Semi-Rationally Designed Short Peptides Self-Assemble and Bind Hemin to Promote Cyclopropanation

Photo-induced imine reduction by a photoredox biocatalyst consisting of a pentapeptide and a Ru bipyridine terpyridine complex

Imine reduction is a useful reaction in the preparation of amine derivatives. Various catalysts have been reported to promote this reaction and photoredox catalysts are promising candidates for sustainable amine synthesis. Improvement of this reaction using biomolecule-based reaction scaffolds is expected to increase the utility of the reaction. In this context, we have recently investigated photoredox Ru complexes with pentapeptide scaffolds via coordination bonds as catalysts for photoreduction of dihydroisoquinoline derivatives. First, Ru bipyridine terpyridine complexes coordinated with five different pentapeptides (XVHVV: X = V, F, W, Y, C) were prepared and characterized by mass spectrometry. Catalytic activities of the Ru complexes with XVHVV were evaluated for photoreduction of dihydroisoquinoline derivatives in the presence of ascorbate and thiol compounds as sacrificial reagents and hydrogen sources. Interestingly, the turnover number of the Ru complex with VVHVV is 531, which is two-fold higher than that of a simple Ru complex with an imidazole ligand. The detailed emission lifetime measurements indicate that the enhanced catalytic activity provided by the peptide scaffold is caused by an efficient reaction with the thiol derivative to accelerate reductive quenching of Ru complex. The quenching behavior suggests formation of an active species such as a Ru(I) complex. These findings reveal that the simple pentapeptide serves as an effective scaffold to enhance the photocatalytic activity of a photoactive Ru complex.

Catalytic Nanomaterials by Conjugation of an Artificial Heme-Peroxidase to Amyloid Fibrils

The self-assembly of proteins and peptides into fibrillar amyloid aggregates is a highly promising route to define the next generation of functional nanomaterials. Amyloid fibrils, traditionally associated with neurodegenerative diseases, offer exceptional conformational and chemical stability and mechanical properties, and resistance to degradation. Here, we report the development of catalytic amyloid nanomaterials through the conjugation of a miniaturized artificial peroxidase (FeMC6*a) to a self-assembling amyloidogenic peptide derived from human transthyretin, TTR(105-115), whose sequence is YTIAALLSPYS. Our synthetic approach relies on fast and selective click ligation upon proper modification of both the peptide and FeMC6*a, leading to TTRLys108@FeMC6*a. Mixing unmodified TTR(105-115) with TTRLys108@FeMC6*a allowed the generation of enzyme-loaded amyloid fibrils, namely, FeMC6*a@fibrils. Catalytic studies, performed in aqueous solution at nearly neutral pH, using ABTS as a model substrate and H2O2 as the oxidizing agent revealed that the enzyme retains its catalytic activity. Moreover, the activity was found to depend on the TTRLys108@FeMC6*a/unmodified TTR(105-115) peptide ratio. In particular, those with the 2:100 ratio showed the highest activity in terms of initial rates and substrate conversion among the screened nanoconjugates and compared to the freely diffusing enzyme. Finally, the newly developed nanomaterials were integrated into a flow system based on a polyvinylidene difluoride membrane filter. Within this flow-reactor, multiple reaction cycles were performed, showcasing the reusability and stability of the catalytic amyloids over extended periods, thus offering significantly improved characteristics compared to the isolated FeMC6*a in the application to a number of practical scenarios.

Ceria nanoparticles immobilized with self-assembling peptide for biocatalytic applications

Peptide-based artificial enzymes exhibit structure and catalytic mechanisms comparable to natural enzymes but they suffer from limited reusability due to their existence in homogenous solutions. Immobilization of self-assembling peptides on the surface of nanoparticles can be used to overcome limitations associated with artificial enzymes. A high, local density of peptides can be obtained on nanoparticles to exert cooperative or synergistic effects, resulting in an accelerated rate of reaction, distinct catalytic properties, and excellent biocompatibility. In this work, we have immobilized a branched, self-assembled, and nanofibrous catalytic peptide, (C12-SHD)2KK(Alloc)-NH2, onto thiolated ceria nanoparticles to generate a heterogeneous catalyst with an enhanced number of catalytic sites. This artificial enzyme mimics the activities of esterase, phosphatase, and haloperoxidase enzymes and the catalytic efficiency remains nearly unaltered when reused. The enzyme-mimicking property is investigated for pesticide detection, bone regeneration, and antibiofouling applications. Overall, this work presents a facile approach to develop a multifunctional heterogeneous biocatalyst that addresses the challenges associated with unstable peptide-based homogeneous catalysts and, thus, shows a strong potential for industrial applications.

