Stabilization of a highly active but unstable alcohol dehydrogenase from yeast using immobilization and post-immobilization techniques

The alcohol dehydrogenase (ADH) from Baker's yeast is very active but extremely unstable under several different conditions. Mild immobilization methods such as one-point attachment to agarose activated with cyanogen bromide groups or ionic adsorption to agarose activated with charged groups allow high activity recoveries (80–100%) but do not promote protein stabilization. In contrast, immobilization methods that force the enzyme to be covalently attached at multiple points on the support fully inactivate the enzyme. Herein, we propose an interesting solution to address the dichotomy between activity and stability. We have developed a protocol in which the enzyme is immobilized on agarose activated with glyoxyl groups in the presence of acetyl cysteine, which results in the recovery of 25% of the enzyme activity but increases the thermal stability of the soluble enzyme 50-fold. However, this immobilization technique does not stabilize the enzyme quaternary structure. Hence, a post-immobilization technique using functionalized polymers has been used to cross-link all enzyme subunits. In this method, polycationic polymers (polyethylenimine) cross-link the quaternary structure with a negligible effect on catalytic activity, which results in a derivative that is 5-fold more stable than non-cross-linked derivatives under very dilute and acidic conditions that highly favor subunit dissociation. Therefore, the stability was increased 500-fold for this optimal derivative compared to diluted soluble enzyme, although the relative expressed activity was low (25%). However, the low expressed activity may be overcome by designing immobilized biocatalysts with high volumetric activities.     

Assay of detergents by rocket electrophoresis in agarose gels containing red blood cells: "rocket hemolysis"

A method is described for quantitation of charged detergents using their hemolytic property in an electrophoresis assay in agarose gels containing red blood cells. After electrophoresis the zone of hemolysis is directly proportional to the concentration of detergent in the sample. Using this technique we have determined the smallest detectable concentration for the negatively charged detergents, sodium dodecyl sulfate (SDS) and Quil A to about 10 micrograms/ml and 25 micrograms/ml, respectively and the positively charged cetyltrimethylammonium bromide (CTAB) to about 10 micrograms/ml.     

Regulation by Mg2+ and Ca2+ of mitochondrial membrane integrity: study of the effects of a cytosolic molecule and Ca2+ antagonists.

The coupling of aliphatic amines to agarose by the cyanogen bromide reaction yields isourea linkages which are positively charged at pH 7. The presence of these cationic sites in affinity gels causes significant non-specific adsorption of proteins. Serum albumin was found to bind to a number of derivatized gels which possessed these charged groups. The use of adipic dihydrazide as the leash moiety yielded affinity gels which were noncharged at pH 7. Serum albumin failed to adsorb to these gels. Beta-galactosidase from Escherichia coli was found to be sensitive to both ionic and hydrophobic groups in an affinity gel. A sample of active-site inhibited enzyme was found to bind to an affinity gel which contained both the cationic isourea and a phenyl structure in the leash. Thus it was concluded that the affinity purification of this enzyme has yet to be demonstrated. These studies dictate against the use of salt and pH gradients to desorb enzymes from affinity sorbents.     

DNA and buffers: the hidden danger of complex formation

The free solution electrophoretic mobility of DNA differs significantly in different buffers, suggesting that DNA-buffer interactions are present in certain buffer systems. Here, capillary and gel electrophoresis data are combined to show that the Tris ions in Tris-acetate-EDTA (TAE) buffers are associated with the DNA helix to approximately the same extent as sodium ions. The borate ions in Tris-borate-EDTA (TBE) buffers interact with DNA to form highly charged DNA-borate complexes, which are stable both in free solution and in polyacrylamide gels. DNA-borate complexes are not observed in agarose gels, because of the competition of the agarose gel fibers for the borate residues. The resulting agarose-borate complexes increase the negative charge of the agarose gel fibers, leading to an increased electroendosmotic flow of the solvent in agarose-TBE gels. The combined results indicate that the buffers in which DNA is studied cannot automatically be assumed to be innocuous.     

