Magnetic amyloid-based biocatalyst for the hydrolysis of urea

The presence of urea in wines and other alcoholic beverages represents a critical problem since it can chemically react with ethanol, which leads to the formation of ethyl carbamate, a carcinogenic agent according to the World Health Organization. Here we report the creation of a biocatalyst for the hydrolysis of urea, which could potentially be used before bottling alcoholic drinks. For this, the effective surface area of streptavidin-labeled magnetic microparticles was amplified by functionalization with biotin-labeled hen egg lysozyme amyloid fibers. Subsequently, by using copper and hydrogen peroxide induced cross-linking of unmodified proteins (CHICUP), soybean urease was immobilized to the fibers. This gave rise to a magnetic biocatalyst with remarkable urease activity, which was maintained even after 10 reuses. We propose that this strategy could be used as a platform for immobilizing other molecules to design and develop a myriad of biocatalysts for the food industry.

Photo-induced protein modifications: a range of biological consequences and applications

Proteins are the most abundant biomolecules in living organisms and tissues and are also present in many natural and processed foods and beverages, as well as in pharmaceuticals and therapeutics. When exposed to UV-visible light, proteins containing endogenous or exogenous chromophores can undergo direct and indirect photochemical processes, resulting in protein modifications including oxidation of residues, cross-linking, proteolysis, covalent binding to molecules and interfaces, and conformational changes. When these modifications occur in an uncontrolled manner in a physiological context, they can lead to biological dysfunctions that ultimately result in cell death. However, rational design strategies involving light-activated protein modification have proven to be a valuable tool for the modulation of protein function or even for the construction of new biomaterials. This mini-review describes the fundamentals of photochemical processes in proteins and explores some of their emerging biomedical and nanobiotechnological applications, such as photodynamic therapy (PDT), photobonding for wound healing, photobioprinting, photoimmobilization of biosensors and enzymes for sensing, and biocatalysis, among others.

Multi-length scale structural investigation of lysozyme self-assembly

Reactive amyloid oligomers are responsible for cytotoxicity in amyloid pathologies and because of their unstable nature characterizing their behavior is a challenge. The physics governing the self-assembly of proteins in crowded conditions is extremely complex and its comprehension, despite its paramount relevance to understanding molecular mechanisms inside cells and optimizing pharmaceutical processes, remains inconclusive. Here, we focus on the amyloid oligomerization process in self-crowded lysozyme aqueous solutions in acidic conditions. We reveal that the amyloid oligomers form at high protein concentration and low pH. Through multi-length scale spectroscopic investigations, we find that amyloid oligomers can further interconnect with each other by weak and non-specific interactions forming an extended network that leads to the percolation of the whole system. Our multi-length scale structural analysis follows the thermal history of amyloid oligomers from different perspectives and highlights the impact of hierarchical self-assembly of biological macromolecules on functional properties.

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Use of multi-length scale spectroscopies to characterize unstable amyloid oligomers

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Lysozyme form thermo-labile amyloid oligomers in self-crowded conditions

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Amyloid oligomers interact and form an extended hydrogel network

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Amyloid oligomers are responsible for the existence of the hydrogel matrix

Protein scaffolds: A tool for multi-enzyme assembly

The synthesis of complex molecules using multiple enzymes simultaneously in one reaction vessel has rapidly emerged as a new frontier in the field of bioprocess technology. However, operating different enzymes together in a single vessel limits their operational performance which needs to be addressed. With this respect, scaffolding proteins play an immense role in bringing different enzymes together in a specific manner. The scaffolding improves the catalytic performance, enzyme stability and provides an optimal micro-environment for biochemical reactions. This review describes the components of protein scaffolds, different ways of constructing a protein scaffold-based multi-enzyme complex, and their effects on enzyme kinetics. Moreover, different conjugation strategies viz; dockerin-cohesin interaction, SpyTag-SpyCatcher system, peptide linker-based ligation, affibody, and sortase-mediated ligation are discussed in detail. Various analytical and characterization tools that have enabled the development of these scaffolding strategies are also reviewed. Such mega-enzyme complexes promise wider applications in the field of biotechnology and bioengineering.

Enzyme-polymeric/inorganic metal oxide/hybrid nanoparticle bio-conjugates in the development of therapeutic and biosensing platforms

Background

Because enzymes can control several metabolic pathways and regulate the production of free radicals, their simultaneous use with nanoplatforms showing protective and combinational properties is of great interest in the development of therapeutic nano-based platforms. However, enzyme immobilization on nanomaterials is not straightforward due to the toxic and unpredictable properties of nanoparticles in medical practice.

