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Volumn 29, Issue 21, 2013, Pages 2714-2721

Accounting for epistatic interactions improves the functional analysis of protein structures

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; LEXA PROTEIN, BACTERIA; PROTEIN; PROTEOME; SERINE PROTEINASE;

EID: 84886063889     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt489     Document Type: Article
Times cited : (21)

References (59)
  • 1
    • 80053453491 scopus 로고    scopus 로고
    • Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites
    • Adikesavan, A.K. et al. (2011) Separation of recombination and SOS response in Escherichia coli RecA suggests LexA interaction sites. PLoS Genet., 7, e1002244.
    • (2011) PLoS Genet. , vol.7
    • Adikesavan, A.K.1
  • 2
    • 0035838976 scopus 로고    scopus 로고
    • Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • DOI 10.1006/jmbi.2001.4870
    • Aloy, P. et al. (2001) Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol., 311, 395-408. (Pubitemid 32744549)
    • (2001) Journal of Molecular Biology , vol.311 , Issue.2 , pp. 395-408
    • Aloy, P.1    Querol, E.2    Aviles, F.X.3    Sternberg, M.J.E.4
  • 5
    • 84858126537 scopus 로고    scopus 로고
    • Automated protein structure modeling with swiss-model workspace and the protein model portal
    • In: Orry, A.J.W. and Abagyan, R. (eds) Humana Press
    • Bordoli, L. et al. (2012) Automated protein structure modeling with swiss-model workspace and the protein model portal. In: Orry, A.J.W. and Abagyan, R. (eds) Homology Modeling, volume 857 of Methods in Molecular Biology. pp. 107-136. Humana Press.
    • (2012) Homology Modeling, Volume 857 of Methods in Molecular Biology , pp. 107-136
    • Bordoli, L.1
  • 6
    • 84867781208 scopus 로고    scopus 로고
    • Epistasis as the primary factor in molecular evolution
    • Breen, M.S. et al. (2012) Epistasis as the primary factor in molecular evolution. Nature, 490, 535538.
    • (2012) Nature , vol.490 , pp. 535538
    • Breen, M.S.1
  • 7
    • 58149518390 scopus 로고    scopus 로고
    • The bacterial lexa transcriptional repressor
    • 10.1007/s00018-008-8378-6
    • Butala, M. et al. (2009) The bacterial lexa transcriptional repressor. Cell. Mol. Life Sci., 66, 82-93. 10.1007/s00018-008-8378-6.
    • (2009) Cell. Mol. Life Sci. , vol.66 , pp. 82-93
    • Butala, M.1
  • 8
    • 78649655423 scopus 로고    scopus 로고
    • Networks of high mutual information define the structural proximity of catalytic sites: Implications for catalytic residue identification
    • Buslje, C.M. et al. (2010) Networks of high mutual information define the structural proximity of catalytic sites: implications for catalytic residue identification. PLoS Comput. Biol., 6, e1000978.
    • (2010) PLoS Comput. Biol. , vol.6
    • Buslje, C.M.1
  • 9
    • 34548133728 scopus 로고    scopus 로고
    • Predicting functionally important residues from sequence conservation
    • DOI 10.1093/bioinformatics/btm270
    • Capra, J.A. and Singh, M. (2007) Predicting functionally important residues from sequence conservation. Bioinformatics, 23, 1875-1882. (Pubitemid 47299827)
    • (2007) Bioinformatics , vol.23 , Issue.15 , pp. 1875-1882
    • Capra, J.A.1    Singh, M.2
  • 10
    • 0029587166 scopus 로고
    • A method to predict functional residues in proteins
    • DOI 10.1038/nsb0295-171
    • Casari, G. et al. (1995) A method to predict functional residues in proteins. Nat. Struct. Biol., 2, 171-178. (Pubitemid 26040653)
    • (1995) Nature Structural Biology , vol.2 , Issue.2 , pp. 171-178
    • Casari, G.1    Sander, C.2    Valencia, A.3
  • 13
    • 0028916599 scopus 로고
    • A hot spot of binding energy in a hormone-receptor interface
    • Clackson, T. and Well, J.A. (1995) A hot spot of binding energy in a hormone-receptor interface. Science, 267, 383-386.