Agarose Gel Electrophoresis for the Separation of DNA Fragments

Agarose gel electrophoresis is the most effective way of separating DNA fragments of varying sizes ranging from 100 bp to 25 kb¹. Agarose is isolated from the seaweed genera Gelidium and Gracilaria, and consists of repeated agarobiose (L- and D-galactose) subunits². During gelation, agarose polymers associate non-covalently and form a network of bundles whose pore sizes determine a gel''s molecular sieving properties. The use of agarose gel electrophoresis revolutionized the separation of DNA. Prior to the adoption of agarose gels, DNA was primarily separated using sucrose density gradient centrifugation, which only provided an approximation of size. To separate DNA using agarose gel electrophoresis, the DNA is loaded into pre-cast wells in the gel and a current applied. The phosphate backbone of the DNA (and RNA) molecule is negatively charged, therefore when placed in an electric field, DNA fragments will migrate to the positively charged anode. Because DNA has a uniform mass/charge ratio, DNA molecules are separated by size within an agarose gel in a pattern such that the distance traveled is inversely proportional to the log of its molecular weight³. The leading model for DNA movement through an agarose gel is "biased reptation", whereby the leading edge moves forward and pulls the rest of the molecule along⁴. The rate of migration of a DNA molecule through a gel is determined by the following: 1) size of DNA molecule; 2) agarose concentration; 3) DNA conformation⁵; 4) voltage applied, 5) presence of ethidium bromide, 6) type of agarose and 7) electrophoresis buffer. After separation, the DNA molecules can be visualized under uv light after staining with an appropriate dye. By following this protocol, students should be able to: 1. Understand the mechanism by which DNA fragments are separated within a gel matrix 2. Understand how conformation of the DNA molecule will determine its mobility through a gel matrix 3. Identify an agarose solution of appropriate concentration for their needs 4. Prepare an agarose gel for electrophoresis of DNA samples 5. Set up the gel electrophoresis apparatus and power supply 6. Select an appropriate voltage for the separation of DNA fragments 7. Understand the mechanism by which ethidium bromide allows for the visualization of DNA bands 8. Determine the sizes of separated DNA fragments       

m-Aminophenylboronate agarose specifically binds capped snRNA and mRNA.

m-Aminophenylboronate-substituted agarose binds specifically RNA chains carrying a mature 5' cap. The binding occurs most effectively at pH greater than 8 and involves diester formation between the negatively charged tetrahedric boronate group and the cisdiol of the ribose of the cap. The positive charge introduced by the m7G methylation is necessary for efficient binding although two closely spaced cis-diol groups alone (as in the cap analog NADH) are sufficient for binding. Non-capped RNA (like poly (U) and rRNA) or decapped RNA are not bound. It is shown that the matrix can be used for the isolation of capped small nuclear RNA and mRNA.     

Darcy permeability of agarose-glycosaminoglycan gels analyzed using fiber-mixture and donnan models

Agarose-glycosaminoglycan (GAG) membranes were synthesized to provide a model system in which the factors controlling the Darcy (or hydraulic) permeability could be assessed in composite gels of biological relevance. The membranes contained a GAG (chondroitin sulfate) that was covalently bound to agarose via terminal amine groups, and the variables examined were GAG concentration and solution ionic strength. The addition of even small amounts of GAG (0.4 vol/vol %) resulted in a twofold reduction in the Darcy permeability of 3 vol/vol % agarose gels. Electrokinetic coupling, caused by the negative charge of the GAG, resulted in an additional twofold reduction in the open-circuit permeability when the ionic strength was decreased from 1 M to 0.01 M. A microstructural hydrodynamic model was developed, based on a mixture of neutral, coarse fibers (agarose fibrils), and fine, charged fibers (GAG chains). Heterogeneity within agarose gels was modeled by assuming that fiber-rich, spherical inclusions were distributed throughout a fiber-poor matrix. That model accurately predicted the Darcy permeability when the ionic strength was high enough to suppress the effects of charge, but underestimated the influence of ionic strength. A more macroscopic approach, based on Donnan equilibria, better captured the reductions in Darcy permeability caused by GAG charge.     

