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Volumn 260, Issue 2, 1996, Pages 277-285

Assessment of protein fold predictions from sequence information: The predicted α/β doubly wound fold of the von Willebrand factor type a domain is similar to its crystal structure

Author keywords

Doubly wound fold; Prediction assessment; Protein fold recognition; Secondary structure prediction; Solvent accessibility prediction; von Willebrand factor

Indexed keywords

COMPLEMENT RECEPTOR; DISULFIDE; FLAVODOXIN; RAS PROTEIN; VON WILLEBRAND FACTOR;

EID: 0030581168     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0398     Document Type: Article
Times cited : (29)

References (31)
  • 1
    • 0025162844 scopus 로고
    • Structural design and molecular evolution of a cytokine receptor superfamily
    • Bazan, J. F. (1990). Structural design and molecular evolution of a cytokine receptor superfamily. Proc. Natl Acad. Sci. USA, 87, 6934-6938.
    • (1990) Proc. Natl Acad. Sci. USA , vol.87 , pp. 6934-6938
    • Bazan, J.F.1
  • 2
    • 0027943361 scopus 로고
    • Predicting protein crystal structures
    • Benner, S. A., Gerloff, D. L. & Jenny, T. F. (1994). Predicting protein crystal structures. Science, 265, 1642-1644.
    • (1994) Science , vol.265 , pp. 1642-1644
    • Benner, S.A.1    Gerloff, D.L.2    Jenny, T.F.3
  • 5
    • 0025807693 scopus 로고
    • The superfamily of proteins with von Willebrand factor-type A-like domains: One theme common to components of extracellular matrix, hemostasis, cellular adhesion and defense mechanisms
    • Colombatti, A. & Bonaldo, P. (1991). The superfamily of proteins with von Willebrand Factor-type A-like domains: one theme common to components of extracellular matrix, hemostasis, cellular adhesion and defense mechanisms. Blood, 77, 2305-2315.
    • (1991) Blood , vol.77 , pp. 2305-2315
    • Colombatti, A.1    Bonaldo, P.2
  • 6
    • 0023512802 scopus 로고
    • Prediction of secondary structure by evolutionary comparison: Application to the a subunit of tryptophan synthase
    • Crawford, I. P., Niermann, T. & Kirschner, K. (1987). Prediction of secondary structure by evolutionary comparison: application to the a subunit of tryptophan synthase. Proteins: Struct. Funct. Genet. 2, 118-129.
    • (1987) Proteins: Struct. Funct. Genet. , vol.2 , pp. 118-129
    • Crawford, I.P.1    Niermann, T.2    Kirschner, K.3
  • 7
    • 4244135790 scopus 로고
    • Prediction of the fold of the von Willebrand Factor type A domain as an open twisted β-sheet flanked by α-helices: Possible identification with human ras-p21 and bacterial elongation factor EF-Tu and implications for evolution
    • Chester, U.K.
    • Edwards, Y. J. K. & Perkins, S. J. (1994). Prediction of the fold of the von Willebrand Factor type A domain as an open twisted β-sheet flanked by α-helices: possible identification with human ras-p21 and bacterial elongation factor EF-Tu and implications for evolution. Genes, Proteins and Computers: An International Conference on Bioinformatics, Networking and Computing in Molecular Biology, September 1994. Chester, U.K.
    • (1994) Genes, Proteins and Computers: An International Conference on Bioinformatics, Networking and Computing in Molecular Biology, September 1994
    • Edwards, Y.J.K.1    Perkins, S.J.2
  • 8
    • 0028959231 scopus 로고
    • The protein fold of the von Willebrand Factor type A domain is predicted to be similar to the open twisted β-sheet flanked by α-helices found in human ras-p21
    • Edwards, Y. J. K. & Perkins, S. J. (1995a). The protein fold of the von Willebrand Factor type A domain is predicted to be similar to the open twisted β-sheet flanked by α-helices found in human ras-p21. FEBS Letters, 358, 283-286.
    • (1995) FEBS Letters , vol.358 , pp. 283-286
    • Edwards, Y.J.K.1    Perkins, S.J.2
  • 9
    • 85030209375 scopus 로고
    • Assessment of a method for protein fold predictions prior to crystal structure determinations: The von Willebrand Type A domain
    • University of Bath, U.K.
