A predicted consensus structure for the C terminus of the beta and gamma chains of fibrinogen

Proteins: Structure, Function and Genetics

Volumn 27, Issue 2, 1997, Pages 279-289

  Gerloff, Dietlind L ^a   Cohen, Fred E ^a,b   Benner, Steven A ^c,d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c ETH Zentrum ^*  (United States)

^d ETH ZURICH   (Switzerland)

Author keywords

CASP2; compensatory covariation; prediction contest; protein sequence alignment; protein structure prediction

Indexed keywords

FIBRINOGEN;

ARTICLE; CARBOXY TERMINAL SEQUENCE; FIBRIN FORMATION; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

AMINO ACID SEQUENCE; FIBRINOGEN; MOLECULAR SEQUENCE DATA; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY;

EID: 0031042554     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(199702)27:2<279::AID-PROT13>3.0.CO;2-J     Document Type: Article

References (35)

1. Benner, S.A. Patterns of divergence in homologous 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;1520, 1992.
4. Musacchio, A., Gibson, T., Lehto, V.-P., Saraste, M. SH3: An abundant protein domain in search of a function. FEBS Lett. 307:55-61, 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 asparte 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, 1986:163-168.
7. Benner, S.A., Gerloff, D.L., Jenny, T.F. Predicting protein crystal structures. Science 265:1642-1644, 1994.
8. Benner, S.A., Ellington, A.D. Evolution and structural theory: The frontier between chemistry and biochemistry. Bioorg. Chem. Front. 1:1-70, 1990.
9. Benner, S.A. Predicting the conformation of proteins from sequence data. In "Protein Engineering: A Guide to Design and Production." Craik, C.S., Cleland, J. (eds.). 1996:71-99.
10. Chothia, C., Lesk, A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826.
11. Benner, S.A., Chelvanayagam, G., Turcotte, M. Bona fide predictions of protein secondary structure using transparent analyses of multiple sequence alignments. Chem. Rev., submitted, 1996.
12. Jenny, T.F., Benner, S.A. Evaluating predictions of secondary structure in proteins. Biochem. Biophys. Res. Commun. 200:149-155, 1994.
13. Jenny, T.F., Benner, S.A. A prediction of the secondary structure of the pleckstrin homology domain. Proteins 20: 1-4, 1994.
14. Musacchio, A., Gibson, T., Rice, P., Thompson, J., Sarasate M. The PH domain: A common piece in the structural patchwork of signaling proteins. Trends Biochem. Sci. 18: 343-348, 1993.
15. Gerloff, D.L., Jenny, T.F., Knecht, L.J., Benner, S.A. A secondary structure prediction of the hemorrhagic metalloprotease family. Biochem. Biophys. Res. Commun. 194: 560-565, 1993.
16. Benner, S.A., Gerloff, D.L., Chelvanayagam, G. The phospho-beta-galactosidase and synaptotagmin predictions. Proteins 23:446-453, 1995.
17. Bazan, J.F. Helix fold prediction for the cyclin box. Proteins 24:18-34, 1996.
18. Edwards, Y.J.K., Perkins, S.J. The protein fold of the von Willebrand factor type A domain is predicted to be similar to the open twisted beta-sheet flanked by alpha helices found in human Ras-p21. FEBS Lett. 358:283-286, 1995.
19. Jenny, T.F., Gerloff, D.L., Cohen, M.A., Benner, S.A. Predicted secondary and supersecondary structure for the serine/threonine specific protein phosphatase family. Proteins 21:1-10, 1995.
20. Livinston, C.D., Barton, G.J. Secondary structure prediction from multiple sequence data: Blood clotting factor XIII and Yersinia protein-tyrosine phosphatase. Int. J. Peptide Protein Res. 44:239-244, 1994.
21. Lupas, A., Koster, A.J., Walz, J., Baumeister, W. Predicted seconday structure of the 20 S proteasome and model structure of the putative peptide channel. FEBS Lett. 354: 45-49, 1994.
22. Doolittle, R.F. Fibrinogen and fibrin. Annu. Rev. Biochem. 53:195-229, 1984.
23. Weisel, J.W., Stauffacher, C.V., Bullitt, E., Cohen, C. A model for fibrinogen: Domains and sequence. Science 230: 1388-1391, 1985.
24. Bairoch, A., Boeckmann, B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 20:2019-2022, 1992.
25. Gonnet, G.H., Benner, S.A. Computational biochemistry research at ETH. Tech. Rep. Dept. Inform. 154, 1991.
26. Gonnet, G.H., Cohen, M.A., Benner, S.A. Exhaustive matching of the entire protein sequence dtabase. Science 256:1443-1445, 1992.
27. Benner, S.A., Badcoe, I., Cohen, M.A., Gerloff, D.L. Bona fide prediction 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.
28. 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, 191.
29. Göbel, U., Sander, C., Schneider, R., Valencia, A. Correlated mutations and residue contacts in proteins. Proteins 18:309-317, 1994.
30. Neher, E. How frequent are correlated changes in families of protein sequences? Proc. Natl. Acad. Sci. USA 91:98-102, 1994.
31. Shindyalov, I.N., Kolchanov, N.A., Sander, C. Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? Protein Eng. 7:349-358, 1994.
32. Taylor, W.R., Hatrick, K.L. Compensating changes in protein multiple sequence alignments. Protein Eng. 7:341-348, 1994.
33. Chelvanayagam, G., Eggenschwiler, A., Knecht, L., Gonnet, G.H., Benner, S.A. An analysis of simultaneous vriation in protein structures. Proteins, submitted.
34. di Francesco, V., Gamier, J., Munson, P.J. Improving protein secondary structure prediction with aligned homologous sequences. Protein Sci. 5:106-113, 1996.
35. Doolittle, R.F. A detailed consideration of a principal domain of vertebrate fibrinogen and its relatives. Protein Sci. 1:1563-1577, 1992.