Protocellular Heme and Iron-Sulfur Clusters

ConspectusCentral to the quest of understanding the emergence of life is to uncover the role of metals, particularly iron, in shaping prebiotic chemistry. Iron, as the most abundant of the accessible transition metals on the prebiotic Earth, played a pivotal role in early biochemical processes and continues to be indispensable to modern biology. Here, we discuss our recent contributions to probing the plausibility of prebiotic complexes with iron, including heme and iron-sulfur clusters, in mediating chemistry beneficial to a protocell. Laboratory experiments and spectroscopic findings suggest plausible pathways, often facilitated by UV light, for the synthesis of heme and iron-sulfur clusters. Once formed, heme displays catalytic, peroxidase-like activity when complexed with amphiphiles. This activity could have been beneficial in two ways. First, heme could have catalytically removed a molecule (H2O2) that could have had degradative effects on a protocell. Second, heme could have helped in the synthesis of the building blocks of life by coupling the reduction of H2O2 with the oxidation of organic substrates. The necessity of amphiphiles to avoid the formation of inactive complexes of heme is telling, as the modern-day electron transport chain possesses heme embedded within a lipid membrane. Conversely, prebiotic iron-sulfur peptides have yet to be reported to partition into lipid membranes, nor have simple iron-sulfur peptides been found to be capable of participating in the synthesis of organic molecules. Instead, iron-sulfur peptides span a wide range of reduction potentials complementary to the reduction potentials of hemes. The reduction potential of iron-sulfur peptides can be tuned by the type of iron-sulfur cluster formed, e.g., [2Fe-2S] versus [4Fe-4S], or by the substitution of ligands to the metal center. Since iron-sulfur clusters easily form upon stochastic encounters between iron ions, hydrosulfide, and small organic molecules possessing a thiolate, including peptides, the likelihood of soluble iron-sulfur clusters seems to be high. What remains challenging to determine is if iron-sulfur peptides participated in early prebiotic chemistry or were recruited later when protocellular membranes evolved that were compatible with the exploitation of electron transfer for the storage of energy as a proton gradient. This problem mirrors in some ways the difficulty in deciphering the origins of metabolism as a whole. Chemistry that resembles some facets of extant metabolism must have transpired on the prebiotic Earth, but there are few clues as to how and when such chemistry was harnessed to support a (proto)cell. Ultimately, unraveling the roles of hemes and iron-sulfur clusters in prebiotic chemistry promises to deepen our understanding of the origins of life on Earth and aids the search for life elsewhere in the universe.

Designing Pathway-Controlled Multicomponent Ultrashort Peptide Hydrogels with Diverse Functionalities at the Nanoscale for Directing Cellular Behavior

Tuning self-assembling pathways by implementing different external stimuli has been extensively studied, owing to their effective control over structural and mechanical properties. Consequently, multicomponent peptide hydrogels with high structural tunability and stimuli responsiveness are crucial in dictating cellular behavior. Herein, we have implemented both coassembly approach and pathway-dependent self-assembly to design nonequilibrium nanostructures to understand the thermodynamic and kinetic aspects of peptide self-assembly toward controlling cellular response. Our system involved an ultrashort peptide gelator and a hydrophilic surfactant which coassembled through different pathways, i.e., heat-cool and sonication methods with variable energy input. Interestingly, it was possible to access diverse structural and mechanical properties at the nanoscale in a single coassembled system. Further, the hydrophilic surfactant provided additional surface functionalities, thus creating an efficient hydrophilic matrix for cellular interaction. Such diverse functionalities in a single coassembled system could lead to the development of advanced scaffolds, with applications in various biomedical fields.

