PRACTICAL I: Protein Assay by the BCA method

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1 PRACTICAL I: Protein Assay by the BCA method The BCA protein assay is a detergent-compatible formulation based on bicinchoninic acid (BCA) for the colorimetric detection and quantitation of total protein. This method combines the well-known reduction of Cu 2+ to Cu + by protein in an alkaline medium (the biuret reaction) with the highly sensitive and selective colorimetric detection of the cuprous cation (Cu + ) using a unique reagent containing bicinchoninic acid. The purple-colored reaction product of this assay is formed by the chelation of two molecules of BCA with one cuprous ion. This water-soluble complex exhibits a strong absorbance at 562 nm that is nearly linear with increasing protein concentrations over a broad working range (20-2,000 µg/ml). BCA Protein Assay Reagent Kit, BSA (standard), a protein extract. A standard curve for BSA and protein concentration of the sample. Eppendorf tubes Microwell plate Incubator ELISA reader Unknown samples BSA stock solution (2000 µg/ml) Distilled water BCA protein assay kit METHODS 1. Preparation of diluted BSA standards Please do calculations before practical Prepare by serial dilution (2x) of BSA standards: 2000 µg/ml, 1000 µg/ml, 500 µg/ml, 250 µg/ml, 125 µg/ml, 62.5 µg/ml from the BSA stock solution (2000 µg/ml). The final volume for each diluted standard should be > 60 µl. 2. Preparation of diluted unknown samples Take out the protein extracts from the freezer. Transfer 100 µl into a new eppendorf tube, then dilute 2X and 4X with distilled water. The final volume for each diluted standard should be > 60 µl. 3. Preparation of the BCA Working Reagent Prepare the BCA working reagent by mixing 50 parts of BCA Reagent A (5 ml) with 1 part of BCA Reagent B (100 µl) in a 15 ml tube. 4. Assay a. Pipette 25 µl of each standard or unknown sample into an appropriate microwell plate wells. Use 25 µl of the diluent (e.g. distilled water) for the blank wells. Duplicates should be done for each standard, unknown sample, and blank. b. Add 200 µl of the BCA working reagent to each well, mix the plate well on a plate shaker for 30 seconds. 1

2 c. Cover the plate with foil and incubate the plate at 37 C for 30 min. d. After incubation, cool the plate to RT then measure the absorbance at or near 562 nm on an ELISA reader. e. Subtract the average A 562 reading for the blanks from the A 562 reading for each standard or unknown sample. f. Prepare a standard curve by plotting the average blank-corrected A 562 reading for each BSA standard vs. its concentration in µg/ml. QUESTIONS 1. Determine the protein concentration of your unknown sample. 2. How do your results agree with those of other groups? Comment on any differences if any. 2

3 PRACTICAL II: Protein Separation by SDS-PAGE This practical will allow you to separate and detect those proteins by SDS-PAGE followed by Coomassie blue staining, and make a comparison on the protein profile between two samples. 2 tubes containing two protein extracts. One polyacrylamide gel - one where the proteins are separated by molecular weight (SDS-PAGE) Part 1 Pre-stained low molecular weight protein markers Polyacrylamide gel Gel tank and power pack SDS-PAGE electrophoresis buffer (see Appendix 3.2) Part 2 Fixative solution (see Appendix 3.2) Coomassie Blue staining solution (see Appendix 3.2) Destaining solution (see Appendix 3.2) Staining box METHODS Part 1 1. Take out two tubes of the protein extracts. Transfer 10 µl from each tube to new Eppendorf tubes, and add 10 µl of 2xSDS-PAGE sample buffer to each. Boil the samples and at 95 C for 5 min. 2. Spin the samples at 13,000 rpm on the bench-top centrifuge for 5 min. 3. Set up the SDS-PAGE gel in the electrophoresis tank. 4. Add SDS-PAGE electrophoresis buffer into the inner chamber to above the inner shorter plate. 5. Load the gel as follows (10 µl in each lane): Lane 1: Protein marker Lane 2: Protein extract A Lane 3: Protein extract B Lane 4: Protein extract A Lane 3: Extract B etc, etc 6. Add SDS-PAGE electrophoresis buffer into the lower chamber to cover the 3

