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Volumn 269, Issue 3, 1997, Pages 423-439

Recognition of analogous and homologous protein folds: Analysis of sequence and structure conservation

Author keywords

Fold recognition; Protein evolution; Protein structure prediction; Sequence identity; Substitution matrices

Indexed keywords

PROTEIN;

EID: 0031566432     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1997.1019     Document Type: Article
Times cited : (175)

References (49)
  • 1
    • 0030310296 scopus 로고    scopus 로고
    • Fast protein fold recognition via sequence to structure alignment and contact capacity potentials
    • Singapore: World Scientific Publishing Co
    • Alexandrov N. N., Nussinov R., Zimmer R. M. Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. Pacific Symposium on Biocomputing. 1996;World Scientific Publishing Co, Singapore.
    • (1996) Pacific Symposium on Biocomputing
    • Alexandrov, N.N.1    Nussinov, R.2    Zimmer, R.M.3
  • 2
    • 0023660022 scopus 로고
    • Correlation of co-ordinate amino acid substitutions with function in viruses related to tobacco mosaic virus
    • Altschuh D., Lesk A. M., Bloomer A. C., Klug A. Correlation of co-ordinate amino acid substitutions with function in viruses related to tobacco mosaic virus. J. Mol. Biol. 193:1987;693-707.
    • (1987) J. Mol. Biol. , vol.193 , pp. 693-707
    • Altschuh, D.1    Lesk, A.M.2    Bloomer, A.C.3    Klug, A.4
  • 3
    • 0025303764 scopus 로고
    • Protein multiple sequence alignment and flexible pattern matching
    • Barton G. J. Protein multiple sequence alignment and flexible pattern matching. Methods Enzymol. 183:1990;403-428.
    • (1990) Methods Enzymol. , vol.183 , pp. 403-428
    • Barton, G.J.1
  • 4
    • 0027412196 scopus 로고
    • Alscript: A tool to format multiple sequence alignments
    • Barton G. J. Alscript: a tool to format multiple sequence alignments. Protein Eng. 6:1993;37-40.
    • (1993) Protein Eng. , vol.6 , pp. 37-40
    • Barton, G.J.1
  • 5
    • 0023518540 scopus 로고
    • A strategy for the rapid multiple alignment of protein sequences: Confidence levels from tertiary structure comparisons
    • Barton G. J., Sternberg M. J. E. A strategy for the rapid multiple alignment of protein sequences: confidence levels from tertiary structure comparisons. J. Mol. Biol. 198:1987;327-337.
    • (1987) J. Mol. Biol. , vol.198 , pp. 327-337
    • Barton, G.J.1    Sternberg, M.J.E.2
  • 7
    • 0020483945 scopus 로고
    • Evolution of proteins formed by β-sheets. I. Plastocyanin and azurin
    • Chothia C., Lesk A. M. Evolution of proteins formed by β-sheets. I. Plastocyanin and azurin. J. Mol. Biol. 160:1982;309-323.
    • (1982) J. Mol. Biol. , vol.160 , pp. 309-323
    • Chothia, C.1    Lesk, A.M.2
  • 8
    • 0022706389 scopus 로고
    • The relation between the divergence of sequence and structure in proteins
    • Chothia C., Lest A. M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:1986;823-826.
    • (1986) EMBO J. , vol.5 , pp. 823-826
    • Chothia, C.1    Lest, A.M.2
  • 9
    • 0009130599 scopus 로고    scopus 로고
    • A structural explanation of the twilight zone or protein sequence homology
    • Chung S. Y., Subbiah S. A structural explanation of the twilight zone or protein sequence homology. Curr. Biol. 4:1996;1123-1127.
    • (1996) Curr. Biol. , vol.4 , pp. 1123-1127
    • Chung, S.Y.1    Subbiah, S.2
  • 10
    • 0000228203 scopus 로고
    • A model of evolutionary change in proteins, matrices for detecting distant relationships
    • Washington: National Biomedical Research Foundation
    • Dayhoff M. O., Schwartz R. M., Orcutt B. C. A model of evolutionary change in proteins, matrices for detecting distant relationships. Atlas of Protein Sequence and Structure. 1978;National Biomedical Research Foundation, Washington.
    • (1978) Atlas of Protein Sequence and Structure
    • Dayhoff, M.O.1    Schwartz, R.M.2    Orcutt, B.C.3
  • 11
    • 0029874551 scopus 로고    scopus 로고
    • Protein fold recognition using sequence-derived predictions
    • Fischer D., Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5:1996;947-955.
    • (1996) Protein Sci. , vol.5 , pp. 947-955
    • Fischer, D.1    Eisenberg, D.2
  • 12
    • 0027485083 scopus 로고
