Emergent Catalytic Behavior of Self-Assembled Low Molecular Weight Peptide-Based Aggregates and Hydrogels

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.

Molecularly imprinted peptide-based enzyme mimics with enhanced activity and specificity

We herein report the construction of peroxidase (POD)-mimicking catalysts based on the strategy of peptide assembly and molecular imprinting. Upon co-assembly of Fmoc-FFH and Hemin, we firstly fabricated CA-H/Hemin which displayed POD-like catalytic activity and showed a 21-fold rate acceleration in the oxidation of 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulphonate) (ABTS) compared to the uncatalyzed reaction. Then, upon combining CA-H/Hemin with the ABTS-imprinted polymer, the obtained imprinted catalyst (MIP-H/Hemin) showed 52-fold acceleration due to the enhanced re-binding toward ABTS. Moreover, by introducing cationic monomers, a 137-fold rate enhancement was further achieved for the positively charged imprinted catalyst (MIP+-H/Hemin), from the synergistic effect of molecular imprinting and electrostatic attraction. Remarkably, by comparing the catalytic activity of these POD mimics towards ABTS and 3,3',5,5'-tetramethylbenzidine (TMB), we also highlighted the substrate specificity of MIP-H/Hemin and MIP+-H/Hemin toward ABTS. This study provides a promising approach to improve the catalytic activity and specificity of peptide-based enzyme mimics.

Self-assembling behaviour of a modified aromatic amino acid in competitive medium

Aromatic amino acid, specifically phenylalanine (Phe), is one of the most studied building blocks in peptide synthesis due to its importance in biology. It is reported in the literature that Phe-containing peptides have a high tendency to form different self-assembled materials due to efficient aromatic-aromatic interactions. In this article, we have tuned the supramolecular interactions of phenylalanine by making it electron-deficient upon introduction of the nitro group in the ring. The presence of the nitro group has a profound influence on the self-assembly process. It has been observed that 4-nitrophenylalanine (4NP) is a highly efficient gelator compared with the native phenylalanine in DMSO solvent in terms of minimum gelation concentration and it forms hydrogen bonding mediated crystals in water. The change of self-assembling patterns of 4NP in these solvents was studied using X-ray diffraction, UV-Vis spectroscopy, FE-SEM and other techniques. With the help of different experimental data and density functional theory (DFT), we have simulated the theoretical structure of 4NP in DMSO. The theoretical structure of 4NP in DMSO is different compared with that of crystals in water. We then studied the self-assembly process of 4NP in the mixed solvent of DMSO (polar aprotic) and water (polar protic). Different competitive non-covalent interactions of solvents as well as the ratio of the solvent mixture guide the final self-assembly state of 4NP.

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.

Thermodynamic and Evolutionary Coupling between the Native and Amyloid State of Globular Proteins

The amyloid-like aggregation propensity present in most globular proteins is generally considered to be a secondary side effect resulting from the requirements of protein stability. Here, we demonstrate, however, that mutations in the globular and amyloid state are thermodynamically correlated rather than simply associated. In addition, we show that the standard genetic code couples this structural correlation into a tight evolutionary relationship. We illustrate the extent of this evolutionary entanglement of amyloid propensity and globular protein stability. Suppressing a 600-Ma-conserved amyloidogenic segment in the p53 core domain fold is structurally feasible but requires 7-bp substitutions to concomitantly introduce two aggregation-suppressing and three stabilizing amino acid mutations. We speculate that, rather than being a corollary of protein evolution, it is equally plausible that positive selection for amyloid structure could have been a driver for the emergence of globular protein structure.

Conjugating Catalytic Polyproline Fragments with a Self-Assembling Peptide Produces Efficient Artificial Hydrolases

