Nano-scale proteomics approach using two-dimensional fibrin zymography combined with fluorescent SYPRO ruby dye

Journal of Biochemistry and Molecular Biology

Volumn 37, Issue 3, 2004, Pages 298-303

  Choi, Nack Shick ^a,b   Yoo, Ki Hyun ^a   Yoon, Kab Seog ^a   Maeng, Pil Jae ^b   Kim, Seung Ho ^a  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b Chungnam National University   (South Korea)

Author keywords

Bacillus; Proteomics; SYPRO ruby; Two dimension; Zymography

Indexed keywords

ADENOSINE TRIPHOSPHATE; CASEIN; DYE; FIBRIN; GELATIN; METALLOPROTEINASE; PROTEINASE;

ARTICLE; BACILLUS; BACILLUS SUBTILIS; BACTERIAL STRAIN; CANCER CELL CULTURE; CONTROLLED STUDY; FERMENTATION; FLUORESCENCE ANALYSIS; KOREA; MATRIX ASSISTED LASER DESORPTION IONIZATION TIME OF FLIGHT MASS SPECTROMETRY; NONHUMAN; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN ANALYSIS; PROTEOMICS; STAINING; YEAST; ZYMOGRAPHY;

BACILLUS SP.; BACILLUS SP. DJ-4; BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS);

EID: 3142783406     PISSN: 12258687     EISSN: None     Source Type: Journal    
DOI: 10.5483/bmbrep.2004.37.3.298     Document Type: Article

References (26)

