A.1. Transformation of Plasmid into Bacteria (Day 1)
f. BL21 cells (Thermo Scientific Catalog number: EC0114)
g. 2 mL microcentrifuge tube
h. SOC (Super Optimal broth with Catabolite repression) Media (Thermo Scientific Catalog number: 15544034)
i. plasmid DNA (encoding cDNA of desired protein as described in reference [1])
j. plasmid of chaperone protein DNA (to help with protein folding)
k. floating foam tube rack (Fisherbrand, Catalog number: 36-099-2328)
l. incubator shaker (Eppendorf New Brunswick Innova 44)
m. incubator set to 37 ºC
n. water bath set at 42 ºC
o. LB agar plate with ampicillin and kanamycin (as described in reference [1])
p. micropipettes (1-10 μl, 20-100 μl, 100 μl-1000 μl)
r. spreader to spread transformed cells onto LB agar plate
A.2. Pre-Culture (Before Bulk Culture) (Day 2)
i. cart (to hold autoclave bin and supplies)
k. 250 ml Erlenmeyer flask
m. 125 ml of deionized water
n. ampicillin solution (25 mg of ampicillin in 250 μl of deionized water)
o. kanamycin solution (12.5 mg of kanamycin in 250 μl of deionized water)
A.3. Bulk Culture (Induction of Protein Expression) (Day 3 then Days 4-6)
e. Incubator shaker (Innova)
g. 47.5 g of TB media for each 1-L of bulk culture (6 L total)
h. 5 ml of glycerol for each 1-L of bulk culture (6 L total)
j. thiamine solution (2.38 g thiamine in 14 ml of water)
k. Double beam UV/Vis spectrophotometer (VWR, UV-6300PC)
l. 1 ml disposable cuvette (to check the optical density 600 nm after inducing protein expression)
m. IPTG solution (1.67 g of IPTG in 14 ml of water for the induction of cysteine protease)
n. arabinose solution (6.3 g of arabinose in 14 ml of water for the induction of chaperone proteins)
o. Graduated cylinder (100 mL)
p. Overnight pre-culture solution from Section A.2.
r. Ti 45 rotor (for the ultracentrifuge in the next section)
B.1. Harvesting and Lysing the Cells (Day 7)
d. Centrifuge (Beckman Coulter, Avanti JXN-26)
e. Ohaus scale (2kg-5lb Capacity, Harvard Trip I400/I500 Series)
f. 6x 1 L centrifuge bottles
j. Cold box (refrigerator)
(i) Tris HCl (1 M, 50 mL),
(iv) EDTA disodium salt (93 mg))
o. Sonic dismembrator (Fisherbrand, Model CL-334)
B.2. Centrifuging the Lysed Cells (Day 7)
d. Centrifuge (Beckman Coulter, Avanti JXN-26)
e. Ohaus scale (2kg-5lb Capacity, Harvard Trip I400/I500 Series)
f. Lysed Cells from Step 15 in the previous section (Purification of the Proteins I)
g. Ultracentrifuge (Beckman Coulter, Optima XPN-80)
h. 6x ultracentrifuge tubes (for Ti-45 rotor)
i. Cooled down Ti-45 Rotor from Section A.3. (for ultracentrifuge)
k. Beckman Coulter tube removal tool (Beckman Coulter 301875) (can also use skinny spatula)
B.3. Purification of the Supernatant from the Ultracentrifuge Step (Day 7)
d. Ni nitriloacetic acid (NTA) resin (500 ml commercial bottle, Thermo Scientific Product #88223)
g. Cold box (refrigerator)
l. 50 mL Plastic disposable syringe
m. Clamp to hold the column
n. Stand to hold the clamp for the column
o. 50 mL Falcon tubes to collect the protein fractions (up to 20)
p. Tube rack to hold the 50 mL Falcon tubes