Computation-Driven Rational Design of Self-Assembled Short Peptides for Catalytic Hydrogen Production

Self-assembling peptides represent a captivating area of study in nanotechnology and biomaterials. This interest is largely driven by their unique properties and the vast application potential across various fields such as catalytic functions. However, design complexities, including high-dimensional sequence space and structural diversity, pose significant challenges in the study of such systems. In this work, we explored the possibility of self-assembled peptides to catalyze the hydrolysis of hydrosilane for hydrogen production using ab initio calculations and carried out wet-lab experiments to confirm the feasibility of these catalytic reactions under ambient conditions. Further, we delved into the nuanced interplay between sequence, structural conformation, and catalytic activity by combining modeling with experimental techniques such as transmission electron microscopy and nuclear magnetic resonance and proposed a dual mode of the microstructure of the catalytic center. Our results reveal that although research in this area is still at an early stage, the development of self-assembled peptide catalysts for hydrogen production has the potential to provide a more sustainable and efficient alternative to conventional hydrogen production methods. In addition, this work also demonstrates that a computation-driven rational design supplemented by experimental validation is an effective protocol for conducting research on functional self-assembled peptides.

Avoiding common pitfalls in designing kinetic protocols for catalytic amyloid studies

Kinetic characterization of catalytic amyloids arguably presents a most challenging type of kinetic experiment where careful consideration of many factors is required. Here we outline common pitfalls in devising kinetic studies in such systems. Unlike the more specific protocols for various applications described in this volume, this chapter deals with general issues in setting up kinetic experiments that are incredibly important but often go without explicit mention in the specialized literature. The kinetic fundamentals described here can be also be of use to the enzymologists working with more traditional catalysts.

Computational modelling of supramolecular metallopeptide assemblies

Among the important questions in supramolecular peptide self-assemblies are their interactions with metallic compounds and ions. In the last decade, intensive efforts have been devoted to understanding the structural properties of these interactions including their dynamical and catalytic impact in natural and de novo systems. Since structural insights from experimental approaches could be particularly challenging, computational chemistry methods are interesting complementary tools. Here, we present the general multiscale strategies we developed and applied for the study of metallopeptide assemblies. These strategies include prediction of metal binding site, docking of metallic moieties, classical and accelerated molecular dynamics and finally QM/MM calculations. The systems of choice for this chapter are, on one side, peptides involved in neurodegenerative diseases and, on the other, de novo fibrillar systems with catalytic properties. Both successes and remaining challenges are highlighted so that the protocol could be apply to other system of this kind.

Life Cycle of Functional All-Green Biocompatible Fibrous Materials Based on Biodegradable Polyhydroxybutyrate and Hemin: Synthesis, Service Life, and the End-of-Life via Biodegradation

This article addresses the entire life cycle of the all-green fibrous materials based on poly(3-hydroxybutyrate) (PHB) containing a natural biocompatible additive Hemin (Hmi): from preparation, service life, and the end of life upon in-soil biodegradation. Fibrous PHB/Hmi materials with a highly developed surface and interconnected porosity were prepared by electrospinning (ES) from Hmi-containing feed solutions. Structural organization of the PHB/Hmi materials (porosity, uniform structure, diameter of fibers, surface area, distribution of Hmi within the PHB matrix, phase composition, etc.) is shown to be governed by the ES conditions: the presence of even minor amounts of Hmi in the PHB/Hmi (below 5 wt %) serves as a powerful tool for the control over their structure, performance, and biodegradation. Service characteristics of the PHB/Hmi materials (wettability, prolonged release of Hmi, antibacterial activity, breathability, and mechanical properties) were studied by different physicochemical methods (scanning electron microscopy, Fourier transform infrared spectroscopy, energy-dispersive X-ray spectroscopy, differential scanning calorimetry, contact angle measurements, antibacterial tests, etc.). The effect of the structural organization of the PHB/Hmi materials on their in-soil biodegradation at the end of life was analyzed, and key factors providing efficient biodegradation of the PHB/Hmi materials at all stages (from adaptation to mineralization) are highlighted (high surface area and porosity, thin fibers, release of Hmi, etc.). The proposed approach allows for target-oriented preparation and structural design of the functional PHB/Hmi nonwovens when their structural supramolecular organization with a highly developed surface area controls both their service properties as efficient antibacterial materials and in-soil biodegradation upon the end of life.

