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This assay allows to determine whether proteins possess oxidative activity-the ability to introduce disulfide bond in vitro. The substrate for potential oxidases is a ribonuclease A which, for its activity, needs 4 properly formed disulfide bonds (Raines, 1998).
RNase A activity can be detected by:

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Detection of Protein Oxidative Activity Using Reduced RNase A

Microbiology > Microbial biochemistry > Protein > Activity
Authors: Magdalena Grzeszczuk
Magdalena GrzeszczukAffiliation: Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
Bio-protocol author page: a2995
Katarzyna Bocian-Ostrzycka
Katarzyna Bocian-OstrzyckaAffiliation: Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
Bio-protocol author page: a2996
Anna Lasica
Anna LasicaAffiliation: Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
Bio-protocol author page: a2997
 and E. Katarzyna Jagusztyn-Krynicka
E. Katarzyna Jagusztyn-KrynickaAffiliation: Department of Bacterial Genetics, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
For correspondence: kjkryn@biol.uw.edu.pl
Bio-protocol author page: a2998
Vol 6, Iss 6, 3/20/2016, 533 views, 0 Q&A, How to cite
DOI: http://dx.doi.org/10.21769/BioProtoc.1766

[Abstract] This assay allows to determine whether proteins possess oxidative activity-the ability to introduce disulfide bond in vitro. The substrate for potential oxidases is a ribonuclease A which, for its activity, needs 4 properly formed disulfide bonds (Raines, 1998).
RNase A activity can be detected by:

Keywords: Thiol oxidoreductases, Disulfide bonds, Oxidative folding

  1. Monitoring the digestion of RNA (Lambert and Freedman, 1983);
  2. Methylene Blue assay (Greiner-Stoeffele et al., 1996);
  3. Analyzing the cleavage of the cyclic CMP (Lyles and Gilbert, 1991; Lyles and Gilbert, 1991).

We here describe method for measurements of oxidative activity, based on the cleavage of cCMP. Oxidative activity will be tested by measuring spectrophotometrically RNase A cleavage of cyclic-2’, 3’-cytidinemonophosphate (cCMP) to 3’-cytidinemonophosphate (3’ CMP), which results in an increase in absorption at 296 nm.
The reaction equation: RNase A +2’ 3’-cCMP→RNase A + 3’ CMP.

Materials and Reagents

  1. Flat-bottomed clear 96-well microplates (Optimum Line, catalog number: GP700)
  2. Ribonuclease A from bovine pancreas (RNase A) (store -20 °C) (Sigma-Aldrich, catalog number: R6513-10 mg)
  3. Desalting columns-Biorad Econo-Pac 10DG Desalting Columns, 30 units (Bio-Rad Laboratories, catalog number: 7322010)
  4. Bio-Scale Mini Profinity IMAC Cartridges (Bio-Rad Laboratories, catalog number: 7324614)
  5. ENrichTM SEC 70 size exclusion columns (Bio-Rad Laboratories, catalog number: 7801070)
  6. PierceTM Protein Concentrators, 9K MWCO (7 ml) (Thermo Fisher Scientific, catalog number: 89884A) or Amicon Ultra-4 Centrifugal Filter Unit with Ultracel-10 membrane (EMD Millipore Corporation, catalog number: UFC801008)
  7. Proteins of interest (purified to homogeneity proteins, concentration approx 7-8 mg/ml)
  8. Phosphate buffered saline (PBS) (Sigma-Aldrich, catalog number: P4417-50TAB)
  9. L-Glutathione oxidized disodium salt (GSSG) (Sigma-Aldrich, catalog number: G4626-100 mg)
  10. L-Glutathione reduced (GSH) (Sigma-Aldrich, catalog number: G6529-1 g)
  11. DL-Dithiothreitol (DTT) (AppliChem GmbH, catalog number: 3483-12-3; Sigma-Aldrich, catalog number: 43815-1 G)
  12. Guanidine hydrochloride (Gdn-HCl) (AppliChem GmbH, catalog number: A11061000)
  13. 1 M Tris (pH 8.0) (Eurx, catalog number: E0273-01)
  14. 0.5 M EDTA (pH 8.0) (Eurx, catalog number: E240-01)
  15. DTNB (Ellman’s Reagent) (5, 5-dithio-bis-(2-nitrobenzoic acid) (Thermo Fisher Scientific, catalog number: 22582)
  16. Sodium phosphate dibasic (pH 8.0) (Sigma-Aldrich, catalog number: S3264-250 G)
  17. Cytidine 2’:3’-cyclic monophosphate monosodium salt (cCMP) (store -20 °C) (Sigma-Aldrich, catalog number: C9630-100 mg)
  18. 2x Reaction buffer (see Recipes)
  19. Reduction buffer (see Recipes)

