메뉴 건너뛰기




Volumn 65, Issue 5, 2007, Pages 485-495

Coevolutionary patterns in cytochrome c oxidase subunit I depend on structural and functional context

Author keywords

Coevolution; Cytochrome c oxidase; Markov chain; Proton pump channels; Residue interaction

Indexed keywords

CYTOCHROME C OXIDASE; PROTON PUMP;

EID: 36148966864     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-007-9018-8     Document Type: Article
Times cited : (22)

References (52)
  • 1
    • 0020484234 scopus 로고
    • Structural prediction of membrane-bound proteins
    • Argos P, Rao JK, Hargrave PA (1982) Structural prediction of membrane-bound proteins. Eur J Biochem 128:565-575
    • (1982) Eur J Biochem , vol.128 , pp. 565-575
    • Argos, P.1    Rao, J.K.2    Hargrave, P.A.3
  • 2
    • 0033977832 scopus 로고    scopus 로고
    • Correlation among amino acid sites in bHLH protein domains: An information theoretic analysis
    • Atchley WR, Wollenberg KR, Fitch WM, Terhalle W, Dress AW (2000) Correlation among amino acid sites in bHLH protein domains: An information theoretic analysis. Mol Biol Evol 17:164-178
    • (2000) Mol Biol Evol , vol.17 , pp. 164-178
    • Atchley, W.R.1    Wollenberg, K.R.2    Fitch, W.M.3    Terhalle, W.4    Dress, A.W.5
  • 4
    • 0031566950 scopus 로고    scopus 로고
    • Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation
    • Bahar I, Jernigan RL (1997) Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation. J Mol Biol 266:195-214
    • (1997) J Mol Biol , vol.266 , pp. 195-214
    • Bahar, I.1    Jernigan, R.L.2
  • 5
    • 27544473473 scopus 로고    scopus 로고
    • Quantitative trait loci analysis using the false discovery rate
    • Benjamini Y, Yekutieli D (2005) Quantitative trait loci analysis using the false discovery rate. Genetics 171:783-790
    • (2005) Genetics , vol.171 , pp. 783-790
    • Benjamini, Y.1    Yekutieli, D.2
  • 9
    • 0037013278 scopus 로고    scopus 로고
    • The effects of modifying the surface charge on the catalytic activity of a thermolysinlike protease
    • de Kreij A, van den Burg B, Venema G, Vriend G, Eijsink VGH, Nielsen JE (2002) The effects of modifying the surface charge on the catalytic activity of a thermolysinlike protease. J Biol Chem 277:15432-15438
    • (2002) J Biol Chem , vol.277 , pp. 15432-15438
    • De Kreij, A.1    Van Den Burg, B.2    Venema, G.3    Vriend, G.4    Eijsink, V.G.H.5    Nielsen, J.E.6
  • 12
    • 23944476399 scopus 로고    scopus 로고
    • A model-based approach for detecting coevolving positions in a molecule
    • Dutheil J, Pupko T, Jean-Marie A, Galtier N (2005) A model-based approach for detecting coevolving positions in a molecule. Mol Biol Evol 22:1919-1928
    • (2005) Mol Biol Evol , vol.22 , pp. 1919-1928
    • Dutheil, J.1    Pupko, T.2    Jean-Marie, A.3    Galtier, N.4
  • 13
    • 0242318326 scopus 로고    scopus 로고
    • Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes
    • Faith JJ, Pollock DD (2003) Likelihood analysis of asymmetrical mutation bias gradients in vertebrate mitochondrial genomes. Genetics 165:735-745
    • (2003) Genetics , vol.165 , pp. 735-745
    • Faith, J.J.1    Pollock, D.D.2
  • 14
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J (1981) Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17:368-376
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 15
    • 0000122573 scopus 로고
    • Phylogeny inference package
    • Felsenstein J (1989) Phylogeny inference package. Cladistics 5:164-166
    • (1989) Cladistics , vol.5 , pp. 164-166
    • Felsenstein, J.1
  • 16
    • 2942580743 scopus 로고    scopus 로고
    • An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels
