Proteomic analysis of the subunit composition of complex I (NADH:Ubiquinone oxidoreductase) from bovine heart mitochondria

Methods in Molecular Biology

Volumn 357, Issue , 2007, Pages 103-125

  Fearnley, Ian M ^a   Carroll, Joe ^a   Walker, John E ^a  

^a NONE

Author keywords

Chromatography; Complex I; Electrophoresis; Isoelectric focusing; Mass spectrometry; Mitochondria; NADH:ubiquinone oxidoreductase; Protein complex; Protein modification; Respiratory complex; RP HPLC

Indexed keywords

BOVINAE; MAMMALIA;

CYSTEINE; MITOCHONDRIAL PROTEIN; PROTEOME; REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE (UBIQUINONE); TRYPSIN;

ANIMAL; ARTICLE; CATTLE; HEART MITOCHONDRION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; ISOELECTRIC FOCUSING; ISOLATION AND PURIFICATION; MASS SPECTROMETRY; METABOLISM; METHODOLOGY; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROTEIN PROCESSING; PROTEOMICS; REPRODUCIBILITY; TANDEM MASS SPECTROMETRY; TWO DIMENSIONAL GEL ELECTROPHORESIS;

ANIMALS; CATTLE; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; CYSTEINE; ELECTRON TRANSPORT COMPLEX I; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ISOELECTRIC FOCUSING; MITOCHONDRIA, HEART; MITOCHONDRIAL PROTEINS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; PROTEOMICS; REPRODUCIBILITY OF RESULTS; SPECTROMETRY, MASS, MATRIX-ASSISTED LASER DESORPTION-IONIZATION; TANDEM MASS SPECTROMETRY; TRYPSIN;

EID: 36549021003     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1385/1-59745-214-9:103     Document Type: Article

References (44)

