Nickel Ferrite Nanoparticles as an Adsorbent for Immobilized Metal Affinity Chromatography of Proteins

A simple method of preparing amorphous nickel ferrite nanoparticles of about 5 nm diameter is described. These particles were characterized by dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FT-IR), transmission electron microscopy (TEM) and selected area electron diffraction (SAED). The nanoparticles were evaluated for their use as a magnetic material for immobilized metal affinity chromatography (IMAC). The ferrite nanoparticles bound to bovine serum albumin (BSA) and the binding fitted Langmuir isotherm model. A high capacity of 916 mg BSA/g dried nanoparticle was observed. Six proteins (Soybean trypsin inhibitor (STI), lactate dehydrogenase (LDH), papain, catalase, β-galactosidase and casein) were used and all were found to bind at >90% level (except papain which showed 84% binding). All the proteins except LDH and β-galactosidase could be eluted with 1 M imidazole and with % activity recovery of >80%. Papain could be purified from its dried crude latex by 5-fold and purified papain showed a single band on SDS-PAGE. These nanoparticles constitute a high capacity and are magnetic material useful for IMAC and do not require any pre-functionalization.

Intrinsic disorder in proteins: Relevance to protein assemblies, drug design and host-pathogen interactions

Intrinsic disorder in proteins resulting in considerable variation in structure can lead to multiple functions including multi-specificity and diverse pathologies. Protein interfaces can involve disordered regions that assemble through a concerted-fold-and-bind mechanism. The binding involves both enthalpic and entropic gains by exploiting 'hot spots' on the partner and displacing water molecules placed in thermodynamically unfavorable situations. The examples of Rad51-BRCA2 and Artemis-DNA-PKCs/LigIV complexes illustrate this in the context of drug design. This overview tracks the seamless involvement of protein disorder in multi-specificity of biocatalysts, protein assembly formations and host-pathogen interactions, where intrinsic disorder can in Mycobacteria, compensate for genome reduction by carrying out multiple functions and in some RNA viruses facilitate adaption to the host. These present challenging opportunities for designing new drugs and interventions.

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.

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.

Effectiveness of cross-linked enzyme aggregates of cellulolytic enzymes in hydrolyzing wheat straw

Development of industrially potent cellulolytic enzymes is one of the greatest challenges faced in lignocellulosic feed-stock based bio-refining. In the current work cross-linked enzyme aggregates (CLEAs) of commercial cellulase mix were successfully prepared and their performance to be used as potential industrial enzymes in terms of stability and wheat straw hydrolysis was evaluated. The CLEAs were more stable compared to native enzymes with half-lives being 2.30-, 1.56-, 3.07- and 1.67-fold higher at 70°C for filter paper activity (FPA), endoglucanase, β-glucosidase and xylanase, respectively. CLEAs retained 77.4% of endoglucanase and 85.9% of xylanase activity after five cycles of hydrolysis of soluble substrates such as carboxymethyl cellulose and xylan, respectively. A maximum saccharification yield of 31.8% by soluble enzymes and 32.9% by CLEAs were obtained when alkali-pretreated wheat straw was subjected to hydrolysis. On repeated batch hydrolysis for five consecutive cycles of 24 h each, the CLEAs showed an overall higher saccharification yield of 43.3% compared to 31.8% with soluble enzymes.

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.

The family 6 Carbohydrate Binding Module (CtCBM6) of glucuronoxylanase (CtXynGH30) of Clostridium thermocellum binds decorated and undecorated xylans through cleft A

CtCBM6 of glucuronoxylan-xylanohydrolase (CtXynGH30) from Clostridium thermocellum was cloned, expressed and purified as a soluble ~14 kDa protein. Quantitative binding analysis with soluble polysaccharides by affinity electrophoresis and ITC revealed that CtCBM6 displays similar affinity towards decorated and undecorated xylans by binding wheat- and rye-arabinoxylans, beechwood-, birchwood- and oatspelt-xylan. Protein melting studies confirmed thermostable nature of CtCBM6 and that Ca(2+) ions did not affect its structure stability and binding affinity significantly. The CtCBM6 structure was modeled and refined and CD spectrum displayed 44% β-strands supporting the predicted structure. CtCBM6 displays a jelly roll β-sandwich fold presenting two potential carbohydrate binding clefts, A and B. The cleft A, is located between two loops connecting β4-β5 and β8-β9 strands. Tyr28 and Phe84 present on these loops make a planar hydrophobic binding surface to accommodate sugar ring of ligand. The cleft B, is located on concave surface of β-sandwich fold. Tyr34 and Tyr104 make a planar hydrophobic platform, which may be inaccessible to ligand due to hindrance by Pro68. Site-directed mutagenesis revealed Tyr28 and Phe84 in cleft A, playing a major role in ligand binding. The results suggest that CtCBM6 interacts with carbohydrates through cleft A, which recognizes equally well both decorated and un-decorated xylans.

