Structural details (kinks and non-α conformations) in transmembrane helices are intrahelically determined and can be predicted by sequence pattern descriptors

Nucleic Acids Research

Volumn 31, Issue 15, 2003, Pages 4625-4631

  Rigoutsos, Isidore ^c   Riek, Peter ^a   Graham, Robert M ^a,b   Novotny, Jiri ^a  

^a ST VINCENT S HOSPITAL   (Australia)

^b UNIVERSITY OF NEW SOUTH WALES   (Australia)

^c IBM T J WATSON RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; POLYPEPTIDE; PROTEIN; MEMBRANE PROTEIN; RHODOPSIN;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; EMBL NUCLEOTIDE SEQUENCE DATABASE; METHODOLOGY; PREDICTION; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ACTIVITY RELATION; STRUCTURE ANALYSIS; SWISS-PROT; X RAY CRYSTALLOGRAPHY; CHEMICAL STRUCTURE; CHEMISTRY; INTERNET; MOLECULAR GENETICS; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT;

AMINO ACID SEQUENCE; INTERNET; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN STRUCTURE, SECONDARY; RHODOPSIN; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN;

EID: 0041660896     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg639     Document Type: Article

References (22)

1. Epstein,C.J. (1966) Role of amino-acid 'code' and selection for conformation in the evolution of proteins. Nature, 210, 25-28.
2. Epstein,C.J. (1967) Non-randomness of amino-acid changes in the evolution of homologous proteins. Nature, 215, 355-359.
3. Chothia,C. (1992) Proteins - 1000 families for the molecular biologist. Nature, 357, 543-544.
4. Govindarajan,S., Recabarren,R. and Goldstein,R.A. (1999) Estimating the total number of protein folds. Proteins, 35, 408-414.
5. Bashford,D., Chothia,C. and Lesk,A.M. (1987) Determinants of a protein fold: unique features of the globin amino acid sequences. J. Mol. Biol., 196, 199-216.
6. Pearson,W.R. (1996) Effective protein sequence comparison. Methods Enzymol., 266, 227-258.
7. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
8. Smith,T.F. and Waterman,M.S. (1981) Identification of common molecular subsequences. J. Mol. Biol., 147, 195-197.
9. Thompson,T.J., Higgins,D.G. and Gibson,T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res., 22, 4673-4680.
10. Karplus,K., Barrett,C. and Hughey,R. (1998) Hidden Markov models for detecting remote protein homologies. Bioinformatics, 14, 846-856.
11. Rigoutsos,I. and Floratos,A. (1998) Combinatorial pattern discovery in biological sequences: the TEIRESIAS algorithm. Bioinformatics, 14, 55-67.
12. Rigoutsos,I., Floratos,A., Ouzounis,C., Gao,Y. and Parida,L. (1999) Dictionary building via unsupervised hierarchical motif discovery in the sequence space of natural proteins. Proteins, 37, 264-277.
13. Bairoch,A. and Apweiler,R. (2000) The Swiss-Prot protein sequence database and its supplement TrEMBL in 2000. Nucleic Acids Res., 28, 45-48.
14. Rigoutsos,I., Huynh,T., Floratos,A., Parida,L. and Platt,D. (2002) Dictionary-driven protein annotation. Nucleic Acids Res., 30, 3901-3916.
15. Shibuya,T. and Rigoutsos,I. (2002) Dictionary-driven prokaryotic gene finding. Nucleic Acids Res., 30, 2710-2725.
16. Popot,J.L. and Engelman,D.M. (2000) Helical membrane protein folding, stability and evolution. Annu. Rev. Biochem., 69, 881-922.
17. Riek,R.P., Rigoutsos,I., Novotny,J. and Graham,R.M. (2001) Non-α-helical elements modulate polytopic membrane architecture. J. Mol. Biol., 306, 349-362.
18. Ubarretxena-Belandia,I. and Engelman,D.M. (2001) Helical membrane proteins: diversity of functions in the context of simple architecture. Curr. Opin. Struct. Biol., 11, 370-376.
19. Pauling,L., Corey,R.B. and Branson,H.R. (1951) The structure of proteins: two hydrogen bonded helical conformations of the polypeptide chain. Proc. Natl Acad. Sci. USA, 37, 205-211.
20. Barlow,D.J. and Thornton,J.M. (1988) Helix geometry in proteins. J. Mol. Biol., 201, 601-619.
21. LoConte,L., Brenner,S.E., Hubbard,T.J.P., Chothia,C. and Murzin,A.G. (2002) SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res., 30, 264-267.
22. Chen,S., Lin,F., Xu,M., Riek,P., Novotny,J. and Graham,R.M. (2002) Mutation of a single TMVI residue, Phe(282), in the beta(2)-adrenergic receptor results in structurally distinct activated receptor conformations. Biochemistry, 41, 6045-6053.