1. Schultz, B. E. and Chan, S. I. (2001) Structures and proton-pumping strategies of mitochondrial respiratory enzymes. Annu. Rev. Biophys. Biomol. Struct. 30, 23-65.
2. Nicholls, D. G. and Ferguson, S. J. (2002) Bioenergetics 3 Academic Press, London.
3. Walker, J. E. (1992) The NADH-ubiquinone oxidoreductase (complex I) of respiratory chains. Q. Rev. Biophys. 25, 253-324.
4. Friedrich, T. (2001) Complex I: a chimera of a redox and conformation driven proton pump? J. Bioenerg. Biomembr. 33, 169-177.
5. Hirst, J., Carroll, J., Fearnley, I. M., Shannon, R. J., and Walker, J. E. (2003) The nuclear encoded subunits of complex I from bovine heart mitochondria. Biochim. Biophys. Acta 1604, 135-150.
6. Grigorieff, N. (1999) Structure of the respiratory NADH:ubiquinone oxidoreductase (complex I). Curr. Opin. Struct. Biol. 9, 476-483.
7. Grigorieff, N. (1998) Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 Å in ice. J. Mol. Biol. 277, 1033-1046.
8. Guénebaut, V., Schlitt, A., Weiss, H., Leonard, K., and Friedrich, T. (1998) Consistent structure between bacterial and mitochondrial NADH:ubiquinone oxidoreductase (complex I). J. Mol. Biol. 276, 105-112.
9. Chomyn, A., Mariottini, P., Cleeter, M. W. J., et al. (1985) Six unidentified reading frames of human mitochondrial DNA encode components of the respiratory chain NADH dehydrogenase. Nature 314, 592-597.
10. Pilkington, S. J. and Walker, J. E. (1988) Mitochondrial NADH-ubiquinone reductase: complementary DNA sequences of import precursors of the bovine and human 24 kDa subunit. Biochemistry 28, 3257-3264.
11. Runswick, M. J., Gennis, R. B., Fearnley, I. M., and Walker, J. E. (1989) Mitochondrial NADH:ubiquinone reductase: complementary DNA sequence of the import precursor of the bovine 75-kDa subunit. Biochemistry 28, 9452-9459.
12. Fearnley, I. M., Runswick, M. J., and Walker, J. E. (1989) A homologue of the nuclear encoded 49 kD subunit of bovine mitochondrial NADH-ubiquinone reductase is coded in chloroplast DNA. EMBO J. 8, 665-672.
13. Pilkington, S. J., Skehel, J. M., Gennis, R. B., and Walker, J. E. (1991) Relationship between mitochondrial NADH-ubiquinone reductase and a bacterial NAD-reducing hydrogenase. Biochemistry 30, 2166-2175.
14. Fearnley, I. M., Finel, M., Skehel, J. M., and Walker, J. E. (1991) NADH-ubiquinone reductase from bovine heart mitochondria: cDNA sequences of the import precursors of the 39 kDa and 42 kDa subunits. Biochem. J. 278, 821-829.
15. Dupuis, A., Skehel, J. M., and Walker, J. E. (1991) A homologue of nuclearcoded iron-sulfur protein subunit of bovine mitochondrial complex I is encoded in chloroplast genomes. Biochemistry 30, 2954-2960.
16. Arizmendi, J. M., Runswick, M. J., Skehel, J. M., and Walker, J. E. (1992) NADH: ubiquinone oxidoreductase from bovine heart mitochondria. A fourth nuclear encoded subunit with a homologue encoded in chloroplast genomes. FEBS Lett. 301, 237-242.
17. Walker, J. E., Arizmendi, J. M., Dupuis, A., et al. (1992) Sequences of twenty subunits of NADH: ubiquinone oxidoreductase from bovine heart mitochondria: application of a novel strategy for sequencing proteins using the polymerase chain reaction, J. Mol. Biol. 226, 1051-1072.
18. Arizmendi, J. M., Skehel, J. M., Runswick, M. J., Fearnley, I. M., and Walker, J. E. (1992) Complementary DNA sequences of two 14.5 kDa subunits of NADH: ubiquinone oxidoreductase from bovine heart mitochondria. Completion of the primary structure of the complex? FEBS Lett. 313, 80-84.
19. Skehel, J. M., Fearnley, I. M., and Walker, J. E. (1998) NADH:ubiquinone oxidoreductase from bovine heart mitochondria: sequence of a novel 17.2 kDa subunit. FEBS Lett. 438, 301-305.
20. Murray, J., Zhang, B., Taylor, S. W., et al. (2003) The subunit composition of the human NADH dehydrogenase obtained by a rapid one step immunopurification. J. Biol. Chem. 278, 13,619-13,622.
21. Schilling, B., Bharath, M. M. S., Row, R. H., et al. (2005) Rapid purification and mass spectrometric characterization of mitochondrial NADH dehydrogenase (complex I) from rodent brain and a dopaminergic neuronal cell line. Mol. Cell. Proteomics 4, 84-96.
22. Finel, M., Skehel, J. M., Albracht, S. P. J., Fearnley, I. M., and Walker, J. E. (1992) Resolution of NADH-ubiquinone oxidoreductase from bovine heart mitochondria into two subcomplexes, one of which contains the redox centres of the enzyme. Biochemistry 31, 11,425-11,434.
