메뉴 건너뛰기




Volumn 22, Issue 7, 2005, Pages 1627-1634

Networks of coevolving sites in structural and functional domains of serpin proteins

Author keywords

Coevolution; Covariation; Factor analysis; Mutual information; Protein structure; Serpin

Indexed keywords

SERINE PROTEINASE INHIBITOR;

EID: 20444426807     PISSN: 07374038     EISSN: None     Source Type: Journal    
DOI: 10.1093/molbev/msi157     Document Type: Article
Times cited : (31)

References (45)
  • 1
    • 0035182669 scopus 로고    scopus 로고
    • Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions
    • Afonnikov, D. A., D. Y. Oshchepkov, and N. A. Kolchanov. 2001. Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. Bioinformatics 17:1035-1046.
    • (2001) Bioinformatics , vol.17 , pp. 1035-1046
    • Afonnikov, D.A.1    Oshchepkov, D.Y.2    Kolchanov, N.A.3
  • 2
    • 16344379182 scopus 로고    scopus 로고
    • Covarion structure in plastid genome evolution: A new statistical test
    • Ane, C., J. G. Burleigh, M. M. McMahon, and M. J. Sanderson. 2005. Covarion structure in plastid genome evolution: a new statistical test. Mol. Biol. Evol. 22:914-924.
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 914-924
    • Ane, C.1    Burleigh, J.G.2    McMahon, M.M.3    Sanderson, M.J.4
  • 3
    • 0034897644 scopus 로고    scopus 로고
    • Phylogenetic analyses of amino acid variation in the serpin proteins
    • Atchley, W. R., T. Lokot, K. Wollenberg, A. Dress, and H. Ragg. 2001. Phylogenetic analyses of amino acid variation in the serpin proteins. Mol. Biol. Evol. 18:1502-1511.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 1502-1511
    • Atchley, W.R.1    Lokot, T.2    Wollenberg, K.3    Dress, A.4    Ragg, H.5
  • 4
    • 0032925848 scopus 로고    scopus 로고
    • Positional dependence, cliques, and predictive motifs in the bHLH protein domain
    • Atchley, W. R., W. Terhalle, and A. Dress. 1999. Positional dependence, cliques, and predictive motifs in the bHLH protein domain. J. Mol. Evol. 48:501-516.
    • (1999) J. Mol. Evol. , vol.48 , pp. 501-516
    • Atchley, W.R.1    Terhalle, W.2    Dress, A.3
  • 5
    • 0033977832 scopus 로고    scopus 로고
    • Correlations among amino acid sites in bHLH protein domains: An information theoretic analysis
    • Atchley, W. R., K. R. Wollenberg, W. M. Fitch, W. Terhalle, and A. W. Dress. 2000. Correlations 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
  • 7
    • 0142095053 scopus 로고    scopus 로고
    • Mutation of the highly conserved tryptophan in the serpin breach region alters the inhibitory mechanism of plasminogen activator inhibitor-1
    • Blouse, G. E., M. J. Perron, J. O. Kvassman, S. Yunus, J. H. Thompson, R. L. Betts, L. C. Lutter, and J. D. Shore. 2003. Mutation of the highly conserved tryptophan in the serpin breach region alters the inhibitory mechanism of plasminogen activator inhibitor-1. Biochemistry 42:12260-12272.
    • (2003) Biochemistry , vol.42 , pp. 12260-12272
    • Blouse, G.E.1    Perron, M.J.2    Kvassman, J.O.3    Yunus, S.4    Thompson, J.H.5    Betts, R.L.6    Lutter, L.C.7    Shore, J.D.8
  • 9
    • 0028832687 scopus 로고
    • Covariation of residues in the homeodomain sequence family
    • Clarke, N. D. 1995. Covariation of residues in the homeodomain sequence family. Protein Sci. 4:2269-2278.
    • (1995) Protein Sci. , vol.4 , pp. 2269-2278
    • Clarke, N.D.1
  • 10
    • 0033598346 scopus 로고    scopus 로고