1. Berggren, K., Chernokalskaya, E., Steinberg, T. H., Kemper, C., Lopez, M. F., Diwu, Z., Haugland, R. P. and Patton, W. F. (2000) Background-free, high sensitivity staining of proteins in one- and two-dimensional sodium dodecyl sulfate-polyacrylamide gels using a luminescent ruthenium complex. Electrophoresis 21, 2509-2521.
2. Berggren, K., Steinberg, T. H., Lauber, W. M., Carroll, J. A., Lopez, M. F., Chernokalskaya, E., Zieske, L., Diwu, Z. and Haugland, R. P. (1999) A luminescent ruthenium complex for ultrasensitive detection of proteins immobilized on membrane supports. Anal. Biochem. 276, 129-143.
3. Bradford, M. M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-252.
4. Choi, N. S., Kim, B. Y., Lee, J. Y., Yoon, K. S., Han, K. Y. and Kim, S. H. (2002) Relationship between acrylamide concentration and enzymatic activity in an improved single fibrin zymogram gel system. J. Biochem. Mol. Biol. 35, 236-238.
5. Choi, N. S. and Kim, S. H. (1999) Application of fibrin zymography for determining the optimum culture time for protease activity. Biotechnol. Techniq. 13, 899-901.
6. Choi, N. S. and Kim, S. H. (2000) Two fibrin zymography methods for analysis of lasminogen activators on gels. Anal. Biochem. 281, 236-238.
7. Choi, N. S. and Kim, S. H. (2001) The effect of sodium chloride on the serine-type fibrinolytic enzymes and the thermostability of extracellular protease from Bacillus amyloliquefaciens DJ-4. J. Biochem. Mol. Biol 34, 134-138.
8. Choi, N. S., Lee, J. Y., Yoon, K. S., Han, K. Y. and Kim, S. H. (2001a) Identification of total extracellular fibrinase from Bacillus sp. DJ using one- or two-dimensional fibrin zymography for proteomic approach. J. Microbiol. Biotechnol. 11, 1111-1114.
9. Choi, N. S., Yoon, K. S., Lee, J. Y., Han, K. Y. and Kim, S. H. (2001b) Comparison of three substrates (casein, fibrin and gelatin) in zymographic gel. J. Biochem. Mol. Biol. 34, 531-536.
10. Hirushi, S. and Kadota, H. (1976) Intracellular protease of Bacillus subtilis. Agric. Biol. Chem. 40, 1047-1049.
11. Kim, S. H. and Choi, N. S. (1999) Electrophoretic analysis of protease inhibitors in fibrin zymography. Anal. Biochem. 270, 179-181.
12. Kim, S. H. and Choi, N. S. (2000) Purification and characterization of subtilisin DJ-4 secreted by Bacillus sp. strain DJ-4 screened from Doen-Jang. Biosci. Biotechnol. Biochem. 64, 1722-1725.
13. Kim, S. H., Choi, N. S. and Lee, W. Y. (1998) Fibrin zymography: A direct analysis of fibrinolytic enzyme on gels. Anal. Biochem. 263, 115-116.
14. Kim, W., Choi, K., Kim, Y., Park, H., Choi, J., Lee, Y., Oh, H., Kwon, I. and Lee, S. (1996) Purification and characterization of a fibrinolytic enzyme produced from Bacillus sp. strain CK 11-4 screened from Chungkook-Jang. Appl. Environ. Microbiol. 62, 2482-2488.
15. Kleiner, D. E. and Stetler-Stevenson, W. G. (1994) Quantitative zymography: Detection of picogram quantities of gelatinases. Anal. Biochem. 218, 325-329.
16. Lauber, W. M., Carroll, J. A., Dufield, D. R., Kiesel, J. R., Radabaugh, M. R. and Malone, J. P. (2001) Mass spectrometry compatibility of two-dimensional gel protein stains. Electrophoresis 22, 906-918.
17. Lopez, M. F., Berggren, K., Chernokalskaya, E., Lazarev, A., Robinson, M. and Patton, W. F. (2000) A comparison of silver stain and SYPRO Ruby Protein Gel Stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis 21, 3673-3683.
18. Malone, J. P., Radabaugh, M. R., Leimgruber, R. M. and Gerstenecker, G. S. (2001) Practical aspects of fluorescent staining for proteomic applications. Electrophoresis 22, 919-932.
19. Raser, K. J., Posner, A. and Wang, K. K. W. (1995) Casein zymography: A method to study mu-calpain, m-calpain, and their inhibitor agents. Arch. Biochem. Biophys. 319, 211-216.
20. Robertson, E. F., Dannelly, K., Malloy, P. J. and Reeves, H. C. (1987) Rapid isoelectric focusing in a vertical polyacrylamide minigel system. Anal. Biochem. 167, 290-294.
21. Steinberg, T. H., Chernokalskaya, E., Berggren, K., Lopez, M. F., Diwu, Z., Haugland, R. P. and Patton, W. F. (2000) Ultrasensitive fluorescence protein detection in isoelectric focusing gels using a ruthenium metal chelate stain. Electrophoresis 21, 486-496.
22. Strongin, A. Y., Izotova, L. S., Abramov, Z. T., Gorodetsky, D. I., Ermakova, L. H., Baratova, L. A., Belyanova, L. P. and Stepanov, V. M. (1978) Intracellular serine protease of Bacillus subtilis; sequence homology with extracellular subtilisins. J. Bacteriol. 133, 1401-1411.
23. Sumi, H., Hamada, K., Nakanishi, K. and Hiratani, H. (1990) Enhancement of the fibrinolytic activity in plasma by oral administration of nattokinase. Acta Haematol. 84, 139-143.
24. Sumi, H., Hamada, H., Tsushima, H., Mihara, H. and Muraki, H. (1987) A novel fibrinolytic enzyme (nattokinase) in the vegetable cheese natto; a typical and popular soybean food in the Japanese diet. Experentia 43, 1110-1111.
25. Valdes, I., Pitarch, A., Gil, C., Bermudez, A., Llorente, M., Nombela, C. and Mendez, E. (2000) Novel procedure for the identification of proteins by mass fingerprinting combining two-dimensional electrophoresis with fluorescent SYPRO Red staining. J. Mass Spectrom. 35, 672-682.
26. Yan, J. X., Harry, R. A., Spibey, C. and Dunn, M. J. (2000) Postelectrophoretic staining of proteins separated by two-dimensional gel electrophoresis using SYPRO dye. Electrophoresis 21, 3657-3665.