Equipment

  1. Plate reader (Tecan, Infinite®, model: 200 PRO series)

Procedure

  1. Preparation of proteins for assay (approx 1 week) (Chim et al., 2013)
    1. Purify proteins.
      Note: We overexpressed proteins by autoinduction (Studier, 2005) and then purified by affinity chromatography using the NGC chromatography system (see Optional materials).
    2. To obtain higher purity, load your proteins onto size exclusion columns and elute with PBS.
    3. Determine the amount of protein by nanodrop.
    4. Oxidize proteins with 50 mM oxidized glutathione (GSSG) and incubate for 1 h at RT (5-7 mg in 1 ml).
    5. Exchange buffer on desalting columns according to manufacturer’s guidelines.
    6. Determine the amount of protein by nanodrop.
    7. Follow the Ellman assay to confirm proper redox state.
    8. Concentrate if necessary (using protein concentration columns). For this assay you need approx 3 mg/ml.
    9. Use fresh or in the next couple of days.

  2. Reduction and denaturation of RNase A (2 days) (Daniels et al., 2010)
    1. Resuspend 10 mg of RNase A in 1 ml of reduction buffer (in 1.5 ml tube).
      Note: 10 mg of RNase A permit to perform approx. 20 assays.
    2. Incubate overnight at RT without shaking.
    3. Desalinate on columns and elute with PBS (according to manufacturer’s guidelines).
    4. Determine the amount of protein by nanodrop.
    5. If necessary, concentrate (for Ellman assay you need 2.5 mg/ml of RNase A).
    6. Follow the Ellman assay to confirm proper redox state.
    7. Use the same day.

  3. Oxidative folding of reduced RNase A (1 day) (Daniels et al., 2010)
    1. Prepare 2x reaction buffer.
    2. Prepare mixture of protein and reduced RNase A in a volume of 100 μl (add PBS if necessary) in a 96-well plate (40 μM protein and 20 μM RNase A).
      Note: With concentration of 2.5 mg/ml you need to add 11 μl to the well to achieve 20 μM of RNase A.
    3. Add 100 μl of 2x reaction buffer to the mixture of protein and RNase A; mix gently by pipetting up and down.
    4. Insert plate into the plate reader and start program.

Representative data


Figure 1. The results from one representative experiment. EcDsbA stands for main oxidase in E. coli.

Notes

  1. Notes about microplate reader settings (Table 1).

Table 1. Universal settings for microplate reader

Recipes

  1. 2x reaction buffer
    200 mM Tris/HCl (pH 8.0)
    4 mM EDTA
    0.4 mM GSSG
    2 mM GSH
    9 mM cCMP
  2. Reduction buffer
    100 mM Tris/HCl (pH 8.0)
    6 M Gdn-HCl
    140 mM DTT

Acknowledgements

The work was supported by the National Science Centre (grant no. 2012/05/B/NZ1/00039).

References

  1. Chim, N., Harmston, C. A., Guzman, D. J. and Goulding, C. W. (2013). Structural and biochemical characterization of the essential DsbA-like disulfide bond forming protein from Mycobacterium tuberculosis. BMC Struct Biol 13: 23.
  2. Daniels, R., Mellroth, P., Bernsel, A., Neiers, F., Normark, S., von Heijne, G. and Henriques-Normark, B. (2010). Disulfide bond formation and cysteine exclusion in gram-positive bacteria. J Biol Chem 285(5): 3300-3309.
  3. Greiner-Stoeffele, T., Grunow, M. and Hahn, U. (1996). A general ribonuclease assay using methylene blue. Anal Biochem 240(1): 24-28.
  4. Lambert, N. and Freedman, R. B. (1983). Kinetics and specificity of homogeneous protein disulphide-isomerase in protein disulphide isomerization and in thiol-protein-disulphide oxidoreduction. Biochem J 213(1): 235-243.
  5. Lyles, M. M. and Gilbert, H. F. (1991). Catalysis of the oxidative folding of ribonuclease A by protein disulfide isomerase: dependence of the rate on the composition of the redox buffer. Biochemistry 30(3): 613-619.
  6. Lyles, M. M. and Gilbert, H. F. (1991). Catalysis of the oxidative folding of ribonuclease A by protein disulfide isomerase: pre-steady-state kinetics and the utilization of the oxidizing equivalents of the isomerase. Biochemistry 30(3): 619-625.
  7. Raines, R. T. (1998). Ribonuclease A. Chem Rev 98(3): 1045-1066.
  8. Studier, F. W. (2005). Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41(1): 207-234.



How to cite this protocol: Grzeszczuk, M., Bocian-Ostrzycka, K., Lasica, A. and Jagusztyn-Krynicka, E. K. (2016). Detection of Protein Oxidative Activity Using Reduced RNase A. Bio-protocol 6(6): e1766. DOI: 10.21769/BioProtoc.1766; Full Text



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