Aim of review

In fact, because of the ability to load enzymes on nano-based supports and increase their renewability, scientific groups have been tempted to create potential therapeutic enzymes in this field. Therefore, this study not only pays attention to the therapeutic and diagnostic applications of diseases by enzyme-nanoparticle (NP) bio-conjugate (abbreviated as: ENB), but also considers the importance of nanoplatforms used based on their toxicity, ease of application and lack of significant adverse effects on loaded enzymes. In the following, based on the published reports, we explained that the immobilization of enzymes on polymers, inorganic metal oxide and hybrid compounds provide hopes for potential use of ENBs in medical activities. Then, the use of ENBs in bioassay activities such as paper-based or wearing biosensors and lab-on-chip/microfluidic biosensors were evaluated. Finally, this review addresses the current challenges and future perspective of ENBs in biomedical applications.

Key scientific concepts of review

This literature may provide useful information regarding the application of ENBs in biosensing and therapeutic platforms.

Industrial biotransformations catalyzed by microbial lipases: screening platform and commercial aspects

The successfulness of a lipase-catalyzed industrial process depends on a proper lipase selection. In this work, an alternative screening platform for industrially important biotransformations catalyzed by microbial lipases was proposed. Thus, the reactivity of sixty lipase activities from spore-forming microorganisms towards hydrolytic and transesterification reactions by using p-nitrophenyl palmitate as a chromogenic acyl donor substrate was explored. Only three biocatalysts were capable of catalyzing all reactions tested. Fourteen biocatalysts did not show hydrolytic activity at all; however, they displayed transesterification activities using ethanol, starch, low-methoxyl (LM) pectin, high-methoxyl (HM) pectin, or vitamin C as acyl acceptors. Using heat-treated biocatalysts, hydrolytic activities were not highly correlated with the corresponding transesterification activities using ethanol (r =  -0.058, p = 0.660), starch (r = 0.431, p = 0.001), LM pectin (r =  -0.010, p = 0.938), HM pectin (r = 0.167, p = 0.202), and vitamin C (r =  -0.048, p = 0.716) as acyl acceptor. In addition, to the best of our knowledge, several transesterification activities produced from microorganisms of the genus Bacillus, Brevibacillus, Lysinibacillus, Geobacillus, or Sporosarcina were reported for first time. Finally, the global lipase market was presented and segmented by date, application, geography and player highlighting the commercial contribution of microbial lipases.

Engineering bioscaffolds for enzyme assembly

With the demand for green, safe, and continuous biocatalysis, bioscaffolds, compared with synthetic scaffolds, have become a desirable candidate for constructing enzyme assemblages because of their biocompatibility and regenerability. Biocompatibility makes bioscaffolds more suitable for safe and green production, especially in food processing, production of bioactive agents, and diagnosis. The regenerability can enable the engineered biocatalysts regenerate through simple self-proliferation without complex re-modification, which is attractive for continuous biocatalytic processes. In view of the unique biocompatibility and regenerability of bioscaffolds, they can be classified into non-living (polysaccharide, nucleic acid, and protein) and living (virus, bacteria, fungi, spore, and biofilm) bioscaffolds, which can fully satisfy these two unique properties, respectively. Enzymes assembled onto non-living bioscaffolds are based on single or complex components, while enzymes assembled onto living bioscaffolds are based on living bodies. In terms of their unique biocompatibility and regenerability, this review mainly covers the current advances in the research and application of non-living and living bioscaffolds with focus on engineering strategies for enzyme assembly. Finally, the future development of bioscaffolds for enzyme assembly is also discussed. Hopefully, this review will attract the interest of researchers in various fields and empower the development of biocatalysis, biomedicine, environmental remediation, therapy, and diagnosis.

