Examining structure-activity correlations of some high activity enzyme preparations for low water media

Enzyme-Coated Micro-Crystals: An Almost Forgotten but Very Simple and Elegant Immobilization Strategy

The immobilization of enzymes using protein coated micro-crystals (PCMCs) was reported for the first time in 2001 by Kreiner and coworkers. The strategy is very simple. First, an enzyme solution must be prepared in a concentrated solution of one compound (salt, sugar, amino acid) very soluble in water and poorly soluble in a water-soluble solvent. Then, the enzyme solution is added dropwise to the water soluble solvent under rapid stirring. The components accompanying the enzyme are called the crystal growing agents, the solvent being the dehydrating agent. This strategy permits the rapid dehydration of the enzyme solution drops, resulting in a crystallization of the crystal formation agent, and the enzyme is deposited on this crystal surface. The reaction medium where these biocatalysts can be used is marked by the solubility of the PCMC components, and usually these biocatalysts may be employed in water soluble organic solvents with a maximum of 20% water. The evolution of these PCMC was to chemically crosslink them and further improve their stabilities. Moreover, the PCMC strategy has been used to coimmobilize enzymes or enzymes and cofactors. The immobilization may permit the use of buffers as crystal growth agents, enabling control of the reaction pH in the enzyme environments. Usually, the PCMC biocatalysts are very stable and more active than other biocatalysts of the same enzyme. However, this simple (at least at laboratory scale) immobilization strategy is underutilized even when the publications using it systematically presented a better performance of them in organic solvents than that of many other immobilized biocatalysts. In fact, many possibilities and studies using this technique are lacking. This review tried to outline the possibilities of this useful immobilization strategy.

Protein promiscuity in drug discovery, drug-repurposing and antibiotic resistance

Proteins are supposed to bind to their substrates/ligands in a specific manner via their pre-formed binding sites, according to classical biochemistry. In recent years, several types of deviations from this norm have been observed and called promiscuous behavior. Enzymatic promiscuities allow several biochemical functions to be carried out by the same enzyme. The promiscuous activity can also be the origin of "new proteins" via gene duplication. In more recent years, proteins from prokaryotes, eukaryotes and viruses have been found to have intrinsic disorder and lack a preformed binding site. Intrinsic disorder is exploited in regulatory proteins such as those that are involved in transcription and signal transduction. Such proteins function by folding locally while binding to their ligands or interacting with other proteins. These phenomena have also been classified as examples of protein promiscuity and encompass diverse kinds of ligands that can bind to a protein. Given the significant extent of structural homology in many protein families, it is not surprising that ligands also have been found to display promiscuity. Promiscuous behavior of proteins offers both challenges and opportunities to the drug discovery programs such as drug repurposing. Pathogens when exposed to antibiotics exploit protein promiscuity in several ways to develop resistance to the drug. There is increasing evidence now to support that the disorder in proteins is a major tool used by pathogens for virulence and evade drug action by exploiting protein promiscuity. This review provides a holistic view of this multi-faceted phenomenon called protein promiscuity.

Tailoring enzyme microenvironment: State-of-the-art strategy to fulfill the quest for efficient bio-catalysis

Enzymes as green industrial biocatalysts have become a powerful norm that offers several advantages over traditional catalytic agents with regard to process efficiency, reusability, sustainability, and overall cost-effective ratio. However, enzymes obtained from natural origins are often engineered/tailored since their native forms do not fulfill the acute need for the industrial application. Revolutionary developments in protein engineering provide excellent opportunities for designing and constructing novel industrial biocatalysts with improved functional properties including catalytic activity, stability, substrate specificity, and reaction product inhibition. Momentum in enzyme immobilization has enabled robustness and optimal functions in extreme industrial environments, such as high temperature or organic solvents. The emergence of multi-enzyme catalytic cascade based on a combination of biocatalysts presents multifarious opportunities in biosynthesis, biocatalysis, and biotransformation. This review focuses on the emerging and state-of-the-art enzyme engineering trends and approaches to constructing innovative nano- and microstructured biocatalysts with enhanced catalytic activity and stability features requisite for industrial exploitation. Continuous key developments in this direction together with protein engineering in unique ways might offer ever-increasing opportunities for future biocatalysis-based industrial bioprocesses.

