Protein and Enzyme Technology

Practical Exercise

Aim

To investigate some of the properties of immobilised enzymes.

Introduction

The four-session practical exercise is designed to give some insight into the preparation and properties of immobilised enzymes. 

It consists of three parts:

Before starting work, read through the Methods and Results sections. This practical is very demanding and must be approached with thought and care. It will be necessary to retain samples of the soluble enzyme before and after coupling (as well as the immobilised enzyme, of course) for protein and activity assay (see Appendix A) in order to determine the amount of enzyme coupled. You are expected to work in teams of three with a named team leader. You must plan and organise your experiments carefully, for which marks will be awarded. a-amylase is an enzyme produced and purified from Bacillus. It hydrolyses the a-1-4 links in starch randomly along its structure (i.e. it is an endo-glycosidase). It cannot hydrolyse a-1-6 links. Complete hydrolysis of starch by a-amylase produces a mixture of short glucose oligomers (e.g. maltose, maltotriose), some limit dextrin containing a-1-6 links but relatively little glucose. The quality of hydrolysed starches is given in terms of its dextrose equivalent (DE), which equals the percentage of the starch that is hydrolysed. ('Dextrose' is another word for glucose). 

a-Amylase is assayed by the creation of new reducing (terminal; equivalent in reducing power to glucose) sugar by the catalysed hydrolysis of soluble starch.

In this practical, a-amylase is immobilised by means of covalent and non-covalent binding to solid supports. The amount of enzyme attached to the supports is determined and the activities of the immobilised enzymes are compared to that of the free (non-immobilised) enzyme. Packed bed reactors containing the immobilised enzymes are prepared and their ability to hydrolyse starch compared.

 

Amylopectin (alpha-linked 1,4-D-glucose with alpha-linked 1,6 branchpoints) is hydrolysed randomly by bacillus alpha-amylase to give limit dextrin. It does not hydrolyse alpha 1,6 links or their neighbouring alpha 1,4 links

Plan
During week 1 you should

During week 2 you should 

During weeks 3 and 4 you should run the stirred tank and packed bed reactors and analyse their products.

Covalent Immobilisation of a-amylase (Methods Enzymol. 44, pp. 98-99)

Safety note: The following makes use of nitrous acid. This gives off toxic brown fumes of nitrogen oxides, if warmed. It is important from both a safety and experimental point of view that it is kept ICE-COLD.

Week 1. Weigh out 1.0 g Enzacryl AA gel. (This is a gel based on a polyacrylamide matrix with aromatic amino groups present as the reactive moieties). Add to 50 ml ICE-COLD 2 M HCl, stir at 0°C, and gradually add 40 ml ICE-COLD 2% sodium nitrite solution (Together these produce nitrous acid, HNO2).

NaNO2 + HCl HNO2 + NaCl

Keep the beaker surrounded by ice during addition. This should take about 10 - 15 minutes. (This creates the reactive diazonium groups from the aromatic amino groups. If these are allowed to warm up, they decompose to give nitrogen gas with the loss of their specific reactivity)

 

aromatic amine + HNO2 --> diazonium salt --> couples to enzyme tyrosine groups

Stir for another 15 minutes, then filter the gel on a filter paper disc on a Buchner funnel, by suction. Wash with 200 ml ICE-COLD 20 mM phosphate buffer, pH 7.0, 0.1 mM CaCl2 (a-amylase buffer). Add the buffer in 25 ml batches, and KEEP IT COLD. At this stage, the amino groups of the gel matrix should be diazotized. Quickly scrape gel off the filter into a test tube. Add 5 ml of an ICE-COLD solution of a-amylase (2 mg/ml in phosphate buffer). Cap, label ('Cov') swirl in an ice bath for about an hour and leave in the fridge until next week. (This allows the diazo groups to covalently couple to the tyrosine phenolic groups on the enzyme)

Non-Covalent Immobilisation of a-amylase

Safety note: The following makes use of a fine powder. Treat it with care and do not allow this to form a dust cloud Clean all spillages with slightly damp tissue.

Resin structure

Complex poly phenol with some quinone groups

Week 1. Weigh out 0.6 g dry phenolic resin (invented and patented by M. F. Chaplin, J Chem Soc., Perkin 1, 1979, pp 2144-2153), suspend in 20 ml 20 mM K phosphate pH 7.0, 0.1 mM CaCl2 (a-amylase buffer) for 10 minutes. Filter and re-suspend in 5 ml of 2 mg/ml a-amylase in the 20 mM phosphate buffer. Cap, label ('Non') swirl for 30 min and leave in the fridge until next week

N.B.: Keep a solution of the free enzyme (0.5 ml 2 mg/ml) similarly capped in the fridge as a comparison for both 'Cov' and 'Non' above (label 'Enz').

