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Volumn 4, Issue , 2004, Pages

Reconstruction of ancestral protein sequences and its applications

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PROTEIN;

EID: 8744259751     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-4-33     Document Type: Article
Times cited : (95)

References (58)
  • 1
    • 84959747425 scopus 로고
    • Toward defining the course of evolution: Minimum change for a specific tree topology
    • Fitch WM: Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971, 20:406-416.
    • (1971) Syst Zool , vol.20 , pp. 406-416
    • Fitch, W.M.1
  • 2
    • 0002329356 scopus 로고
    • Minimum evolution fits to a given tree
    • Hartigan JA: Minimum evolution fits to a given tree. Biometrics 1973, 29:53-65.
    • (1973) Biometrics , vol.29 , pp. 53-65
    • Hartigan, J.A.1
  • 3
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nucleotide and amino acid sequences
    • Yang Z, Kumar S, Nei M: A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 1995,141:1641-1650.
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 4
    • 0029881442 scopus 로고    scopus 로고
    • Probabilistic reconstruction of ancestral protein sequences
    • Koshi JM, Goldstein RA: Probabilistic reconstruction of ancestral protein sequences. J Mol Evol 1996, 42:313-320.
    • (1996) J Mol Evol , vol.42 , pp. 313-320
    • Koshi, J.M.1    Goldstein, R.A.2
  • 5
    • 0034117082 scopus 로고    scopus 로고
    • A fast algorithm for joint reconstruction of ancestral amino acid sequences
    • Pupko T, Pe'er I, Shamir R, Graur D: A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol Biol Evol 2000, 17:890-896.
    • (2000) Mol Biol Evol , vol.17 , pp. 890-896
    • Pupko, T.1    Pe'er, I.2    Shamir, R.3    Graur, D.4
  • 6
    • 0031025677 scopus 로고    scopus 로고
    • Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods
    • Zhang J, Nei M: Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J Mol Evol 1997, 44 Suppl 1:S139-146.
    • (1997) J Mol Evol , vol.44 , Issue.1 SUPPL.
    • Zhang, J.1    Nei, M.2
  • 8
    • 0019797407 scopus 로고
    • Evolutionary trees from DNA sequences: A maximum likelihood approach
    • Felsenstein J: Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981, 17:368-376.
    • (1981) J Mol Evol , vol.17 , pp. 368-376
    • Felsenstein, J.1
  • 9
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou N, Nei M: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987,4:406-425.
    • (1987) Mol Biol Evol , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 10
    • 0033984609 scopus 로고    scopus 로고
    • Weighted neighbor joining: A likelihood-based approach to distance-based phylogeny reconstruction
    • Bruno WJ, Socci ND, Halpern AL: Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 2000, 17:189-197.
    • (2000) Mol Biol Evol , vol.17 , pp. 189-197
    • Bruno, W.J.1    Socci, N.D.2    Halpern, A.L.3
  • 11
    • 0030807655 scopus 로고    scopus 로고
    • BIONJ: An improved version of the NJ algorithm based on a simple model of sequence data
    • Gascuel O: BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data. Mol Biol Evol 1997,14:685-695.
    • (1997) Mol Biol Evol , vol.14 , pp. 685-695
    • Gascuel, O.1
  • 12
    • 0015219691 scopus 로고
    • Fitting discrete probability distributions to evolutionary events
    • Uzzell T, Corbin KW: Fitting discrete probability distributions to evolutionary events. Science 1971, 172:1089-1896.
    • (1971) Science , vol.172 , pp. 1089-1896
    • Uzzell, T.1    Corbin, K.W.2
  • 13
    • 0027132974 scopus 로고
    • Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
    • Yang Z: Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Mol Biol Evol 1993, 10:1396-1401.
    • (1993) Mol Biol Evol , vol.10 , pp. 1396-1401
    • Yang, Z.1
  • 14
    • 0014211361 scopus 로고
    • Construction of phylogenetic trees
    • Fitch WM, Margoliash E: Construction of phylogenetic trees. Science 1967, 155:279-284.
    • (1967) Science , vol.155 , pp. 279-284
    • Fitch, W.M.1    Margoliash, E.2
  • 15
    • 0023058718 scopus 로고
    • The estimate of total nucleotide substitutions from pairwise differences is biased
    • Fitch WM: The estimate of total nucleotide substitutions from pairwise differences is biased. Philos Trans R Soc Lond B Biol Sci 1986, 312:317-324.