Solid state fluorescence of proteins in high throughput mode and its applications

Direct comparison between fluorescence spectra of a sample in solution and solid state form is valuable to monitor the changes in protein structure when it is “dried” or immobilized on a solid surface (for biocatalysis or sensor applications). We describe here a simple method for recording fluorescence emission spectra of protein powders without using any dedicated accessory for solid samples in a high-throughput format. The 96-well plate used in our studies, was coated black from all the sides and the excitation and emission paths are identical and are from the top of the well. These two features minimize scatter and provide fairly noise free spectra. Even then the fluorescence intensity may be dependent upon many factors such as the extent of protein aggregation, morphology and sizes of the protein particles. Hence, (changes in) λ _max emission may be a more reliable metric in the case of fluorescence spectra of proteins in the solid state. However, any large changes in the intensity could indicate changes in the microenvironment of the fluorophore. The fluorescence emission spectra were blue-shifted (4 to 9 nm), showed an increase in the intensity for different proteins studied upon lyophilization, and were similar to what has been reported by others using available commercial accessories for solid state samples. After validating that our method worked just as well as the dedicated accessories, we applied the method to compare the fluorescence emission spectra of α-chymotrypsin in solution, precipitated form, and the lyophilized powder form. We further examined the fluorescence emission spectra of green fluorescent protein (GFP) in solution and solid form. We also analyzed fluorescence resonance energy transfer (FRET) between tryptophan (Trp57) and the cyclic chromophore of GFP. These findings pointed towards the change in the microenvironment around the cyclic chromophore in GFP upon lyophilization.

Cross-Linked Enzyme Aggregates for Applications in Aqueous and Nonaqueous Media

Extensive cross-linking of a precipitate of a protein by a cross-linking reagent (glutaraldehyde has been most commonly used) creates an insoluble enzyme preparation called cross-linked enzyme aggregates (CLEAs). CLEAs show high stability and performance in conventional aqueous as well as nonaqueous media. These are also stable at fairly high temperatures. CLEAs with more than one kind of enzyme activity can be prepared, and such CLEAs are called combi-CLEAs or multipurpose CLEAs. Extent of cross-linking often influences their morphology, stability, activity, and enantioselectivity.

Protein-Coated Microcrystals, Combi-Protein-Coated Microcrystals, and Cross-Linked Protein-Coated Microcrystals of Enzymes for Use in Low-Water Media

Protein-coated microcrystals (PCMC) are a high-activity preparation of enzymes for use in low-water media. The protocols for the preparation of PCMCs of Subtilisin Carlsberg and Candida antarctica lipase B (CAL B) are described. The combi-PCMC concept is useful both for cascade and non-cascade reactions. It can also be beneficial to combine two different specificities of a lipase when the substrate requires it. Combi-PCMC of CALB and Palatase used for the conversion of coffee oil present in spent coffee grounds to biodiesel is described. Cross-linked protein-coated microcrystals (CL-PCMC) in some cases can give better results than PCMC. Protocols for the CLPCMC of Subtilisin Carlsberg and Candida antarctica lipase B (CAL B) are described. A discussion of their applications is also provided.

Dual bioimprinting of Thermomyces lanuginosus lipase for synthesis of biodiesel

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High activity TLL is made by dually bioimprinting with substrate alcohol and a surfactant.

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TLL (28 U/g of oil) bioimprinted with only the surfactants could yield 99% biodiesel from soybean oil in about 4 h.