A polyproline fragment containing a catalytic dyad of His-His or Ser-His was coupled with a self-assembling peptide MAX1 to design new hydrolases (H2H5 and H2S5) for catalyzing ester hydrolysis. Circular dichroism measurements indicated that the peptides change their conformation from random coils to β-sheets when pH increases from 5 to 10. IR spectra also displayed the vibration modes corresponding to their β-structures at pH 9.0. Transmission electron microscopy (TEM) and atomic force microscopy (AFM) measurements showed that in solution, the designed peptides self-assemble into network fibrils having a significantly increased catalytic efficiency on ester hydrolysis. On p-nitrophenyl acetate (p-NPA) substrate, the designed peptides exhibit high catalytic efficiency at pH 9.0 (k_cat/K_M = 12.1 M^-1 s^-1 for H2H5, 13.3 M^-1 s^-1 for H2S5), and their efficiency is even better at pH 10.0 (k_cat/K_M = 24.3 M^-1 s^-1 for H2H5, 99.4 M^-1 s^-1 for H2S5). Additionally, H2H5 and H2S5 also display good activity on catalyzing the hydrolysis of p-nitrophenyl-(2-phenyl)-propanoate (p-NPP) and p-nitrophenyl methoxyacetate (p-NPMA). Combining the polyproline-based catalytic scaffold with a self-assembling peptide generates an efficient hydrolase, providing a new design for effective artificial enzymes.

Catalytic Gels for a Prebiotically Relevant Asymmetric Aldol Reaction in Water: From Organocatalyst Design to Hydrogel Discovery and Back Again

This paper reports an investigation into organocatalytic hydrogels as prebiotically relevant systems. Gels are interesting prebiotic reaction media, combining heterogeneous and homogeneous characteristics with a structurally organized active "solid-like" catalyst separated from the surrounding environment, yet in intimate contact with the solution phase and readily accessible via "liquid-like" diffusion. A simple self-assembling glutamine amide derivative 1 was initially found to catalyze a model aldol reaction between cyclohexanone and 4-nitrobenzaldehyde, but it did not maintain its gel structure during reaction. In this study, it was observed that compound 1 could react directly with the benzaldehyde to form a hydrogel in situ based on Schiff base 2 as a low-molecular-weight gelator (LMWG). This new dynamic gel is a rare example of a two-component self-assembled LMWG hydrogel and was fully characterized. It was demonstrated that glutamine amide 1 could select an optimal aldehyde component and preferentially assemble from mixtures. In the hunt for an organocatalyst, reductive conditions were applied to the Schiff base to yield secondary amine 3, which is also a highly effective hydrogelator at very low loadings with a high degree of nanoscale order. Most importantly, the hydrogel based on 3 catalyzed the prebiotically relevant aldol dimerization of glycolaldehyde to give threose and erythrose. In buffered conditions, this reaction gave excellent conversions, good diastereoselectivity, and some enantioselectivity. Catalysis using the hydrogel of 3 was much better than that using non-assembled 3-demonstrating a clear benefit of self-assembly. The results suggest that hydrogels offer a potential strategy by which prebiotic reactions can be promoted using simple, prebiotically plausible LMWGs that can selectively self-organize from complex mixtures. Such processes may have been of prebiotic importance.

Prebiotic Peptides: Molecular Hubs in the Origin of Life

The fundamental roles that peptides and proteins play in today's biology makes it almost indisputable that peptides were key players in the origin of life. Insofar as it is appropriate to extrapolate back from extant biology to the prebiotic world, one must acknowledge the critical importance that interconnected molecular networks, likely with peptides as key components, would have played in life's origin. In this review, we summarize chemical processes involving peptides that could have contributed to early chemical evolution, with an emphasis on molecular interactions between peptides and other classes of organic molecules. We first summarize mechanisms by which amino acids and similar building blocks could have been produced and elaborated into proto-peptides. Next, non-covalent interactions of peptides with other peptides as well as with nucleic acids, lipids, carbohydrates, metal ions, and aromatic molecules are discussed in relation to the possible roles of such interactions in chemical evolution of structure and function. Finally, we describe research involving structural alternatives to peptides and covalent adducts between amino acids/peptides and other classes of molecules. We propose that ample future breakthroughs in origin-of-life chemistry will stem from investigations of interconnected chemical systems in which synergistic interactions between different classes of molecules emerge.

Covalent Catalysis by Cross β Amyloid Nanotubes

The binding pockets of extant enzymes feature precise positioning of amino acid residues that facilitate multiple complex transformations exploiting covalent and non-covalent interactions. Reversible covalent anchoring is extensively used as an efficient tool by Nature for activating modern enzymes such as esterases and dehydratases and also for proteins like opsins for the complex process of visual phototransduction. Here we construct paracrystalline amyloid surfaces through the self-propagation of short peptides which offer binding pockets exposed with arrays of imidazoles and lysines. As covalent catalysis is utilized by modern-day enzymes, these homogeneous amyloid nanotubes exploit Schiff imine formation via the exposed lysines to efficiently hydrolyze both activated and inactivated esters. Controls where lysines were mutated with charged residues accessed similar morphologies but did not augment the rate. The designed amyloid microphases thus foreshadow the generation of binding pockets of advanced proteins and have the potential to contribute to the development of functional materials.

