challenge of systems-level design to access complex functions that emerge when multiple reactions and interactions are coordinated and integrated. We discuss key features relevant to systems-level design, including regulating supramolecular order and disorder, development of active and adaptive systems by considering kinetic and thermodynamic design aspects and combinatorial dynamic covalent and noncovalent interactions. Finally, we discuss how structural and dynamic design concepts, including preorganization and induced fit, are critical to the ability to develop adaptive materials with adaptive and tunable photonic, electronic, and catalytic properties. Finally, we highlight examples where multiple features are combined, resulting in chemical systems and materials that display adaptive properties that cannot be achieved without this level of integration.

Photothermally switchable peptide nanostructures towards modulating catalytic hydrolase activity

Enzymes are the most efficient catalysts in nature that possess an impressive range of catalytic activities, albeit limited by stability in adverse conditions. Functional peptides have emerged as alternative robust biocatalysts to mimic complex enzymes. Here, a rational design of minimalistic amyloid-inspired peptides 1-2 is demonstrated, which leads to pathway-driven self-assembly triggered by heat, light and chemical cues to render 1D and 2D nanostructures by the interplay of hydrogen bonding, host-guest interaction and reversible photodimerization. Such in situ transformable peptide nanostructures by means of external cues are envisaged as a catalytic amyloid for the first time to mimic the hydrolase enzyme activity. Michaelis Menten's enzyme kinetic parameters for the hydrolysis rate correlate the external cue-mediated structure-function augmentation with the twisted bundles, 1_TB being the most efficient biocatalyst among all the dimensionally diverse nanostructures. Unlike the natural enzyme, the peptide nanostructures exhibited the robust nature of the hydrolase activity over a broad range of temperature and pH. Finally, the peptide nanostructures are explored as efficient heterogeneous flow catalysts to improve the turnover number for the hydrolase activity.

Biocatalysts Based on Peptide and Peptide Conjugate Nanostructures

Peptides and their conjugates (to lipids, bulky N-terminals, or other groups) can self-assemble into nanostructures such as fibrils, nanotubes, coiled coil bundles, and micelles, and these can be used as platforms to present functional residues in order to catalyze a diversity of reactions. Peptide structures can be used to template catalytic sites inspired by those present in natural enzymes as well as simpler constructs using individual catalytic amino acids, especially proline and histidine. The literature on the use of peptide (and peptide conjugate) α-helical and β-sheet structures as well as turn or disordered peptides in the biocatalysis of a range of organic reactions including hydrolysis and a variety of coupling reactions (e.g., aldol reactions) is reviewed. The simpler design rules for peptide structures compared to those of folded proteins permit ready ab initio design (minimalist approach) of effective catalytic structures that mimic the binding pockets of natural enzymes or which simply present catalytic motifs at high density on nanostructure scaffolds. Research on these topics is summarized, along with a discussion of metal nanoparticle catalysts templated by peptide nanostructures, especially fibrils. Research showing the high activities of different classes of peptides in catalyzing many reactions is highlighted. Advances in peptide design and synthesis methods mean they hold great potential for future developments of effective bioinspired and biocompatible catalysts.

Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet

The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.

Tripeptide Self-Assembly into Bioactive Hydrogels: Effects of Terminus Modification on Biocatalysis

Bioactive hydrogels based on the self-assembly of tripeptides have attracted great interest in recent years. In particular, the search is active for sequences that are able to mimic enzymes when they are self-organized in a nanostructured hydrogel, so as to provide a smart catalytic (bio)material whose activity can be switched on/off with assembly/disassembly. Within the diverse enzymes that have been targeted for mimicry, hydrolases find wide application in biomaterials, ranging from their use to convert prodrugs into active compounds to their ability to work in reverse and catalyze a plethora of reactions. We recently reported the minimalistic l-His-d-Phe-d-Phe for its ability to self-organize into thermoreversible and biocatalytic hydrogels for esterase mimicry. In this work, we analyze the effects of terminus modifications that mimic the inclusion of the tripeptide in a longer sequence. Therefore, three analogues, i.e., N-acetylated, C-amidated, or both, were synthesized, purified, characterized by several techniques, and probed for self-assembly, hydrogelation, and esterase-like biocatalysis. This work provides useful insights into how chemical modifications at the termini affect self-assembly into biocatalytic hydrogels, and these data may become useful for the future design of supramolecular catalysts for enhanced performance.

Synergistic Interactions Are Prevalent in Catalytic Amyloids

Interactions between multiple functional groups are key to catalysis. Previously, we reported synergistic interactions in catalytic amyloids formed by mixtures of heptameric peptides that lead to significant improvements in esterase activity. Herein, we describe the in-depth investigation of synergistic interactions within a family of amyloid fibrils, exploring the results of functional group interactions, the effects of chirality and the use of mixed enantiomers within fibrils. Remarkably, we find that synergistic interactions (either positive or negative) are found in the vast majority of binary mixtures of catalytic amyloid-forming peptides. The productive arrangements of functionalities rapidly identified by mixing different peptides will undoubtedly lead to the development of more active catalysts for a variety of different transformations.