Lipase catalyzed transesterification of castor oil by straight chain higher alcohols

Biolubricants from Castor oil were produced enzymatically by transesterification with higher alcohols using a lipase mixture of immobilized Mucor miehei (RMIM) and immobilized Candida antarctica lipase B (Novozym 435) under low water conditions. The conversions were in the range of 80-95% under the optimized conditions.

Simultaneous purification and refolding of proteins by affinity precipitation and macro (affinity ligand)-facilitated three phase partitioning (MLFTPP)

This chapter describes two simple interrelated non-chromatographic methods of protein purification. In the first method, called affinity precipitation, inherent affinity of reversibly soluble-insoluble polymers (also called stimuli-sensitive or smart polymers) is exploited to form an affinity complex in free solution with target protein. The affinity complex is precipitated by a suitable change in the medium. The desired protein is dissociated from the smart polymer. In the second method called macro (affinity ligand)-facilitated three phase partitioning (MLFTPP), the affinity complex is precipitated at an interface between upper t-butanol-rich phase and lower aqueous phase. These three phases are achieved by adding appropriate amounts of ammonium sulfate and t-butanol to the initial crude extract. In the first protocol, sequential MLFTPP is used with two different smart polymers to purify pectinase and cellulase from a single crude preparation. The second protocol illustrates the application of the affinity precipitation in simultaneous purification and refolding of a urea-denatured xylanase.

A novel α-L-arabinofuranosidase of family 43 glycoside hydrolase (Ct43Araf) from Clostridium thermocellum

The study describes a comparative analysis of biochemical, structural and functional properties of two recombinant derivatives from Clostridium thermocellum ATCC 27405 belonging to family 43 glycoside hydrolase. The family 43 glycoside hydrolase encoding α-L-arabinofuranosidase (Ct43Araf) displayed an N-terminal catalytic module CtGH43 (903 bp) followed by two carbohydrate binding modules CtCBM6A (405 bp) and CtCBM6B (402 bp) towards the C-terminal. Ct43Araf and its truncated derivative CtGH43 were cloned in pET-vectors, expressed in Escherichia coli and functionally characterized. The recombinant proteins displayed molecular sizes of 63 kDa (Ct43Araf) and 34 kDa (CtGH43) on SDS-PAGE analysis. Ct43Araf and CtGH43 showed optimal enzyme activities at pH 5.7 and 5.4 and the optimal temperature for both was 50°C. Ct43Araf and CtGH43 showed maximum activity with rye arabinoxylan 4.7 Umg(-1) and 5.0 Umg(-1), respectively, which increased by more than 2-fold in presence of Ca(2+) and Mg(2+) salts. This indicated that the presence of CBMs (CtCBM6A and CtCBM6B) did not have any effect on the enzyme activity. The thin layer chromatography and high pressure anion exchange chromatography analysis of Ct43Araf hydrolysed arabinoxylans (rye and wheat) and oat spelt xylan confirmed the release of L-arabinose. This is the first report of α-L-arabinofuranosidase from C. thermocellum having the capacity to degrade both p-nitrophenol-α-L-arabinofuranoside and p-nitrophenol-α-L-arabinopyranoside. The protein melting curves of Ct43Araf and CtGH43 demonstrated that CtGH43 and CBMs melt independently. The presence of Ca(2+) ions imparted thermal stability to both the enzymes. The circular dichroism analysis of CtGH43 showed 48% β-sheets, 49% random coils but only 3% α-helices.

Green synthesis of nanocomposites consisting of silver and protease alpha chymotrypsin

The synergy of ultrasonication and the exposure to light radiation was found to be necessary in the formation of nanocomposites of silver and a protease alpha chymotrypsin. The reaction was carried out in aqueous medium and the process took just less than 35 min. Ultrasonication alone formed very negligible number of nanoparticles of <100 nm size whereas light alone produced enough number but the size of the particles was >100 nm. The effects of pH (in the range of 3-5, 9-10), ultrasonication time periods (0-30 min), ultrasonication intensity (33-83 W cm(-2)), energy of light radiation (short UV, long UV and Fluorescent light) and time period of exposure (5-60 min) to different light radiations were studied. The formation of nanocomposites under these effects was followed by surface plasmon resonance (SPR) spectra, dynamic light scattering (DLS), transmission electron microscopy (TEM). Ag-chymotrypsin nanocomposites of sizes ranging from 13 to 72 nm were formed using the synergy of ultrasonication and exposure to short UV radiation. Results show that ultrasonication promoted nuclei formation, growth and reduction of polydispersity by Ostwald ripening.