    • Comparison of conformational characteristics in structurally similar protein pairs
    • Flores T. P., Orengo C. A., Moss D. S., Thornton J. M. Comparison of conformational characteristics in structurally similar protein pairs. Protein Sci. 2:1993;1811-1826.
    • (1993) Protein Sci. , vol.2 , pp. 1811-1826
    • Flores, T.P.1    Orengo, C.A.2    Moss, D.S.3    Thornton, J.M.4
  • 13
    • 0026656815 scopus 로고
    • Exhaustive matching of the entire protein sequence database
    • Gonnet G. H., Cohen M. A., Benner S. A. Exhaustive matching of the entire protein sequence database. Science. 256:1992;1443-1444.
    • (1992) Science , vol.256 , pp. 1443-1444
    • Gonnet, G.H.1    Cohen, M.A.2    Benner, S.A.3
  • 14
    • 0026602877 scopus 로고
    • Comparison of the hemocyanin β-barrel with other greek key β-barrels: Possible improtance of the "β-zipper" in protein structure and folding
    • Hazes B., Hol W. G. J. Comparison of the hemocyanin β-barrel with other greek key β-barrels: possible improtance of the "β-zipper" in protein structure and folding. Proteins: Struct. Funct. Genet. 12:1992;278-298.
    • (1992) Proteins: Struct. Funct. Genet. , vol.12 , pp. 278-298
    • Hazes, B.1    Hol, W.G.J.2
  • 15
    • 0026458378 scopus 로고
    • Amino acid substitution matrices from protein blocks
    • Henikoff S., 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
  • 16
    • 0029785147 scopus 로고    scopus 로고
    • Mapping the protein universe
    • Holm L., Sander C. Mapping the protein universe. Science. 273:1996a;595-602.
    • (1996) Science , vol.273 , pp. 595-602
    • Holm, L.1    Sander, C.2
  • 17
    • 0029918694 scopus 로고    scopus 로고
    • The fssp database - Fold classification based on structure alignment of proteins
    • Holm L., Sander C. The fssp database - fold classification based on structure alignment of proteins. Nucl. Acids Res. 24:1996b;206-209.
    • (1996) Nucl. Acids Res. , vol.24 , pp. 206-209
    • Holm, L.1    Sander, C.2
  • 18
    • 0000338489 scopus 로고
    • Comparison of solvent-inaccessible cores of homologous proteins - Definitions useful for protein modelling
    • Hubbard T. J. P., Blundell T. L. Comparison of solvent-inaccessible cores of homologous proteins - definitions useful for protein modelling. Protein Eng. 1:1987;159-171.
    • (1987) Protein Eng. , vol.1 , pp. 159-171
    • Hubbard, T.J.P.1    Blundell, T.L.2
  • 19
    • 0027305858 scopus 로고
    • Alignment and searching for common protein folds using a data bank of structural templates
    • Johnson M. S., Overginton J. P., Blundell T. L. Alignment and searching for common protein folds using a data bank of structural templates. J. Mol. Biol. 231:1993;735-752.
    • (1993) J. Mol. Biol. , vol.231 , pp. 735-752
    • Johnson, M.S.1    Overginton, J.P.2    Blundell, T.L.3
  • 20
    • 0026691182 scopus 로고
    • The rapid generation of mutation data matrices from protein sequences
    • Jones D. T., Taylor W. R., Thornton J. M. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8:1992;275-282.
    • (1992) Comput. Appl. Biosci. , vol.8 , pp. 275-282
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 21
    • 0020997912 scopus 로고
    • A dictionary of protein secondary structure
    • Kabsch W., Sander C. A dictionary of protein secondary structure. Biopolymers. 22:1983;2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 22
    • 0028579713 scopus 로고
    • Different protein sequences can give rise to highly similar folds through different stabilizing interactions
    • Laurents D. V., Subbiah S., Levitt M. Different protein sequences can give rise to highly similar folds through different stabilizing interactions. Protein Sci. 3:1994;1938-1944.
    • (1994) Protein Sci. , vol.3 , pp. 1938-1944
    • Laurents, D.V.1    Subbiah, S.2    Levitt, M.3
  • 23
    • 0028818340 scopus 로고
    • Protein-structure prediction by threading methods - Evaluation of current techniques
    • Lemer C. M. R., Rooman M. J., Wodak S. J. Protein-structure prediction by threading methods - evaluation of current techniques. Proteins: Struct. Funct. Genet. 23:1995;337-355.
    • (1995) Proteins: Struct. Funct. Genet. , vol.23 , pp. 337-355
    • Lemer, C.M.R.1    Rooman, M.J.2    Wodak, S.J.3
  • 24
    • 0019332167 scopus 로고