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Dually bioimprinted TLL (only 1.4 U/g of oil) was able to yield 99% biodiesel within 48 h

Use of biodiesel as an alternative to non-renewable sources of energy has become an attractive option in recent years. The enzymatic synthesis of biodiesel by transesterification of fats/oils with an alcohol is a much more sustainable route than the chemical method. However, cost effectiveness of the enzymatic route is a major barrier in its commercialization. In this work, a high activity biocatalyst design of Thermomyces lanuginosus lipase is made by dually bioimprinting it with substrate and a surfactant (which is believed to open up the lid covering the active site of the lipase) during precipitation of the lipase in organic solvent. When the lipase was bioimprinted with only the surfactants, 28 U of the enzyme/g of oil could yield 99% biodiesel from soybean oil in about 4 h. However, when dually bioimprinted even very low enzyme load 1.4 U/g of oil, yielded 99% biodiesel within 48 h.

Molecular bioimprinting of lipases with surfactants and its functional consequences in low water media

Lipases from Thermomyces lanuginosa (TLL), Candida rugosa (CRL) and Burkholderia cepacia (BCL) were obtained in the 'open lid' form by adding surfactant molecules like n-octyl-β-d-glucopyranoside (OG), hexadecyl trimethyl ammonium bromide (CTAB), Bis(2-ethylhexyl) sulfosuccinate sodium salt (AOT) and triton X-100 for this purpose. The enzymes were 'dried' by precipitating with 4× (v/v) excess of organic solvents. The imprint surfactant molecules were removed by extensive washing with organic solvents. TLL imprinted with 0.05% CTAB showed 11-fold increase in the transesterification activity and was a better preparation to kinetically resolve (±)-1-phenylethanol. Fluorescence emission spectra confirmed that Trp89 of the lid was indeed affected during bioimprinting. With CRL, bioimprinting with OG gave 7-fold increase in the transesterification rates and resulted in reversal of enantioselectivity of CRL and gave R-phenylethyl acetate instead of the S-product as with the unimprinted precipitate. Bioimprinted BCL was also a 7-fold better catalyst for transesterification as well as enantioselectivity.

Increasing importance of protein flexibility in designing biocatalytic processes

Enzymes require some flexibility for catalysis. Biotechnologists prefer stable enzymes but often this stabilization comes at the cost of reduced efficiency. Enzymes from thermophiles have low flexibility but poor catalytic rates. Enzymes from psychrophiles are less stable but show good catalytic rates at low temperature. In organic solvents enzymes perform poorly as the prior drying makes the enzyme molecules very rigid. Adding water or increasing reaction temperature improves flexibility and catalytic rates. In case of hydrolases, flexibility and enantioselectivity have interdependence. Understanding the complex role of protein flexibility in biocatalysis can help in designing biotechnological processes.

Immobilization of Candida rugosa lipase on superparamagnetic Fe3O4 nanoparticles for biocatalysis in low-water media

A simple immobilization method for Candida rugosa lipase on superparamagnetic Fe3O4 nanoparticles is described. The Fe3O4 nanoparticles were coated with PEI and Candida rugosa lipase was adsorbed on these particles via electrostatic interactions. The immobilization resulted in marginal simultaneous purification. However, the immobilized preparation showed 110× higher transesterification activity in low-water media. It was also efficient in kinetic resolution of (±)-1-phenylethanol with eep of 99 % and E = 412 within 24 h.

High activity preparations of lipases and proteases for catalysis in low water containing organic solvents and ionic liquids

Simple precipitation of enzymes has shown impressive catalytic efficiencies in organic solvents. In asmuch as these can be recovered after the reaction, these can be viewed as immobilized preparations just like more extensively used cross-linked enzyme aggregates (CLEAs). This chapter describes three protocols which use these enzyme precipitated and rinsed with propanol/some other appropriate organic solvent. The first two protocols show their applications in ionic liquids for a transesterification reaction and a kinetic resolution. The third protocol presumably incorporates an "imprinting" effect so that the precipitates are now able to efficiently catalyze transesterification of tributyrin with tertiary alcohols.