Microwave assisted solubilization of inclusion bodies

Background

Production of recombinant proteins in bacterial hosts often produces insoluble intracellular particles called inclusion bodies. Recovery of active protein from inclusion bodies generally requires their solubilization in chemical denaturants followed by a refolding strategy. The solubilization is carried out with shaking/stirring and takes several hours.

Results

Using inclusion bodies of seven diverse kinds of recombinant proteins [mutants of controller of cell division or death protein B (CcdB), human CD4D12, thioredoxin fusion protein (malETrx), mutants of maltose binding protein (MBP), single chain variable fragment (ScFv) b12 and single chain antigen binding fragment (ScFab) b12 (anti-HIV-1)], it is shown that exposure to microwave irradiation (200 W) for 2 min, solubilized these inclusion bodies completely. This was confirmed by data based upon turbidity measurements at 400 nm and dynamic light scattering studies. These solubilized inclusion bodies could be refolded correctly in all the cases by known methods. The refolding was confirmed by fluorescence emission spectra and biological activity studies.

Conclusion

Solubilization of the inclusion bodies before refolding is a part of protein production processes for several recombinant proteins which are overexpressed in the bacterial host systems. Our results show that microwave assistance can considerably shorten the process time.

WITHDRAWN: Smart polymer-coated microplate wells: Applications in protein purification, protein refolding, and sensing of analytes

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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.

Role of smart polymers in protein purification and refolding

Affinity precipitation is a non-chromatographic method which is useful for purification and refolding of proteins. Quite often, a stimuli-sensitive polymer can be identified which selectively binds to the desired protein. For separation, the protein can be recovered from the precipitate of the protein-smart polymer complex. In case of a refolding experiment, binding of the solubilized protein (in its denatured form) with the polymer leads to the refolding of the protein.

Non-chromatographic strategies for protein refolding

Overexpression of recombinant proteins in bacterial systems (such as E. coli) often leads to formation of inactive and insoluble ' inclusion bodies' . Protein refolding refers to folding back the proteins after solubilizing/unfolding the misfolded proteins of the inclusion bodies. Protein aggregation, a concentration dependent phenomenon, competes with refolding pathway. The refolding strategies largely aim at reducing aggregation and/or promoting correct folding. This review focuses on non-chromatographic strategies for refolding like dilution, precipitation, three phase partitioning and macro-(affinity ligand) facilitated three phase partitioning. The nanomaterials which disperse well in aqueous buffers are also discussed in the context of facilitating protein refolding. Apart from general results with these methods, the review also covers the use of non-chromatographic methods in protein refolding in the patented literature beyond 2000. The patented literature generally describes use of cocktail of additives which results in increase in refolding yield. Such additives include low concentration of chaotropic agents, redox systems, ions like SO4(2-) and Cl-, amines, carboxylic acids and surfactants. Some novel approaches like use of a "pressure window" or ionic liquids for refolding and immobilized diselenide compounds for ensuring correct -S-S- bonds pairing have also been discussed in various patents. In most of the patented literature, focus naturally has been on refolding in case of pharmaceutical proteins.

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

A first study of the comparison of structures of enzymes (by FT-IR and CD) in different high activity (in low water media) preparations is reported. Using chymotrypsin and subtilisin as models, we have studied various factors that distinguish enzyme precipitated and rinsed with propanol (EPRP), crosslinked enzyme aggregates (CLEA), protein coated microcrystals (PCMC) and crosslinked protein coated microcrystals (CLPCMC). The suspensions in organic media were assayed for catalytic activity, and structures were probed by FT-IR and CD measurements. CD studies of enzyme suspensions were possible by using a rotating cell accessory. There was a generally good correlation between higher catalytic activity and retention of native structures. Activity and retention of native structure was always higher if aqueous enzyme solution was added to propanol rather than vice versa in the precipitation step of these preparations. The work identifies factors which may lead to better biocatalyst designs for low water media.

Enzyme stabilization via cross-linked enzyme aggregates

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 both conventional aqueous media as well as nonaqueous media. These are also stable at fairly high temperatures. CLEAs having 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.