Metal Ions Can Modulate the Self-Assembly and Activity of Catalytic Peptide Amyloids

Rational design of peptides has become a powerful tool to produce self-assembled nanostructures with the ability to catalyze different chemical reactions, paving the way to develop minimalistic enzyme-like nanomaterials. Catalytic amyloid-like assemblies have emerged among the most versatile and active, but they often require additional factors for activity. Elucidating how these factors influence the structure and activity is key for the design. Here, we showed that biologically relevant metal ions can guide and modulate the self-assembly of a small peptide into diverse amyloid architectures. The morphology and catalytic activity of the resulting fibrils were tuned by the specific metal ion decorating the surface, whereas X-ray structural analysis of the amyloids showed ion-dependent shape sizes. Molecular dynamics simulations showed that the metals can strongly affect the local conformational space, which can trigger major rearrangements of the fibrils. Our results demonstrate that the conformational landscape of catalytic amyloids is broad and tunable by external factors, which can be critical for future design strategies.

Screening of oxidative behavior in catalytic amyloid assemblies

Once considered a thermodynamic minimum of the protein fold or as simply by-products of a misfolding process, amyloids are increasingly showing remarkable potential for promoting enzyme-like catalysis. Recent studies have demonstrated a diverse range of catalytic behaviors that amyloids can promote way beyond the hydrolytic behaviors originally reported. We and others have demonstrated the strong propensity of catalytic amyloids to facilitate redox reactions both in the presence and in the absence of metal cofactors. Here, we present a detailed protocol for measuring the oxidative ability of supramolecular peptide assemblies.

Asymmetric Michael addition catalysed by copper-amyloid complexes

We developed self-assembled peptides containing a partial amyloid β protein sequence and a metal-coordination site. The amyloid fibril-copper complexes exhibited excellent reactivity and moderate enantioselectivity in Michael addition reactions with 2-azachalcone and dimethylmalonate. The catalytic amyloids were characterized using various measurements to confirm their amyloid-like nanofibre structures.

Mechanisms and pathology of protein misfolding and aggregation

Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.

Rational Design and Self-Assembly of Histidine-Rich Peptides on a Graphite Surface

Histidine-rich peptides (HRPs) have been investigated to create functional biomolecules based on the nature of histidine, such as ion binding and catalytic activity. The organization of these HRPs on a solid surface can lead to surface functionalization with the well-known properties of HRPs. However, immobilization of HRPs on the surface has not been realized. Here, we design a series of octapeptides with histidine repeat units, aiming to establish their self-assembly on a graphite surface to produce a highly robust and active nanoscaffold. The new design has (XH)₄, and we incorporated various types of hydrophobic amino acids at X in the sequence to facilitate their interaction with the surface. The effect of the pair of amino acids on their self-assembly was investigated by atomic force microscopy. Contact angle measurement revealed that these assemblies functionalized graphite surfaces with different wetting chemistry. Moreover, the secondary structure of peptides was characterized by Fourier transform infrared spectroscopy (FTIR), which gives us further insights into the conformation of histidine repeat peptides on the surface. Our results showed a new approach to applying histidine-rich peptides on the surface and tuning the self-assembly behavior by introducing different counter amino acids that could be integrated with a wide range of biosensing and biotechnology applications.

A covalent crosslinking strategy to construct a robust peptide-based artificial esterase

Peptide-based artificial enzymes derived from the supramolecular assembly of short peptides have attracted growing attention in recent years. However, the stability of these artificial enzymes is still a problem since their noncovalent supramolecular structure is quite sensitive and frail under environmental conditions. In this study, we reported a covalent crosslinking strategy for the fabrication of a robust peptide-based artificial esterase. Inspired by the di-tyrosine bonds in many natural structural proteins, multi-tyrosines were designed into a peptide sequence with histidine as the catalytic residue for the ester hydrolysis reaction. Upon the photo-induced oxidation reaction, the short peptide YYHYY rapidly transferred into nanoparticle-shaped aggregates (CL-YYHYY) and displayed improved esterase-like catalytic activity than some previously reported noncovalent-based artificial esterases. Impressively, CL-YYHYY showed outstanding reusability and superior stability under high temperature, strong acid and alkaline and organic solvent conditions. This study provides a promising approach to improving the catalytic activity and stability of peptide-based artificial enzymes.

