Combinatorial High-Throughput Screening of Complex Polymeric Enzyme Immobilization Supports

Recent advances have demonstrated the promise of complex multicomponent polymeric supports to enable supra-biological enzyme performance. However, the discovery of such supports has been limited by time-consuming, low-throughput synthesis and screening. Here, we describe a novel combinatorial and high-throughput platform that enables rapid screening of complex and heterogeneous copolymer brushes as enzyme immobilization supports, named combinatorial high-throughput enzyme support screening (CHESS). Using a 384-well plate format, we synthesized arrays of three-component polymer brushes in the microwells using photoactivated surface-initiated polymerization and immobilized enzymes in situ. The utility of CHESS to identify optimal immobilization supports under thermally and chemically denaturing conditions was demonstrated usingBacillus subtilisLipase A (LipA). The identification of supports with optimal compositions was validated by immobilizing LipA on polymer-brush-modified biocatalyst particles. We further demonstrated that CHESS could be used to predict the optimal composition of polymer brushes a priori for the previously unexplored enzyme, alkaline phosphatase (AlkP). Our findings demonstrate that CHESS represents a predictable and reliable platform for dramatically accelerating the search of chemical compositions for immobilization supports and further facilitates the discovery of biocompatible and stabilizing materials.

Supramolecular bioamphiphile facilitated bioemulsification and concomitant treatment of recalcitrant hydrocarbons in petroleum refining industry oily waste

Bioremediation of real-time petroleum refining industry oily waste (PRIOW) is a major challenge due to the poor emulsification potential and oil sludge disintegration efficiency of conventional bioamphiphile molecules. The present study was focused on the design of a covalently engineered supramolecular bioamphiphile complex (SUBC) rich in hydrophobic amino acids for proficient emulsification of hydrocarbons followed by the concomitant degradation of total petroleum hydrocarbons (TPH) in PRIOW using the hydrocarbonoclastic microbial bio-formulation system. The synthesis of SUBC was carried out by pH regulated microbial biosynthesis process and the yield was obtained to be 450.8 mg/g of petroleum oil sludge. The FT-IR and XPS analyses of SUBC revealed the anchoring of hydrophilic moieties of monomeric bioamphiphilic molecules, resulting in the formation of SUBC via covalent interaction. The SUBC was found to be lipoprotein in nature. The maximum loading capacity of SUBC onto surface modified rice hull (SMRH) was achieved to be 45.25 mg/g SMRH at the optimized conditions using RSM-CCD design. The SUBC anchored SMRH was confirmed using SEM, FT-IR, XRD and TGA analyses. The adsorption isotherm models of SUBC onto SMRH were performed. The integrated approach of SUBC-SMRH and hydrocarbonoclastic microbial bio-formulation system, emulsified oil from PRIOW by 92.86 ± 2.26% within 24 h and degraded TPH by 89.25 ± 1.75% within 4 days at the optimum dosage ratio of SUBC-SMRH (0.25 g): PRIOW (1 g): mass of microbial-assisted biocarrier material (0.05 g). The TPH degradation was confirmed by SARA fractional analysis, FT-IR, ¹H NMR and GC-MS analyses. The study suggested that the application of covalently engineered SUBC has resulted in the accelerated degradation of real-time PRIOW in a very short duration without any secondary sludge generation. Thus, the SUBC integrated approach can be considered to effectively manage the hydrocarbon contaminants from petroleum refining industries under optimal conditions.

Is enzyme immobilization a mature discipline? Some critical considerations to capitalize on the benefits of immobilization

Enzyme immobilization has been developing since the 1960s and although many industrial biocatalytic processes use the technology to improve enzyme performance, still today we are far from full exploitation of the field. One clear reason is that many evaluate immobilization based on only a few experiments that are not always well-designed. In contrast to many other reviews on the subject, here we highlight the pitfalls of using incorrectly designed immobilization protocols and explain why in many cases sub-optimal results are obtained. We also describe solutions to overcome these challenges and come to the conclusion that recent developments in material science, bioprocess engineering and protein science continue to open new opportunities for the future. In this way, enzyme immobilization, far from being a mature discipline, remains as a subject of high interest and where intense research is still necessary to take full advantage of the possibilities.