    • (1995) Science , vol.267 , pp. 383-386
    • Clackson, T.1    Well, J.A.2
  • 14
    • 77955344995 scopus 로고    scopus 로고
    • Surface residues dynamically organize water bridges to enhance electron transfer between proteins
    • de la Lande, A. et al. (2010) Surface residues dynamically organize water bridges to enhance electron transfer between proteins. Proc. Natl Acad. Sci. USA, 107, 11799-11804.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 11799-11804
    • De La-Lande, A.1
  • 15
    • 59149089414 scopus 로고    scopus 로고
    • Joint evolutionary trees: A large-scale method to predict protein interfaces based on sequence sampling
    • Engelen, S. et al. (2009) Joint evolutionary trees: a large-scale method to predict protein interfaces based on sequence sampling. PLoS Comput. Biol., 5, e1000267.
    • (2009) PLoS Comput. Biol. , vol.5
    • Engelen, S.1
  • 16
    • 77649271360 scopus 로고    scopus 로고
    • Evolutionary trace annotation of protein function in the structural proteome
    • Erdin, S. et al. (2010) Evolutionary trace annotation of protein function in the structural proteome. J. Mol. Biol., 396, 1451-1473.
    • (2010) J. Mol. Biol. , vol.396 , pp. 1451-1473
    • Erdin, S.1
  • 17
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • DOI 10.1093/bioinformatics/19.1.163
    • Glaser, F. et al. (2003) ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics, 19, 163-164. (Pubitemid 36150199)
    • (2003) Bioinformatics , vol.19 , Issue.1 , pp. 163-164
    • Glaser, F.1    Pupko, T.2    Paz, I.3    Bell, R.E.4    Bechor-Shental, D.5    Martz, E.6    Ben-Tal, N.7
  • 18
    • 0042674397 scopus 로고    scopus 로고
    • Using a neural network and spatial clustering to predict the location of active sites in enzymes
    • Gutteridge, A. et al. (2003) Using a neural network and spatial clustering to predict the location of active sites in enzymes. J. Mol. Biol., 330, 719-734.
    • (2003) J. Mol. Biol. , vol.330 , pp. 719-734
    • Gutteridge, A.1
  • 19
    • 68749107059 scopus 로고    scopus 로고
    • Protein sectors: Evolutionary units of three-dimensional structure
    • Halabi, N. et al. (2009) Protein sectors: evolutionary units of three-dimensional structure. Cell, 138, 774-786.
    • (2009) Cell , vol.138 , pp. 774-786
    • Halabi, N.1
  • 20
    • 9944263528 scopus 로고    scopus 로고
    • Searching for new allosteric sites in enzymes
    • DOI 10.1016/j.sbi.2004.10.009, PII S0959440X0400185X
    • Hardy, J.A. et al. (2004) Searching for new allosteric sites in enzymes. Curr. Opin. Struct. Biol., 14, 706-715. (Pubitemid 39592582)
    • (2004) Current Opinion in Structural Biology , vol.14 , Issue.6 , pp. 706-715
    • Hardy, J.A.1    Wells, J.A.2
  • 22
    • 34547600100 scopus 로고    scopus 로고
    • SiteFiNDER-3D: A web-based tool for predicting the location of functional sites in proteins
    • Innis, C.A. (2007) siteFiNDER-3D: a web-based tool for predicting the location of functional sites in proteins. Nucleic Acids Res., 35, W489-W494.
    • (2007) Nucleic Acids Res. , vol.35
    • Innis, C.A.1
  • 23
    • 38849090164 scopus 로고    scopus 로고
    • Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
    • Kristensen, D.M. et al. (2008) Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. BCM Bioinformatics, 9, 17.
    • (2008) BCM Bioinformatics , vol.9 , pp. 17
    • Kristensen, D.M.1
  • 24
    • 13444254300 scopus 로고    scopus 로고
    • PDBsum more: New summaries and analyses of the known 3D structures of proteins and nucleic acids
    • DOI 10.1093/nar/gki001
    • Laskowski, R. et al. (2005) PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res., 33, D266-D268. (Pubitemid 40207875)
    • (2005) Nucleic Acids Research , vol.33 , Issue.DATABASE ISS.
