Biophysics and bioinformatics reveal structural differences of the two peripheral stalk subunits in chloroplast ATP synthase

Journal of Biochemistry

Volumn 141, Issue 3, 2007, Pages 411-420

  Poetsch, Ansgar ^a   Berzborn, Richard J ^a   Heberle, Joachim ^b,e   Link, Thomas A ^c   Dencher, Norbert A ^d   Seelert, Holger ^d  

^a RUHR UNIVERSITY BOCHUM   (Germany)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

^c GOETHE UNIVERSITY   (Germany)

^d DARMSTADT UNIVERSITY OF TECHNOLOGY   (Germany)

^e BIELEFELD UNIVERSITY   (Germany)

Author keywords

Bioinformatics; CD spectroscopy; Dimerization; F0F1; FTIR

Indexed keywords

HOMODIMER; PROTON; PROTON TRANSPORTING ADENOSINE TRIPHOSPHATE SYNTHASE;

ALPHA HELIX; ARTICLE; BIOINFORMATICS; CATALYSIS; CHLOROPLAST; CIRCULAR DICHROISM; CONTROLLED STUDY; CYANOBACTERIUM; DIMERIZATION; ENZYME PURIFICATION; ENZYME STRUCTURE; ENZYME SUBUNIT; HYDROPHILICITY; INFRARED SPECTROSCOPY; NONHUMAN; PHOTOSYNTHESIS; PLANT STEM; PREDICTION; PROTEIN DOMAIN; PROTEIN EXPRESSION; SPINACH;

AMINO ACID SEQUENCE; BIOPHYSICS; CHLOROPLAST PROTON-TRANSLOCATING ATPASES; COMPUTATIONAL BIOLOGY; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS; SEQUENCE ALIGNMENT; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; SPINACIA OLERACEA;

BACTERIA (MICROORGANISMS); CYANOBACTERIA; SPINACIA OLERACEA;

EID: 34248676587     PISSN: 0021924X     EISSN: None     Source Type: Journal    
DOI: 10.1093/jb/mvm045     Document Type: Article

References (54)