Self-assembly and multifunctionality of peptide organogels: oil spill recovery, dye absorption and synthesis of conducting biomaterials

The self-assembly of a series of low molecular weight gelator dipeptides containing para amino benzoic acid has been studied in mechanistic detail. All four dipeptides form phase selective, thermoreversible, rigid gels in a large range of organic solvents and fuels such as petrol, diesel, and kerosene. The mechanism of self-assembly has been dissected in detail using several experimental techniques. Self-assembly is driven mainly by aromatic and hydrophobic interactions. Hydrogen bonding groups, though present, seem to make a trivial contribution towards the self-assembly process. Phase selective gelation abilities in fuels in the presence of acidic, basic and saline conditions, together with the easy recovery of fuels from the organogels, render the peptides potential candidates for addressing oil-spill recovery. Being electron rich systems, these organogelators can absorb cationic dyes with >90% efficiency from wastewater. Finally, conducting biomaterials have been synthesized by the insertion of reduced graphene oxide into the organogels. Such small peptide based gelator molecules, being economically viable and easy to prepare, in addition to being multifunctional, are a hot area of research in the field of materials chemistry.

Aldolase Cascade Facilitated by Self-Assembled Nanotubes from Short Peptide Amphiphiles

Early evolution benefited from a complex network of reactions involving multiple C-C bond forming and breaking events that were critical for primitive metabolism. Nature gradually chose highly evolved and complex enzymes such as lyases to efficiently facilitate C-C bond formation and cleavage with remarkable substrate selectivity. Reported here is a lipidated short peptide which accesses a homogenous nanotubular morphology to efficiently catalyze C-C bond cleavage and formation. This system shows morphology-dependent catalytic rates, suggesting the formation of a binding pocket and registered enhancements in the presence of the hydrogen-bond donor tyrosine, which is exploited by extant aldolases. These assemblies showed excellent substrate selectivity and templated the formation of a specific adduct from a pool of possible adducts. The ability to catalyze metabolically relevant cascade transformations suggests the importance of such systems in early evolution.

Self-Assembly of an Amino Acid Derivative into an Antimicrobial Hydrogel Biomaterial

N-(4-Nitrobenzoyl)-Phe self-assembled into a transparent supramolecular hydrogel, which displayed high fibroblast and keratinocyte cell viability. The compound showed a mild antimicrobial activity against E. coli both as a hydrogel and in solution. Single-crystal XRD data revealed packing details, including protonation of the C-terminus due to an apparent pK_a shift, as confirmed by pH titrations. MicroRaman analysis revealed almost identical features between the gel and crystal states, although more disorder in the former. The hydrogel is thermoreversible and disassembles within a range of temperatures that can be fine-tuned by experimental conditions, such as gelator concentration. At the minimum gelling concentration of 0.63 wt %, the hydrogel disassembles in a physiological temperature range of 39-42 °C, thus opening the way to its potential use as a biomaterial.

Visible-light photooxidation in water by 1O2-generating supramolecular hydrogels

An aqueous photocatalytic system exploits photophysical properties arising from the formation of supramolecular hydrogels, with properties and assembly modulated by the amino acids appended to an organic chromophore.

Electrostatic-driven self-sorting and nanostructure speciation in self-assembling tetrapeptides

Significant efforts in the field of supramolecular materials have strived to co-assemble small molecules in order to realize individual nanostructures with multiple, tunable activities. The design of self-assembling motifs bearing opposite charges is one commonly used method, with favorable electrostatic interactions used to promote mixing in a resulting co-assembly. This approach, at the same time, contrasts with a typical thermodynamic preference for self-sorting. Moreover, rigorous experimental techniques which can clearly elucidate co-assembly from self-sorting are limited. Here we describe the self-assembly of two oppositely charged tetrapeptides yielding highly disparate nanostructures of fibrillar and spherical assemblies. Upon mixing at different ratios, the disparate nanostructure of the parent peptides remain. Interestingly, while the assemblies appear self-sorted, surface-mediated interactions between spherical and fibrous assemblies translate to increased mechanical properties through enhanced fiber bundling. Moreover, the observed self-sorting is a thermodynamic product and not a result of kinetically trapped pre-existing structures. Taken together, and with the benefit of disparate nanostructures in the parent peptides, we have shown in our system experimental evidence for electrostatic-driven self-sorting in oligopeptide self-assembly.