    • How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    • Lesk A. M., Chothia C. How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. J. Mol. Biol. 136:1980;225-270.
    • (1980) J. Mol. Biol. , vol.136 , pp. 225-270
    • Lesk, A.M.1    Chothia, C.2
  • 25
    • 0020429363 scopus 로고
    • Evolution of proteins formed by β-sheets II. The core of the immunoglobulin domains
    • Lesk A. M., Chothia C. Evolution of proteins formed by β-sheets II. The core of the immunoglobulin domains. J. Mol. Biol. 160:1982;325-342.
    • (1982) J. Mol. Biol. , vol.160 , pp. 325-342
    • Lesk, A.M.1    Chothia, C.2
  • 26
    • 0029165589 scopus 로고
    • Thioredoxin - A fold for all reasons
    • Martin J. L. Thioredoxin - a fold for all reasons. Structure. 3:1995;245-250.
    • (1995) Structure , vol.3 , pp. 245-250
    • Martin, J.L.1
  • 27
    • 0027373949 scopus 로고
    • Crystal structure of the DsbA protein required for disulphide bond formation in vivo
    • Martin J. L., Bardwell J. C. A., Kuriyan J. Crystal structure of the DsbA protein required for disulphide bond formation in vivo. Nature. 365:1993;464-468.
    • (1993) Nature , vol.365 , pp. 464-468
    • Martin, J.L.1    Bardwell, J.C.A.2    Kuriyan, J.3
  • 29
    • 0028961335 scopus 로고
    • Scop: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin A., Brenner S. E., Hubbard T., Chothia C. scop: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 30
    • 0027162768 scopus 로고
    • Sweet tasting protein monellin is related to the cystatin family of thiol proteinase inhibitors
    • Murzin A. G. Sweet tasting protein monellin is related to the cystatin family of thiol proteinase inhibitors. J. Mol. Biol. 230:1993a;689-694.
    • (1993) J. Mol. Biol. , vol.230 , pp. 689-694
    • Murzin, A.G.1
  • 31
    • 0027372804 scopus 로고
    • Can homologous proteins evolve different enzymatic activities?
    • Murzin A. G. Can homologous proteins evolve different enzymatic activities? J. Mol. Biol. 18:1993b;403-405.
    • (1993) J. Mol. Biol. , vol.18 , pp. 403-405
    • Murzin, A.G.1
  • 32
    • 0026556882 scopus 로고
    • β-trefoil fold patterns of structure and sequence in the Kunitz inhibitors interleukins-1β and 1α and fibroblast growth factors
    • Murzin A. G., Lesk A. M., Chothia C. β-trefoil fold patterns of structure and sequence in the Kunitz inhibitors interleukins-1β and 1α and fibroblast growth factors. J. Mol. Biol. 223:1992;531-543.
    • (1992) J. Mol. Biol. , vol.223 , pp. 531-543
    • Murzin, A.G.1    Lesk, A.M.2    Chothia, C.3
  • 33
    • 0027479161 scopus 로고
    • OB(oligonucleotide/oligosaccharide binding)-fold: Common structural and functional solution for non-homologous sequences
    • Murzin A. Z. OB(oligonucleotide/oligosaccharide binding)-fold: common structural and functional solution for non-homologous sequences. EMBO J. 12:1993;861-867.
    • (1993) EMBO J. , vol.12 , pp. 861-867
    • Murzin, A.Z.1
  • 35
    • 0028593509 scopus 로고
    • Protein superfamilies and domain superfolds
    • Orengo C. A., Jones D. T., Thornton J. M. Protein superfamilies and domain superfolds. Nature. 372:1994;631-634.
    • (1994) Nature , vol.372 , pp. 631-634
    • Orengo, C.A.1    Jones, D.T.2    Thornton, J.M.3
  • 36
    • 0025104478 scopus 로고
    • Tertiary structural constraints on protein evolutionary diversity: Templates, key residues and structure prediction
    • Overington J., Johnson M. S., Sali A., Blundell T. L. Tertiary structural constraints on protein evolutionary diversity: templates, key residues and structure prediction. Proc. Roy. Soc. ser. B. 241:1990;132-145.
    • (1990) Proc. Roy. Soc. Ser. B , vol.241 , pp. 132-145
    • Overington, J.1    Johnson, M.S.2    Sali, A.3    Blundell, T.L.4
  • 37
    • 0026511848 scopus 로고
    • A data bank merging related protein structures and sequences
    • Pascarella S., Argos P. A data bank merging related protein structures and sequences. Protein Eng. 5:1992;121-137.
    • (1992) Protein Eng. , vol.5 , pp. 121-137
    • Pascarella, S.1    Argos, P.2
  • 38
    • 0026452698 scopus 로고
    • Evaluation of the sequence template method for protein structure prediction. Discrimination of the β/α-barrel fold
    • Pickett S. D., Saqi M. A. S., Sternberg M. J. E. Evaluation of the sequence template method for protein structure prediction. Discrimination of the β/α-barrel fold. J. Mol. Biol. 228:1992;170-187.
