The transmembrane helices of the L, M, and N subunits of Complex i from E. coli can be assigned on the basis of conservation and hydrophobic moment analysis

FEBS Letters

Volumn 585, Issue 8, 2011, Pages 1180-1184

  Vik, Steven B ^a  

^a SOUTHERN METHODIST UNIVERSITY   (United States)

Author keywords

Complex I; Conservation; Discontinuous helix; Hydrophobic moment; Hydrophobicity; Transmembrane helix

Indexed keywords

REDUCED NICOTINAMIDE ADENINE DINUCLEOTIDE DEHYDROGENASE (UBIQUINONE);

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME SUBUNIT; ESCHERICHIA COLI; GENETIC CONSERVATION; HYDROPHOBICITY; LIPID MEMBRANE; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN INTERACTION; PROTEIN LOCALIZATION; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ELECTRON TRANSPORT COMPLEX I; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENETIC VARIATION; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MEMBRANE PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEIN SUBUNITS;

ESCHERICHIA COLI;

EID: 79954435633     PISSN: 00145793     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.febslet.2011.03.029     Document Type: Article

References (31)

1. U. Brandt Energy converting NADH:quinone oxidoreductase (Complex I) Annu. Rev. Biochem. 75 2006 69 92 (Pubitemid 44118026)
2. L.A. Sazanov, and P. Hinchliffe Structure of the hydrophilic domain of respiratory Complex I from Thermus thermophilus Science 311 2006 1430 1436 (Pubitemid 43376691)
3. R.G. Efremov, R. Baradaran, and L.A. Sazanov The architecture of respiratory Complex I Nature 465 2010 441 445
4. C. Hunte, V. Zickermann, and U. Brandt Functional modules and structural basis of conformational coupling in mitochondrial Complex I Science 329 2010 448 451
5. T. Friedrich The NADH:ubiquinone oxidoreductase (complex I) from Escherichia coli Biochim. Biophys. Acta 1364 1998 134 146 (Pubitemid 28291836)
6. L.A. Sazanov Respiratory Complex I: Mechanistic and structural insights provided by the crystal structure of the hydrophilic domain Biochemistry 46 2007 2275 2288 (Pubitemid 46362402)
7. T. Swartz, S. Ikewada, O. Ishikawa, M. Ito, and T. Krulwich The Mrp system: a giant among monovalent cation/proton antiporters? Extremophiles 9 2005 345 354 (Pubitemid 41428347)
8. P.J. Holt, D.J. Morgan, and L.A. Sazanov The location of NuoL and NuoM subunits in the membrane domain of the Escherichia coli complex I: implications for the mechanism of proton pumping J. Biol. Chem. 278 2003 43114 43120 (Pubitemid 37345929)
9. T. Ohnishi, E. Nakamaru-Ogiso, and S.T. Ohnishi A new hypothesis on the simultaneous direct and indirect proton pump mechanisms in NADH-quinone oxidoreductase (complex I) FEBS Lett. 584 2010 4131 4137
10. D.C. Rees, H. Komiya, T.O. Yeates, J.P. Allen, and G. Feher The bacterial photosynthetic reaction center as a model for membrane proteins Annu. Rev. Biochem. 58 1989 607 633 (Pubitemid 19172982)
11. D. Eisenberg, E. Schwarz, M. Komaromy, and R. Wall Analysis of membrane and surface protein sequences with the hydrophobic moment plot J. Mol. Biol. 179 1984 125 142 (Pubitemid 16223392)
12. D. Eisenberg, R.M. Weiss, and T.C. Terwilliger The hydrophobic moment detects periodicity in protein hydrophobicity Proc. Natl. Acad. Sci. USA 81 1984 140 144 (Pubitemid 14180843)
13. o ATP synthase using variational and hydrophobic moment analyses Biochim. Biophys. Acta 1140 1992 199 207
14. T. Beuming, and H. Weinstein A knowledge-based scale for the analysis and prediction of buried and exposed faces of transmembrane domain proteins Bioinformatics 20 2004 1822 1835 (Pubitemid 39199046)