Supramolecular Gel as the Template for Catalysis, Inorganic Superstructure, and Pharmaceutical Crystallization

A supramolecular gel is a fascinating combination of flexibility and orderliness. While the supramolecular nature of crosslinking contributes towards the adaptivity and the reversibility of the system, orderliness at the molecular level amplifies the functional output and induces extraordinary selectivity into the system. Therefore, use of supramolecular gels as the soft template is an emerging area of research, which includes but not limited to catalysis of a chemical or a photochemical process, transcription of gel property to a substrate, or even controlling the nucleation of drug molecules. This review aims to highlight the template effect of supramolecular gels in the above-mentioned areas relevant to novel fundamental chemistry, technology, and healthcare.

The aromaticity of the phenyl ring imparts thermal stability to a supramolecular hydrogel obtained from low molecular mass compound

Using Fmoc-phenylalanine and Fmoc-cyclohexylalanine, we show that the aromaticity of the phenyl ring imparts significant thermal stability to a supramolecular hydrogel system and its significance depends on the method of inducing hydrogelation.

Constructing peptide-based artificial hydrolases with customized selectivity

The substrate selectivity of peptide-based artificial enzymes can be customized by combining molecularly imprinted polymers as binding sites with peptide nanofibers as catalytic moieties.

Achieving biopolymer synergy in systems chemistry

Synthetic and materials chemistry initiatives have enabled the translation of the macromolecular functions of biology into synthetic frameworks. These explorations into alternative chemistries of life attempt to capture the versatile functionality and adaptability of biopolymers in new orthogonal scaffolds. Information storage and transfer, however, so beautifully represented in the central dogma of biology, require multiple components functioning synergistically. Over a single decade, the emerging field of systems chemistry has begun to catalyze the construction of mutualistic biopolymer networks, and this review begins with the foundational small-molecule-based dynamic chemical networks and peptide amyloid-based dynamic physical networks on which this effort builds. The approach both contextualizes the versatile approaches that have been developed to enrich chemical information in synthetic networks and highlights the properties of amyloids as potential alternative genetic elements. The successful integration of both chemical and physical networks through β-sheet assisted replication processes further informs the synergistic potential of these networks. Inspired by the cooperative synergies of nucleic acids and proteins in biology, synthetic nucleic-acid-peptide chimeras are now being explored to extend their informational content. With our growing range of synthetic capabilities, structural analyses, and simulation technologies, this foundation is radically extending the structural space that might cross the Darwinian threshold for the origins of life as well as creating an array of alternative systems capable of achieving the progressive growth of novel informational materials.

Designed peptides that assemble into cross-α amyloid-like structures

Amyloids adopt 'cross-β' structures composed of long, twisted fibrils with β-strands running perpendicular to the fibril axis. Recently, a toxic peptide was proposed to form amyloid-like cross-α structures in solution, with a planar bilayer-like assembly observed in the crystal structure. Here we crystallographically characterize designed peptides that assemble into spiraling cross-α amyloid-like structures, which resemble twisted β-amyloid fibrils. The peptides form helical dimers, stabilized by packing of small and apolar residues, and the dimers further assemble into cross-α amyloid-like fibrils with superhelical pitches ranging from 170 Å to 200 Å. When a small residue that appeared critical for packing was converted to leucine, it resulted in structural rearrangement to a helical polymer. Fluorescently tagged versions of the designed peptides form puncta in mammalian cells, which recover from photobleaching with markedly different kinetics. These structural folds could be potentially useful for directing in vivo protein assemblies with predetermined spacing and stabilities.