    • (1992) J. Mol. Biol. , vol.228 , pp. 170-187
    • Pickett, S.D.1    Saqi, M.A.S.2    Sternberg, M.J.E.3
  • 39
    • 0029186289 scopus 로고
    • TOPITS: Treading one-dimensional predictions into three-dimensional structures
    • C. Rawlings, D. Clark, R. Altman, L. Hunter, T. Lengauer, & S. Wodak. Menlo Park: AAAI Press
    • Rost B. TOPITS: treading one-dimensional predictions into three-dimensional structures. Rawlings C., Clark D., Altman R., Hunter L., Lengauer T., Wodak S. Proc. 3rd. Int. Conf. Intel. Sys. Mol. Biol. 1995;AAAI Press, Menlo Park.
    • (1995) Proc. 3rd. Int. Conf. Intel. Sys. Mol. Biol.
    • Rost, B.1
  • 40
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost B., Sander C. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232:1993;584-599.
    • (1993) J. Mol. Biol. , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 41
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost B., Sander C. Conservation and prediction of solvent accessibility in protein families. Proteins: Struct. Funct. Genet. 20:1994;216-226.
    • (1994) Proteins: Struct. Funct. Genet. , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 42
    • 0028064006 scopus 로고
    • Redefining the goals of protein secondary structure prediction
    • Rost B., Sander C., Schneider R. Redefining the goals of protein secondary structure prediction. J. Mol. Biol. 235:1994;13-26.
    • (1994) J. Mol. Biol. , vol.235 , pp. 13-26
    • Rost, B.1    Sander, C.2    Schneider, R.3
  • 43
    • 0026743174 scopus 로고
    • Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels
    • Russell R. B., Barton G. J. Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels. Proteins: Struct. Funct. Genet. 14:1992;309-323.
    • (1992) Proteins: Struct. Funct. Genet. , vol.14 , pp. 309-323
    • Russell, R.B.1    Barton, G.J.2
  • 44
    • 0027765576 scopus 로고
    • The limits of protein secondary structure prediction accuracy from multiple sequence alignment
    • Russell R. B., Barton G. J. The limits of protein secondary structure prediction accuracy from multiple sequence alignment. J. Mol. Biol. 234:1993;951-957.
    • (1993) J. Mol. Biol. , vol.234 , pp. 951-957
    • Russell, R.B.1    Barton, G.J.2
  • 45
    • 0028081403 scopus 로고
    • Structural features can be unconserved in proteins with similar folds: An analysis of side-chain to side-chain contacts, secondary structure and accessibility
    • Russell R. B., Barton G. J. Structural features can be unconserved in proteins with similar folds: An analysis of side-chain to side-chain contacts, secondary structure and accessibility. J. Mol. Biol. 244:1994;332-350.
    • (1994) J. Mol. Biol. , vol.244 , pp. 332-350
    • Russell, R.B.1    Barton, G.J.2
  • 46
    • 84995072940 scopus 로고
    • Protein fold recognition from secondary structure assignments
    • L. Hunter, & B.D. Shriver. Los Alamitos: IEEE Computer Society Press
    • Russell R. B., Copley R. R., Barton G. J. Protein fold recognition from secondary structure assignments. Hunter L., Shriver B. D. Proc. 28th Hawaii. Int. Conf. Sys. Sci. 1995;IEEE Computer Society Press, Los Alamitos.
    • (1995) Proc. 28th Hawaii. Int. Conf. Sys. Sci.
    • Russell, R.B.1    Copley, R.R.2    Barton, G.J.3
  • 47
    • 0029951995 scopus 로고    scopus 로고
    • Protein fold recognition by mapping predicted secondary structures
    • Russell R. B., Copley R. R., Barton G. J. Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259:1996;349-365.
    • (1996) J. Mol. Biol. , vol.259 , pp. 349-365
    • Russell, R.B.1    Copley, R.R.2    Barton, G.J.3
  • 48
    • 0019887799 scopus 로고
    • Identification of common molecular subsequences
    • Smith T. F., Waterman M. S. Identification of common molecular subsequences. J. Mol. Biol. 147:1981;195-197.
    • (1981) J. Mol. Biol. , vol.147 , pp. 195-197
    • Smith, T.F.1    Waterman, M.S.2
  • 49
    • 0022591495 scopus 로고
    • Classification of amino acid conservation
    • Taylor W. R. Classification of amino acid conservation. J. Theoret. Biol. 119:1986;205-218.
    • (1986) J. Theoret. Biol. , vol.119 , pp. 205-218
    • Taylor, W.R.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.