    • Edwards, Y. J. K. & Perkins, S. J. (1995b). Assessment of a method for protein fold predictions prior to crystal structure determinations: the von Willebrand Type A domain. Perspectives on Protein Engineering: Molecular Bioinformatics Meeting, September 1995. University of Bath, U.K.
    • (1995) Perspectives on Protein Engineering: Molecular Bioinformatics Meeting, September 1995
    • Edwards, Y.J.K.1    Perkins, S.J.2
  • 10
    • 0026690571 scopus 로고
    • A new approach to protein fold recognition
    • Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition. Nature, 358, 86-89.
    • (1992) Nature , vol.358 , pp. 86-89
    • Jones, D.T.1    Taylor, W.R.2    Thornton, J.M.3
  • 11
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
    • (1983) Biopolymers , vol.22 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 12
    • 0028105794 scopus 로고
    • Yeast chromosome III: New gene functions
    • Koonin, E. V., Bork, P. & Sander, C. (1994). Yeast chromosome III: new gene functions. EMBO J. 13, 493-503.
    • (1994) EMBO J. , vol.13 , pp. 493-503
    • Koonin, E.V.1    Bork, P.2    Sander, C.3
  • 13
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B. & Richards, F. M. (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
  • 14
    • 0028986196 scopus 로고
    • Crystal structure of the A domain from the α subunit of integrin CR3 (CD11b/CD18)
    • Lee, J.-O., Rieu, P., Arnaout, M. A. & Liddington, R. (1995). Crystal structure of the A domain from the α subunit of integrin CR3 (CD11b/CD18). Cell, 80, 631-638.
    • (1995) Cell , vol.80 , pp. 631-638
    • Lee, J.-O.1    Rieu, P.2    Arnaout, M.A.3    Liddington, R.4
  • 15
    • 0027483226 scopus 로고
    • A novel divalent cation-binding site in the A domain of the β2 integrin CR3 (CD11b/CD18) is essential for ligand binding
    • Michishita, M., Videm, V. & Arnaout, M. A. (1993). A novel divalent cation-binding site in the A domain of the β2 integrin CR3 (CD11b/CD18) is essential for ligand binding. Cell, 72, 857-867.
    • (1993) Cell , vol.72 , pp. 857-867
    • Michishita, M.1    Videm, V.2    Arnaout, M.A.3
  • 17
    • 0023189868 scopus 로고
    • A structural model for the retroviral proteases
    • Pearl, L. H. & Taylor, W. R. (1987). A structural model for the retroviral proteases. Nature, 329, 351-354.
    • (1987) Nature , vol.329 , pp. 351-354
    • Pearl, L.H.1    Taylor, W.R.2
  • 18
    • 0023916526 scopus 로고
    • A study of the structure of human complement component Factor H by Fourier transform infrared spectroscopy and secondary structure averaging methods
    • Perkins, S. J., Haris, P. I., Sim, R. B. & Chapman, D. (1988). A study of the structure of human complement component Factor H by Fourier transform infrared spectroscopy and secondary structure averaging methods. Biochemistry, 27, 4004-4012.
    • (1988) Biochemistry , vol.27 , pp. 4004-4012
    • Perkins, S.J.1    Haris, P.I.2    Sim, R.B.3    Chapman, D.4
  • 19
    • 0028360720 scopus 로고
    • The secondary structure of the von Willebrand Factor type A domain in Factor B of human complement by fourier-transform infrared spectroscopy. Its occurrence in collagen type-VI, type-VII, type-XII and type-XIV, the integrins and other proteins by averaged structure predictions
    • Perkins, S. J., Smith, K. F., Williams, S. C., Haris, P. I., Chapman, D. & Sim, R. B. (1994). The secondary structure of the von Willebrand Factor type A domain in Factor B of human complement by fourier-transform infrared spectroscopy. Its occurrence in collagen type-VI, type-VII, type-XII and type-XIV, the integrins and other proteins by averaged structure predictions. J. Mol. Biol. 238, 104-119.
    • (1994) J. Mol. Biol. , vol.238 , pp. 104-119
    • Perkins, S.J.1    Smith, K.F.2    Williams, S.C.3    Haris, P.I.4    Chapman, D.5    Sim, R.B.6
  • 20
    • 0027291015 scopus 로고
    • Prediction of protein secondary structure at better than 70% accuracy
    • Rost, B. & Sander, C. (1993). Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232, 584-599.
    • (1993) J. Mol. Biol. , vol.232 , pp. 584-599
    • Rost, B.1    Sander, C.2