15. J. Pei, and N.V. Grishin AL2CO: calculation of positional conservation in a protein sequence alignment Bioinformatics 17 2001 700 712 (Pubitemid 32851378)
16. G. von Heijne Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule J. Mol. Biol. 225 1992 487 494
17. D.M. Engelman, T.A. Steitz, and A. Goldman Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins Annu. Rev. Biophys. Biophys. Chem. 15 1986 321 353
18. D.G. Higgins, A.J. Bleasby, and R. Fuchs CLUSTAL V: improved software for multiple sequence alignment Comput. Appl. Biosci. 8 1992 189 191
19. E. Screpanti, and C. Hunte Discontinuous membrane helices in transport proteins and their correlation with function J. Struct. Biol. 159 2007 261 267 (Pubitemid 47095395)
20. J. Vonck, T.K. von Nidda, T. Meier, U. Matthey, D.J. Mills, W. Kuhlbrandt, and P. Dimroth Molecular architecture of the undecameric rotor of a bacterial Na+-ATP synthase J. Mol. Biol. 321 2002 307 316
21. J. Liu, M. Fujisawa, D.B. Hicks, and T.A. Krulwich Characterization of the functionally critical AXAXAXA and PXXEXXP Motifs of the ATP synthase c-Subunit from an Alkaliphilic Bacillus J. Biol. Chem. 284 2009 8714 8725
22. P. Nollert, W.E.C. Harries, D. Fu, L.J.W. Miercke, and R.M. Stroud Atomic structure of a glycerol channel and implications for substrate permeation in aqua(glycero)porins FEBS Lett. 504 2001 112 117 (Pubitemid 32787058)
23. J.A. Birrell, and J. Hirst Truncation of subunit ND2 disrupts the threefold symmetry of the antiporter-like subunits in complex I from higher metazoans FEBS Lett. 584 2010 4247 4252
24. C. Mathiesen, and C. Hägerhäll Transmembrane topology of the NuoL, M and N subunits of NADH:quinone oxidoreductase and their homologues among membrane-bound hydrogenases and bona fide antiporters Biochim. Biophys. Acta 1556 2002 121 132 (Pubitemid 35379670)
25. J. Torres-Bacete, P.K. Sinha, N. Castro-Guerrero, A. Matsuno-Yagi, and T. Yagi Features of subunit NuoM (ND4) in Escherichia coli NDH-1: Topology and implication of conserved Glu144 for coupling site 1 J. Biol. Chem. 284 2009 33062 33069
26. B. Amarneh, and S.B. Vik Transmembrane topology of subunit N of complex I (NADH:ubiquinone oxidoreductase) from Escherichia coli J. Bioenerg. Biomembr. 42 2010 511 516
27. B. Amarneh, and S.B. Vik Mutagenesis of subunit N of the Escherichia coli Complex I. Identification of the initiation codon and the sensitivity of mutants to decylubiquinone Biochemistry 42 2003 4800 4808 (Pubitemid 36532031)
28. J. Torres-Bacete, E. Nakamaru-Ogiso, A. Matsuno-Yagi, and T. Yagi Characterization of the nuoM (ND4) subunit in Escherichia coli NDH-1: conserved charged residues essential for energy-coupled activities J. Biol. Chem. 282 2007 36914 36922
29. L. Euro, G. Belevich, M.I. Verkhovsky, M. Wikström, and M. Verkhovskaya Conserved lysine residues of the membrane subunit NuoM are involved in energy conversion by the proton-pumping NADH:ubiquinone oxidoreductase (Complex I) Biochim. Biophys. Acta 1777 2008 1166 1172
30. E. Nakamaru-Ogiso, M.C. Kao, H. Chen, S.C. Sinha, T. Yagi, and T. Ohnishi The membrane subunit NuoL(ND5) is involved in the indirect proton pumping mechanism of E. coli complex I J. Biol. Chem. 285 2010 39070 39078
31. J. Michel, J. DeLeon-Rangel, S. Zhu, K. Van Ree, and S.B. Vik Mutagenesis of the L, M, and N subunits of Complex I from Escherichia coli indicates a common role in function PLoS ONE 6 2011 e17420