    • (1986) Philos Trans R Soc Lond B Biol Sci , vol.312 , pp. 317-324
    • Fitch, W.M.1
  • 16
    • 0030734575 scopus 로고    scopus 로고
    • A simple method for estimating the parameter of substitution rate variation among sites
    • Gu X, Zhang J: A simple method for estimating the parameter of substitution rate variation among sites. Mol Biol Evol 1997,14:1106-1113.
    • (1997) Mol Biol Evol , vol.14 , pp. 1106-1113
    • Gu, X.1    Zhang, J.2
  • 17
    • 0034818755 scopus 로고    scopus 로고
    • Taking variation of evolutionary rates between sites into account in inferring phylogenies
    • Felsenstein J: Taking variation of evolutionary rates between sites into account in inferring phylogenies. J Mol Evol 2001,53:447-455.
    • (2001) J Mol Evol , vol.53 , pp. 447-455
    • Felsenstein, J.1
  • 18
    • 0031153858 scopus 로고    scopus 로고
    • Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA
    • Nielsen R: Site-by-site estimation of the rate of substitution and the correlation of rates in mitochondrial DNA. Syst Biol 1997, 46:346-353.
    • (1997) Syst Biol , vol.46 , pp. 346-353
    • Nielsen, R.1
  • 19
    • 0036677932 scopus 로고    scopus 로고
    • A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families
    • Pupko T, Pe'er I, Hasegawa M, Graur D, Friedman N: A branch-andbound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. Bioinformatics 2002, 18:1116-1123.
    • (2002) Bioinformatics , vol.18 , pp. 1116-1123
    • Pupko, T.1    Pe'er, I.2    Hasegawa, M.3    Graur, D.4    Friedman, N.5
  • 20
    • 0034922289 scopus 로고    scopus 로고
    • Modeling amino acid replacement
    • Muller T, Vingron M: Modeling amino acid replacement. J Comput Biol 2000, 7:761-776.
    • (2000) J Comput Biol , vol.7 , pp. 761-776
    • Muller, T.1    Vingron, M.2
  • 22
    • 0029067458 scopus 로고
    • Evalution of Several Methods for Estimating Phylogenetic Trees When Substitution Rates Differ over Nucleotide Sites
    • Yang Z: Evalution of Several Methods for Estimating Phylogenetic Trees When Substitution Rates Differ over Nucleotide Sites. J Mol Evol 1995, 40:689-697.
    • (1995) J Mol Evol , vol.40 , pp. 689-697
    • Yang, Z.1
  • 23
    • 1042264059 scopus 로고    scopus 로고
    • Searching for functional sites in protein structures
    • Jones S, Thornton JM: Searching for functional sites in protein structures. Curr Opin Chem Biol 2004, 8:3-7.
    • (2004) Curr Opin Chem Biol , vol.8 , pp. 3-7
    • Jones, S.1    Thornton, J.M.2
  • 24
    • 0036468670 scopus 로고    scopus 로고
    • Evolutionary predictions of binding surfaces and interactions
    • Lichtarge O, Sowa ME: Evolutionary predictions of binding surfaces and interactions. Curr Opin Struct Biol 2002, 12:21-27.
    • (2002) Curr Opin Struct Biol , vol.12 , pp. 21-27
    • Lichtarge, O.1    Sowa, M.E.2
  • 25
    • 0034843597 scopus 로고    scopus 로고
    • AL2CO: Calculation of positional conservation in a protein sequence alignment
    • Pei J, Grishin NV: AL2CO: calculation of positional conservation in a protein sequence alignment. Bioinformatics 2001,17:700-712.
    • (2001) Bioinformatics , vol.17 , pp. 700-712
    • Pei, J.1    Grishin, N.V.2
  • 26
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge O, Bourne HR, Cohen FE: An evolutionary trace method defines binding surfaces common to protein families. J Mol Biol 1996, 257:342-358.
    • (1996) J Mol Biol , vol.257 , pp. 342-358
    • Lichtarge, O.1    Bourne, H.R.2    Cohen, F.E.3
  • 27
    • 0027157960 scopus 로고
    • Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees
    • Tamura K, Nei M: Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993, 10:512-526.