    • Laskowski, R.A.1    Chistyakov, V.V.2    Thornton, J.M.3
  • 25
    • 38349144394 scopus 로고    scopus 로고
    • Understanding the molecular machinery of genetics through 3D structures
    • Laskowski, R.A. and Thornton, J.M. (2008) Understanding the molecular machinery of genetics through 3D structures. Nat. Rev. Genet., 9, 141-145.
    • (2008) Nat. Rev. Genet. , vol.9 , pp. 141-145
    • Laskowski, R.A.1    Thornton, J.M.2
  • 26
    • 77955570809 scopus 로고    scopus 로고
    • Evolution: A guide to perturb protein function and networks
    • Lichtarge, O. and Wilkins, A. (2010) Evolution: a guide to perturb protein function and networks. Curr. Opin. Struct. Biol., 20, 351-359.
    • (2010) Curr. Opin. Struct. Biol. , vol.20 , pp. 351-359
    • Lichtarge, O.1    Wilkins, A.2
  • 27
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • DOI 10.1006/jmbi.1996.0167
    • Lichtarge, O. et al. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257, 342-358. (Pubitemid 26114038)
    • (1996) Journal of Molecular Biology , vol.257 , Issue.2 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 28
    • 0024832465 scopus 로고
    • - mutant LexA proteins
    • DOI 10.1016/0022-2836(89)90121-6
    • Lin, L.L. and Little, J.W. (1989) Autodigestion and RecA-dependent cleavage of Ind mutant LexA proteins. J. Mol. Biol., 210, 439-452. (Pubitemid 20030382)
    • (1989) Journal of Molecular Biology , vol.210 , Issue.3 , pp. 439-452
    • Lin, L.-L.1    Little, J.W.2
  • 30
    • 1542379652 scopus 로고    scopus 로고
    • Evolutionary Trace of G Protein-coupled Receptors Reveals Clusters of Residues That Determine Global and Class-specific Functions
    • DOI 10.1074/jbc.M312671200
    • Madabushi, S. et al. (2004) Evolutionary trace of G protein-coupled receptors reveals clusters of residues that determine global and class-specific functions. J. Biol. Chem., 279, 8126-8132. (Pubitemid 38294703)
    • (2004) Journal of Biological Chemistry , vol.279 , Issue.9 , pp. 8126-8132
    • Madabushi, S.1    Gross, A.K.2    Philippi, A.3    Meng, E.C.4    Wensel, T.G.5    Lichtarge, O.6
  • 31
    • 80053129150 scopus 로고    scopus 로고
    • Allostery in pharmacology: Thermodynamics, evolution and design
    • Maksay, G. (2011) Allostery in pharmacology: thermodynamics, evolution and design. Prog. Biophys. Mol. Biol., 106, 463-473.
    • (2011) Prog. Biophys. Mol. Biol. , vol.106 , pp. 463-473
    • Maksay, G.1
  • 32
    • 0037485769 scopus 로고    scopus 로고
    • Combining inference from evolution and geometric probability in protein structure evaluation
    • DOI 10.1016/S0022-2836(03)00663-6
    • Mihalek, I. et al. (2003) Combining inference from evolution and geometric probability in protein structure evaluation. J. Mol. Biol., 331, 263-279. (Pubitemid 36870792)
    • (2003) Journal of Molecular Biology , vol.331 , Issue.1 , pp. 263-279
    • Mihalek, I.1    Res, I.2    Yao, H.3    Lichtarge, O.4
  • 33
    • 1242339659 scopus 로고    scopus 로고
    • A family of evolution-entropy hybrid methods for ranking protein residues by importance
    • DOI 10.1016/j.jmb.2003.12.078
    • Mihalek, I. et al. (2004) A family of evolution-entropy hybrid methods for ranking protein residues by importance. J. Mol. Biol., 336, 1265-1282. (Pubitemid 38229712)
    • (2004) Journal of Molecular Biology , vol.336 , Issue.5 , pp. 1265-1282
    • Mihalek, I.1    Res, I.2    Lichtarge, O.3
  • 34
    • 33645024859 scopus 로고    scopus 로고
    • Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins
    • Mihalek, I. et al. (2006a) Evolutionary and structural feedback on selection of sequences for comparative analysis of proteins. Proteins, 63, 87-99.
