A predicted consensus structure for the N-terminal fragment of the heat shock protein HSP90 family

Proteins: Structure, Function and Genetics

Volumn 27, Issue 3, 1997, Pages 450-458

  Gerloff, Dietlind L ^a   Cohen, Fred E ^a   Korostensky, Chantal ^c   Turcotte, Marcel ^b   Gonnet, Gaston H ^b   Benner, Steven A ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of Florida ^*  (United States)

^c NONE

Author keywords

prediction contest; protein sequence alignment; protein structure prediction

Indexed keywords

HEAT SHOCK PROTEIN 90;

AMINO ACID SEQUENCE; ARTICLE; AUTOANALYSIS; HEAT SHOCK; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

ALGORITHMS; BINDING SITES; DNA GYRASE; DNA TOPOISOMERASES, TYPE II; HSP90 HEAT-SHOCK PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 0030889010     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199703)27:3<450::AID-PROT12>3.0.CO;2-K     Document Type: Article

References (26)

1. Benner, S.A. Patterns of divergence in homologos proteins as indicators of tertiary and quaternary structure. Adv. Enzymol. Reg. 28:219-236, 1989.
2. Pananoyotou, G., Bax, B., Gout, I., Federwisch, M., Wroblowski, B., Dhand, R., Fry, M.J., Blundell, T.L., Wollmer, A., Waterfield, M.D. Interaction of the p85 subunit of PI 3-kinase and its N-terminal SH2 domain with a PDGF receptor phosphorylation site. EMBO J. 11:4261-4272, 1992.
3. Russell, R.B., Breed, J., Barton, G.J. Conservation analysis and structure prediction of the SH2 family of phosphotyrosine binding domains. FEBS Lett. 304:15-20, 1992.
4. Musacchio, A., Gibson, T., Lehto, V.-P., Saraste, M. SH3. An abundant protein domain in search of a function. FEBS Lett. 304:15-20, 1992.
5. Bazan, J.F. Structural design and molecular evolution of a cytokine receptor superfamily. Proc. Natl. Acad. Sci. USA 87:6934-6937, 1990.
6. Moe, G.R., Koshland Jr., D.E. Transmembrane signalling through the aspartate receptor. In: "Microbial Energy Transduction, Genetics, Structure and Function of Membrane Proteins." Youvan, D.C., Daldal, F. (eds.). Cold Spring Harbor, NY: Cold Spring Harbor Press, 1986.
7. Benner, S.A., Gerloff, D.L., Jenny, T.F. Predicting protein crystal structures. Science 265:1642-1644, 1994.
8. Benner, S.A. Chelvanyagam, G., Turcotte, M. Bona fide predictions of protein secondary structure using transparent analyses of multiple sequence alignments. Chem. Rev. 1996. (submitted).
9. Benner, S.A., Ellington, A.D. Evolution and structural theory: The frontier between chemistry and biochemistry. Bioorg. Chem. Front. 1:1-70, 1990.
10. Benner, S.A. Predicting the conformation of proteins from sequence data. Prot. Eng. 71:99, 1996.
11. Chothia, C., Lesk, A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826, 1986.
12. Rost, B., Sander, C. Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 231:584-599, 1983.
13. DeFay, T., Cohen, F.E. Evaluation of current techniques for ab initio predictions. Proteins 23:431, 1995.
14. Moult, J., Pedersen, J.T., Judson, R., Fidelis, K. A large-scale experiment to assess protein structure prediction methods. Proteins 23:R2, 1995.
15. Bairoch, A., Boeckmann, B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 20:2019-2022, 1992.
16. Gonnet, G.H., Benner, S.A. Computational biochemistry research at ETH. Tech. Rep. 154, 1991.
17. Gonnet, G.H., Cohen, M.A., Benner, S.A. Exhaustive matching of the entire protein sequence database. Science 256: 1443-1445, 1992.
18. Korostensky, C., Gonnet, G.H. Evaluation measures of multiple sequence alignments. Symp. Discrete Algorithms, 1997. (in preparation).
19. Benner, S.A., Badcoe, I., Cohen, M.A., Gerloff, D.L. Bona fide predicton of aspects of protein conformation: Assigning interior and surface residues from patterns of variation and conservation in homologous protein sequences. J. Mol. Biol. 235:926-958, 1994.
20. Benner, S.A., Gerloff, D. Patterns of divergence in homologous proteins as indicators of secondary and tertiary structure: The catalytic domain of protein kinases. Adv. Enzymol. Reg. 31:121-181, 1991.
21. Csermely, P., Kahn, C.R. Yhe 90-kDa heat shock protein (hsp-90) possesses an ATP binding site and autophosphorylating activity. J. Biol. Chem. 266:4943-4950, 1991.
22. Murzin, A.G., Brenner, S.E., Hubbard, T., Chothia, C. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:536-540, 1995.
23. Wigley, D.B., Davies, G.J., Dodson, E.J., Maxwell, A., Dodson, G. Crystal structure of an N-terminal fragment of the DNA gyrase B protein. Nature 351:624-629, 1991.
24. Jenny, T.F., Benner, S.A. Evaluating predictions of secondary structure in proteins. Biochem. Biophys. Res. Commun. 200:149-155, 1994.
25. Bowie, J.U., Luthy, R., Eisenberg, D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253:164-170, 1991.
26. Russell, R.B., Copley, R.R., Barton, G.J. Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259:349-365, 1996.