    • Familial dementia caused by polymerization of mutant neuroserpin
    • Davis, R. L., A. E. Shrimpton, P. D. Holohan et al. (20 co-authors). 1999. Familial dementia caused by polymerization of mutant neuroserpin. Nature 401:376-379.
    • (1999) Nature , vol.401 , pp. 376-379
    • Davis, R.L.1    Shrimpton, A.E.2    Holohan, P.D.3
  • 11
    • 1542510099 scopus 로고    scopus 로고
    • Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting
    • Desper, R., and O. Gascuel. 2004. Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21:587-598.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 587-598
    • Desper, R.1    Gascuel, O.2
  • 12
    • 17744409446 scopus 로고    scopus 로고
    • Wild-type alpha 1-antitrypsin is in the canonical inhibitory conformation
    • Elliott, P. R., J. P. Abrahams, and D. A. Lomas. 1998. Wild-type alpha 1-antitrypsin is in the canonical inhibitory conformation. J. Mol. Biol. 275:419-425.
    • (1998) J. Mol. Biol. , vol.275 , pp. 419-425
    • Elliott, P.R.1    Abrahams, J.P.2    Lomas, D.A.3
  • 13
    • 0015162378 scopus 로고
    • Rate of change of concomitantly variable codons
    • Fitch, W. M. 1971. Rate of change of concomitantly variable codons. J. Mol. Evol. 1:84-96.
    • (1971) J. Mol. Evol. , vol.1 , pp. 84-96
    • Fitch, W.M.1
  • 14
    • 0014860857 scopus 로고
    • An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
    • Fitch, W. M., and E. Markowitz. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem. Genet. 4:579-593.
    • (1970) Biochem. Genet. , vol.4 , pp. 579-593
    • Fitch, W.M.1    Markowitz, E.2
  • 15
    • 0035895207 scopus 로고    scopus 로고
    • Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors
    • Gaucher, E. A., M. M. Miyamoto, and S. A. Benner. 2001. Function-structure analysis of proteins using covarion-based evolutionary approaches: elongation factors. Proc. Natl. Acad. Sci. USA 98:548-552.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 548-552
    • Gaucher, E.A.1    Miyamoto, M.M.2    Benner, S.A.3
  • 16
    • 0037125184 scopus 로고    scopus 로고
    • The F-helix of serpins plays an essential, active role in the proteinase inhibition mechanism
    • Gettins, P. G. 2002a. The F-helix of serpins plays an essential, active role in the proteinase inhibition mechanism. FEBS Lett. 523:2-6.
    • (2002) FEBS Lett. , vol.523 , pp. 2-6
    • Gettins, P.G.1
  • 17
    • 0036882395 scopus 로고    scopus 로고
    • Serpin structure, mechanism, and function
    • -. 2002b. Serpin structure, mechanism, and function. Chem. Rev. 102:4751-4804.
    • (2002) Chem. Rev. , vol.102 , pp. 4751-4804
  • 19
    • 0027182969 scopus 로고
    • Effects of mutations in the hinge region of serpins
    • Hopkins, P. C., R. W. Carrell, and S. R. Stone. 1993. Effects of mutations in the hinge region of serpins. Biochemistry 32:7650-7657.
    • (1993) Biochemistry , vol.32 , pp. 7650-7657
    • Hopkins, P.C.1    Carrell, R.W.2    Stone, S.R.3
  • 20
  • 21
    • 3042601821 scopus 로고    scopus 로고
    • Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies
    • Inagaki, Y., E. Susko, N. M. Fast, and A. J. Roger. 2004. Covarion shifts cause a long-branch attraction artifact that unites microsporidia and archaebacteria in EF-1alpha phylogenies. Mol. Biol. Evol. 21:1340-1349.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1340-1349
    • Inagaki, Y.1    Susko, E.2    Fast, N.M.3    Roger, A.J.4