Preparation of Amyloid Fibrils Using Recombinant Technology

Amyloid fibrils are widely investigated as they are directly associated with various neurodegenerative diseases. For example, a vast of experimental results have shown that the oligomeric and fibrillar aggregates of the amyloid β-peptide (Aβ) play a critical role in the pathogenesis of Alzheimer's disease (AD). Therefore, the accessibility of certain amounts of pure Aβ peptide is necessary for the studies of the mechanism of neurotoxicity. In this regard, recombinant methods provide the possibility to synthesize the Aβ peptide in vitro and thus promote the investigation of the relationship between peptide structure and pathogenic mechanism. These investigations further provide the fundamental supports for developing potential drugs for AD treatment. In addition to providing support for the study of pathogenic mechanisms, the recombination of Aβ peptides also offers the possibility to utilize these unique protein nanomaterials. For example, Aβ peptides tend to assemble into chiral amyloid fibrils with an ultra-high aspect ratio. These unique nano features, together with the inherent protein characteristics, of amyloid fibrils, allow them to be used in biomedical and environmental fields. Accordingly, herein, we aim to introduce the recombinant protocols for the synthesis of Aβ peptides. The experimental route to assemble these peptides to amyloid fibrils is also summarized in this chapter.

Highly reusable invertase biocatalyst: Biological fibrils functionalized by photocrosslinking

Here we report a novel strategy for the immobilization of invertase using amyloid-like fibrils as a support. Optimal conditions to get Tyr-Tyr covalent binding between invertase and the support were determined using a photocrosslinking approach. The biological fibrils with invertase activity turn into microstructured catalysts according to electron microscopy outcomes. Thermal and storage stability as well as optimal pH and temperature of the enzyme were conserved. Moreover, the immobilized enzyme recovered by low g-force centrifugation retained 83% of its initial enzymatic activity after 15 reuse cycles. Considering that enzyme cost is the most significant part of the overall fee of enzymatic biomass conversion, the highly efficient recovery/reuse strategy described herein becomes relevant. Besides, it can also be applied to the immobilization of other enzymes for industrial biocatalysis.

Half a century of amyloids: past, present and future

Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.

Control of microbial biofilm formation as an approach for biomaterials synthesis

The search for new biomaterials with superior mechanical properties is the focus in the area of materials science. A promising pathway is drawing inspiration from nature to design and develop materials with enhanced properties. In this work, a novel strategy to produce functionalized supramolecular bionanomaterials from the microbial biofilm is reported. Tuneable biofilms with specific characteristics were obtained by controlling the culture condition of the microorganism. When the exopolysaccharide (EPS) production was desired the tryptone was the best nutritional component for the EPS production into the biofilm. However, for the expression of a high amount of amyloid protein the combination of peptone and glucose was the best nutritional choice. Each biofilm obtained showed its owner rheology properties. These properties were altered by the addition of extracellular DNA, which increased the viscosity of the biofilm and induced a viscoelastic hydrogel behavior. Besides, as a proof of concept of bionanomaterial, a novel supramolecular polymeric hybrid EPS-Amyloid protein (EPAP) was obtained from the biofilm and it was tested as a new natural functionalized support for enzyme immobilization. The results suggest that this technology could be used as a new concept to obtain biomaterials from biofilms by controlling the nutritional conditions of a microorganism. Understanding environmental factors affecting biofilm formation will help the development of methods for controlling biofilm production and therefore obtaining new biomaterials.

Architecture and physicochemical characterization of Bacillus biofilm as a potential enzyme immobilization factory

Biocatalysis for industrial application is based on the use of enzymes to perform complex transformations. However, these systems have some disadvantage related to the costs of the biocatalyst. In this work, an alternative strategy for producing green immobilized biocatalysts based on biofilm was developed.A study of the rheological behavior of the biofilm from Bacillus sp. Mcn4, as well as the determination of its composition, was carried out. The dynamic rheological measurements, viscosity (G") and elasticity (G') module, showed that the biofilm presents appreciable elastic components, which is a recognized property for enzymes immobilization. After the partial purification, the exopolysaccharidewas identified as a levan with a non-Newtonian behavior. Extracellular DNA with fragments between 10,000 and 1000bp was detected also in the biofilm, and amyloid protein in the extracellular matrix using a fluorescence technique was identified. Bacillus sp. Mcn4 biofilms were developed on different surfaces, being the most stable those developed on hydrophilic supports. The biofilm showed lipase activity suggesting the presence of constitutive lipases entrapped into the biofilm. Indeed, two enzymes with lipase activity were identified in native PAGE. These were used as biocatalysts, whose reuse showed a residual lipase activity after more than one cycle of catalysis. The components identified in the biofilm could be the main contributors of the rheological characteristic of this material, giving an exceptional environment to the lipase enzyme. Based on these findings, the current study proposes green and natural biopolymers matrix as support for the enzyme immobilization for industrial applications.