Functional Assemblies Emerging in Complex Mixtures of Peptides and Nucleic Acid-Peptide Chimeras

Striking synergy between nucleic acids and proteins is exhibited in living cells. Whether such mutual activity can be performed using simple supramolecular nucleic acid-peptide (NA-pep) architectures remains a mystery. To shed light on this question, we studied the emergence of a primitive synergy in assemblies of short DNA-peptide chimeras. Specifically, we characterized multiple structures forming along gradual mixing trajectory, in which a peptide solution was seeded with increasing amounts of NA-pep chimeras. We report on the systematic change from β-sheet-peptide-based fibrillar architectures into the spherical structures formed by the conjugates. Remarkably, we find that through forming onion-like structures, the conjugates exhibit increased DNA hybridization stability and bind small molecules more efficiently than the peptides or DNA alone. A brief discussion highlights the implications of our findings for the production of new materials and for research on the origin of life.

Peptide Amyloids in the Origin of Life

How life can emerge from non-living matter is one of the fundamental mysteries of the universe. A bottom-up approach to this problem focuses on the potential chemical precursors of life, in particular the nature of the first replicative molecules. Such thinking has led to the currently most popular idea: that an RNA-like molecule played a central role as the first replicative and catalytic molecule. Here, we review an alternative hypothesis that has recently gained experimental support, focusing on the role of amyloidogenic peptides rather than nucleic acids, in what has been by some termed "the amyloid-world" hypothesis. Amyloids are well-ordered peptide aggregates that have a fibrillar morphology due to their underlying structure of a one-dimensional crystal-like array of peptides in a β-strand conformation. While they are notorious for their implication in several neurodegenerative diseases including Alzheimer's disease, amyloids also have many biological functions. In this review, we will elaborate on the following properties of amyloids in relation to their fitness as a prebiotic entity: they can be formed by very short peptides with simple amino acids sequences; as aggregates they are more chemically stable than their isolated component peptides; they can possess diverse catalytic activities; they can form spontaneously during the prebiotic condensation of amino acids; they can act as templates in their own chemical replication; they have a structurally repetitive nature that enables them to interact with other structurally repetitive biopolymers like RNA/DNA and polysaccharides, as well as with structurally repetitive surfaces like amphiphilic membranes and minerals.

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.

Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities

A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.

Chiral organocatalysts based on lipopeptide micelles for aldol reactions in water

A comprehensive study of the self-assembly in water of a lipopeptide consisting of a sequence of l-proline, l-arginine and l-tryptophan with a hydrocarbon chain has been performed. Fluorescence assays were used to determine the critical aggregation concentration. In situ small-angle X-ray scattering (SAXS) and molecular dynamics simulations showed the presence of spherical micelles with diameters around 6 nm. In agreement with these results, cryo-TEM images showed globular aggregates with diameters ranging from ≈4 nm up to ≈9 nm. Furthermore, the lipopeptide catalytic activity has been tested for the direct aldol reaction between cyclohexanone and p-nitrobenzaldehyde, and we have observed that the self-association of the organocatalyst played a critical role in the enhanced activity. Water affects the selectivity, and poor results are obtained under neat reaction conditions. The location of the catalytic groups at the lipopetide/water solvent interface also endowed unusual selectivity in the catalyzed aldol reactions. Under optimized reaction conditions, high yields (up to >99%), good enantioselectivity (ee up to 85%) and high diastereoselectivity (ds up to 92 : 8) were obtained.

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.

Expanding the informational chemistries of life: peptide/RNA networks

The RNA world hypothesis simplifies the complex biopolymer networks underlining the informational and metabolic needs of living systems to a single biopolymer scaffold. This simplification requires abiotic reaction cascades for the construction of RNA, and this chemistry remains the subject of active research. Here, we explore a complementary approach involving the design of dynamic peptide networks capable of amplifying encoded chemical information and setting the stage for mutualistic associations with RNA. Peptide conformational networks are known to be capable of evolution in disease states and of co-opting metal ions, aromatic heterocycles and lipids to extend their emergent behaviours. The coexistence and association of dynamic peptide and RNA networks appear to have driven the emergence of higher-order informational systems in biology that are not available to either scaffold independently, and such mutualistic interdependence poses critical questions regarding the search for life across our Solar System and beyond.This article is part of the themed issue 'Reconceptualizing the origins of life'.