4 electric wire. Run at constant voltage 100 V (or 10 ma) until the bromophenol blue front reaches the resolving gel, then increase the voltage to 120 V (or 15 ma) until the dye front reaches to about cm above the bottom of the gel. Stop the electrophoresis. Part 2 Coomassie Blue Staining 1. Dismantle the apparatus and open the glass sandwich gently, leaving the gel on one plate. 2. Place the gel in a staining box containing Coomassie blue staining solution and incubate with gentle shaking for 30 minutes at room temperature. 3. Wash the gel with destaining solution once and leave the gel in destaining solution for several hours to overnight. Change the destaining solution as needed until the gel is destained (background of the gel is clear). Alternatively, put the gel in a microwave suitable container with distilled water, and place it in microwave oven for 1-2 min at medium level, repeat a few times until the Coomassie blue is destained. 4. Take the picture of destained gels. QUESTIONS 1. Work out the molecular weight of the most abundant protein? Record the % of the gel you need to consult your lecture notes to assign which markers are observed. 2. Revision: What is the function of stacking gel in SDS-PAGE? What is the mechanism of separation of proteins by SDS-PAGE? 4

5 PRACTICAL III: Protein Separation by IEF This practical will allow you to separate and detect those proteins by IEF followed by Coomassie blue staining, and make a comparison on the protein profile between two samples. 2 tubes containing two protein extracts. One polyacrylamide gel with ampholytes - one where the proteins are separated by their pi (IEF) Part 1 Pre-stained pi markers Pre-cast IEF gels (ph 3-10) Sample buffer, cationic and anionic buffers (see Appendix 3.3) Gel tank and power pack Same gel tank and power pack as SDS-PAGE Part 2 IEF 1. Take out the two tubes of protein extract from freezer. Transfer 10 µl from each tube to a new Eppendorf tube, and add 10 µl of the IEF sample buffer. Vortex.. 2. Spin the samples and protein markers at 13,000 rpm for 5 min. 3. Set up the IEF gel in the electrophoresis tank. 4. Add cationic buffer into the inner chamber to above the inner shorter plate. 5. Load the gel as follows (10 µl in each lane) as before: Lane 1: Protein marker Lane 2: Protein extract A Lane 3: Protein extract B etc, etc 6. Add anionic buffer into the outer chamber to cover the electric wire. Run at 100 V (1 hr); 200 V (1 hr); 500 V (0.5 hr). The final current should be about 5-6 ma. At the end of the run, the pre-stained markers should be focussed. Part 2 Coomassie Blue Staining 1. Dismantle the apparatus and open the glass sandwich gently. Place the gel in a staining box containing fixative solution for 30 minutes. Then change to Coomassie blue staining solution and incubate with gentle shaking for 30 minutes at room temperature. 2. Wash the gel with destaining solution once and leave the gel in destaining solution for several hours to overnight. Change the destaining solution as needed until the gel is destained (background of the gel is clear). Alternatively, put the gel in a microwave suitable container with distilled water, and place it in microwave oven for 1-2 min at medium level, repeat a few times until the Coomassie blue is destained. 3. Take a picture of destained gels. QUESTIONS 1. What is the pi of the most abundant protein? You will need to know the pi of the marker proteins. 2. Revision: What is the mechanism of separation of proteins by IEF? Why are the fixative solutions different? 5

6 Practical IV: 2D-GEL ELECTROPHORESIS Lab 1: The First Dimension (IEF) In this practical, a mixture of proteins will be separated according to their isoelectric points followed by SDS- PAGE. As IEF is a focussing technique, the protein mixture can be applied across the whole IEF strip, the proteins will migrate to places on the strip corresponding to their isoelectric points when a voltage is applied. Protein extract stored at -20 C. an IEF strip containing focused proteins stored in the 80 C freezer. You should work in pairs for this experiment. Each group should have one 7-cm IEF strip (ph 3-10, linear) one Eppendorf tube containing 125 µl protein extract dissolved in rehydration buffer one micropipette (200 µl) with yellow tips a pair of tweezers disposable Pasteur pipette The following will be shared in common 7 cm focussing tray (BioRad) Paper electrode wicks Sterile deionised water (about 10 ml) one micropipette (20 µl) with yellow tips Mineral oil METHOD Powderless gloves should be worn for this experiment. For most of this experiment you will have to wait your turn as there is only one tray. There are 12 lanes in the focusing tray. Lane 1 is the lane nearest the electrical contacts. You will be allocated one channel to place your IEF strip. 1. Prepare the sample for 2-D electrophoresis by mixing 10 µl of protein extract with 120 µl of rehydration buffer. 2. Place two electrode wicks using a pair of tweezers at both ends of your channel on top of the wire electrodes. 3. Pipette 8 µl of deionised water onto each wick to wet them. Make sure again that the wicks cover the electrodes. 4. Pipette 125 µl of 2-D sample carefully in a line over the whole channel. Avoid introducing bubbles by pipetting the last bits of the sample into the channel. 5. Carefully peel off the plastic backing of the IEF strip with your hand while holding the strip with a pair of tweezers. Note carefully which side of the plastic the gel is on. 6. Note carefully the anodic end of the strip. If you are using a BioRad IEF strip, this is the end of the strip marked with a + and should be placed later in the tray pointing towards the + side. If you are using a 6