  • 22
    • 1542496192 scopus 로고    scopus 로고
    • The 1.5 A crystal structure of a prokaryote serpin: Controlling conformational change in a heated environment
    • Irving, J. A., L. D. Cabrita, J. Rossjohn, R. N. Pike, S. P. Bottomley, and J. C. Whisstock. 2003. The 1.5 A crystal structure of a prokaryote serpin: controlling conformational change in a heated environment. Structure (Camb.) 11:387-397.
    • (2003) Structure (Camb.) , vol.11 , pp. 387-397
    • Irving, J.A.1    Cabrita, L.D.2    Rossjohn, J.3    Pike, R.N.4    Bottomley, S.P.5    Whisstock, J.C.6
  • 23
    • 0034523345 scopus 로고    scopus 로고
    • Phylogeny of the serpin superfamily: Implications of patterns of amino acid conservation for structure and function
    • Irving, J. A., R. N. Pike, A. M. Lesk, and J. C. Whisstock. 2000. Phylogeny of the serpin superfamily: implications of patterns of amino acid conservation for structure and function. Genome Res. 10:1845-1864.
    • (2000) Genome Res. , vol.10 , pp. 1845-1864
    • Irving, J.A.1    Pike, R.N.2    Lesk, A.M.3    Whisstock, J.C.4
  • 26
    • 34250922831 scopus 로고
    • The varimax criterion for analytic rotation in factor analysis
    • Kaiser, H. F. 1958. The varimax criterion for analytic rotation in factor analysis. Psychometrika 23:187-200.
    • (1958) Psychometrika , vol.23 , pp. 187-200
    • Kaiser, H.F.1
  • 28
    • 0027297096 scopus 로고
    • Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: An information theoretic analysis
    • Korber, B. T., R. M. Farber, D. H. Wolpert, and A. S. Lapedes. 1993. Covariation of mutations in the V3 loop of human immunodeficiency virus type 1 envelope protein: an information theoretic analysis. Proc. Natl. Acad. Sci. USA 90:7176-7180.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 7176-7180
    • Korber, B.T.1    Farber, R.M.2    Wolpert, D.H.3    Lapedes, A.S.4
  • 29
    • 0141509877 scopus 로고    scopus 로고
    • Conserved Ser residues, the shutter region, and speciation in serpin evolution
    • Krem, M. M., and E. Di Cera. 2003. Conserved Ser residues, the shutter region, and speciation in serpin evolution. J. Biol. Chem. 278:37810-37814.
    • (2003) J. Biol. Chem. , vol.278 , pp. 37810-37814
    • Krem, M.M.1    Di Cera, E.2
  • 30
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B., and F. M. Richards. 1971. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 31
    • 0035964912 scopus 로고    scopus 로고
    • Role of the connectivity of secondary structure segments in the folding of alpha(1)-antitrypsin
    • Lee, C., E. I. Seo, and M. H. Yu. 2001. Role of the connectivity of secondary structure segments in the folding of alpha(1)-antitrypsin. Biochem. Biophys. Res. Commun. 287:636-641.
    • (2001) Biochem. Biophys. Res. Commun. , vol.287 , pp. 636-641
    • Lee, C.1    Seo, E.I.2    Yu, M.H.3
  • 32
    • 0021747157 scopus 로고
    • Human alpha 1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function
    • Loebermann, H., R. Tokuoka, I. Deisenhofer, and R. Huber. 1984. Human alpha 1-proteinase inhibitor. Crystal structure analysis of two crystal modifications, molecular model and preliminary analysis of the implications for function. J. Mol. Biol. 177:531-557.
    • (1984) J. Mol. Biol. , vol.177 , pp. 531-557
    • Loebermann, H.1    Tokuoka, R.2    Deisenhofer, I.3    Huber, R.4
  • 35
    • 0030743758 scopus 로고    scopus 로고