    • Fleishman SJ, Yifrach O, Ben-Tal N (2004) An evolutionarily conserved network of amino acids mediates gating in voltage-dependent potassium channels. J Mol Biol 340:307-318
    • (2004) J Mol Biol , vol.340 , pp. 307-318
    • Fleishman, S.J.1    Yifrach, O.2    Ben-Tal, N.3
  • 17
    • 0036301488 scopus 로고    scopus 로고
    • Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences
    • Fukami-Kobayashi K, Schreiber DR, Benner SA (2002) Detecting compensatory covariation signals in protein evolution using reconstructed ancestral sequences. J Mol Biol 319:729-743
    • (2002) J Mol Biol , vol.319 , pp. 729-743
    • Fukami-Kobayashi, K.1    Schreiber, D.R.2    Benner, S.A.3
  • 18
    • 0032510965 scopus 로고    scopus 로고
    • Protein structure: Cytochrome c oxidase: One enzyme, two mechanisms?
    • Gennis RB (1998) Protein structure: cytochrome c oxidase: one enzyme, two mechanisms? Science 280:1712-1713
    • (1998) Science , vol.280 , pp. 1712-1713
    • Gennis, R.B.1
  • 19
    • 0037449144 scopus 로고    scopus 로고
    • Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation
    • Govindarajan S, Ness JE, Kim S, Mundorff EC, Minshull J, Gustafsson C (2003) Systematic variation of amino acid substitutions for stringent assessment of pairwise covariation. J Mol Biol 328:1061-1069
    • (2003) J Mol Biol , vol.328 , pp. 1061-1069
    • Govindarajan, S.1    Ness, J.E.2    Kim, S.3    Mundorff, E.C.4    Minshull, J.5    Gustafsson, C.6
  • 20
    • 0016197604 scopus 로고
    • Amino acid difference formula to help explain protein evolution
    • Grantham R (1974) Amino acid difference formula to help explain protein evolution. Science 185:862-864
    • (1974) Science , vol.185 , pp. 862-864
    • Grantham, R.1
  • 21
    • 0035913416 scopus 로고    scopus 로고
    • Role of medium and long-range interactions in discriminating globular and membrane proteins
    • Gromiha MM, Selvaraj S (2001) Role of medium and long-range interactions in discriminating globular and membrane proteins. Int J Biol Macromol 29:25-34
    • (2001) Int J Biol Macromol , vol.29 , pp. 25-34
    • Gromiha, M.M.1    Selvaraj, S.2
  • 22
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov Chains and their applications
    • Hastings WK (1970) Monte Carlo sampling methods using Markov Chains and their applications. Biometrika 57:97-109
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 23
    • 0028133496 scopus 로고
    • Converting trypsin to chymotrypsin-residue-172 is a substrate-specificity determinant
    • Hedstrom L, Perona JJ, Rutter WJ (1994) Converting trypsin to chymotrypsin-residue-172 is a substrate-specificity determinant. Biochemistry (Mosc) 33:8757-8763
    • (1994) Biochemistry (Mosc) , vol.33 , pp. 8757-8763
    • Hedstrom, L.1    Perona, J.J.2    Rutter, W.J.3
  • 24
    • 0028890031 scopus 로고
    • Structure at 2.8?resolution of cytochrome c oxidase from Paracoccus denitrificans
    • Iwata S, Ostermeier C, Ludwig B, Michel H (1995) Structure at 2.8?resolution of cytochrome c oxidase from Paracoccus denitrificans. Nature 376:660-669
    • (1995) Nature , vol.376 , pp. 660-669
    • Iwata, S.1    Ostermeier, C.2    Ludwig, B.3    Michel, H.4
  • 25
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282
    • (1992) Comput Appl Biosci , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 28
    • 0018800255 scopus 로고
    • Local interactions as a structure determinant fro protein molecules: II
    • Krigbaum WR, Komoriya A (1979) Local interactions as a structure determinant fro protein molecules: II. Biochim Biophys Acta 576:204-248
    • (1979) Biochim Biophys Acta , vol.576 , pp. 204-248
    • Krigbaum, W.R.1    Komoriya, A.2
  • 29
    • 2542483466 scopus 로고    scopus 로고