7 Amersham IEF strip, this is the pointed end of the strip and should be placed later in the tray pointing towards the + side, 7. Note the anodic end of the focusing tray. This is the end marked with a Place the strip (gel side downwards) into your allocated channel carefully in the correct direction. Avoid trapping bubbles under the gel. If this happens, lift the strip up and down or press the gel gently. 9. Pipette about 2-3 ml mineral oil over the strip. 10. When everyone has finished placing their strip into the tray, place it in the IEF cell and close the cell and start the run. The IEF cell will apply a low voltage overnight while allowing the strip to swell and rehydrate. It will then apply a high voltage to refocus the proteins. This will take about 5 hours after which it will shut down to a low voltage again. Day 2 The run should be finished 17 hours after starting. Switch off the IEF cell and take the strips out with a pair of tweezers. Hold them vertically over a piece of filter paper to drain the oil and then store in a labeled tube at - 80 C. Lab 2: The Second Dimension At the end of the last practical, the proteins will be focussed as vertical lines on the IEF strip. You may be able to see this if there was an extra strip left over from the previous practical and it has been stained. In this practical, the proteins will migrate from the IEF strip on to an SDS-PAGE gel where they will be separated by the molecular weight. You will then stain this gel and observe the spots on the gel. Each spot should in theory represent one protein and can then be excised and characterised by amino acid sequencing or mass spectrommetry, an IEF strip containing focused proteins stored in the 80 C freezer. a stained SDS-PAGE gel with many spots.. You should work in pairs for this experiment. Each group should have one 7-cm IEF strip from the last experiment one 10% ready cast TrisHCl PAGE gel with a well for an IPG strip a pair of tweezers disposable Pasteur pipettes staining tray/box The following will be shared in common Two 7 cm rehydration tray (BioRad) 7

8 Equilibration buffer I (should be reconstituted just before practical) Equilibration buffer II (should be reconstituted just before practical) one micropipette (5 ml) with white tips one 10 ml measuring cylinder containing Tris/glycine/SDS run buffer Tris/glycine/SDS buffer Orbital shaker Coomassie Blue R-250 staining solution Destaining solution METHOD Gloves must be worn for this experiment. Part 1 Reequilibration (about 1 hour) 1. Place your thawed IEF strip (it should be clear) gel side facing upwards in a rehydration tray (try to use the same channel you were allocated in the last practical). 2. Pipette ml of equilibration buffer I on top of the strip. 3. After all the strips are placed in the tray, place on the orbital shaker and shake for 10 minutes. 4. Remove your strip and place in another empty channel or in a second tray and repeat the same procedure with equilibration buffer II. 5. While waiting, microwave the agarose (about 30 seconds). 6. While waiting in step 4, prepare the PAGE gel by removing the tape at the bottom end of the plate and the comb. Use a filter paper to drain any water in the well. Place the gel on the bench with the long plate on the bottom. 5. Remove your strip and dip briefly in the measuring cylinder containing Tris/glycine/SDS buffer briefly. 6. Use the tweezers to place the IEF strip gel side up onto the long plate. 7. Stand the PAGE gel upright and use a Pasteur pipette to drip the liquefied agarose into the well of the gel. 8. Gently push the IEF strip into the well. Take care not to trap any air bubbles beneath the strip. 9. Leave to solidify for about 10 minutes. Part 2 SDS PAGE (about 1 hour) 1. Mount the gel in the gel tank and fill the reservoirs with Tris/Glycine/SDS running buffer and begin the electrophoresis. The voltage should be constant and 200 V. The run should take minutes. 2. When the bromophenol blue front has reached about 0.5 cm above the bottom of the gel, stop the run. Part 3 Staining (about 1 hour) 1. Remove the gel assembly from the tank. Carefully open the plates with your fingers and gently peel of the gel into a staining tray/box containing enough Coomassie Blue to cover the gel. 2. Place the tray/box on an orbital shaker for 20 min. 3. Decant the staining solution and add destaining solution to the tray and shake on the orbital shaker. Change the destaining solution after 5 minutes, ½ hour, 1 hour until the background is reasonably clear. Or alternatively, put the gel in a microwave suitable container with distilled water, and place it in microwave oven for 1-2 min at med. level for few times until the Coomassie blue is destained. 4. Take a photograph of the gel. Questions 1. Why is the temperature of the IEF step 20 C (normal IEF is usually done at 4 C)? 2. What is the function of the equilibration steps between the 1 st and 2 nd dimensions? 8

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