Biocatalysis of D,L-Peptide Nanofibrillar Hydrogel

Self-assembling peptides are attracting wide interest as biodegradable building blocks to achieve functional nanomaterials that do not persist in the environment. Amongst the many applications, biocatalysis is gaining momentum, although a clear structure-to-activity relationship is still lacking. This work applied emerging design rules to the heterochiral octapeptide sequence His-Leu-DLeu-Ile-His-Leu-DLeu-Ile for self-assembly into nanofibrils that, at higher concentration, give rise to a supramolecular hydrogel for the mimicry of esterase-like activity. The peptide was synthesized by solid-phase and purified by HPLC, while its identity was confirmed by 1H-NMR and electrospray ionization (ESI)-MS. The hydrogel formed by this peptide was studied with oscillatory rheometry, and the supramolecular behavior of the peptide was investigated with transmission electron microscopy (TEM) analysis, circular dichroism (CD) spectroscopy, thioflavin T amyloid fluorescence assay, and attenuated total reflectance (ATR) Fourier-transform infrared (FT-IR) spectroscopy. The biocatalytic activity was studied by monitoring the hydrolysis of p-nitrophenyl acetate (pNPA) at neutral pH, and the reaction kinetics followed an apparent Michaelis-Menten model, for which a Lineweaver-Burk plot was produced to determine its enzymatic parameters for a comparison with the literature. Finally, LC-MS analysis was conducted on a series of experiments to evaluate the extent of, if any, undesired peptide acetylation at the N-terminus. In conclusion, we provide new insights that allow gaining a clearer picture of self-assembling peptide design rules for biocatalysis.

A minimalistic hydrolase based on co-assembled cyclic dipeptides

The self-assembly of small peptides into larger aggregates is an important process for the fundamental understanding of abiogenesis. In this article we demonstrate that blends of cyclic dipeptides (2,5-diketopiperazines - DKPs) bearing either histidine or cysteine in combination with a lipophilic amino acid form highly stable aggregates in aqueous solution with esterase-like activity. We demonstrate that the catalytic activity is based on an intermolecular cooperative behavior between histidine and cysteine. A high control of the molecular arrangement of the peptide assemblies was gained by C-H-π interactions between Phe and Leu or Val sidechains, resulting in a significant increase in catalytic activity. These interactions were strongly supported by Hartree-Fock calculations and finally confirmed via1H-NMR HRMAS NOE spectroscopy.

Bio-inspired nanozyme: a hydratase mimic in a zeolitic imidazolate framework

Nanozymes provide comparative advantages over natural enzymes and conventional artificial enzymes for catalytic reactions. However, nanozymes are only suitable for limited types of reactions, whose catalytic principles are not yet fully revealed. Herein, a new nanozyme based on a bionic zeolitic imidazolate framework is proposed. Zeolitic imidazolate framework-8 (ZIF-8) possesses a similar geometric structure to that of the active center of human carbonic anhydrase II (hCAII) and exhibits catalytic performance analogous to that of the hCAII. The less imidazolate coordinated zinc cations on the external surface of ZIF-8 can act as Lewis acid sites, lowering the pKa of Zn-bound H2O molecules from 14 to 8.4, which facilitates the deprotonation of H2O molecules and generation of zinc-bound hydroxide nucleophiles. The esterase-like ZIF-8 nanozyme shows a similar affinity to p-nitrophenyl acetate compared with hCAII. The ZIF-8 nanozyme also promotes CO2 hydration and acetylthiocholine hydrolysis reaction, and a series of ZIFs are also found with intrinsic enzyme-like activities due to similar compositions and spatial structures. These results imply that the bionic nanoparticles can be developed to fabricate a new generation of nanozymes by mimicking the active sites of natural enzymes.

Ovalbumin self-assembles into amyloid nanosheets that elicit immune responses and facilitate sustained drug release

Amyloids are associated with many neurodegenerative diseases, motivating investigations into their structure and function. Although not linked to a specific disease, albumins have been reported to form many structural aggregates. We were interested in investigating host immune responses to amyloid fibrils assembled from the model protein ovalbumin. Surprisingly, upon subjecting ovalbumin to standard denaturing conditions, we encountered giant protein nanosheets harboring amyloid-like features and hypothesized that these nanosheets might have potential in clinical or therapeutic applications. We found that the nanosheets, without the administration of any additional adjuvant, evoked a strong antibody response in mice that was higher than that observed for native ovalbumin. This suggests that amyloid nanosheets have a self-adjuvanting property. The nanosheet-induced immune response was helper T cell 2 (Th2) biased and negligibly inflammatory. While testing whether the nanosheets might form depots for the sustained release of precursor proteins, we did observe release of ovalbumin that mimicked the conformation of native protein. Moreover, the nanosheets could load the anticancer drug doxorubicin and release it in a slow and sustained manner. Taken together, our results suggest that amyloid nanosheets should be further investigated as either an antigen delivery vehicle or a multifunctional antigen and drug co-delivery system, with potential applications in simultaneous immunotherapy and chemotherapy.