    • Structural elements involved in electron-coupled proton transfer in cytochrome c oxidase
    • Namslauer A, Brzezinski P (2004) Structural elements involved in electron-coupled proton transfer in cytochrome c oxidase. FEBS Lett 567:103-110
    • (2004) FEBS Lett , vol.567 , pp. 103-110
    • Namslauer, A.1    Brzezinski, P.2
  • 31
    • 0028125904 scopus 로고
    • How frequent are correlated changes in families of protein sequences?
    • Neher E (1994) How frequent are correlated changes in families of protein sequences? Proc Natl Acad Sci USA 91:98-102
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 98-102
    • Neher, E.1
  • 32
    • 1942472174 scopus 로고    scopus 로고
    • A cooperative model for proton pumping in cytochrome c oxidase
    • Papa S, Capitanio N, Capitanio G (2004) A cooperative model for proton pumping in cytochrome c oxidase. Biochim Biophys Acta Bioenerg 1655:353-364
    • (2004) Biochim Biophys Acta Bioenerg , vol.1655 , pp. 353-364
    • Papa, S.1    Capitanio, N.2    Capitanio, G.3
  • 33
    • 1942504686 scopus 로고    scopus 로고
    • Proton pathways, ligand binding and dynamics of the catalytic site in haem-copper oxygen reductases: A comparison between the three families
    • Pereira MM, Teixeira M (2004) Proton pathways, ligand binding and dynamics of the catalytic site in haem-copper oxygen reductases: a comparison between the three families. Biochim Biophys Acta Bioenerg 1655:340-346
    • (2004) Biochim Biophys Acta Bioenerg , vol.1655 , pp. 340-346
    • Pereira, M.M.1    Teixeira, M.2
  • 35
    • 0030743758 scopus 로고    scopus 로고
    • Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
    • Pollock DD, Taylor WR (1997) Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution. Protein Eng 10:647-657
    • (1997) Protein Eng , vol.10 , pp. 647-657
    • Pollock, D.D.1    Taylor, W.R.2
  • 36
    • 0033582946 scopus 로고    scopus 로고
    • Coevolving protein residues: Maximum likelihood identification and relationship to structure
    • Pollock DD, Taylor WR, Goldman N (1999) Coevolving protein residues: maximum likelihood identification and relationship to structure. J Mol Biol 287:187-198
    • (1999) J Mol Biol , vol.287 , pp. 187-198
    • Pollock, D.D.1    Taylor, W.R.2    Goldman, N.3
  • 37
    • 0034794239 scopus 로고    scopus 로고
    • Evaluation of a novel method for the identification of coevolving protein residues
    • Pritchard L, Bladon P, Mitchell JMO, Dufton MJ (2001) Evaluation of a novel method for the identification of coevolving protein residues. Protein Eng 14:459-555
    • (2001) Protein Eng , vol.14 , pp. 459-555
    • Pritchard, L.1    Bladon, P.2    Mitchell, J.M.O.3    Dufton, M.J.4
  • 38
    • 0023646665 scopus 로고
    • Rational modification of enzyme catalysis by engineering surface-charge
    • Russell AJ, Fersht AR (1987) Rational modification of enzyme catalysis by engineering surface-charge. Nature 328:496-500
    • (1987) Nature , vol.328 , pp. 496-500
    • Russell, A.J.1    Fersht, A.R.2
  • 39
    • 0042767572 scopus 로고    scopus 로고
    • Using multiple sequence correlation analysis to characterize functionally important protein regions
    • Saraf MC, Moore GL, Maranas CD (2003) Using multiple sequence correlation analysis to characterize functionally important protein regions. Protein Eng 16:397-406
    • (2003) Protein Eng , vol.16 , pp. 397-406
    • Saraf, M.C.1    Moore, G.L.2    Maranas, C.D.3
  • 40
    • 0028084754 scopus 로고
    • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    • Shindyalov I, Kolchanov N, Sander C (1994) Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng 7:349-358
    • (1994) Protein Eng , vol.7 , pp. 349-358
