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Volumn 351, Issue 4, 2006, Pages 1031-1036

A new method for quantifying residue conservation and its applications to the protein folding nucleus

Author keywords

Evolutionary conservation; Folding nucleus; Multiple sequence alignment (MSA); Physicochemical property

Indexed keywords

AMINO ACID;

EID: 33750797530     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.10.157     Document Type: Article
Times cited : (4)

References (38)
  • 1
    • 0036295887 scopus 로고    scopus 로고
    • Residue participating in the protein folding nucleus do not exhibit preferential evolutionary conservation
    • Larson S.M., Ruczinski I., Davidson A.R., Baker D., and Plaxco K.W. Residue participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. J. Mol. Biol. 316 (2002) 225-233
    • (2002) J. Mol. Biol. , vol.316 , pp. 225-233
    • Larson, S.M.1    Ruczinski, I.2    Davidson, A.R.3    Baker, D.4    Plaxco, K.W.5
  • 3
    • 0345062357 scopus 로고    scopus 로고
    • Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function
    • Mirny L.A., and Shakhnovich E.I. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291 (1999) 177-196
    • (1999) J. Mol. Biol. , vol.291 , pp. 177-196
    • Mirny, L.A.1    Shakhnovich, E.I.2
  • 4
    • 0035957514 scopus 로고    scopus 로고
    • Evolutionary conservation of the folding nucleus
    • Mirny L., and Shakhnovich E. Evolutionary conservation of the folding nucleus. J. Mol. Biol. 308 (2001) 123-129
    • (2001) J. Mol. Biol. , vol.308 , pp. 123-129
    • Mirny, L.1    Shakhnovich, E.2
  • 5
    • 0032496419 scopus 로고    scopus 로고
    • Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes?
    • Ptitsyn O.B. Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes?. J. Mol. Biol. 278 (1998) 655-666
    • (1998) J. Mol. Biol. , vol.278 , pp. 655-666
    • Ptitsyn, O.B.1
  • 6
    • 0035178383 scopus 로고    scopus 로고
    • Protein-protein interfaces: analysis of amino acid conservation in homodimers
    • Valdar W.S.J., and Thornton J.M. Protein-protein interfaces: analysis of amino acid conservation in homodimers. Proteins 42 (2001) 108-124
    • (2001) Proteins , vol.42 , pp. 108-124
    • Valdar, W.S.J.1    Thornton, J.M.2
  • 7
    • 0035914476 scopus 로고    scopus 로고
    • Conservation helps to identify biologically relevant crystal contacts
    • Valdar W.S.J., and Thomton J.M. Conservation helps to identify biologically relevant crystal contacts. J. Mol. Biol. 313 (2001) 399-416
    • (2001) J. Mol. Biol. , vol.313 , pp. 399-416
    • Valdar, W.S.J.1    Thomton, J.M.2
  • 8
    • 0014828908 scopus 로고
    • An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity
    • Wu T.T., and Kabat E.A. An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity. J. Exp. Med. 132 (1970) 211-249
    • (1970) J. Exp. Med. , vol.132 , pp. 211-249
    • Wu, T.T.1    Kabat, E.A.2
  • 9
    • 0025612174 scopus 로고
    • Resolution of hypervariable regions in T-cell receptor chains by a modified Wu-Kabat index of amino acid diversity
    • Jores R., Alzari P.M., and Meo T. Resolution of hypervariable regions in T-cell receptor chains by a modified Wu-Kabat index of amino acid diversity. Proc. Natl. Acad. Sci. USA 87 (1990) 9138-9142
    • (1990) Proc. Natl. Acad. Sci. USA , vol.87 , pp. 9138-9142
    • Jores, R.1    Alzari, P.M.2    Meo, T.3
  • 10
    • 0033536602 scopus 로고    scopus 로고
    • Evolutionarily conserved pathways of energetic connectivity in protein families
    • Lockless S.W., and Ranganathan R. Evolutionarily conserved pathways of energetic connectivity in protein families. Science 286 (1999) 295-299
    • (1999) Science , vol.286 , pp. 295-299
    • Lockless, S.W.1    Ranganathan, R.2
  • 11
    • 0026342532 scopus 로고
    • Information-theoretical entropy as a measure of sequence variability
    • Shenkin P.S., Erman B., and Mastrandrea L.D. Information-theoretical entropy as a measure of sequence variability. Proteins 11 (1991) 297-313
    • (1991) Proteins , vol.11 , pp. 297-313
    • Shenkin, P.S.1    Erman, B.2    Mastrandrea, L.D.3
  • 12
    • 0026030641 scopus 로고