    • Effectiveness of correlation analysis in identifying protein residues undergoing correlated evolution
    • Pollock, D. D., and W. R. Taylor. 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, D. D., W. R. Taylor, and N. Goldman. 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., P. Bladon, I. M. O. Mitchell, and M. I. Dufton. 2001. Evaluation of a novel method for the identification of coevolving protein residues. Protein Eng. 14:549-555.
    • (2001) Protein Eng. , vol.14 , pp. 549-555
    • Pritchard, L.1    Bladon, P.2    Mitchell, I.M.O.3    Dufton, M.I.4
  • 38
    • 0002218484 scopus 로고    scopus 로고
    • Rate4Site: An algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues
    • Pupko, T., R. E. Bell, I. Mayrose, F. Glaser, and N. Ben-Tal. 2002. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18 (Suppl. 1):S71-S77.
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 39
    • 0035060052 scopus 로고    scopus 로고
    • Vertebrate serpins: Construction of a conflict-free phytogeny by combining exon-intron and diagnostic site analyses
    • Ragg, H., T. Lokot, P. B. Kamp, W. R. Atchley, and A. Dress. 2001. Vertebrate serpins: construction of a conflict-free phytogeny by combining exon-intron and diagnostic site analyses. Mol. Biol. Evol. 18:577-584.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 577-584
    • Ragg, H.1    Lokot, T.2    Kamp, P.B.3    Atchley, W.R.4    Dress, A.5
  • 40
    • 4644325614 scopus 로고    scopus 로고
    • Serpins in unicellular Eukarya, Archaea, and Bacteria: Sequence analysis and evolution
    • Roberts, T. H., J. Hejgaard, N. F. Saunders, R. Cavicchioli, and P. M. Curmi. 2004. Serpins in unicellular Eukarya, Archaea, and Bacteria: sequence analysis and evolution. J. Mol. Evol. 59:437-447.
    • (2004) J. Mol. Evol. , vol.59 , pp. 437-447
    • Roberts, T.H.1    Hejgaard, J.2    Saunders, N.F.3    Cavicchioli, R.4    Curmi, P.M.5
  • 42
    • 0029589824 scopus 로고
    • What do dysfunctional serpins tell us about molecular mobility and disease?
    • Stein, P. E., and R. W. Carrell. 1995. What do dysfunctional serpins tell us about molecular mobility and disease? Nat. Struct. Biol. 2:96-113.
    • (1995) Nat. Struct. Biol. , vol.2 , pp. 96-113
    • Stein, P.E.1    Carrell, R.W.2
  • 43
    • 0033744204 scopus 로고    scopus 로고
    • Exploring a phylogenetic approach for the detection of correlated substitutions in proteins
    • Tuff, P., and P. Darlu. 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
    • Tuff, P.1    Darlu, P.2
  • 44
    • 19944406094 scopus 로고    scopus 로고
    • Context dependence and coevolution among amino acid residues in proteins
    • Wang, Z. O. and D. D. Pollock. 2005. Context dependence and coevolution among amino acid residues in proteins. Methods Enzmol. 395:779-790.
    • (2005) Methods Enzmol. , vol.395 , pp. 779-790
    • Wang, Z.O.1    Pollock, D.D.2
  • 45
    • 0034695402 scopus 로고    scopus 로고
    • Conformational changes in serpins: I. The native and cleaved conformations of alpha(1)-antitrypsin
    • Whisstock, J. C., R. Skinner, R. W. Carrell, and A. M. Lesk. 2000. Conformational changes in serpins: I. The native and cleaved conformations of alpha(1)-antitrypsin. J. Mol. Biol. 295:651-665.
    • (2000) J. Mol. Biol. , vol.295 , pp. 651-665
    • Whisstock, J.C.1    Skinner, R.2    Carrell, R.W.3    Lesk, A.M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.