23. Finel, M., Majander, A. S., Tyynelä, J., De Jong, A. M. P., Albracht, S. P. J., and Wikström, M. (1994) Isolation and characterisation of subcomplexes of the mitochondrial NADH:ubiquinone oxidoreductase (complex I). Eur. J. Biochem. 226, 237-242.
24. Carroll, J., Fearnley, I. M., Shannon, R. J., Hirst, J., and Walker, J. E. (2003) Analysis of the subunit composition of complex I from bovine heart mitochondria. Mol. Cell. Proteomics 1, 117-126.
25. Fearnley, I. M., Carroll, J., Shannon, R. J., Runswick, M. J., Walker, J. E., and Hirst, J. (2001) GRIM-19, a cell death regulatory gene product, is a subunit of bovine mitochondrial NADH:ubiquinone oxidoreductase (complex I). J. Biol. Chem. 276, 38,345-38,348.
26. Carroll, J., Shannon, R. J., Fearnley, I. M., Walker, J. E., and Hirst, J. (2002) Definition of the nuclear encoded protein composition of bovine heart mitochondrial complex I: identification of two new subunits. J. Biol. Chem. 277, 50,311-50,317.
27. Chen, R., Fearnley, I. M., Peak-Chew, S. Y., and Walker, J. E. (2004) The phosphorylation of subunits of complex I in bovine mitochondria. J. Biol. Chem. 279, 26,036-26,045.
28. Carroll, J., Fearnley, I. M., Skehel, J. M., et al. (2005) The post-translational modifications of the nuclear encoded subunits of complex I from bovine heart mitochondria. Mol. Cell. Proteomics 4, 693-699.
29. Sazanov, L. A., Peak-Chew, S. Y., Fearnley, I. M., and Walker, J. E. (2000) Resolution of the membrane domain of bovine complex I into subcomplexes: implications for the structural organization of the enzyme. Biochemistry 39, 7229-7235.
30. Neuhoff, V., Stamm, R., and Eibl, H. (1985) Clear background and highly sensitive protein staining with Coomassie Blue dyes in Polyacrylamide gels: a systematic analysis. Electrophoresis 6, 427-448.
31. Wessel, D. and Flugge, U. I. (1984) A method for the quantitative recovery of protein in dilute solution in the presence of detergents and lipids. Anal. Biochem. 138, 141-143.
32. Simpson, R. J. (2003) Proteins and Proteomics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, pp. 206-207.
33. Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227, 680-685.
34. Görg, A., Postel, W., and Günther, S. (1988) The current state of two-dimensional electrophoresis with immobilised pH gradients. Electrophoresis 9, 531-546.
35. Chevallet, M., Santoni, V., Poinas, A., et al. (1998) New zwitterionic detergents improve the analysis of membrane proteins by two-dimensional electrophoresis. Electrophoresis 19, 1901-1909.
36. Schägger, H. and von Jagow, G. (1987) Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa. Anal. Biochem. 166, 368-379.
37. Fearnley, I. M., Skehel, J. M., and Walker, J. E. (1994) Electrospray mass spectrometric analysis of subunits of NADH:ubiquinone oxidoreductase (complex I) from bovine heart mitochondria. Biochem. Soc. Trans. 22, 551-555.
38. Shevchenko, A., Wilm, M., Vorm, O., and Mann, M. (1996) Mass spectrometric sequencing of proteins from silver-stained polyacrylamide gels. Anal. Chem. 68, 850-858.
39. Perkins, D. N., Pappin, D. J., Creasy, D. M., and Cottrell, J. S. (1999) Probability-based protein identification by searching sequence databases using mass spectrometry data. Electrophoresis 20, 3551-3567.
40. Mann, M. and Wilm, M. (1994) Error tolerant identification of peptides in sequence databases by peptide sequence tags. Anal. Chem. 66, 4390-4399.
41. Santoni, V., Kieffer, S., Desclaux, D., Masson, F., and Rabilloud, T. (2000) Membrane proteomics: use of additive main effects with multiplicative interaction model to classify plasma membrane proteins according to their solubility and electrophoretic properties. Electrophoresis 21, 3329-3344.
42. Santoni, V., Molloy, M., and Rabilloud, T. (2000) Membrane proteins and proteomics: un amour impossible? Electrophoresis 21, 105-107.
43. Gygi, S. P., Corthals, G. L., Zhang, Y., Rochon, Y., and Aebersold, R. (2000) Evaluation of two-dimensional gel electrophoresis-based proteome analysis technology. Proc. Natl. Acad. Sci. USA 97, 9390-9395.
44. Wilm, M., Shevchenko, A., Houthaeve, T., et al. (1996) Femtomole sequencing of proteins from Polyacrylamide gels by nano-electrospray mass spectrometry. Nature 379, 466-469.