    • (2006) Proteins , vol.63 , pp. 87-99
    • Mihalek, I.1
  • 35
    • 32144437402 scopus 로고    scopus 로고
    • A structure and evolution-guided Monte Carlo sequence selection strategy for multiple alignment-based analysis of proteins
    • DOI 10.1093/bioinformatics/bti791
    • Mihalek, I. et al. (2006b) A structure and evolution guided monte carlo sequence selection strategy for multiple alignment-based analysis of proteins. Bioinformatics, 22, 149-156. (Pubitemid 43205400)
    • (2006) Bioinformatics , vol.22 , Issue.2 , pp. 149-156
    • Mihalek, I.1    Res, I.2    Lichtarge, O.3
  • 36
    • 0030614427 scopus 로고    scopus 로고
    • Receptor and βγ binding sites in the α subunit of the retinal G protein transducin
    • DOI 10.1126/science.275.5298.381
    • Onrust, R. et al. (1997) Receptor and betagamma binding sites in the alpha subunit of the retinal G protein transducin. Science, 275, 381-384. (Pubitemid 27051613)
    • (1997) Science , vol.275 , Issue.5298 , pp. 381-384
    • Onrust, R.1    Herzmark, P.2    Chi, P.3    Garcia, P.D.4    Lichtarge, O.5    Kingsley, C.6    Bourne, H.R.7
  • 37
    • 34548040966 scopus 로고    scopus 로고
    • Crystal structure of an ancient protein: Evolution by conformational epistasis
    • DOI 10.1126/science.1142819
    • Ortlund, E.A. et al. (2007) Crystal structure of an ancient protein: evolution by conformational epistasis. Science, 317, 1544-1548. (Pubitemid 47417432)
    • (2007) Science , vol.317 , Issue.5844 , pp. 1544-1548
    • Ortlund, E.A.1    Bridgham, J.T.2    Redinbo, M.R.3    Thornton, J.W.4
  • 38
    • 1842454912 scopus 로고    scopus 로고
    • Prediction of functional sites by analysis of sequence and structure conservation
    • DOI 10.1110/ps.03465504
    • Panchenko, A.R. et al. (2004) Prediction of functional sites by analysis of sequence and structure conservation. Protein Sci., 13, 884-892. (Pubitemid 38429212)
    • (2004) Protein Science , vol.13 , Issue.4 , pp. 884-892
    • Panchenko, A.R.1    Kondrashov, F.2    Bryant, S.3
  • 39
    • 33745599119 scopus 로고    scopus 로고
    • Phylogeny-independent detection of functional residues
    • DOI 10.1093/bioinformatics/btl104
    • Pazos, F. et al. (2006) Phylogeny-independent detection of functional residues. Bioinformatics, 22, 1440-1448. (Pubitemid 43985314)
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1440-1448
    • Pazos, F.1    Rausell, A.2    Valencia, A.3
  • 40
    • 54349091030 scopus 로고    scopus 로고
    • Protein co-evolution, co-adaptation and interactions
    • Pazos, F. and Valencia, A. (2008) Protein co-evolution, co-adaptation and interactions. EMBO J., 27, 2648-2655.