Heme-Dependent Supramolecular Nanocatalysts: A Review

Enzymes fold into three-dimensional structures to distribute amino acid residues for catalysis, which inspired the supramolecular approach to construct enzyme-mimicking catalysts. A key concern in the development of supramolecular strategies is the ability to confine and orient functional groups to form enzyme-like active sites in artificial materials. This review introduces the design principles and construction of supramolecular nanomaterials exhibiting catalytic functions of heme-dependent enzymes, a large class of metalloproteins, which rely on a heme cofactor and spatially configured residues to catalyze diverse reactions via a complex multistep mechanism. We focus on the structure-activity relationship of the supramolecular catalysts and their applications in materials synthesis/degradation, biosensing, and therapeutics. The heme-free catalysts that catalyze reactions achieved by hemeproteins are also briefly discussed. Towards the end of the review, we discuss the outlook on the challenges related to catalyst design and future prospective, including the development of structure-resolving techniques and design concepts, with the aim of creating enzyme-mimicking materials that possess catalytic power rivaling that of natural enzymes..

Chimeric Biocatalyst Combining Peptidic and Nucleic Acid Components Overcomes the Performance and Limitations of the Native Horseradish Peroxidase

Chimeric peptide-DNAzyme (CPDzyme) is a novel artificial peroxidase that relies on the covalent assembly of DNA, peptides, and an enzyme cofactor in a single scaffold. An accurate control of the assembly of these different partners allows for the design of the CPDzyme prototype G4-Hemin-KHRRH, found to be >2000-fold more active (in terms of conversion number k_cat) than the corresponding but non-covalent G4/Hemin complex and, more importantly, >1.5-fold more active than the corresponding native peroxidase (horseradish peroxidase) when considering a single catalytic center. This unique performance originates in a series of gradual improvements, thanks to an accurate selection and arrangement of the different components of the CPDzyme, in order to benefit from synergistic interactions between them. The optimized prototype G4-Hemin-KHRRH is efficient and robust as it can be used under a wide range of non-physiologically relevant conditions [organic solvents, high temperature (95 °C), and in a wide range of pH (from 2 to 10)], thus compensating for the shortcomings of the natural enzymes. Our approach thus opens broad prospects for the design of ever more efficient artificial enzymes.

Biocompatibility and Antimicrobial Activity of Electrospun Fibrous Materials Based on PHB and Modified with Hemin

The effect of the hemin (Hmi) on the structure and properties of nanocomposite electrospun materials based on poly-3-hydroxybutyrate (PHB) is discussed in the article. The additive significantly affected the morphology of fibers allowed to produce more elastic material and provided high antimicrobial activity. The article considers also the impact of the hemin on the biocompatibility of the nonwoven material based on PHB and the prospects for wound healing.

Bioinspired Electropun Fibrous Materials Based on Poly-3-Hydroxybutyrate and Hemin: Preparation, Physicochemical Properties, and Weathering

The development of innovative fibrous materials with valuable multifunctional properties based on biodegradable polymers and modifying additives presents a challenging direction for modern materials science and environmental safety. In this work, high-performance composite fibrous materials based on semicrystalline biodegradable poly-3-hydroxybutyrate (PHB) and natural iron-containing porphyrin, hemin (Hmi) were prepared by electrospinning. The addition of Hmi to the feed PHB mixture (at concentrations above 3 wt.%) is shown to facilitate the electrospinning process and improve the quality of the electrospun PHB/Hmi materials: the fibers become uniform, their average diameter decreases down to 1.77 µm, and porosity increases to 94%. Structural morphology, phase composition, and physicochemical properties of the Hmi/PHB fibrous materials were studied by diverse physicochemical methods, including electronic paramagnetic resonance, optical microscopy, scanning electron microscopy, and energy-dispersive X-ray spectroscopy, elemental analysis, differential scanning calorimetry, Fourier-transformed infrared spectroscopy, mechanical analysis, etc. The proposed nonwoven Hmi/PHB composites with high porosity, good mechanical properties, and retarded biodegradation due to high antibacterial potential can be used as high-performance and robust materials for biomedical applications, including breathable materials for wound disinfection and accelerated healing, scaffolds for regenerative medicine and tissue engineering.

Catalytically Active Amyloids as Future Bionanomaterials

Peptides and proteins can aggregate into highly ordered and structured conformations called amyloids. These supramolecular structures generally have convergent features, such as the formation of intermolecular beta sheets, that lead to fibrillary architectures. The resulting fibrils have unique mechanical properties that can be exploited to develop novel nanomaterials. In recent years, sequences of small peptides have been rationally designed to self-assemble into amyloids that catalyze several chemical reactions. These amyloids exhibit reactive surfaces that can mimic the active sites of enzymes. In this review, I provide a state-of-the-art summary of the development of catalytically active amyloids. I will focus especially on catalytic activities mediated by hydrolysis, which are the most studied examples to date, as well as novel types of recently reported activities that promise to expand the possible repertoires. The combination of mechanical properties with catalytic activity in an amyloid scaffold has great potential for the development of future bionanomaterials aimed at specific applications.