    • Database of homology-derived protein structures and the structural meaning of sequence alignment
    • Sander C., and Schneider R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9 (1991) 56-68
    • (1991) Proteins , vol.9 , pp. 56-68
    • Sander, C.1    Schneider, R.2
  • 13
    • 0029091249 scopus 로고
    • Average core structures and variability measures for protein families: application to the immunoglobulins
    • Gerstein M., and Altman R.B. Average core structures and variability measures for protein families: application to the immunoglobulins. J. Mol. Biol. 251 (1995) 161-175
    • (1995) J. Mol. Biol. , vol.251 , pp. 161-175
    • Gerstein, M.1    Altman, R.B.2
  • 14
    • 0022591495 scopus 로고
    • The classification of amino acid conservation
    • Taylor W.R. The classification of amino acid conservation. J. Theor. Biol. 119 (1986) 205-218
    • (1986) J. Theor. Biol. , vol.119 , pp. 205-218
    • Taylor, W.R.1
  • 15
    • 0023660653 scopus 로고
    • Prediction of protein secondary structure and active sites using the alignment of homologous sequences
    • Zvelibil M.J., Barton G.J., Taylor W.R., and Sternberg M.J. Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J. Mol. Biol. 195 (1987) 957-961
    • (1987) J. Mol. Biol. , vol.195 , pp. 957-961
    • Zvelibil, M.J.1    Barton, G.J.2    Taylor, W.R.3    Sternberg, M.J.4
  • 16
    • 0029078795 scopus 로고
    • Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters
    • Williamson R.M. Information theory analysis of the relationship between primary sequence structure and ligand recognition among a class of facilitated transporters. J. Theor. Biol. 174 (1995) 179-188
    • (1995) J. Theor. Biol. , vol.174 , pp. 179-188
    • Williamson, R.M.1
  • 17
    • 0029935769 scopus 로고    scopus 로고
    • Evolutionary conservation of RecA genes in relation to protein structure and function
    • Karlin S., and Brocchieri L. Evolutionary conservation of RecA genes in relation to protein structure and function. J. Bacteriol. 178 (1996) 1881-1894
    • (1996) J. Bacteriol. , vol.178 , pp. 1881-1894
    • Karlin, S.1    Brocchieri, L.2
  • 18
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    • Armon A., Graur D., and Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol. 307 (2001) 447-463
    • (2001) J. Mol. Biol. , vol.307 , pp. 447-463
    • Armon, A.1    Graur, D.2    Ben-Tal, N.3
  • 19
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 25 (1997) 4876-4882
    • (1997) Nucleic Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 20
    • 0032900495 scopus 로고    scopus 로고
    • The variable and conserved interfaces of modeled olfactory receptor proteins
    • Pilpel Y., and Lancet D. The variable and conserved interfaces of modeled olfactory receptor proteins. Protein Sci. 8 (1999) 969-977
    • (1999) Protein Sci. , vol.8 , pp. 969-977
    • Pilpel, Y.1    Lancet, D.2
  • 21
    • 0032711731 scopus 로고    scopus 로고
    • Analysis of heregulin symmetry by weighted evolutionary tracing
    • Landgraf R., Fischer D., and Eisenberg D. Analysis of heregulin symmetry by weighted evolutionary tracing. Protein Eng. 12 (1999) 943-951
    • (1999) Protein Eng. , vol.12 , pp. 943-951
    • Landgraf, R.1    Fischer, D.2    Eisenberg, D.3
  • 22
    • 0036681416 scopus 로고    scopus 로고
    • Scoring residue conservation
    • Valdar W.S.J. Scoring residue conservation. Proteins 48 (2002) 227-241
    • (2002) Proteins , vol.48 , pp. 227-241
    • Valdar, W.S.J.1
  • 23
    • 0026527758 scopus 로고
    • Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modeling
    • Smith R.F., and Smith T.F. Pattern-induced multi-sequence alignment (PIMA) algorithm employing secondary structure-dependent gap penalties for use in comparative protein modeling. Protein Eng. 5 (1992) 35-41
    • (1992) Protein Eng. , vol.5 , pp. 35-41
    • Smith, R.F.1    Smith, T.F.2
  • 24
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89 (1992) 10915-10919
    • (1992) Proc. Natl. Acad. Sci. USA , vol.89 , pp. 10915-10919
    • Henikoff, S.1    Henikoff, J.G.2
  • 25
    • 0024544755 scopus 로고