Waste Management in the Agri-Food Industry: The Conversion of Eggshells, Spent Coffee Grounds, and Brown Onion Skins into Carriers for Lipase Immobilization

One of the major challenges in sustainable waste management in the agri-food industry following the “zero waste” model is the application of the circular economy strategy, including the development of innovative waste utilization techniques. The conversion of agri-food waste into carriers for the immobilization of enzymes is one such technique. Replacing chemical catalysts with immobilized enzymes (i.e., immobilized/heterogeneous biocatalysts) could help reduce the energy efficiency and environmental sustainability problems of existing chemically catalysed processes. On the other hand, the economics of the process strongly depend on the price of the immobilized enzyme. The conversion of agricultural and food wastes into low-cost enzyme carriers could lead to the development of immobilized enzymes with desirable operating characteristics and subsequently lower the price of immobilized enzymes for use in biocatalytic production. In this context, this review provides insight into the possibilities of reusing food industry wastes, namely, eggshells, coffee grounds, and brown onion skins, as carriers for lipase immobilization.

Chitosan: An Overview of Its Properties and Applications

Chitosan has garnered much interest due to its properties and possible applications. Every year the number of publications and patents based on this polymer increase. Chitosan exhibits poor solubility in neutral and basic media, limiting its use in such conditions. Another serious obstacle is directly related to its natural origin. Chitosan is not a single polymer with a defined structure but a family of molecules with differences in their composition, size, and monomer distribution. These properties have a fundamental effect on the biological and technological performance of the polymer. Moreover, some of the biological properties claimed are discrete. In this review, we discuss how chitosan chemistry can solve the problems related to its poor solubility and can boost the polymer properties. We focus on some of the main biological properties of chitosan and the relationship with the physicochemical properties of the polymer. Then, we review two polymer applications related to green processes: the use of chitosan in the green synthesis of metallic nanoparticles and its use as support for biocatalysts. Finally, we briefly describe how making use of the technological properties of chitosan makes it possible to develop a variety of systems for drug delivery.

New insights into the degradation of synthetic pollutants in contaminated environments

The environment is contaminated by synthetic contaminants owing to their extensive applications globally. Hence, the removal of synthetic pollutants (SPs) from the environment has received widespread attention. Different remediation technologies have been investigated for their abilities to eliminate SPs from the ecosystem; these include photocatalysis, sonochemical techniques, nanoremediation, and bioremediation. SPs, which can be organic or inorganic, can be degraded by microbial metabolism at contaminated sites. Owing to their diverse metabolisms, microbes can adapt to a wide variety of environments. Several microbial strains have been reported for their bioremediation potential concerning synthetic chemical compounds. The selection of potential strains for large-scale removal of organic pollutants is an important research priority. Additionally, novel microbial consortia have been found to be capable of efficient degradation owing to their combined and co-metabolic activities. Microbial engineering is one of the most prominent and promising techniques for providing new opportunities to develop proficient microorganisms for various biological processes; here, we have targeted the SP-degrading mechanisms of microorganisms. This review provides an in-depth discussion of microbial engineering techniques that are used to enhance the removal of both organic and inorganic pollutants from different contaminated environments and under different conditions. The degradation of these pollutants is investigated using abiotic and biotic approaches; interestingly, biotic approaches based on microbial methods are preferable owing to their high potential for pollutant removal and cost-effectiveness.