Covalent Immobilisation of a-amylase

Filter the gel ('Cov'), using a fluted filter paper, into a test tube; use 5 ml of 20 mM K phosphate buffer pH 7.0 to aid this process. Keep about 2 ml of the filtrate for assay of unbound protein and activity, (Label it 'Cov-supernatant')

NB. As you added 5 ml of buffer to the 5 ml of original enzyme solution, any enzyme remaining in solution has been diluted by a factor of two.

Wash gels to remove any free enzyme, using 3 x 20 ml batches of 20 mM potassium phosphate/500 mM NaCl pH 7.0 ('high salt buffer'). Let the gel damp-dry briefly between each 20 ml portion of buffer. Wash once more in the same buffer without NaCl, and re-suspend the gel in 5 ml in 20 mM K phosphate (pH 7.0). Label it 'Cov-immobilised' and refrigerate until next week.

Non-Covalent Immobilisation of a-amylase

Filter the gel ('Non'), using a fluted filter paper, into a test tube; use a further 5 ml of 20 mM K phosphate buffer pH 7.0 to aid this process. Keep about 2 ml of the filtrate for assay of unbound protein and activity, (Label it 'Non-supernatant'), .

NB. As you added 5 ml of buffer to the 5 ml of original enzyme solution, any enzyme remaining in solution has been diluted by a factor of two.

Wash gels to remove any free enzyme, using 3 x 20 ml batches of 20 mM K phosphate buffer pH 7.0. Re-suspend in 5 ml of this buffer. Label it 'Non-immobilised' and refrigerate until next week.

At this stage During Week 2 you should have the following samples:

Assays (See Appendix for details of the procedures)

Note: you have to dilute the samples until they contain about 50 mg/ml protein so that your determinations are in the right range for the assays. Do not forget to allow for these dilutions when you determine the protein content and a-amylase activity of the original.

Dilute samples 'cov-supernatant' and 'non-supernatant' 1:20 v/v and sample 'enz' 1:40 v/v. Assay these diluted samples of 'cov-supernatant', 'non-supernatant' and 'enz' for protein content (Assay 1) and a-amylase activity by production of reducing equivalents (Assay 3). Ensure that you record how you dilute these samples in your notebook.

Although you know the concentration of protein in sample 'enz' (2 mg/ml), you will probably get a different value as determined in the Dye-binding assays due to the different standard protein (bovine serum albumin not a-amylase) used. Use this value to 'correct' the protein concentrations (i.e. if the apparent Dye-binding concentration of sample 'enz' is 1.5 mg/ml then all final protein concentrations as determined by the Dye-binding method should be multiplied by the factor 2.0/ 1.5).

Tabulate the protein concentration (mg/ml, uncorrected and corrected) and activity (mmol reducing sugar released/min/ml and mmol reducing sugar released/min/mg) of the diluted and original undiluted samples cov-supernatant, non-supernatant and enz. By allowing for the volumes of solutions used in the binding (5 ml) and filtering (another 5 ml), tabulate also the total protein content of the supernatants. 

This Table will allow you to calculate:

  1. the (corrected) weight of a-amylase protein not bound to each immobilisation matrix from the protein concentrations in the unbound residual enzyme samples cov-supernatant and non-supernatant. Make sure that you allow for the dilutions and the final volume of the wash solution (10 ml) and the correction for the use of the bovine serum albumin standard.
  2. the weight of protein bound to each immobilisation matrix, by subtracting the (corrected weight of) protein not bound (from above) from the amount added (5 ml x 2 mg/ml = 10 mg).
  3.  the percentage of the enzyme protein that was added that is bound to each immobilisation matrix.
  4. the specific activity of the original a-amylase solution used (sample 'enz'); Note that the specific activity equals the activity of one mg a-amylase protein. the units are in mmol reducing sugar released per min per mg of protein).
  5. the specific activity of the unbound a-amylase solutions left after each of the immobilisation processes. Note that these would be expected to be identical to the specific activity of the original a-amylase solution used (sample 'enz') unless some denaturation occurred in the immobilisation process.