    • A fast and sensitive multiple sequence alignment algorithm
    • Vingron M., and Argos P. A fast and sensitive multiple sequence alignment algorithm. Comput. Appl. Biosci. 5 (1989) 115-121
    • (1989) Comput. Appl. Biosci. , vol.5 , pp. 115-121
    • Vingron, M.1    Argos, P.2
  • 26
    • 0028043552 scopus 로고
    • Position-based sequence weights
    • Henikoff S., and Henikoff J.G. Position-based sequence weights. J. Mol. Biol. 243 (1994) 574-578
    • (1994) J. Mol. Biol. , vol.243 , pp. 574-578
    • Henikoff, S.1    Henikoff, J.G.2
  • 28
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: calculation of positional conservation in a protein sequence alignment
    • Pei J.M., and Grishin N.V. AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 17 (2001) 700-712
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.M.1    Grishin, N.V.2
  • 29
    • 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., Bell R.E., Mayrose I., Glaser F., and Ben-Tal N. Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues. Bioinformatics 18 (2002) 71-77
    • (2002) Bioinformatics , vol.18 , pp. 71-77
    • Pupko, T.1    Bell, R.E.2    Mayrose, I.3    Glaser, F.4    Ben-Tal, N.5
  • 30
    • 4143051195 scopus 로고    scopus 로고
    • Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior
    • Mayrose I., Graur D., Ben-Tal N., and Pupko T. Comparison of site-specific rate-inference methods for protein sequences: empirical Bayesian methods are superior. Mol. Biol. Evol. 21 (2004) 1781-1791
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1781-1791
    • Mayrose, I.1    Graur, D.2    Ben-Tal, N.3    Pupko, T.4
  • 31
    • 18844426792 scopus 로고    scopus 로고
    • Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account
    • Mayrose I., Mitchell A., and Pupko T. Site-specific evolutionary rate inference: taking phylogenetic uncertainty into account. J. Mol. Evol. 60 (2005) 345-353
    • (2005) J. Mol. Evol. , vol.60 , pp. 345-353
    • Mayrose, I.1    Mitchell, A.2    Pupko, T.3
  • 32
    • 0037058983 scopus 로고    scopus 로고
    • Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics
    • Suzuki Y., Glazko G.V., and Nei M. Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics. Proc. Natl. Acad. Sci. USA 99 (2002) 16138-16143
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16138-16143
    • Suzuki, Y.1    Glazko, G.V.2    Nei, M.3
  • 33
    • 2342464164 scopus 로고    scopus 로고
    • Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters
    • Soyer O.S., and Goldstein R.A. Predicting functional sites in proteins: site-specific evolutionary models and their application to neurotransmitter transporters. J. Mol. Biol. 339 (2004) 227-242
    • (2004) J. Mol. Biol. , vol.339 , pp. 227-242
    • Soyer, O.S.1    Goldstein, R.A.2
  • 34
    • 0029670994 scopus 로고    scopus 로고
    • Conserved residues and the mechanism of protein folding
    • Shaknovich E., Abkevich V., and Ptitsyn O. Conserved residues and the mechanism of protein folding. Nature 379 (1996) 96-98
    • (1996) Nature , vol.379 , pp. 96-98
    • Shaknovich, E.1    Abkevich, V.2    Ptitsyn, O.3
  • 36
    • 0345862295 scopus 로고    scopus 로고
    • Are residues in a protein folding nucleus evolutionarily conserved?
    • Tseng Y.Y., and Liang J. Are residues in a protein folding nucleus evolutionarily conserved?. J. Mol. Biol. 335 (2004) 869-880
    • (2004) J. Mol. Biol. , vol.335 , pp. 869-880
    • Tseng, Y.Y.1    Liang, J.2
  • 37
    • 0031043161 scopus 로고    scopus 로고
    • Nucleation mechanisms in protein folding
    • Fersht A.R. Nucleation mechanisms in protein folding. Curr. Opin. Struct. Biol. 7 (1997) 3-9
    • (1997) Curr. Opin. Struct. Biol. , vol.7 , pp. 3-9
    • Fersht, A.R.1
  • 38
    • 0842332830 scopus 로고    scopus 로고
    • Commitment and nucleation in the protein G transition state
    • Hubner I.A., Shimada J., and Shakhnovich E.I. Commitment and nucleation in the protein G transition state. J. Mol. Biol. 336 (2004) 745-761
    • (2004) J. Mol. Biol. , vol.336 , pp. 745-761
    • Hubner, I.A.1    Shimada, J.2    Shakhnovich, E.I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.