Determination of Benzyl-hexadecyldimethylammonium 1,4-Bis(2-ethylhexyl)sulfosuccinate Vesicle Permeability by Using Square Wave Voltammetry and an Enzymatic Reaction

This report describes the studies performed to determine the permeability coefficient value (P) of 1-naphthyl phosphate (1-NP) through the benzyl-hexadecyldimethylammonium 1,4-bis(2-ethylhexyl)sulfosuccinate (AOT-BHD) vesicle bilayer. 1-NP was added in the external phase and must cross the bilayer of the vesicle to react with the encapsulated enzyme (alkaline phosphatase) to yield 1-naphtholate (NPh^-), the product of the enzymatic hydrolysis. This product is electrochemically detected, at basic pH value, by a square wave voltammetry technique, which can be a good alternative over the spectroscopic one, to measure the vesicle solutions because scattering (due to its turbidity) does not make any influence in the electrochemical signal. The experimental data allow us to propose a mathematical model, and a value of P = (1.00 ± 0.15) × 10^-9 cm s^-1 was obtained. Also, a value of P = (2.0 ± 0.5) × 10^-9 cm s^-1 was found by using an independent technique, ultraviolet-visible spectroscopy, for comparison. It is evident that the P values obtained from both the techniques are comparable (within the experimental error of both techniques) under the same experimental conditions. This study constitutes the first report of the 1-NP permeability determination in this new vesicle. We want to highlight the importance of the introduction of a new method and the electrochemical response of the product generated through an enzymatic reaction that occurs in the inner aqueous phase of the vesicle, where the enzyme is placed.

Lessons learned from protein aggregation: toward technological and biomedical applications

The close relationship between protein aggregation and neurodegenerative diseases has been the driving force behind the renewed interest in a field where biophysics, neurobiology and nanotechnology converge in the study of the aggregate state. On one hand, knowledge of the molecular principles that govern the processes of protein aggregation has a direct impact on the design of new drugs for high-incidence pathologies that currently can only be treated palliatively. On the other hand, exploiting the benefits of protein aggregation in the design of new nanomaterials could have a strong impact on biotechnology. Here we review the contributions of our research group on novel neuroprotective strategies developed using a purely biophysical approach. First, we examine how doxycycline, a well-known and innocuous antibiotic, can reshape α-synuclein oligomers into non-toxic high-molecular-weight species with decreased ability to destabilize biological membranes, affect cell viability and form additional toxic species. This mechanism can be exploited to diminish the toxicity of α-synuclein oligomers in Parkinson's disease. Second, we discuss a novel function in proteostasis for extracellular glyceraldehyde 3-phosphate dehydrogenase (GAPDH) in combination with a specific glycosaminoglycan (GAG) present in the extracellular matrix. GAPDH, by changing its quaternary structure from a tetramer to protofibrillar assembly, can kidnap toxic species of α-synuclein, and thereby interfere with the spreading of the disease. Finally, we review a brighter side of protein aggregation, that of exploiting the physicochemical advantages of amyloid aggregates as nanomaterials. For this, we designed a new generation of insoluble biocatalysts based on the binding of photo-immobilized enzymes onto hybrid protein:GAG amyloid nanofibrils. These new nanomaterials can be easily functionalized by attaching different enzymes through dityrosine covalent bonds.

Self-assembling peptide and protein amyloids: from structure to tailored function in nanotechnology

Self-assembled peptide and protein amyloid nanostructures have traditionally been considered only as pathological aggregates implicated in human neurodegenerative diseases. In more recent times, these nanostructures have found interesting applications as advanced materials in biomedicine, tissue engineering, renewable energy, environmental science, nanotechnology and material science, to name only a few fields. In all these applications, the final function depends on: (i) the specific mechanisms of protein aggregation, (ii) the hierarchical structure of the protein and peptide amyloids from the atomistic to mesoscopic length scales and (iii) the physical properties of the amyloids in the context of their surrounding environment (biological or artificial). In this review, we will discuss recent progress made in the field of functional and artificial amyloids and highlight connections between protein/peptide folding, unfolding and aggregation mechanisms, with the resulting amyloid structure and functionality. We also highlight current advances in the design and synthesis of amyloid-based biological and functional materials and identify new potential fields in which amyloid-based structures promise new breakthroughs.

Determining the substrate permeability through the bilayer of large unilamellar vesicles of DOPC. A kinetic study

In this work we determine the permeability of DOPC vesicles in the presence of different cholesterol contents, by using the enzymatic hydrolysis of N-benzoyl-l-tyrosine p-nitroanilide catalyzed by α-chymotrypsin.