    • Shindyalov, I.1    Kolchanov, N.2    Sander, C.3
  • 41
    • 0036382724 scopus 로고    scopus 로고
    • The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides
    • Svensson-Ek M, Abramson J, Larsson G, Tornroth S, Brzezinski P, Iwata S (2002) The X-ray crystal structures of wild-type and EQ(I-286) mutant cytochrome c oxidases from Rhodobacter sphaeroides. J Mol Biol 321:329-339
    • (2002) J Mol Biol , vol.321 , pp. 329-339
    • Svensson-Ek, M.1    Abramson, J.2    Larsson, G.3    Tornroth, S.4    Brzezinski, P.5    Iwata, S.6
  • 42
    • 0027952860 scopus 로고
    • Compensating changes in protein multiple sequence alignments
    • Taylor W, Hatrick K (1994) Compensating changes in protein multiple sequence alignments. Protein Eng 7:341-348
    • (1994) Protein Eng , vol.7 , pp. 341-348
    • Taylor, W.1    Hatrick, K.2
  • 43
    • 0022386437 scopus 로고
    • Tailoring the Ph-dependence of enzyme catalysis using protein engineering
    • Thomas PG, Russell AJ, Fersht AR (1985) Tailoring the Ph-dependence of enzyme catalysis using protein engineering. Nature 318:375-376
    • (1985) Nature , vol.318 , pp. 375-376
    • Thomas, P.G.1    Russell, A.J.2    Fersht, A.R.3
  • 44
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J, Gibson T, Plewniak F, Jeanmougin F, Higgins D (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
    • (1997) Nucleic Acids Res , vol.25 , pp. 4876-4882
    • Thompson, J.1    Gibson, T.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.5
  • 45
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
    • Thompson J, Higgins D, Gibson T (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
    • (1994) Nucleic Acids Res , vol.22 , pp. 4673-4680
    • Thompson, J.1    Higgins, D.2    Gibson, T.3
  • 47
    • 0033744204 scopus 로고    scopus 로고
    • Exploring a phylogenetic approach for the detection of correlated substitutions in proteins
    • Tuffery P, Darlu P (2000) Exploring a phylogenetic approach for the detection of correlated substitutions in proteins. Mol Biol Evol 17:1753-1759
    • (2000) Mol Biol Evol , vol.17 , pp. 1753-1759
    • Tuffery, P.1    Darlu, P.2
  • 48
    • 0036601150 scopus 로고    scopus 로고
    • Computational methods for the prediction of protein interactions
    • Valencia A, Pazos F (2002) Computational methods for the prediction of protein interactions. Curr Opin Struct Biol 12:368-373
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 368-373
    • Valencia, A.1    Pazos, F.2
  • 49
    • 19944406094 scopus 로고    scopus 로고
    • Context dependence and coevolution among amino acid residues in proteins
    • Wang ZO, Pollock DD (2005) Context dependence and coevolution among amino acid residues in proteins. Methods Enzymol 395:779-790
    • (2005) Methods Enzymol , vol.395 , pp. 779-790
    • Wang, Z.O.1    Pollock, D.D.2
  • 50
    • 0034724418 scopus 로고    scopus 로고
    • Separation of phylogenetic and functional association in biological sequences by using the parametric bootstrap
    • Wollenberg KR, Atchley WR (2000) Separation of phylogenetic and functional association in biological sequences by using the parametric bootstrap. Proc Natl Acad Sci U S A 97:3288-3291
    • (2000) Proc Natl Acad Sci U S a , vol.97 , pp. 3288-3291
    • Wollenberg, K.R.1    Atchley, W.R.2
  • 51
    • 0242657395 scopus 로고    scopus 로고
    • A cytochrome c oxidase proton pumping mechanism that excludes the O2 reduction site
    • Yoshikawa S (2003) A cytochrome c oxidase proton pumping mechanism that excludes the O2 reduction site. FEBS Lett 555:8-12
    • (2003) FEBS Lett , vol.555 , pp. 8-12
    • Yoshikawa, S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.