De novo designed peptides form a highly catalytic ordered nanoarchitecture on a graphite surface

Here we demonstrate that short peptides, de novo designed from first principles, self-assemble on the surface of graphite to produce a highly robust and catalytic nanoarchitecture, which promotes peroxidation reactions with activities that rival those of natural enzymes in both single and multi-substrate reactions. These designable peptides recapitulate the symmetry of the underlying graphite surface and act as molecular scaffolds to immobilize hemin molecules on the electrode in a hierarchical self-assembly manner. The highly ordered and uniform hybrid graphite-peptide-hemin nanoarchitecture shows the highest faradaic efficiency of any hybrid electrode reported. Given the explosive growth of the types of chemical reactions promoted by self-assembled peptide materials, this new approach to creating complex electrocatalytic assemblies will yield highly efficient and practically applicable electrocatalysts.

Designed Amyloid Fibers with Emergent Melanosomal Functions

Short peptides designed to self-associate into amyloid fibers with metal ion-binding ability have been used to catalyze various types of chemical reactions. This manuscript demonstrates that one of these short-peptide fibers coordinated with Cu^II can exhibit melanosomal functions. The coordinated Cu^II and the amyloid structure itself are differentially functional in accelerating oxidative self-association of dopamine into melanin-like species and in regulating their material properties (e.g., water dispersion, morphology, and the density of unpaired electrons). The results have implications for the role of functional amyloids in melanin biosynthesis and for designing peptide-based supramolecular structures with various emergent functions.

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.

The Comparison of Advanced Electrospun Materials Based on Poly(-3-hydroxybutyrate) with Natural and Synthetic Additives

The comparison of the effect of porphyrins of natural and synthetic origin containing the same metal atom on the structure and properties of the semi-crystalline polymer matrix is of current concern. A large number of modifying additives and biodegradable polymers for biomedical purposes, composed of poly(-3-hydroxybutyrate)-porphyrin, are of particular interest because of the combination of their unique properties. The objective of this work are electrospun fibrous material based on poly(-3-hydroxybutyrate) (PHB), hemin (Hmi), and tetraphenylporphyrin with iron (Fe(TPP)Cl). The structure of these new materials was investigated by methods such as optical and scanning electron microscopy, X-ray diffraction analysis, Electron paramagnetic resonance method, and Differential scanning calorimetry. The properties of the electrospun materials were analyzed by mechanical and biological tests, and the wetting contact angle was measured. In this work, it was found that even small concentrations of porphyrin can increase the antimicrobial properties by 12 times, improve the physical and mechanical properties by at least 3.5 times, and vary hydrophobicity by at least 5%. At the same time, additives similar in the structure had an oppositely directed effect on the supramolecular structure, the composition of the crystalline, and the amorphous phases. The article considers assumptions about the nature of such differences due to the influence of Hmi and Fe(TPP)Cl) on the macromolecular and fibrous structure of PHB.

De novo metalloprotein design

Natural metalloproteins perform many functions - ranging from sensing to electron transfer and catalysis - in which the position and property of each ligand and metal, is dictated by protein structure. De novo protein design aims to define an amino acid sequence that encodes a specific structure and function, providing a critical test of the hypothetical inner workings of (metallo)proteins. To date, de novo metalloproteins have used simple, symmetric tertiary structures - uncomplicated by the large size and evolutionary marks of natural proteins - to interrogate structure-function hypotheses. In this Review, we discuss de novo design applications, such as proteins that induce complex, increasingly asymmetric ligand geometries to achieve function, as well as the use of more canonical ligand geometries to achieve stability. De novo design has been used to explore how proteins fine-tune redox potentials and catalyse both oxidative and hydrolytic reactions. With an increased understanding of structure-function relationships, functional proteins including O2-dependent oxidases, fast hydrolases, and multi-proton/multi-electron reductases, have been created. In addition, proteins can now be designed using xeno-biological metals or cofactors and principles from inorganic chemistry to derive new-to-nature functions. These results and the advances in computational protein design suggest a bright future for the de novo design of diverse, functional metalloproteins.