Environmental impact of lignocellulosic wastes and their effective exploitation as smart carriers - A drive towards greener and eco-friendlier biocatalytic systems

In recent years, lignocellulosic wastes have gathered much attention due to increasing economic, social, environmental apprehensions, global climate change and depleted fossil fuel reserves. The unsuitable management of lignocellulosic materials and related organic wastes poses serious environmental burden and causes pollution. On the other hand, lignocellulosic wastes hold significant economic potential and can be employed as promising catalytic supports because of impressing traits such as surface area, porous structure, and occurrence of many chemical moieties (i.e., carboxyl, amino, thiol, hydroxyl, and phosphate groups). In the current literature, scarce information is available on this important and highly valuable aspect of lignocellulosic wastes as smart carriers for immobilization. Thus, to fulfill this literature gap, herein, an effort has been made to signify the value generation aspects of lignocellulosic wastes. Literature assessment spotlighted that all these waste materials display high potential for immobilizing enzyme because of their low cost, bio-renewable, and sustainable nature. Enzyme immobilization has gained recognition as a highly useful technology to improve enzyme properties such as catalytic stability, performance, and repeatability. The application of carrier-supported biocatalysts has been a theme of considerable research, for the past three decades, in the bio-catalysis field. Nonetheless, the type of support matrix plays a key role in the immobilization process due to its influential impact on the physicochemical characteristics of the as-synthesized biocatalytic system. In the past, an array of various organic, inorganic, and composite materials has been used as carriers to formulate efficient and stable biocatalysts. This review is envisioned to provide recent progress and development on the use of different agricultural wastes (such as coconut fiber, sugarcane bagasse, corn and rice wastes, and Brewers' spent grain) as support materials for enzyme immobilization. In summary, the effective utilization of lignocellulosic wastes to develop multi-functional biocatalysts is not only economical but also reduce environmental problems of unsuitable management of organic wastes and drive up the application of biocatalytic technology in the industry.

Label-Free Fluorescence Quantification of Hydrolytic Enzyme Activity on Native Substrates Reveals How Lipase Function Depends on Membrane Curvature

Lipases are important hydrolytic enzymes used in a spectrum of technological applications, such as the pharmaceutical and detergent industries. Because of their versatile nature and ability to accept a broad range of substrates, they have been extensively used for biotechnological and industrial applications. Current assays to measure lipase activity primarily rely on low-sensitivity measurements of pH variations or visible changes of material properties, like hydration, and often require high amounts of proteins. Fluorescent readouts, on the other hand, offer high contrast and even single-molecule sensitivity, albeit they are reliant on fluorogenic substrates that structurally resemble the native ones. Here we present a method that combines the highly sensitive readout of fluorescent techniques while reporting enzymatic lipase function on native substrates. The method relies on embedding the environmentally sensitive fluorescent dye pHrodo and native substrates into the bilayer of liposomes. The charged products of the enzymatic hydrolysis alter the local membrane environment and thus the fluorescence intensity of pHrodo. The fluorescence can be accurately quantified and directly assigned to product formation and thus enzymatic activity. We illustrated the capacity of the assay to report the function of diverse lipases and phospholipases both in a microplate setup and at the single-particle level on individual nanoscale liposomes using total internal reflection fluorescence (TIRF). The parallelized sensitive readout of microscopy combined with the inherent polydispersity in sizes of liposomes allowed us to screen the effect of membrane curvature on lipase function and identify how mutations in the lid region control the membrane curvature-dependent activity. We anticipate this methodology to be applicable for sensitive activity readouts for a spectrum of enzymes where the product of the enzymatic reaction is charged.

Agro-industrial wastes as potential carriers for enzyme immobilization: A review

This review provides a general overview of the suitability of different agro-industrial wastes for enzyme immobilization. For the purposes of this literary study, the support materials are divided into two main groups, called lignocellulosic (coconut fiber, corn cob, spent grain, spent coffee, husk, husk ash, and straw rice, soybean and wheat bran) and not lignocellulosic by-products (eggshell and eggshell membranes). The study pointed out that all of these wastes are materials of great potentiality for enzyme immobilization even if coconut fiber is preferred. This result is of significant interest due to the low cost and great availability of such wastes, which actually are underused and cause significant environmental problems for improper storage. In addition, the development of economic biocatalysts more sustainable, besides reduce environmental impacts, improve the application of enzymatic technology in industry. Therefore, the enzyme immobilization reaction and the application of biocatalysts are reviewed and discussed.

Bacillus subtilis Lipase A—Lipase or Esterase?