Catalytic peptide assemblies

Self-assembly of molecules often results in new emerging properties. Even very short peptides can self-assemble into structures with a variety of physical and structural characteristics. Remarkably, many peptide assemblies show high catalytic activity in model reactions reaching efficiencies comparable to those found in natural enzymes by weight. In this review, we discuss different strategies used to rationally develop self-assembled peptide catalysts with natural and unnatural backbones as well as with metal-containing cofactors.

Dentin Phosphoprotein Mimetic Peptide Nanofibers Promote Biomineralization

Dentin phosphoprotein (DPP) is a major component of the dentin matrix playing crucial role in hydroxyapatite deposition during bone mineralization, making it a prime candidate for the design of novel materials for bone and tooth regeneration. The bioactivity of DPP-derived proteins is controlled by the phosphorylation and dephosphorylation of the serine residues. Here an enzyme-responsive peptide nanofiber system inducing biomineralization is demonstrated. It closely emulates the structural and functional properties of DPP and facilitates apatite-like mineral deposition. The DPP-mimetic peptide molecules self-assemble through dephosphorylation by alkaline phosphatase (ALP), an enzyme participating in tooth and bone matrix mineralization. Nanofiber network formation is also induced through addition of calcium ions. The gelation process following nanofiber formation produces a mineralized extracellular matrix like material, where scaffold properties and phosphate groups promote mineralization. It is demonstrated that the DPP-mimetic peptide nanofiber networks can be used for apatite-like mineral deposition for bone regeneration.

A supramolecular approach to construct a hydrolase mimic with photo-switchable catalytic activity

A supramolecular artificial hydrolase with photo-switchable catalytic activity was developed by the introduction of a photo-responsive group in peptide, which leads to the assembly/disassembly of the peptide nanofibers.

Homogenous graphene oxide-peptide nanofiber hybrid hydrogel as biomimetic polysaccharide hydrolase

Cellulose, an impressive potential sustainable fuel, is difficult to hydrolyze because of the protection of β-1,4-glycosidic bonds through the tight hydrogen bonding network. In this study, homogenous graphene oxide (GO)-peptide nanofiber hybrid hydrogels (GO-PNFs) were designed as a β-glycosyl hydrolase mimetic to achieve efficient degradation of cellobiose and cellopentaose. For comparison, free peptides, graphene oxide mixed with free peptides (GO-peptdies) and self-assembled peptide nanofibers (PNFs) were also studied for their activity as a hydrolase mimetics for degradation of cellobiose. Among these materials, GO-PNFs showed the highest hydrolysis activity. Transmission electron microscopy, atomic force microscopy, fluorescence analysis, circular dichroism spectroscopies, X-ray diffraction, Raman spectra and computational modeling were used to interpret the difference in activity mechanism in these artificially designed enzymes. These investigations suggested that high catalytic performance of GO-PNFs toward cellobiose and cellopentaose hydrolysis could be attributed to the formation of nanofiber structures of peptides, optimal molecular conformation and less steric hindrance to access the substrate. More importantly, GO not only served as a platform for attaching PNFs, but also created a hydrophobic microenvironment and facilitated proton transfer, an essential step in catalytic hydrolysis, thus enhancing catalytic activity. All these provided insights into the potential use of peptides and GO hybrid composite nanoenzymes in efficient cellulose hydrolysis.

Probing the structure-activity relationship of a novel artificial cellobiose hydrolase

The remarkable catalytic properties of enzymes contribute to their unique 3D structures and arrangement of amino acid residues, which provide a blueprint for the design of artificial enzymes. Here, a series of peptide catalysts (PCs) that mimic the unique orientation and function of β-glycosyl hydrolases were designed. Transmission electron microscopy (TEM), fluorescence analysis, circular dichroism spectroscopy, X-ray diffraction and computational modeling were used to investigate and compare the relationship of the fibrinous structure of PCs with its glycoside hydrolysis activity. These results indicated that the catalytic activity of PCs was not only related to their amyloid-like structures, but it can also be influenced by the site, species, molecular arrangement and steric hindrance of the amino acid sequence. What's more, this is the first report on peptide-inspired catalysts that mimic the natural cellobiose hydrolases. All this provided insights into the potential use of peptide nanoenzymes in the generation of efficient artificial enzymes.