    • (2008) EMBO J. , vol.27 , pp. 2648-2655
    • Pazos, F.1    Valencia, A.2
  • 41
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: Calculation of positional conservation in a protein sequence alignment
    • Pei, J. and Grishin, N.V. (2001) AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics, 17, 700-712. (Pubitemid 32851378)
    • (2001) Bioinformatics , vol.17 , Issue.8 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 42
    • 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. et al. (2002) Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics, 18, S71-S77. (Pubitemid 41185639)
    • (2002) Bioinformatics , vol.18 , Issue.SUPPL. 1
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 44
    • 76649113438 scopus 로고    scopus 로고
    • Protein interactions and ligand binding: From protein subfamilies to functional specificity
    • Rausell, A. et al. (2010) Protein interactions and ligand binding: from protein subfamilies to functional specificity. Proc. Natl Acad. Sci. USA, 107, 1995-2000.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 1995-2000
    • Rausell, A.1
  • 45
    • 20444462091 scopus 로고    scopus 로고
    • Correlated evolutionary pressure at interacting transcription factors and DNA response elements can guide the rational engineering of DNA binding specificity
    • DOI 10.1016/j.jmb.2005.04.054, PII S0022283605004808
    • Raviscioni, M. et al. (2005) Correlated evolutionary pressure at interacting transcription factors and dna response elements can guide the rational engineering of dna binding specificity. J. Mol. Biol., 350, 402-415. (Pubitemid 40828903)
    • (2005) Journal of Molecular Biology , vol.350 , Issue.3 , pp. 402-415
    • Raviscioni, M.1    Gu, P.2    Sattar, M.3    Cooney, A.J.4    Lichtarge, O.5
  • 47
    • 77952356281 scopus 로고    scopus 로고
    • Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors
    • Rodriguez, G. et al. (2010) Evolution-guided discovery and recoding of allosteric pathway specificity determinants in psychoactive bioamine receptors. Proc. Natl Acad. Sci. USA, 107, 7787-7792.
    • (2010) Proc. Natl Acad. Sci. USA , vol.107 , pp. 7787-7792
    • Rodriguez, G.1
  • 48
    • 77954065271 scopus 로고    scopus 로고
    • I-TASSER: A unified platform for automated protein structure and function prediction
    • Roy, A. et al. (2010) I-TASSER: a unified platform for automated protein structure and function prediction. Nat. Protocols, 5, 725-738.
    • (2010) Nat. Protocols , vol.5 , pp. 725-738
    • Roy, A.1
  • 49
    • 33644857279 scopus 로고    scopus 로고
    • Beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor
    • Shenoy, S. et al. (2006) Beta-arrestin-dependent, G protein-independent ERK1/2 activation by the beta2 adrenergic receptor. J. Biol. Chem., 281, 261-273.
    • (2006) J. Biol. Chem. , vol.281 , pp. 261-273
    • Shenoy, S.1
  • 52
    • 84866181982 scopus 로고    scopus 로고
    • Disentangling evolutionary signals: Conservation, specificity determining positions and coevolution. Implication for catalytic residue prediction
    • Teppa, E. et al. (2012) Disentangling evolutionary signals: conservation, specificity determining positions and coevolution. implication for catalytic residue prediction. BMC Bioinformatics, 13, 235.
    • (2012) BMC Bioinformatics , vol.13 , pp. 235
    • Teppa, E.1
  • 53
    • 70350635776 scopus 로고    scopus 로고
    • Exploitation of binding energy for catalysis and design
    • Thyme, S.B. et al. (2009) Exploitation of binding energy for catalysis and design. Nature, 461, 1300-1304.
    • (2009) Nature , vol.461 , pp. 1300-1304
    • Thyme, S.B.1
  • 54
    • 27544435126 scopus 로고    scopus 로고
    • Fast protein classification with multiple networks
    • DOI 10.1093/bioinformatics/bti1110
    • Tsuda, K. et al. (2005) Fast protein classification with multiple networks. Bioinformatics, 21 (Suppl. 2), ii59-ii65. (Pubitemid 41535429)
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Tsuda, K.1    Shin, H.J.2    Scholkopf, B.3
  • 56
    • 78650798477 scopus 로고    scopus 로고
    • Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities
    • Venner, E. et al. (2010) Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. PLoS One, 5, e14286.
    • (2010) PLoS One , vol.5
    • Venner, E.1
  • 57
    • 47849086673 scopus 로고    scopus 로고
    • De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features
    • Ward, R.M. et al. (2008) De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features. PLoS One, 7;3, e2136.
    • (2008) PLoS One , vol.7 , Issue.3
    • Ward, R.M.1
  • 58
    • 77953963521 scopus 로고    scopus 로고
    • Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation
    • Wilkins, A.D. et al. (2010) Sequence and structure continuity of evolutionary importance improves protein functional site discovery and annotation. Protein Sci., 19, 1296-1311.
    • (2010) Protein Sci. , vol.19 , pp. 1296-1311
    • Wilkins, A.D.1


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