The question of how to distinguish between lipases and esterases is about as old as the definition of the subclassification is. Many different criteria have been proposed to this end, all indicative but not decisive. Here, the activity of lipases in dry organic solvents as a criterion is probed on a minimal α/β hydrolase fold enzyme, the Bacillus subtilis lipase A (BSLA), and compared to Candida antarctica lipase B (CALB), a proven lipase. Both hydrolases show activity in dry solvents and this proves BSLA to be a lipase. Overall, this demonstrates the value of this additional parameter to distinguish between lipases and esterases. Lipases tend to be active in dry organic solvents, while esterases are not active under these circumstances.

Immobilization of lipase in silica gel from rice husk ash and its activity assay to hydrolyze palm oil

A free lipase is one of the biocatalysts used for industrial applications, especially to catalyze the hydrolysis of palm oil. However, it is unstable in an extreme condition so it is easy to denature. Immobilization of lipase improve the enzyme's stability since the cage of the immobilization matrix around the lipase can minimalize denaturation. Silica gel is the most chosen matrix because of its high thermal stability and inertness. Lipase was immobilized in silica gel extracted from rice husk ash. Silica gel was prepared in a sodium silicate solution. Sol-gel process occurred when phosphoric acid was added into the sodium silicate solution until it reached a pH of 7. The immobilization process was initiated by reacting lipase in Phosphate Buffer Solution (PBS) added to the sol solution to produce hydrogel. Hydrogel was got into the dry process to form xerogel. The activity assay was conducted in the hydrolysis reaction by titrimetric method. The immobilized lipase resulted had an immobilization percentage of 67.71% and reusability for 6 cycles.

Direct observation of Thermomyces lanuginosus lipase diffusional states by Single Particle Tracking and their remodeling by mutations and inhibition

Lipases are interfacially activated enzymes that catalyze the hydrolysis of ester bonds and constitute prime candidates for industrial and biotechnological applications ranging from detergent industry, to chiral organic synthesis. As a result, there is an incentive to understand the mechanisms underlying lipase activity at the molecular level, so as to be able to design new lipase variants with tailor-made functionalities. Our understanding of lipase function primarily relies on bulk assay averaging the behavior of a high number of enzymes masking structural dynamics and functional heterogeneities. Recent advances in single molecule techniques based on fluorogenic substrate analogues revealed the existence of lipase functional states, and furthermore so how they are remodeled by regulatory cues. Single particle studies of lipases on the other hand directly observed diffusional heterogeneities and suggested lipases to operate in two different modes. Here to decipher how mutations in the lid region controls Thermomyces lanuginosus lipase (TLL) diffusion and function we employed a Single Particle Tracking (SPT) assay to directly observe the spatiotemporal localization of TLL and rationally designed mutants on native substrate surfaces. Parallel imaging of thousands of individual TLL enzymes and HMM analysis allowed us to observe and quantify the diffusion, abundance and microscopic transition rates between three linearly interconverting diffusional states for each lipase. We proposed a model that correlate diffusion with function that allowed us to predict that lipase regulation, via mutations in lid region or product inhibition, primarily operates via biasing transitions to the active states.

Integrating computational and experimental methods for efficient biocatalytic synthesis of polyesters

The research on biocatalyzed polycondensation has delivered an array of polyesters having molecular weights below 20,000gmol^-1 but characterized by controlled structures and desired functionalities. Their unique catalytic efficiency under mild conditions enables enzymes to catalyze the polycondensation of monomers bearing labile lateral moieties that can be easily accessed via post-polymerization modifications. Despite this great potential, nowadays biocatalysts are not employed for polycondensation on industrial scale due to some bottlenecks related to the formulation of biocatalysts and the process configuration, which make the enzymatic technology non-economic. Recycling the enzymatic catalysts is not only a matter of producing an active and robust formulation, but it also requires the optimal integration of such biocatalyst within a specific reactor and process configuration that must enable efficient mass-transfer while preserving the integrity of the enzymatic preparation. In this chapter, we describe examples of integrated experimental-computational approaches for the rational planning and implementation of enzymatic polycondensation using lipase B from Candida antarctica and cutinase 1 from Thermobifida cellulosilytica. They rely on molecular visualization, molecular modeling and chemometrics, which are methods requiring very modest computational power and approachable by operators who do not have specific computational background. The examples also address the sustainability issue, by describing solvent-free processes involving bio-based monomers and biocatalysts immobilized on renewable carriers.