    • (1993) Mol Biol Evol , vol.10 , pp. 512-526
    • Tamura, K.1    Nei, M.2
  • 28
    • 0028064845 scopus 로고
    • Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods
    • Yang Z: Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 1994, 39:306-314.
    • (1994) J Mol Evol , vol.39 , pp. 306-314
    • Yang, Z.1
  • 30
    • 0030683599 scopus 로고    scopus 로고
    • PAML: A program package for phylogenetic analysis by maximum likelihood
    • Yang Z: PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci 1997, 13:555-556.
    • (1997) Comput Appl Biosci , vol.13 , pp. 555-556
    • Yang, Z.1
  • 34
    • 0027479161 scopus 로고
    • OB(oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences
    • Murzin AG: OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. Embo J 1993, 12:861-867.
    • (1993) Embo J , vol.12 , pp. 861-867
    • Murzin, A.G.1
  • 36
    • 0031743421 scopus 로고    scopus 로고
    • Profile hidden Markov models
    • Eddy SR: Profile hidden Markov models. Bioinformatics 1998,14:755-763.
    • (1998) Bioinformatics , vol.14 , pp. 755-763
    • Eddy, S.R.1
  • 38
    • 0028942595 scopus 로고
    • Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase
    • Muller-Dieckmann HJ, Schulz GE: Substrate specificity and assembly of the catalytic center derived from two structures of ligated uridylate kinase. J Mol Biol 1995, 246:522-530.
    • (1995) J Mol Biol , vol.246 , pp. 522-530
    • Muller-Dieckmann, H.J.1    Schulz, G.E.2
  • 39
    • 0035031966 scopus 로고    scopus 로고
    • A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
    • Whelan S, Goldman N: A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001, 18:691-699.
    • (2001) Mol Biol Evol , vol.18 , pp. 691-699
    • Whelan, S.1    Goldman, N.2
  • 41
    • 0035906714 scopus 로고    scopus 로고
    • Crystal structure of the PDZ1 domain of human Na(+)/H(+) exchanger regulatory factor provides insights into the mechanism of carboxyl-terminal leucine recognition by class I PDZ domains
    • Karthikeyan S, Leung T, Birrane G, Webster G, Ladias JA: Crystal structure of the PDZ1 domain of human Na(+)/H(+) exchanger regulatory factor provides insights into the mechanism of carboxyl-terminal leucine recognition by class I PDZ domains. J Mol Biol 2001, 308:963-973.
    • (2001) J Mol Biol , vol.308 , pp. 963-973
    • Karthikeyan, S.1    Leung, T.2    Birrane, G.3    Webster, G.4    Ladias, J.A.5
  • 42
    • 0023881841 scopus 로고
    • Refined crystal structure of Streptomyces griseus trypsin at 1.7 a resolution
    • Read RJ, James MN: Refined crystal structure of Streptomyces griseus trypsin at 1.7 A resolution. J Mol Biol 1988, 200:523-551.
    • (1988) J Mol Biol , vol.200 , pp. 523-551
    • Read, R.J.1    James, M.N.2
  • 43
    • 0000471429 scopus 로고
    • High-resolution structure of the complex between carboxypeptidase a and L-phenyl lactate
    • Teplyakov A: High-resolution structure of the complex between carboxypeptidase A and L-phenyl lactate. Acta Crystallogr D Biol Crystallogr 1993, 49:534-540.
    • (1993) Acta Crystallogr D Biol Crystallogr , vol.49 , pp. 534-540
    • Teplyakov, A.1
  • 44
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
    • (1995) J Mol Biol , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 45
    • 0034644783 scopus 로고    scopus 로고
    • Analysis and prediction of functional sub-types from protein sequence alignments
    • Hannenhalli SS, Russell RB: Analysis and prediction of functional sub-types from protein sequence alignments. J Mol Biol 2000,303:61-76.
    • (2000) J Mol Biol , vol.303 , pp. 61-76
    • Hannenhalli, S.S.1    Russell, R.B.2
  • 46
    • 0036352010 scopus 로고    scopus 로고
    • Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors
    • Mirny LA, Gelfand MS: Using orthologous and paralogous proteins to identify specificity-determining residues in bacterial transcription factors. J Mol Biol 2002, 321:7-20.