Peptide-based ambidextrous bifunctional gelator: applications in oil spill recovery and removal of toxic organic dyes for waste water management

A low molecular weight peptide-based ambidextrous gelator molecule has been discovered for efficient control of water pollution. The gelator molecules can gel various organic solvents with diverse polarity, e.g. n-hexane, n-octane, petroleum ether, petrol, diesel, aromatic solvents like chlorobenzene, toluene, benzene, o-xylene and even aqueous phosphate buffer of pH 7.5. These gels have been thoroughly characterized using various techniques including field emission scanning electron microscopy, Fourier transform infrared spectroscopy, X-ray powder diffraction analysis, small angle X-ray scattering and rheological experiments. Interestingly, hydrogel obtained from the gelator molecule has been found to absorb toxic organic dyes (both cationic and anionic dyes) from dye-contaminated water. The gelator molecule can be reused for several cycles, indicating its possible future use in waste water management. Moreover, this gelator can selectively gel petrol, diesel, pump oil from an oil-water mixture in the presence of a carrier solvent, ethyl acetate, suggesting its efficient application for oil spill recovery. These results indicate that the peptide-based ambidextrous gelator produces soft materials (gels) with dual function: (i) removal of toxic organic dyes in waste water treatment and (ii) oil spill recovery.

Switchable Hydrolase Based on Reversible Formation of Supramolecular Catalytic Site Using a Self-Assembling Peptide

The reversible regulation of catalytic activity is a feature found in natural enzymes which is not commonly observed in artificial catalytic systems. Here, we fabricate an artificial hydrolase with pH-switchable activity, achieved by introducing a catalytic histidine residue at the terminus of a pH-responsive peptide. The peptide exhibits a conformational transition from random coil to β-sheet by changing the pH from acidic to alkaline. The β-sheet self-assembles to form long fibrils with the hydrophobic edge and histidine residues extending in an ordered array as the catalytic microenvironment, which shows significant esterase activity. Catalytic activity can be reversible switched by pH-induced assembly/disassembly of the fibrils into random coils. At higher concentrations, the peptide forms a hydrogel which is also catalytically active and maintains its reversible (de-)activation.

Emergence of a New Self-Replicator from a Dynamic Combinatorial Library Requires a Specific Pre-Existing Replicator

Our knowledge regarding the early steps in the formation of evolvable life and what constitutes the minimal molecular basis of life remains far from complete. The recent emergence of systems chemistry reinvigorated the investigation of systems of self-replicating molecules to address these questions. Most of these studies focus on single replicators and the effects of replicators on the emergence of other replicators remains under-investigated. Here we show the cross-catalyzed emergence of a novel self-replicator from a dynamic combinatorial library made from a threonine containing peptide building block, which, by itself, only forms trimers and tetramers that do not replicate. Upon seeding of this library with different replicators of different macrocycle size (hexamers and octamers), we observed the emergence of hexamer replicator consisting of six units of the threonine peptide only when it is seeded with an octamer replicator containing eight units of a serine building block. These results reveal for the first time how a new replicator can emerge in a process that relies critically on the assistance by another replicator through cross-catalysis and that replicator composition is history dependent.

Emergence of native peptide sequences in prebiotic replication networks

Biopolymer syntheses in living cells are perfected by an elaborate error correction machinery, which was not applicable during polymerization on early Earth. Scientists are consequently striving to identify mechanisms by which functional polymers were selected and further amplified from complex prebiotic mixtures. Here we show the instrumental role of non-enzymatic replication in the enrichment of certain product(s). To this end, we analyzed a complex web of reactions in β-sheet peptide networks, focusing on the formation of specific intermediate compounds and template-assisted replication. Remarkably, we find that the formation of several products in a mixture is not critically harmful, since efficient and selective template-assisted reactions serve as a backbone correction mechanism, namely, for keeping the concentration of the peptide containing the native backbone equal to, or even higher than, the concentrations of the other products. We suggest that these findings may shed light on molecular evolution processes that led to current biology.The synthesis of biopolymers in living cells is perfected by complex machinery, however this was not the case on early Earth. Here the authors show the role of non-enzymatic replication in the enrichment of certain products within prebiotically relevant mixtures.