Directly covalent immobilization of Candida antarctica lipase B on oxidized aspen powder by introducing poly‑lysines: An economical approach to improve enzyme performance

In our previous study, we could achieve high soluble expression of Candida antarctica lipase B (CalB) in E. coli by fusion poly‑amino acid tags on CalB (pCalB). Herein, we are surprised to find that pCalB can be easily and directly covalent binding on a simply oxidized aspen powder (OAP) by the aid of poly‑lysine tags. Under the optimal conditions, 72.9 ± 3.6% of the total protein could be immobilized, and the activity recovery of immobilized pCalB (pCalB-OAP) was 98.9 ± 3.8%. The analysis of scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) indicated that OAP was a suitable carrier for enzyme immobilization. The immobilized pCalB-OAP could exhibit excellent thermal stabilities, and it retained a residual activity of 58.4 ± 2.8% at 55 °C, whereas only 21.2 ± 2.2% of its initial activity for free pCalB was observed. And it could also display a nice tolerance for the changes of pH environment, compared with that of free pCalB. The results that pCalB-OAP could retained 73.6 ± 2.9% of their initial activity in (R, S)-NEMPAME hydrolysis after the tenth cycles, suggested that pCalB-OAP could be effectively recycled. The immobilization strategies established here were simple and inexpensive.

Safer bio-based solvents to replace toluene and tetrahydrofuran for the biocatalyzed synthesis of polyesters

With increased awareness of environmental issues caused by traditional petrochemical processes, both academia and industry are making enormous efforts towards the development of sustainable practices using renewable biomass as a feedstock. In this work, the biocatalyzed synthesis of polyesters derived from renewable monomers was performed in safer, bio-derivable organic solvents. Candida antarctica lipase B (CaLB), an enzyme belonging to the Ser-hydrolase family (adsorbed on methacrylic resin, also known as Novozym 435) was tested for its performance in the synthesis of adipate- and furandicarboxylate-based polyesters. In addition, the traditional solvents toluene and tetrahydrofuran were compared with a series of green solvents, 2,2,5,5-tetramethyloxolane, 2-methyltetrahydrofuran, 2,5-dimethyltetrahydrofuran and pinacolone for the enzymatic polymerizations. We can conclude that the monomer conversions and molecular masses of the obtained polyesters in all the tested alternative solvents were suitable, and in some cases superior, with CaLB immobilized via physisorption on acrylic resin being the optimal biocatalyst for all reactions. Strikingly, it was found that for the majority of the new solvents, lower reaction temperatures gave comparable monomer conversions and polymers with similar molecular weights whilst pinacolone yielded better polymers with M n > 2000 Da and conversions of over 80%.

Rice Husk as an Inexpensive Renewable Immobilization Carrier for Biocatalysts Employed in the Food, Cosmetic and Polymer Sectors

The high cost and environmental impact of fossil-based organic carriers represent a critical bottleneck to their use in large-scale industrial processes. The present study demonstrates the applicability of rice husk as inexpensive renewable carrier for the immobilization of enzymes applicable sectors where the covalent anchorage of the protein is a pre-requisite for preventing protein contamination while assuring the recyclability. Rice husk was oxidized and then functionalized with a di-amino spacer. The morphological characterization shed light on the properties that affect the functionalization processes. Lipase B from Candida antarctica (CaLB) and two commercial asparaginases were immobilized covalently achieving higher immobilization yield than previously reported. All enzymes were immobilized also on commercial epoxy methacrylic resins and the CaLB immobilized on rice husk demonstrated a higher efficiency in the solvent-free polycondensation of dimethylitaconate. CaLB on rice husk appears particularly suitable for applications in highly viscous processes because of the unusual combination of its low density and remarkable mechanical robustness. In the case of the two asparaginases, the biocatalyst immobilized on rice husk performed in aqueous solution at least as efficiently as the enzyme immobilized on methacrylic resins, although the rice husk loaded a lower amount of protein.