Rheological Study of the Gelation Process of Agarose-Based Solutions

The gelation of agarose is investigated by rheological methods and electron microscopy, as well as the thickening properties of xanthan. The gelling and thickening agents have been investigated in pure water to compare the results with theoretical models. The gelation of agarose was shown to follow two steps upon cooling, which could be addressed to the formation of helices and their aggregation. In addition to the rheology, transmission electron micrographs of freeze-dried samples have been taken to underline the date by corresponding structures at different stages of the gelling process. The xanthan molecules, which have been approximated by rigid highly charged rodlike molecules, undergo a jamming transition at a critical concentration. This concentration shows a strong dependence on the length of the molecules, which supports the high thickening effect of xanthan. When both, agarose and xanthan are mixed, the gel structure becomes very different. The gelling process is now determined by one step only. It is proposed that the jamming xanthan molecules prevent the formation of the aggregates of the agarose gel. The gels themselves appear then less elastic, and should yield a better mouth feeling.     

Adhesion of the marine fouling diatom amphora coffeaeformis to non‐solid gel surfaces

Diatom adhesion to different gel surfaces was tested under different shear conditions, using the fouling marine diatom Amphora coffeaeformis as test organism. Four polymers were selected to obtain a test matrix containing gels with different surface charge as well as different surface energies, viz. agarose, alginate, chitosan and chemically modified polyvinylalcohol (PVA‐SbQ). Three experimental systems were applied to obtain different shear rates. Experimental system 1 consisted of gels cast in a cell culturing well plate for comparing initial adhesion as well as long term biofilm development in the absence of shear. In experimental system 2, microscope slide based test surfaces were tested in aquaria under low shear conditions. A rotating annular biofilm reactor was used to obtain high and controlled shear rates. At high shear rates A. coffeaeformis cells adhered better to the charged polymer gels (alginate and chitosan) than to the low charged polymer gels (agarose and PVA‐SbQ). In the system where shear was absent A. coffeaeformis cells developed a biofilm on agarose equivalent to the charged polymer gels, while adhesion to PVA‐SbQ remained low at all shear rates. It is concluded that non‐solid surfaces did not represent an obstacle to settling and growth of this organism. As observed for solid surfaces, low charge density led to reduced attachment, particularly at high shear.     

Stabilization of multimeric sucrose synthase from Acidithiobacillus caldus via immobilization and post-immobilization techniques for synthesis of UDP-glucose

Sucrose synthases (SuSys) have been attracting great interest in recent years in industrial biocatalysis. They can be used for the cost-effective production of uridine 5′-diphosphate glucose (UDP-glucose) or its in situ recycling if coupled to glycosyltransferases on the production of glycosides in the food, pharmaceutical, nutraceutical, and cosmetic industry. In this study, the homotetrameric SuSy from Acidithiobacillus caldus (SuSyAc) was immobilized-stabilized on agarose beads activated with either (i) glyoxyl groups, (ii) cyanogen bromide groups, or (iii) heterogeneously activated with both glyoxyl and positively charged amino groups. The multipoint covalent immobilization of SuSyAc on glyoxyl agarose at pH 10.0 under optimized conditions provided a significant stabilization factor at reaction conditions (pH 5.0 and 45 °C). However, this strategy did not stabilize the enzyme quaternary structure. Thus, a post-immobilization technique using functionalized polymers, such as polyethyleneimine (PEI) and dextran-aldehyde (dexCHO), was applied to cross-link all enzyme subunits. The coating of the optimal SuSyAc immobilized glyoxyl agarose with a bilayer of 25 kDa PEI and 25 kDa dexCHO completely stabilized the quaternary structure of the enzyme. Accordingly, the combination of immobilization and post-immobilization techniques led to a biocatalyst 340-fold more stable than the non-cross-linked biocatalyst, preserving 60% of its initial activity. This biocatalyst produced 256 mM of UDP-glucose in a single batch, accumulating 1 M after five reaction cycles. Therefore, this immobilized enzyme can be of great interest as a biocatalyst to synthesize UDP-glucose.