Activation of alpha chymotrypsin by three phase partitioning is accompanied by aggregation

Precipitation of alpha chymotrypsin in the simultaneous presence of ammonium sulphate and t-butanol (three phase partitioning) resulted in preparations which showed self aggregation of the enzyme molecules. Precipitation with increasing amounts of ammonium sulphate led to increasing size of aggregates. While light scattering estimated the hydrodynamic diameter of these aggregates in the range of 242-1124 nm; Nanoparticle tracking analysis (NTA) gave the value as 130-462 nm. Scanning electron microscopy and gel filtration on Sephadex G-200 showed extensive aggregation in these preparations. Transmission electron microscopy showed that the aggregates had irregular shapes. All the aggregates had about 3× higher catalytic activity than the native enzyme. These aggregates did not differ in λ(max) of fluorescence emission which was around 340 nm. However, all the aggregates showed higher fluorescence emission intensity. Far-UV and near-UV circular dichroism also showed no significant structural changes as compared to the native molecule. Interestingly, HPLC gel filtration (on a hydroxylated silica column) gave 14 nm as the diameter for all preparations. Light scattering of preparations in the presence of 10% ethylene glycol also dissociated the aggregates to monomers of 14 nm. Both these results indicated that hydrophobic interactions were the driving force behind this aggregation. These results indicate: (1) Even without any major structural change, three phase partitioning led to protein molecules becoming highly prone to aggregation. (2) Different methods gave widely different estimates of sizes of aggregates. It was however possible to reconcile the data obtained with various approaches. (3) The nature of the gel filtration column is crucial and use of this technique for refolding and studying aggregation needs a rethink.

Alpha chymotrypsin coated clusters of Fe3O4 nanoparticles for biocatalysis in low water media

Background

Enzymes in low water containing non aqueous media are useful for organic synthesis. For example, hydrolases in such media can be used for synthetic purposes. Initial work in this area was carried out with lyophilized powders of enzymes. These were found to have poor activity. Drying (removing bulk water) by precipitation turned out to be a better approach. As enzymes in such media are heterogeneous catalysts, spreading these precipitates over a large surface gave even better results. In this context, nanoparticles with their better surface to volume ratio provide obvious advantage. Magnetic nanoparticles have an added advantage of easy separation after the reaction. Keeping this in view, alpha chymotrypsin solution in water was precipitated over a stirred population of Fe₃O₄ nanoparticles in n-propanol. This led to alpha chymotrypsin activity coated over clusters of Fe₃O₄ nanoparticles. These preparations were found to have quite high transesterification activity in low water containing n-octane.

Results

Precipitation of alpha chymotrypsin over a stirred suspension of Fe₃O₄ nanoparticles (3.6 nm diameter) led to the formation of enzyme coated clusters of nanoparticles (ECCNs). These clusters were also magnetic and their hydrodynamic diameter ranged from 1.2- 2.6 microns (as measured by dynamic light scattering). Transmission electron microscopy (TEM), showed that these clusters had highly irregular shapes. Transesterification assay of various clusters in anhydrous n-octane led to optimization of concentration of nanoparticles in suspension during precipitation. Optimized design of enzyme coated magnetic clusters of nanoparticles (ECCN 3) showed the highest initial rate of 465 nmol min^-1 mg^-1protein which was about 9 times higher as compared to the simple precipitates with an initial rate of 52 nmol min^-1 mg^-1 protein.

Circular Dichroism (CD)(with a spinning cell accessory) showed that secondary structure content of the alpha Chymotrypsin in ECCN 3 [15% α-helix, 37% β-sheet and 48% random coil] was identical to the simple precipitates of alpha chymotrypsin.

Conclusion

A strategy for obtaining a high activity preparation of alpha chymotrypsin for application in low water media is described. Such high activity biocatalysts are useful in organic synthesis.