Effect of the Hemin Molecular Complexes on the Structure and Properties of the Composite Electrospun Materials Based on Poly(3-hydroxybutyrate)

The creation of innovative fibrous materials based on biodegradable semicrystalline polymers and modifying additives is an urgent scientific problem. In particular, the development of biomedical materials based on molecular complexes and biopolymers with controlled properties is of great interest. The paper suggests an approach to modifying the structure and properties of the composite materials based on poly(3-hydroxybutyrate) (PHB) obtained by the electrospinning method using molecular complexes of hemin. The introduction of 1-5 wt. % of hemin has a significant effect on the supramolecular structure, morphology and properties of PHB-based fibers. Changes in the supramolecular structure intensified with the increasing hemin concentration. On the one hand, a decrease in the fraction of the crystalline phase by 8-10% was observed. At the same time, there is a decrease in the density of the amorphous phase by 15-70%. Moreover, the addition of hemin leads to an improvement in the strength characteristics of the material: the elongation at break increased by 1.5 times, and in the tensile strength, it increased by 3 times. The antimicrobial activity of the hemin-containing composite materials against Escherichia coli and Staphylococcus aureus was confirmed. The obtained materials are proposed to be used in the creation of composite systems for regenerative medicine.

Catalytic amyloids: Is misfolding folding?

Originally regarded as a disease symptom, amyloids have shown a rich diversity of functions, including biologically beneficial ones. As such, the traditional view of polypeptide aggregation into amyloid-like structures being 'misfolding' should rather be viewed as 'alternative folding.' Various amyloid folds have been recently used to create highly efficient catalysts with specific catalytic efficiencies rivaling those of enzymes. Here we summarize recent developments and applications of catalytic amyloids, derived from both de novo and bioinspired designs, and discuss how progress in the last 2 years reflects on the field as a whole.

Structural Water Stabilizes Protein Motifs in Liquid Protein Phase: The Folding Mechanism of Short β-Sheets Coupled to Phase Transition

Macromolecular associates, such as membraneless organelles or lipid-protein assemblies, provide a hydrophobic environment, i.e., a liquid protein phase (LP), where folding preferences can be drastically altered. LP as well as the associated phase change from water (W) is an intriguing phenomenon related to numerous biological processes and also possesses potential in nanotechnological applications. However, the energetic effects of a hydrophobic yet water-containing environment on protein folding are poorly understood. Here, we focus on small β-sheets, the key motifs of proteins, undergoing structural changes in liquid–liquid phase separation (LLPS) and also model the mechanism of energy-coupled unfolding, e.g., in proteases, during W → LP transition. Due to the importance of the accurate description for hydrogen bonding patterns, the employed models were studied by using quantum mechanical calculations. The results demonstrate that unfolding is energetically less favored in LP by ~0.3–0.5 kcal·mol⁻¹ per residue in which the difference further increased by the presence of explicit structural water molecules, where the folded state was preferred by ~1.2–2.3 kcal·mol⁻¹ per residue relative to that in W. Energetics at the LP/W interfaces was also addressed by theoretical isodesmic reactions. While the models predict folded state preference in LP, the unfolding from LP to W renders the process highly favorable since the unfolded end state has >1 kcal·mol⁻¹ per residue excess stabilization.

Self-Assembled Peptide Nano-Superstructure towards Enzyme Mimicking Hydrolysis

The structural arrangement of amino acid residues in native enzymes underlies their remarkable catalytic properties, thus providing a notable point of reference for designing potent yet simple biomimetic catalysts. Herein, we describe a minimalistic approach to construct a dipeptide-based nano-superstructure with enzyme-like activity. The self-assembled biocatalyst comprises one peptide as a single building block, readily synthesized from histidine. Through coordination with zinc ion, the peptide self-assembly procedure allows the formation of supramolecular β-sheet ordered nanocrystals, which can be used as basic units to further construct higher-order superstructure. As a result, remarkable hydrolysis activity and enduring stability are demonstrated. Our work exemplifies the use of a bioinspired supramolecular assembly approach to develop next-generation biocatalysts for biotechnological applications.