q. Sharpee to label Falcon tubes
r. Buffers for eluting the protein out of the nickel column:
-Buffer B (500 mL volume of: 100 mM pH 7.4 KPhos, 100 μM DTT, 20% glycerol (v/v)):
(i) K2HPO4 (potassium phosphate dibasic, 6.059 g)
(ii) KH2PO4 (potassium phosphate monobasic, 2.07 g)
-Buffer C (300 mM imidazole of "Buffer B"):
-Buffer D (40 mM imidazole of "Buffer B"):
-Alternative Method for Buffer D (40 mM imidazole of "Buffer B"):
-Buffer E (70 mM imidazole of "Buffer B"):
-Alternative Method for Buffer E (70 mM imidazole of "Buffer B"):
s. Amicon filter (30 kDa, Millipore Sigma, catalog number: UFC903024)
t. Centrifuge (Beckman Coulter, Avanti JXN-26)
C.1. Analysis of the Purified Proteins I: SDS Protein Gel Electrophoresis (Days 7-8)
d. Power Supply for Electrophoresis (Thermo Scientific, EPS 300X)
e. Invitrogen Gels (4-20% Tris-Glycine gel, 1.0 mm x 15 well, Catalog #: XP04205BOX)
g. Gel loading tips for 10 μL micropipette (longer tips)
h. Protein Ladder (10-250 kDa protein ladder, Thermo Scientific, Catalog #: 26619)
i. pH meter for making solutions (SI Analytics, Lab 850)
j. Analytical balance (to weigh miligram to g quantities)
k. pipettes (100-1000 μL volume)
n. Denaturing solution for proteins (10 mL of 4x stock solution):
(i) 1 M Tris HCl buffer, pH 6.8 [Amount: 2.5 mL] (121.1 g of tris base in 800 mL of water and the pH
is adjusted using a pH meter to 6.8 using concentrated HCl)
(ii) Water [Amount: 0.5 mL]
(iii) Sodium dodecyl sulfate (SDS) [Amount: 1.0 g]
(iv) Bromophenol blue [Amount: 0.8 mL of 0.1% w/v solution] (Dissolve 10 mg of bromophenol
blue in 1 mL of water to make a 0.1% w/v solution)
(v) Glycerol [Amount: 4.0 mL]
(iv) Beta-mercaptoethanol [Amount: 2.0 mL]
o. Eluted protein samples from Ni-column (Section B.3., Step 15)
p. Styrofoam floaty (to heat 2-mL microcentrifuge tubes)
q. 2 mL microcentrifuge tubes (at least 10, for each protein sample)
s. Running Buffer (10X, pH 8.3):
(iii) Sodium dodecyl sulfate (10 g)
t. Running Buffer (1X - make fresh or gel will not stain properly - it will smear):
(i) 10X Running Buffer (100 mL)
u. Pyrex Crystallizing Dish (for staining solution, 740 mL capacity)
v. Pyrex Crystallizing Dish (for destaining solution, 740 mL capacity)
y. Staining solution for protein gel (500 mL)
(i) Coomassie brilliant blue G-250 (1 g)
(ii) Acetic acid (100 mL)
z. Destaining solution for protein gel (500 mL)
C.2. Analysis of the Purified Proteins II: BCA Assay to Quantify Purified Protein (Day 8)
d. Double beam UV/Vis spectrophotometer (VWR, UV-6300PC)
e. BCA assay kit (Thermo Scientific, PierceTM Bicinchoninic Acid) Protein Assay Kit, Product #:
(i) BCA Protein Assay Reagent A (Product # 23228)
(ii) BCA Protein Assay Reagent B (Product # 1859078)
(iii) Bovine Serum Albumin (BSA) Standard (2 mg/mL concentration) (Product # 23209)
f. 50 mL Falcon tube to make the working reagent (WR)
h. 20x 2 mL microcentrifuge tubes
i. 37 ºC shaking water bath
k. Microsoft Excel on computer to make the calibration curve of Solutions A-F (Abs at 562 nm vs. concentration, y vs. x)