     

Lectin affinity electrophoresis for the separation of fluorescently labeled sugar derivatives.

Lectin affinity electrophoresis was applied to the separation of charged, fluorescent conjugates of disaccharides. Four fluorescent conjugates were prepared by reductive amination of alpha-D-Man-(1----3)-D-Man, alpha-D-Gal-(1----4)-D-Glc, alpha-D-Gal-(1----6)-D-Glc, and beta-D-Gal-(1----4)-D-Glc in the presence of 7-amino-1,3-naphthalenedisulfonic acid. These charged fluorescent-disaccharide conjugates all have identical molecular weight and in the absence of conconavalin A lectin failed to separate either by agarose or by polyacrylamide gel electrophoresis. In the presence of either free or immobilized concanavalin A, agarose gel electrophoresis and polyacrylamide gel electrophoresis could separate the fluorescent conjugate of alpha-D-Man-(1----3)-D-Man from that of alpha-D-Gal-(1----4)-D-Gal, alpha-D-Gal-(1----6)-D-Glc, and beta-D-Gal-(1----4)-D-Glc.     

Electrophoretic charge density and persistence length of DNA as measured by fluorescence microscopy

Individual ethidium-stained DNA molecules, embedded in an agarose gel made with electrophoresis buffer (0.05 molar salt), are observed using a fluorescence microscope. In the first experiment, open circular 66 kilobase pair (kbp) plasmids, immobilized by agarose fibers threaded through their centers, display entropic "rubber" elasticity. The charged molecules extend in an electric field of several volts per centimeter and contract to a compact random coil when the field is removed. The extension of the plasmids as a function of field strength is consistent with the freely jointed chain model when the effective electrophoretic charge density is set at 15 e-per persistence length. In a second experiment, stained linear 48.5 kbp DNA molecules are observed as random coils immobilized in agarose. A measure of their size, here named the "maximal-X-extent," is taken for 100 molecules and found to average 1.47 mu. A Monte Carlo computer simulation of random coils (freely jointed chain model) gives the same maximal-X-extent value when the persistence length is set at 0.08 mu.     

Further studies on the contribution of electrostatic and hydrophobic interactions to protein adsorption on dye-ligand adsorbents.

The adsorption equilibria of bovine serum albumin (BSA), gamma-globulin, and lysozyme to three kinds of Cibacron blue 3GA (CB)-modified agarose gels, 6% agarose gel-coated steel heads (6AS), Sepharose CL-6B, and a home-made 4% agarose gel (4AB), were studied. We show that ionic strength has irregular effects on BSA adsorption to the CB-modified affinity gels by affecting the interactions between the negatively charged protein and CB as well as CB and the support matrix. At low salt concentrations, the increase in ionic strength decreases the electrostatic repulsion between negatively charged BSA and the negatively charged gel surfaces, thus resulting in the increase of BSA adsorption. This tendency depends on the pore size of the solid matrix, CB coupling density, and the net negative charges of proteins (or aqueous - phase pH value). Sepharose gel has larger average pore size, so the electrostatic repulsion-effected protein exclusion from the small gel pores is observed only for the affinity adsorbent with high CB coupling density (15.4 micromol/mL) at very low ionic strength (NaCl concentration below 0.05 M in 10 mM Tris-HCl buffer, pH 7.5). However, because CB-6AS and CB-4AB have a smaller pore size, the electrostatic exclusion effect can be found at NaCl concentrations of up to 0.2 M. The electrostatic exclusion effect is even found for CB-6AS with a CB density as low as 2.38 micromol/mL. Moreover, the electrostatic exclusion effect decreases with decreasing aqueous-phase pH due to the decrease of the net negative charges of the protein. For gamma-globulin and lysozyme with higher isoelectric points than BSA, the electrostatic exclusion effect is not observed. At higher ionic strength, protein adsorption to the CB-modified adsorbents decreases with increasing ionic strength. It is concluded that the hydrophobic interaction between CB molecules and the support matrix increases with increasing ionic strength, leading to the decrease of ligand density accessible to proteins, and then the decrease of protein adsorption. Thus, due to the hybrid effect of electrostatic and hydrophobic interactions, in most cases studied there exists a salt concentration to maximize BSA adsorption.     