1. 1. J. Mol. Biol. 281, 757-762
2. Stock, D., Leslie, A.G., and Walker, J.E. (1999) Molecular architecture of the rotary motor in ATP synthase. Science 286, 1700-1705
3. +-ATPase from Ilyobacter tartaricus. Science 308, 659-662
4. +-ATPase from Enterococcus hirae. Science 308, 654-659
5. Seelert, H., Poetsch, A., Dencher, N.A., Engel, A., Stahlberg, H., and Müller, D.J. (2000) Structural biology. Proton-powered turbine of a plant motor. Nature 405, 418-419
6. +-ATP synthase has an undecameric rotor. EMBO Rep. 2, 229-233
7. Rastogi, V.K. and Girvin, M.E. (1999) Structural changes linked to proton translocation by subunit c of the ATP synthase. Nature 402, 263-268
8. 1 J Mol. Biol. 295, 387-391
9. 1 as a dimer and through the δ subunit. J. Biol. Chem. 272, 31058-31064
10. 0-ATPase. J. Biol. Chem. 272, 21233-21239
11. Hong, S. and Pedersen, P.L. (2003) ATP synthases: insights into their motor functions from sequence and structural analyses. J. Bioenerg. Biomembr. 35, 95-120
12. Del Rizzo, P.A., Bi, Y., Dunn, S.D., and Shilton, B.H. (2002) The "second stalk" of Escherichia coli ATP synthase: structure of the isolated dimerization domain. Biochemistry 41, 6875-6884
13. Dunn, S.D., Revington, M., Cipriano, D.J., and Shilton, B.H. (2000) The b subunit of Escherichia coli ATP synthase. J. Bioenerg. Biomembr. 32, 347-355
14. Dickson, V.K., Silvester, J.A., Fearnley, I.M., Leslie, A.G., and Walker, J.E. (2006) On the structure of the stator of the mitochondrial ATP synthase. EMBO J. 25, 2911-2918
15. Dunn, S.D., Kellner, E., and Lill, H. (2001) Specific heterodimer formation by the cytoplasmic domains of the b and b′ subunits of cyanobacterial ATP synthase. Biochemistry 40, 187-192
16. 0-II from spinach is a real, ninth subunit of chloroplast ATP synthase. FEBS Lett. 326, 192-198
17. 0 subunits. Z. Naturforsch. [C] 52, 789-798
18. 1 ATP synthase. J. Biol. Chem. 274, 15598-15604
19. 1 sector. J. Biol. Chem. 267, 7630-7636
20. 1 via an α-subunit in the Escherichia coli ATP synthase. J. Biol. Chem. 273, 29406-29410
21. 0-ATP synthase. J. Biol. Chem. 279, 11253-11258
22. 0-ATP synthase in Escherichia coli. J. Biol. Chem. 273, 27873-27878
23. 0 ATP synthase in Escherichia coli. J. Biol. Chem. 274, 36261-36266
24. 0-ATP synthase. J. Biol. Chem. 278, 34751-34756
25. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402
26. Lupas, A., Van Dyke, M., and Stock, J. (1991) Predicting coiled coils from protein sequences. Science 252, 1162-1164
27. Berger, B., Wilson, D.B., Wolf, E., Tonchev, T., Milla, M., and Kim, P.S. (1995) Predicting coiled coils by use of pairwise residue correlations. Proc. Natl. Acad. Sci. U.S.A. 92, 8259-8263
28. Delorenzi, M. and Speed, T. (2002) An HMM model for coiled-coil domains and a comparison with PSSM-based predictions. Bioinformatics 18, 617-625
29. Rost, B. and Sander, C. (1994) Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19, 55-72
30. Karplus, K., Karchin, R., Draper, J., Casper, J., Mandel-Gutfreund, Y., Diekhans, M., and Hughey, R. (2003) Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction. Proteins 53(Suppl 6), 491-196
31. Baldi, P., Brunak, S., Frasconi, P., Soda, G., and Pollastri, G. (1999) Exploiting the past and the future in protein secondary structure prediction. Bioinformatics 15, 937-946
32. Jones, D.T. (1999) Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292, 195-202
33. Fromme, P., Boekema, E.J., and Gräber, P. (1987) Isolation and characterization of a supramolecular complex of subunit III of the ATP synthase from chloroplasts. Z. Naturforsch. [C] 42c, 1239-1245
34. Pick, U. and Racker, E. (1979) Purification and reconstitution of the N,N′-dicyclohexylcarbodiimide-sensitive ATPase complex from spinach chloroplasts. J. Biol. Chem. 254, 2793-2799
35. +-ATP synthase. Biochem. Biophys. Res. Commun. 265, 520-524
36. Oakley, B.R., Kirsch, D.R., and Morris, N.R. (1980) A simplified ultrasensitive silver stain for detecting proteins in polyacrylamide gels. Anal. Biochem. 105, 361-363
37. Poduslo, J.F. (1981) Glycoprotein molecular-weight estimation using sodium dodecyl sulfate-pore gradient electrophoresis: comparison of tris-glycine and tris-borate-EDTA buffer systems. Anal. Biochem. 114, 131-139
38. Kyhse-Andersen, J. (1984) Electroblotting of multiple gels: a simple apparatus without buffer tank for rapid transfer of proteins from polyacrylamide to nitrocellulose. J. Biochem. Biophys. Methods 10, 203-209
39. Böhm, G., Muhr, R., and Jaenicke, R. (1992) Quantitative analysis of protein far UV circular dichroism spectra by neural networks. Protein Eng. 5, 191-195
40. Poetsch, A., Rexroth, S., Heberle, J., Link, T.A., Dencher, N.A., and Seelert, H. (2003) Characterisation of subunit III and its oligomer from spinach chloroplast ATP synthase. Biochim. Biophys. Acta 1618, 59-66
41. McLachlin, D.T., Bestard, J.A., and Dunn, S.D. (1998) The b and delta subunits of the Escherichia coli ATP synthase interact via residues in their C-terminal regions. J. Biol. Chem. 273, 15162-15168
42. +-translocating ATPase of chloroplasts. Biochim. Biophys. Acta 1101, 97-104
43. Dunn, S.D., McLachlin, D.T., and Revington, M. (2000) The second stalk of Escherichia coli ATP synthase. Biochim. Biophys. Acta 1458, 356-363
44. 0-ATPase. J. Biol. Chem. 274, 31094-31101
45. 0 subunit IV in proton conduction. J. Biol. Chem. 265, 12474-12480
46. 0 polypeptides. J. Biol. Chem. 265, 12481-12485
47. Tiburzy, H.J., Zimmermann, M., Oworah-Nkruma, R., and Berzborn, R.J. (1999) Z Naturforsch [C] Vol. 54, pp. 230-238
48. Greie, J.C., Deckers-Hebestreit, G., and Altendorf, K. (2000) Secondary structure composition of reconstituted subunit b of the Escherichia coli ATP synthase. Eur. J. Biochem. 267, 3040-3048
49. 0 ATP synthase. Protein Sci. 11, 1227-1238
50. 0 ATP synthase. J. Biol. Chem. 279, 31205-31211
51. +-ATPase. Acta Physiol. Scand. Suppl. 607, 275-278
52. 1-ATPase in a mutant strain of Escherichia coli K12. Biochim. Biophys. Acta 1015, 195-199
53. Lill, H., Steinemann, D., and Nelson, N. (1994) Mutagenesis of the b′-subunit of Synechocystis sp. PCC 6803 ATP-synthase. Biochim. Biophys. Acta 1184, 284-290
54. Berzborn, R.J. (2000) Probing Photosynthesis (Yunus, M., Pathre, U., and Mohanty, P. eds) pp. 70-107 TAYLOR and Francis, London, New York