Partially Acetylated or Benzoylated Arabinose Derivatives as Structurally Simple Organogelators: Effect of the Ester Protecting Group on Gel Properties

Sugar-based low-molecular-weight gelators (LMWGs) have been used for various applications for a long time. Herein, structurally simple, ester-protected arabinosides are reported as low-molecular-weight organogelators (LMOGs) that are able to gel aromatic solvents, as well as petrol and diesel. Studies on the mechanical strength of the gels, through detailed rheological experiments, indicate that gels from the 1,2-dibenzoylated arabinose gelator possess better mechanical properties than those from the 1,2-diacetylated gelator. These results are interpreted in terms of the tendency of the former to form fibers with comparatively lower diameter than those of the latter, based on detailed field-emission SEM and AFM studies. Investigations of the interactions responsible for the self-assembly of gelators through IR spectroscopy and wide-angle X-ray scattering reveal that the primary interactions responsible are hydrogen bonds between the hydroxyl groups and ester C=O, which is absent in the solid state of the gelators. In addition, π interactions present in the 1,2-dibenzoylated derivative result in a more regular arrangement, which, in turn, leads to better mechanical properties of the gels compared with those of the 1,2-diacetylated gelator.

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.

Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine

Catalysis is an essential feature of living systems biochemistry, and probably, it played a key role in primordial times, helping to produce more complex molecules from simple ones. However, enzymes, the biocatalysts par excellence, were not available in such an ancient context, and so, instead, small molecule catalysis (organocatalysis) may have occurred. The best candidates for the role of primitive organocatalysts are amino acids and short random peptides, which are believed to have been available in an early period on Earth. In this review, we discuss the occurrence of primordial organocatalysts in the form of peptides, in particular commenting on reports about seryl-histidine dipeptide, which have recently been investigated. Starting from this specific case, we also mention a peptide fragment condensation scenario, as well as other potential roles of peptides in primordial times. The review actually aims to stimulate further investigation on an unexplored field of research, namely one that specifically looks at the catalytic activity of small random peptides with respect to reactions relevant to prebiotic chemistry and early chemical evolution.

Bipyridine based metallogels: an unprecedented difference in photochemical and chemical reduction in the in situ nanoparticle formation

Metal co-ordination induced supramolecular gelation of low molecular weight organic ligands is a rapidly expanding area of research due to the potential in creating hierarchically self-assembled multi-stimuli responsive materials. In this context, structurally simple O-methylpyridine derivatives of 4,4'-dihydroxy-2,2'-bipyridine ligands are reported. Upon complexation with Ag(i) ions in aqueous dimethyl sulfoxide (DMSO) solutions the ligands spontaneously form metallosupramolecular gels at concentrations as low as 0.6 w/v%. The metal ions induce the self-assembly of three dimensional (3D) fibrillar networks followed by the spontaneous in situ reduction of the Ag-centers to silver nanoparticles (AgNPs) when exposed to daylight. Significant size and morphological differences of the AgNP's was observed between the standard chemical and photochemical reduction of the metallogels. The gelation ability, the nanoparticle formation and rheological properties were found to be depend on the ligand structure, while the strength of the gels is affected by the water content of the gels.

A tripeptide-based self-shrinking hydrogel for waste-water treatment: removal of toxic organic dyes and lead (Pb2+) ions

A tripeptide-based supramolecular automatically self-shrinking superhydrogel has been discovered for the efficient removal of toxic organic dyes and Pb²⁺ ions from waste-water.

Prebiotic synthesis of 2-deoxy-d-ribose from interstellar building blocks promoted by amino esters or amino nitriles

Amino esters and amino nitriles can promote the selective formation of 2-deoxy-d-ribose from materials present in interstellar ices. The use of amino nitriles suggests the possibility that carbohydrates may have existed before amino acids on the prebiotic Earth.

Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions

In this review, we describe the recent advances in supramolecular helical assemblies formed from chiral and achiral small molecules, oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been observed in or achieved by biological systems. In addition, a brief historical overview of the helical assemblies of small molecules and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.

Fine-Tuning of Saponification-Triggered Gelation by Strategic Modification of Peripheral Substituents: Gelation Regulators

A pioneering approach towards controlling the efficiency of saponification assisted gelation in ethyl ester based Zn^II -complexes have been described. Using four new ester containing bis-salen Zn^II complexes (C1-C4) involving different para-azo phenyl substituted ligands it has been clearly shown that gelation efficiency is greatly influenced by the electronic effects of the substituents (-H (C1), -CH₃ (C2), -NO₂ (C3), and -OCH₃ (C4)). Morphological, photophysical, and rheological investigations corroborated the experimental observations well and established that gelation efficiency was enhanced with electron-withdrawing characteristics of substituents (C4<C2<C1<C3). This conclusion was also supported by DFT studies.