  • 21
    • 0028109886 scopus 로고
    • Conservation and prediction of solvent accessibility in protein families
    • Rost, B. & Sander, C. (1994). Conservation and prediction of solvent accessibility in protein families. Proteins: Struct. Fund. Genet. 20, 216-226.
    • (1994) Proteins: Struct. Fund. Genet. , vol.20 , pp. 216-226
    • Rost, B.1    Sander, C.2
  • 22
    • 0027765576 scopus 로고
    • The limits of protein secondary structure prediction accuracy from multiple sequence alignment
    • Russell, R. B. & Barton, G. J. (1993). The limits of protein secondary structure prediction accuracy from multiple sequence alignment. J. Mol. Biol. 234, 951-957.
    • (1993) J. Mol. Biol. , vol.234 , pp. 951-957
    • Russell, R.B.1    Barton, G.J.2
  • 24
    • 0025317502 scopus 로고
    • The definition of topological equivalence in homologous and analogous structures: A procedure involving a comparison of local properties and relationships
    • Šali, A. & Blundell, T. L. (1990). The definition of topological equivalence in homologous and analogous structures: a procedure involving a comparison of local properties and relationships. J. Mol. Biol. 212, 403-428.
    • (1990) J. Mol. Biol. , vol.212 , pp. 403-428
    • Šali, A.1    Blundell, T.L.2
  • 26
    • 0026484847 scopus 로고
    • Structure of recombinant N-terminal globule of type VI collagen α3 chain and its binding to heparin and hyaluronan
    • Specks, U., Mayer, U., Nischt, R., Spissinger, T., Mann, K., Timpl, R., Engel, J. & Chu, M.-L. (1992). Structure of recombinant N-terminal globule of type VI collagen α3 chain and its binding to heparin and hyaluronan. EMBO J. 11, 4281-4290.
    • (1992) EMBO J. , vol.11 , pp. 4281-4290
    • Specks, U.1    Mayer, U.2    Nischt, R.3    Spissinger, T.4    Mann, K.5    Timpl, R.6    Engel, J.7    Chu, M.-L.8
  • 27
    • 0027220648 scopus 로고
    • An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure
    • Srinivasan, N. & Blundell, T. L. (1993). An evaluation of the performance of an automated procedure for comparative modelling of protein tertiary structure. Protein Eng. 6, 501-512.
    • (1993) Protein Eng. , vol.6 , pp. 501-512
    • Srinivasan, N.1    Blundell, T.L.2
  • 28
    • 0001433241 scopus 로고
    • Knowledge-based modelling of homologous proteins. Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures
    • Sutcliffe, M. J., Haneef I., Carney, D. & Blundell, T. L. (1987). Knowledge-based modelling of homologous proteins. Part I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng. 1, 377-384.
    • (1987) Protein Eng. , vol.1 , pp. 377-384
    • Sutcliffe, M.J.1    Haneef, I.2    Carney, D.3    Blundell, T.L.4
  • 29
    • 0028304961 scopus 로고
    • Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures
    • Wako, H. & Blundell, T. L. (1994a). Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. II. Secondary structures. J. Mol. Biol. 238, 693-708.
    • (1994) J. Mol. Biol. , vol.238 , pp. 693-708
    • Wako, H.1    Blundell, T.L.2
  • 30
    • 0028239337 scopus 로고
    • Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. I. Solvent accessibility classes
    • Wako, H. & Blundell, T. L. (1994b). Use of amino acid environment-dependent substitution tables and conformational propensities in structure prediction from aligned sequences of homologous proteins. I. Solvent accessibility classes. J. Mol. Biol. 238, 682-692.
    • (1994) J. Mol. Biol. , vol.238 , pp. 682-692
    • Wako, H.1    Blundell, T.L.2
  • 31
    • 0027168828 scopus 로고
    • Antitermination of amidase expression in Pseudomonas aeruginosa is controlled by a novel cytoplasmic amide-binding protein
    • Wilson, S. A., Wachira, S. J., Drew, R. H., Jones, D. & Pearl, L. H. (1993). Antitermination of amidase expression in Pseudomonas aeruginosa is controlled by a novel cytoplasmic amide-binding protein. EMBO J. 12, 3637-3642.
    • (1993) EMBO J. , vol.12 , pp. 3637-3642
    • Wilson, S.A.1    Wachira, S.J.2    Drew, R.H.3    Jones, D.4    Pearl, L.H.5


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