Stabilization of Candida rugosa lipase during transacetylation with vinyl acetate

An optimally prepared Candida rugosa lipase aggregate cross-linked with bovine serum albumin, was found to overcome acetaldehyde deactivation during transacetylation of a series of benzyl alcohols with vinyl acetate. The formulation, under the same reaction conditions, exhibited 4-30x enhancement in the reaction rate as compared to the celite immobilized lyophilized formulation and 25-133x enhancement as compared to the free lyophilized enzyme depending upon the alcohol chosen. The racemic 1-phenylethanol, taken as one of the alcohols, underwent a more efficient enantioselective transacetylation giving 80% enantiomeric excess of the product, (R)-1-phenylethyl acetate, at 38% conversion (E = 15) within 24h while the enzyme immobilized on celite gave 83% enantiomeric excess at 18% conversion (E = 13) during the same period of time.

Purification and characterization of an alcohol dehydrogenase with an unusual specificity towards glycerol from Thermus thermophilus

The purification and characterization of an NAD(+)-dependent and zinc containing alcohol dehydrogenase (ADH) from Thermus thermophilus (TTHADH) is described. The enzyme could be purified with 25-fold purification and 68% yield using a single chromatographic step. The enzyme was found to be a tetramer (170 kDa) of identical subunits. The pH optimum of the purified enzyme was 8.8 and the temperature optimum was found to be 80 degrees C. Thermal denaturation curves were determined by monitoring the CD values at 222 nm and the T(m) was found to be 89 degrees C. The enzyme showed much higher activity towards glycerol as compared to short chain primary and secondary alcohols. This thermostable enzyme was also highly stereospecific in oxidation of glycerol and converted glycerol into d-glyceraldehyde. The enzyme which converts glycerol into a chiral molecule like d-glyceraldehyde opens up several synthetic opportunities.

A Smart Bioconjugate of Trypsin with Alginate

Alginate is a polymer of guluronic acid and mannuronic acid residues and is an inexpensive, nontoxic polysaccharide of marine origin. Trypsin was immobilized noncovalently on alginate with 100% retention of activity. The enzyme did not leach off the polymer even in the presence of 0.01 M HCl and Triton X-100 (0.2% vv(-1)). The V(max)/K(m) values did not change significantly on immobilization. There was 22% loss of activity in first cycle of pH change and after that the conjugate could be reused upto 4 precipitation cycles without any further loss of activity. This smart bioconjugate was also found to have better operational stability in the presence of casein than free enzyme. Fluorescence studies were carried out to probe structural changes upon immobilization.

Applications of Alginate in Bioseparation of Proteins

Alginate is a polysaccharide that is a block polymer consisting of block units of guluronic acid and mannuronic acid. It shows inherent biological affinity for a variety of enzymes such as pectinase, lipase, phospholipase D, a and ss amylases and glucoamylase. Taking advantage of its precipitation with Ca2+ and the above-mentioned property, alginate has been used for purification of these enzymes by affinity precipitation, aqueous two phase separation, macroaffinity ligand facilitated three phase partitioning, immobilized metal affinity chromatography and expanded bed affinity chromatography. Thus, this versatile marine resource has tremendous potential in bioseparation of proteins.

Preparation and Properties of Thermoresponsive Bioconjugates of Trypsin

Covalent attachment of enzymes and other proteins to the smart polymer, poly(N-isopropylacrylamide) [poly (NIPAAm)], has been widely used as a method for the preparation of thermosensitive protein conjugates. In the present study, reversible soluble-insoluble polymer-enzyme conjugates were prepared by conjugating a copolymer of NIPAAm with 5-mol % of 6-acrylaminohexanoic acid to trypsin by the carbodiimide-NHS (N-hydroxysuccinimide) coupling method. Four bioconjugates with different units of enzyme coupled to the matrix were prepared. Increased enzymatic activity in terms of high effectiveness factor (in the range of 3-5) was found in the conjugates. Kinetic parameters for the immobilized and free enzyme were determined. The Vmax/Km value of the enzyme significantly increased on immobilization by the factors in the range of 12-28. The immobilized enzyme also showed stability to autolysis at 50 degrees C.

Refolding and simultaneous purification by three-phase partitioning of recombinant proteins from inclusion bodies

Many recombinant eukaryotic proteins tend to form insoluble aggregates called inclusion bodies, especially when expressed in Escherichia coli. We report the first application of the technique of three-phase partitioning (TPP) to obtain correctly refolded active proteins from solubilized inclusion bodies. TPP was used for refolding 12 different proteins overexpressed in E. coli. In each case, the protein refolded by TPP gave either higher refolding yield than the earlier reported method or succeeded where earlier efforts have failed. TPP-refolded proteins were characterized and compared to conventionally purified proteins in terms of their spectral characteristics and/or biological activity. The methodology is scaleable and parallelizable and does not require subsequent concentration steps. This approach may serve as a useful complement to existing refolding strategies of diverse proteins from inclusion bodies.