Spatially confined lignin nanospheres for biocatalytic ester synthesis in aqueous media

Dehydration reactions proceed readily in water-filled biological cells. Development of biocatalysts that mimic such compartmentalized reactions has been cumbersome due to the lack of low-cost nanomaterials and associated technologies. Here we show that cationic lignin nanospheres function as activating anchors for hydrolases, and enable aqueous ester synthesis by forming spatially confined biocatalysts upon self-assembly and drying-driven aggregation in calcium alginate hydrogel. Spatially confined microbial cutinase and lipase retain 97% and 70% of their respective synthetic activities when the volume ratio of water to hexane increases from 1:1 to 9:1 in the reaction medium. The activity retention of industrially most frequently used acrylic resin-immobilized Candida antarctica lipase B is only 51% under similar test conditions. Overall, our findings enable fabrication of robust renewable biocatalysts for aqueous ester synthesis, and provide insight into the compartmentalization of diverse heterogeneous catalysts.

Spatially confined lignin nanospheres for biocatalytic ester synthesis in aqueous media

Dehydration reactions proceed readily in water-filled biological cells. Development of biocatalysts that mimic such compartmentalized reactions has been cumbersome due to the lack of low-cost nanomaterials and associated technologies. Here we show that cationic lignin nanospheres function as activating anchors for hydrolases, and enable aqueous ester synthesis by forming spatially confined biocatalysts upon self-assembly and drying-driven aggregation in calcium alginate hydrogel. Spatially confined microbial cutinase and lipase retain 97% and 70% of their respective synthetic activities when the volume ratio of water to hexane increases from 1:1 to 9:1 in the reaction medium. The activity retention of industrially most frequently used acrylic resin-immobilized Candida antarctica lipase B is only 51% under similar test conditions. Overall, our findings enable fabrication of robust renewable biocatalysts for aqueous ester synthesis, and provide insight into the compartmentalization of diverse heterogeneous catalysts.

Development of biocatalysts that mimic compartmentalized reactions in cells has been cumbersome due to the lack of low-cost materials and associated technologies. Here the authors show that cationic lignin nanospheres function as activating anchors for hydrolases, and enable aqueous ester synthesis by forming spatially confined biocatalysts.

His-Tag Immobilization of Cutinase 1 From Thermobifida cellulosilytica for Solvent-Free Synthesis of Polyesters

For many years, lipase B from Candida antarctica (CaLB) was the primary biocatalyst used for enzymatic esterification and polycondensation reactions. More recently, the need for novel biocatalysts with different selectivity has arisen in the biotechnology and biocatalysis fields. The present work describes how the catalytic potential of Thermobifida cellulosilytica cutinase 1 (Thc_Cut1) was exploited for polyester synthesis. In a first step, Thc_Cut1 was immobilized on three different carriers, namely Opal, Coral, and Amber, using a novel non-toxic His-tag method based on chelated Fe(III) ions (>99% protein bounded). In a second step, the biocatalyzed synthesis of an array of aliphatic polyesters was conducted. A selectivity chain study in a solvent-free reaction environment showed how, in contrast to CaLB, Thc_Cut1 presents a certain preference for C₆ -C₄ ester-diol combinations reaching monomer conversions up to 78% and M_w of 878 g mol^-1 when the Amber immobilized Thc_Cut1 was used. The synthetic potential of this cutinase was also tested in organic solvents, showing a marked activity decrease in polar media like that observed for CaLB. Finally, recyclability studies were performed, which showed an excellent stability of the immobilized Thc_Cut1 (retained activity >94%) over 24 h reaction cycles when a solvent-free workup was used. Concerning a practical application of the biocatalyst's preparation, the production of oligomers with M_n values below 10 kDa is usually desired for the production of nanoparticles and for the synthesis of functional pre-polymers for coating applications that can be crosslinked in a second reaction step.