Note: you have to dilute the samples until they contain about 50 mg/ml protein so that your determinations are in the right range for the assays. Do not forget to allow for these dilutions when you determine the protein content and a-amylase activity of the original solutions.

Figure 1

Prepare two small packed bed reactors containing all of the covalently and non-covalently immobilised a-amylase ('cov-immobilised' and 'non-immobilised'). Do not allow them to run dry. (Note that if they are allowed to develop an air lock, they will not flow and must be repacked) Run 5 ml of 1% starch in 20 mM K phosphate pH 7.0, 0.1 mM CaCl2. through each column.

Immobilised enzyme column

Reduce the flow rate through the columns to about 1 ml per 10 min (i.e. about one drop every 30 seconds), allow the starch solution to run through for about 15 min and then collect 2 ml from each column for analysis, label 'cov-eluent' from the 'cov-immobilised' column and 'non-eluent 'from the 'non-immobilised' column and set to one side.

Wash the packed bed reactors with 3 column volumes of phosphate buffer (20 mM K phosphate, pH 7) without starch and store refrigerated until week 4.

Assay the partially-hydrolysed starch samples cov-eluent and non-eluent for reducing equivalents (Assay 2).

 Remove the gels ('cov-immobilised' and 'non-immobilised') from the columns. Using all of the samples of immobilised enzymes determine (separately) their activity in a stirred reactors (beaker) containing 50 ml of 1.0% w/v starch in 20 mM K phosphate pH 7.0, 0.1 mM CaCl2. Withdraw samples at intervals (e.g. 1 min, 5 min, 10 min, etc.) to determine their reducing sugar content. 

From the assay of the stirred tank and packed bed reactors you should calculate :

  1. the concentration of reducing equivalent in the partially-hydrolysed starch samples (mmoles of reducing equivalent produced per ml per reactor).
  2. the productivity of the reactors (mmoles of reducing equivalent produced per minute per reactor), 
  3. the fractional conversions, X (X = moles of reducing equivalents produced/moles of potential glucose units in the starch solution); Note that to calculate the number of moles of potential glucose in the 1% starch, solution, the apparent M.Wt of potential glucose is 180 - 18 = 162, as water is necessary to release the glucose; the complete hydrolysis of 162 g of starch produces one mole (180 g) of glucose, Also remember that the number of moles in a sample is the weight in grams divided by the weight of one mole (i.e. weight/ M.Wt). Also, note that because a-amylase cannot hydrolyse limit dextrins, maltose, maltotriose or maltotetraose, the highest value expected for the fractional conversion, X, is about 0.2.
  4. the dextrose equivalent DE of the products (in this case the fractional conversion, X, expressed as a percentage), 
  5. the activity of the immobilised enzymes (mmoles of reducing equivalent produced per minute per g resin).
  6.  the specific activity of the immobilised enzymes (mmoles of reducing equivalent produced per minute per mg enzyme) by using the known amount of protein immobilised (determined previously).
  7. the effectiveness factors for the immobilised enzymes. Note that the effectiveness factor is the specific activity of the immobilised enzyme divided by the specific activity of an equal quantity of the free enzyme (calculated previously).

Assay samples 'cov-immobilised', 'non-immobilised' and 'enz' for a-amylase activity by loss of iodine reactive material (Assay 4). This reaction may be very rapid with excess free enzyme. For the free and immobilised enzymes estimate the % digestion of the starch when the iodine reactive material has been used up, by comparing these results with your specific activity results from the production of reducing equivalents.

  1. determine the relative specific activities of the immobilised enzymes compared with the free a-amylase. Use the reciprocals of the times needed to decolourise the blue starch-iodide divided by the amounts of a-amylase protein present.
  2. compare these specific activities with those calculated earlier. Explain your results on the basis that starch molecules, once next to an immobilised a-amylase, have difficulty diffusing away due to their bulk. Thus, immobilised a-amylase is expected to produce some starch that is completely hydrolysed before other starch molecules are hydrolysed at all, whereas free a-amylase hydrolyses all starch molecules roughly equally.

 Practical: Appendices

Assays
Note that all assays should be done in duplicate, where possible. Ensure all the cuvettes are clean by checking their absorption against each other at the assay wavelength before use. 

1 Dye-binding Protein Assay 
1.5 ml of protein sample solution (0 - 50 mg/ml) is mixed with 1.5 ml Coomassie blue reagent (0.6% dye in dilute perchloric acid). Use 1.5 ml distilled water plus 1.5 ml Coomassie blue reagent as blank to zero the spectrophotometer. Read the absorbency at 620 nm. 