Unique modification of human heart glycerol 3-phosphate dehydrogenase by blue agarose

The major form of glycerol phosphate dehydrogenase in human heart (GPDH-1) is a minor form (less than 15%) in brain and other tissues and is extremely labile. After GPDH-1 was eluted from an agarose column to which Cibacron blue F3GA had been covalently linked, (a) it was no longer labile (t 1/2 at 40 degrees C changed from 1.6 min to greater than 180 min); (b) it could now be stained for activity on native gels following electro-phoresis; and (c) it now migrated with the bromphenol blue dye front. The results suggest that this stabilized form of GPDH-1 is due to the covalent binding of charged ligands from the column and that this technique may be useful for studying the molecular structure and/or the active site of GPHD-1 and possibly of other enzymes which bind to blue agarose.     

An affinity gel for the inhibition, binding, and isolation of serine proteases

A preparation procedure for gels for the specific binding and inhibition of serine proteases is described. Phosphoryl trifluoride was synthesized and reacted with two different types of agarose gels, a crosslinked agarose (Sepharose CL-4B) and an agarose containing spacer arms with terminal vicinal-diol groups (a hydrolyzed epoxy-activated Sepharose 6B). The phosphoryl difluoride groups coupled to the gels were, in both cases, further modified by treatment with isopropanol to obtain isopropyl fluorophosphate groups covalently bound to the matrix. It was found that both modified gels absorbed and inhibited plasmin, but that the modified gel with spacer arms was markedly more efficient.     

Quantitative measurement of lipoprotein surface charge by agarose gel electrophoresis.

The electrophoretic mobilities of low density lipoprotein (LDL) and six pure proteins in a 0.5% agarose gel have been compared to literature electrophoretic mobility values determined by the Tiselius moving boundary method. There is a strong correlation (r = 0.99) between the electrophoretic mobilities determined by the two techniques. The electrophoretic behavior of charged particles smaller than very low density lipoproteins (VLDL) is not markedly perturbed by a 0.5% agarose matrix, and variations in mobility primarily reflect differences in particle valence and density of surface charge. Application of electrokinetic theory to derive protein and lipoprotein net charges from the electrophoretic mobilities in agarose yields a quantitative delineation of lipoprotein electrophoretic migration patterns wherein the beta mobility region comprises a surface potential range of -4.5 to -7.0 mV; the pre-beta region a range of -7.0 to -10.5 mV; the alpha mobility region a range of -10.5 to -12.5 mV and the serum albumin region a range of -12.5 to -14.0 mV. Because protein conformation and charge are critical in metabolic regulation, the agarose gel electrophoresis technique provides a valuable analytical tool that should help to elucidate further details of the structure-function relationships of serum lipoprotein particles.     

Light-activated immobilization of biomolecules to agarose hydrogels for controlled cellular response

We describe a new method of synthesizing photolabile hydrogel materials for convenient photoimmobilization of biomolecules on surfaces or in 3-D matrixes. Dissolved agarose was modified with photolabile S-(2-nitrobenzyl)cysteine (S-NBC) via 1,1'-carbonyldiimidazole (CDI) activation of primary hydroxyl groups. S-NBC-modified agarose remained soluble and gelable with up to 5% S-NBC substitution, yet gelation was slower and the elastic modulus of the resulting gel was lower than those of unmodified agarose. Irradiating S-NBC-grafted agarose resulted in the loss of the protecting 2-nitrobenzyl groups, thereby exposing free sulfhydryl groups for biomolecular coupling. When appropriately activated with sulfhydryl-reactive groups, either peptides or proteins were effectively immobilized to the photoirradiated hydrogel matrixes, with the irradiation energy dose (i.e., irradiation time) used to control the amount of biomolecule immobilization. When the GRGDS peptide was immobilized on agarose, it was shown to be cell-adhesive and to promote neurite outgrowth from primary, embryonic chick dorsal root ganglion neurons. The immobilized GRGDS surface ligand concentration affected the cellular response: neurite length and density increased with GRGDS surface concentration at low adhesion ligand concentration and then plateaued at higher GRGDS concentration. Grafting 2-nitrobenzyl-protected compounds to hydrogel materials is useful for creating new photolabile hydrogel substrates for light-activated functional group generation and biomolecular immobilization.     

