Identification of enzymes and activity from two-dimensional gel electrophoresis

Nature Protocols

Volumn 2, Issue 10, 2007, Pages 2318-2324

  Afjehi Sadat, Leila ^a   Lubec, Gert ^a  

^a MEDICAL UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME;

ANIMAL; ARTICLE; CHEMISTRY; ENZYMOLOGY; MASS SPECTROMETRY; METHODOLOGY; PROTEOMICS; RAT; SPINAL CORD; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ANIMALS; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ENZYMES; PROTEOMICS; RATS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; SPINAL CORD;

EID: 38449119746     PISSN: 17542189     EISSN: 17502799     Source Type: Journal    
DOI: 10.1038/nprot.2007.317     Document Type: Article

References (23)

1. Chen, W.Q., Kang, S.U. & Lubec, G. Protein profiling by the combination of two independent mass spectrometry techniques. Nat. Protoc. 1, 1446-1452 (2006).
2. Lubec, G., Afjehi-Sadat, L., Yang, J.W. & John, J.P. Searching for hypothetical proteins: theory and practice based upon original data and literature. Prog. Neurobiol. 77, 90-127 (2005).
3. John, J.P. et al. Nitricoxideandoxygen radicalattackon GDP-dissociation inhibitor 2 (GDI-2) in spinal cord injury of the rat. J. Proteome Res. 6, 1500-1509 (2007).
4. Chou, K.C. & Elrod, D.W. Prediction of enzyme family classes. J. Proteome Res. 2, 183-190 (2003).
5. Chou, K.C. & Cai, Y.D. Predicting enzyme family class in a hybridization space. Protein Sci. 13, 2857-2863 (2004).
6. Chou, K.C. Using amphiphilic pseudo amino acid composition to predict enzyme subfamily classes. Bioinformatics 21, 10-19 (2005).
7. Chou, K.C. & Cai, Y.D. Predicting enzyme family class in a hybridization space. Using GO-PseAA predictor to predict enzyme sub-class. Biochem. Biophys. Res. Commun. 325, 506-509 (2004).
8. Kuznetsova, E. etal. Enzyme genomics: application ofgeneralenzymaticscreens to discover new enzymes. FEMS Microbiol. Rev. 29, 263-279 (2005).
9. Schmidt, A.J., Ryjenkov, D.A. & Gomelsky, M. The ubiquitous protein domain EAL is a cyclic diguanylate-specific phosphodiesterase: enzymatically active and inactive EAL domains. J. Bacteriol. 187, 4774-4781 (2005).
10. Prakash, P., Aruna, B., Sardesai, A.A. & Hasnain, S.E. Purified recombinant hypothetical protein coded by open reading frame Rv1885c of Mycobacterium tuberculosis exhibits a monofunctional AroQ class of periplasmic chorismate mutase activity. J. Biol. Chem. 280, 19641-19648 (2005).
11. Thuswaldner, S. et al. Identification, expression, and functional analyses of a thylakoid ATP/ADP carrier from Arabidopsis. J. Biol. Chem. 282, 8848-8859 (2007).
12. Fumic, K. et al. Functional analysis of human S-adenosylhomocysteine hydrolase isoforms SAHH-2 and SAHH-3. Eur. J. Hum. Genet. 15, 347-351 (2007).
13. Hager, D.A. & Burgess, R.R. Elution of proteins from sodium dodecyl sulfatepolyacrylamide gels, removal of sodium dodecyl sulfate, and renaturation of enzymatic activity: results with sigma subunit of Escherichia coli RNA polymerase, wheat germ DNA topoisomerase, and other enzymes. Anal. Biochem. 109, 76-86 (1980).
14. Afjehi-Sadat, L. et al. Structural and functional analysis of hypothetical proteins in mouse hippocampus from two-dimensional gel electrophoresis. J. Proteome Res. 6, 711-723 (2007).
15. Bradford, M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 72, 248-254 (1976).
16. Howell, A., Dubrac, S., Noone, D., Varughese, K.I. & Devine, K. Interactions between the YycFG and PhoPR two-component systems in Bacillus subtilis: the PhoR kinase phosphorylates the non-cognate YycF response regulator upon phosphate limitation. Mol. Microbiol. 59, 1199-1215 (2006).
17. Genda, T., Nakamatsu, T. & Ozak, H.: Purification and characterization of malate dehydrogenase from Corynebacterium glutamicum. J. Biosci. Bioeng. 95, 562-566 (2003).
18. Habig, W. & Racusen, D. An apparent oligomer of malate dehydrogenase from bean leaves. Plant Physiol. 53, 402-410 (1974).
19. Harris, D.G., Marx, D.P., Anderson, J.M., McCune, R.W. & Zimmerman, S.S. Kinetic and molecular modeling of nucleoside and nucleotide inhibition of malate dehydrogenase. Nucleosides Nucleotides Nucleic Acids 21, 813-823 (2002).
20. Hung, H.C., Chien, Y.C., Hsieh, J.Y., Chang, G.G. & Liu, G.Y. Functional roles of ATP-binding residues in the catalytic site of human mitochondrial NAD(P)+-dependent malic enzyme. Biochemistry 44, 12737-12745 (2005).
21. Yan, J.X. et al: A modified silver staining protocol for visualization of proteins compatible with matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry. Electrophoresis 21, 3666-3672 (2000).
22. Yao, H. & Sem, D.S. Cofactor fingerprinting with STD NMR to characterize proteins of unknown function: identification of a rare cCMP cofactor preference. FEBS Lett. 579, 661-666 (2005).
23. Kleemann, R. et al. Specific reduction of insulin disulfides by macrophage migration inhibitory factor (MIF) with glutathione and dihydrolipoamide: potential role in cellular redox processes. FEBS Lett. 430, 191-196 (1998).