    • (2002) J Mol Biol , vol.321 , pp. 7-20
    • Mirny, L.A.1    Gelfand, M.S.2
  • 47
    • 0028998836 scopus 로고
    • High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer
    • Abele U, Schulz GE: High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer. Protein Sci 1995, 4:1262-1271.
    • (1995) Protein Sci , vol.4 , pp. 1262-1271
    • Abele, U.1    Schulz, G.E.2
  • 49
    • 0038853525 scopus 로고    scopus 로고
    • Crystal structures of myoglobin-ligand complexes at near-atomic resolution
    • Vojtechovsky J, Chu K, Berendzen J, Sweet RM, Schlichting I: Crystal structures of myoglobin-ligand complexes at near-atomic resolution. Biophys J 1999, 77:2153-2174.
    • (1999) Biophys J , vol.77 , pp. 2153-2174
    • Vojtechovsky, J.1    Chu, K.2    Berendzen, J.3    Sweet, R.M.4    Schlichting, I.5
  • 50
    • 0030604722 scopus 로고    scopus 로고
    • Crystal structures of a complexed and peptide-free membrane protein-binding domain: Molecular basis of peptide recognition by PDZ
    • Doyle DA, Lee A, Lewis J, Kim E, Sheng M, MacKinnon R: Crystal structures of a complexed and peptide-free membrane protein-binding domain: molecular basis of peptide recognition by PDZ. Cell 1996, 85:1067-1076.
    • (1996) Cell , vol.85 , pp. 1067-1076
    • Doyle, D.A.1    Lee, A.2    Lewis, J.3    Kim, E.4    Sheng, M.5    MacKinnon, R.6
  • 51
    • 0029617615 scopus 로고
    • Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain
    • Ferguson KM, Lemmon MA, Schlessinger J, Sigler PB: Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain. Cell 1995,83:1037-1046.
    • (1995) Cell , vol.83 , pp. 1037-1046
    • Ferguson, K.M.1    Lemmon, M.A.2    Schlessinger, J.3    Sigler, P.B.4
  • 55
    • 0030220960 scopus 로고    scopus 로고
    • Molecular basis for the binding of SH3 ligands with non-peptide elements identified by combinatorial synthesis
    • Feng S, Kapoor TM, Shirai F, Combs AP, Schreiber SL: Molecular basis for the binding of SH3 ligands with non-peptide elements identified by combinatorial synthesis. Chem Biol 1996,3:661-670.
    • (1996) Chem Biol , vol.3 , pp. 661-670
    • Feng, S.1    Kapoor, T.M.2    Shirai, F.3    Combs, A.P.4    Schreiber, S.L.5
  • 56
    • 0032512422 scopus 로고    scopus 로고
    • Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: Crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes
    • Stoll VS, Eger BT, Hynes RC, Martichonok V, Jones JB, Pai EF: Differences in binding modes of enantiomers of 1-acetamido boronic acid based protease inhibitors: crystal structures of gamma-chymotrypsin and subtilisin Carlsberg complexes. Biochemistry 1998, 37:451-462.
    • (1998) Biochemistry , vol.37 , pp. 451-462
    • Stoll, V.S.1    Eger, B.T.2    Hynes, R.C.3    Martichonok, V.4    Jones, J.B.5    Pai, E.F.6
  • 57
    • 0032830481 scopus 로고    scopus 로고
    • Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events
    • Wolf YI, Aravind L, Grishin NV, Koonin EV: Evolution of aminoacyl-tRNA synthetases--analysis of unique domain architectures and phylogenetic trees reveals a complex history of horizontal gene transfer events. Genome Res 1999, 9:689-710.
    • (1999) Genome Res , vol.9 , pp. 689-710
    • Wolf, Y.I.1    Aravind, L.2    Grishin, N.V.3    Koonin, E.V.4
  • 58
    • 0027526039 scopus 로고
    • Statistical tests of models of DNA substitution
    • Goldman N: Statistical tests of models of DNA substitution. J Mol Evol 1993, 36:182-198.
    • (1993) J Mol Evol , vol.36 , pp. 182-198
    • Goldman, N.1


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