Self-Assembling Catalytic Peptide Nanomaterials Capable of Highly Efficient Peroxidase Activity

The self-assembly of short peptides gives rise to versatile nanomaterials capable of promoting efficient catalysis. We have shown that short, seven-residue peptides bind hemin to produce functional catalytic materials which display highly efficient peroxidation activity, reaching a catalytic efficiency of 3×105  m-1  s-1 . Self-assembly is essential for catalysis as non-assembling controls show no activity. We have also observed peroxidase activity even in the absence of hemin, suggesting the potential to alter redox properties of substrates upon association with the assemblies. These results demonstrate the practical utility of self-assembled peptides in various catalytic applications and further support the evolutionary link between amyloids and modern-day enzymes.

Design and engineering of artificial metalloproteins: from de novo metal coordination to catalysis

Metalloproteins are essential to sustain life. Natural evolution optimized them for intricate structural, regulatory and catalytic functions that cannot be fulfilled by either a protein or a metal ion alone. In order to understand this synergy and the complex design principles behind the natural systems, simpler mimics were engineered from the bottom up by installing de novo metal sites in either natural or fully designed, artificial protein scaffolds. This review focuses on key challenges associated with this approach. We discuss how proteins can be equipped with binding sites that provide an optimal coordination environment for a metal cofactor of choice, which can be a single metal ion or a complex multinuclear cluster. Furthermore, we highlight recent studies in which artificial metalloproteins were engineered towards new functions, including electron transfer and catalysis. In this context, the powerful combination of de novo protein design and directed evolution is emphasized for metalloenzyme development.

De Novo-Designed β-Sheet Heme Proteins

The field of de novo protein design has met with considerable success over the past few decades. Heme, a cofactor, has often been introduced to impart a diverse array of functions to a protein, ranging from electron transport to respiration. In nature, heme is found to occur predominantly in α-helical structures over β-sheets, which has resulted in significant designs of heme proteins utilizing coiled-coil helices. By contrast, there are only a few known β-sheet proteins that bind heme and designs of β-sheets frequently result in amyloid-like aggregates. This review reflects on our success in designing a series of multistranded β-sheet heme binding peptides that are well folded in both aqueous and membrane-like environments. Initially, we designed a β-hairpin peptide that self-assembles to bind heme and performs peroxidase activity in membrane. The β-hairpin was optimized further to accommodate a heme binding pocket within multistranded β-sheets for catalysis and electron transfer in membranes. Furthermore, we de novo designed and characterized β-sheet peptides and miniproteins that are soluble in an aqueous environment capable of binding single and multiple hemes with high affinity and stability. Collectively, these studies highlight the substantial progress made toward the design of functional β-sheets.

Covalent Linkage and Macrocylization Preserve and Enhance Synergistic Interactions in Catalytic Amyloids

The self-assembly of short peptides into catalytic amyloid-like nanomaterials has proven to be a powerful tool in both understanding the evolution of early proteins and identifying new catalysts for practically useful chemical reactions. Here we demonstrate that both parallel and antiparallel arrangements of β-sheets can accommodate metal ions in catalytically productive coordination environments. Moreover, synergistic relationships, identified in catalytic amyloid mixtures, can be captured in macrocyclic and sheet-loop-sheet species, that offer faster rates of assembly and provide more complex asymmetric arrangements of functional groups, thus paving the way for future designs of amyloid-like catalytic proteins. Our findings show how initial catalytic activity in amyloid assemblies can be propagated and improved in more-complex molecules, providing another link in a complex evolutionary chain between short, potentially abiotically produced peptides and modern-day enzymes.

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.

Artificial Metalloenzymes: From Selective Chemical Transformations to Biochemical Applications

Artificial metalloenzymes (ArMs) comprise a synthetic metal complex in a protein scaffold. ArMs display performances combining those of both homogeneous catalysts and biocatalysts. Specifically, ArMs selectively catalyze non-natural reactions and reactions inspired by nature in water under mild conditions. In the past few years, the construction of ArMs that possess a genetically incorporated unnatural amino acid and the directed evolution of ArMs have become of great interest in the field. Additionally, biochemical applications of ArMs have steadily increased, owing to the fact that compartmentalization within a protein scaffold allows the synthetic metal complex to remain functional in a sea of inactivating biomolecules. In this review, we present updates on: 1) the newly reported ArMs, according to their type of reaction, and 2) the unique biochemical applications of ArMs, including chemoenzymatic cascades and intracellular/in vivo catalysis. We believe that ArMs have great potential as catalysts for organic synthesis and as chemical biology tools for pharmaceutical applications.