Use of biotin-labeled nucleic acids for protein purification and agarose-based chemiluminescent electromobility shift assays

We have employed biotin-labeled RNA to serve two functions. In one, the biotin tethers the RNA to streptavidin-agarose beads, creating an affinity resin for protein purification. In the other, the biotin functions as a label for use in a modified chemiluminescent electromobility shift assay (EMSA), a technique used to detect the formation of protein-RNA complexes. The EMSA that we describe avoids the use not only of radioactivity but also of neurotoxic acrylamide by using agarose as the gel matrix in which the free nucleic acid is separated from protein-nucleic acid complexes. After separation of free from complexed RNA in agarose, the RNA is electroblotted to positively charged nylon. The biotin-labeled RNA is readily bound by a streptavidin-alkaline phosphatase conjugate, allowing for very sensitive chemiluminescent detection ( approximately 0.1-1.0 fmol limit). Using our system, we were able to purify both known iron-responsive proteins (IRPs) from rat liver and assess their binding affinity to RNA containing the iron-responsive element (IRE) using the same batch of biotinylated RNA. We show data indicating that agarose is especially useful for cases when large complexes are formed, although smaller complexes are even better resolved.     

Optimal spacer arm microenvironment for the immobilization of recombinant Protein A on heterofunctional amino-epoxy agarose supports

In this study, recombinant Staphylococcus Protein A (rSPA) was immobilized on three different amino-epoxy agaroses: traditional amino-epoxy, butanediol diglycidyl-amino and glycidyl-amino agarose (coded as AE, BDA and GA agarose, respectively), for obtaining affinity adsorbents to bind human immunoglobulin G (hIgG). The effects of the spacer arm microenvironment of the support on the rSPA immobilization were investigated. Compared with the AE agarose, the GA agarose presents ionized amino groups far from the support. Therefore, the rSPA immobilization efficiency of 92 % is slightly higher than that of 88 % on AE agarose due to the weak steric hindrance. Moreover, the BDA agarose exhibited the lowest immobilization efficiency of 58 %, attributing to the existence of hydrophobic butylidene groups on the BDA agarose. Ethanolamine was used as the blocking agent to obtain three affinity adsorbents. The hIgG-binding capacity from the human plasma was determined to be 18.7, 34.7 and 38.7 mg/mL for rSPA-BDA, rSPA-AE and rSPA-GA, respectively. Furthermore, the maximum hIgG-binding capacity was calculated by the Langmuir model of adsorption isotherm to be 25.1, 44.8 and 52.2 mg/mL for rSPA-BDA, rSPA-AE and rSPA-GA, respectively. Therefore, the GA agarose bears the optimal spacer arm microenvironment for preparing the rSPA adsorbent with high hIgG-binding capacity.     

Efficient electroblotting of human very-low-density lipoproteins and low-density lipoproteins from composite gradient gels to nylon membranes

Rinsing of gradient composite acrylamide/agarose gels with 1% Triton X-100 permits the efficient electrotransfer of very-low-density and low-density lipoproteins from the gels and does not appear to interfere with subsequent capture of the lipoproteins by charged nylon membranes. Overall efficiency of the transfer/capture process can approach 95% and does not appear to be significantly affected by total lipoprotein concentrations up to 5000 mg/dl. Direct immunoquantification of transferred apolipoproteins on the membrane is feasible as well. The nylon membranes used, however, must be pretested to ensure capture efficiency.