A standard curve is prepared by using the stock solution of bovine serum albumin (BSA, 50 mg/ml) using at least four data points in duplicate. e.g. 0.4 ml stock + 1.1 ml water (= 0.4/1.5 x 50 mg/ml = 13.3 mg/ml), 0.8 ml stock + 0.7 ml water, etc. N.B. only the concentration within the 1.5 ml 'sample' solution is relevant; the (constant) amount of reagent added is not relevant for sample concentration calculations

2 Reducing Sugar Assay 
2.0 ml of DNS reagent (ready prepared; 3,5-dinitrosalicylic acid and sodium potassium tartrate dissolved in dilute sodium hydroxide) is added to sample (200 ml, 0.2 ml), containing 0 - 2 mg reducing sugar (i.e. 0 - 10 mg/ml). The tube is placed in a boiling water bath and the solution heated at 100°C for 5 minutes. Rapidly cool in ice to room temperature. Use 0.2 ml distilled water plus 2.0 ml DNS reagent, heated as above, as blank to zero the spectrophotometer. Read absorbency at 570 nm. A standard curve is prepared by using the stock solution of maltose (10 mg/ml) using at least four data points in duplicate. e.g. 0.05 ml stock + 0.15 ml water (= 0.05/0.2 x 10 mg/ml = 2.5 mg/ml), 0.1 ml stock + 0.1 ml water, etc. N.B. only the concentration within the 0.2 ml 'sample' solution is relevant; the (constant) amount of reagent added is not relevant for sample concentration calculations. You are reminded that the M.Wt. of maltose is 342 and maltose contains a single reducing group (i.e. 342 g maltose contains one mole of reducing group/equivalent). For your graphs, you must calculate the molar concentration of reducing groups in the standard maltose solutions.

3 Assay of a-amylase by production of reducing equivalents 
Add 0.8 ml 20 mM K phosphate (a-amylase buffer) to 0.2 ml soluble enzyme in phosphate buffer (containing about 10 mg amylase). Note that the enzyme solutions must be diluted before they are assayed). Pre-incubate for about 4 minutes at 37°C. Add 1.0 ml, 1% starch in phosphate buffer (pre-warmed to 37°C). Incubate for exactly 5 minutes at 37°C. Stop the reaction by removing 0.2 ml of the incubated mixture and adding this to 2 ml of DNS reagent. 

The tube should be placed in a boiling water bath and the solution heated at 100°C for 5 minutes to develop the reducing sugar assay colour. Rapidly cool in ice to room temperature and read absorbency at 570 nm. Use 0.1 ml buffer plus 0.1 ml starch plus 2.0 ml DNS reagent, heated as above, as a blank to zero the spectrophotometer. Note that the reducing sugars in only 0.2 ml of the 2.0 ml in the 37°C incubation mixture is used in the reducing sugar assay and allowance should be made for this when calculating the amount of reducing sugar produced by the enzyme in the 0.2 ml original sample.

4 Assay of a-amylase by loss of iodine reactive material 
Make a mixture of 0.1 ml buffer plus 0.1 ml starch for use as blank. Add one drop to one drop of K phosphate containing 0.05% iodine. A blue coloration will be observed. 

Free enzyme assay: Add 0.8 ml K phosphate (20 mM, pH 7, 'a-amylase buffer') to 0.2 ml enzyme (containing about 10 µg free amylase). Incubate for 4 minutes at 37°C. Add 1 ml 1% starch (pre-warmed to 37°C) and incubate at 37°C. At known times (e.g. 0, 30 s, 1, 2, 5, 10 min etc), remove 1 drop and drop into 1 ml K phosphate containing 0.05% iodine. 

Immobilised enzyme assay: Add 1.0 ml K phosphate (20 mM, pH 7, 'a-amylase buffer') to half the immobilised enzyme. Incubate for 4 minutes at 37°C as above. Add 1 ml 1% starch. Keep the immobilised enzymes agitated. At known times (e.g. 0, 30 s, 1, 2, 5, 10 min etc), remove one drop and drop into one drop of K phosphate containing 0.05% iodine. In both assays, blue coloration will be observed while macromolecular starch is still present. The enzyme activity is inversely proportional to the time taken. If no blue colour is observed in the first samples, repeat the assay as either (1) the reaction has already occurred at to rapid a pace, or (2) you forgot to add the enzyme/ iodine/starch/etc.