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Relationship between Amino Acids Sequences and Protein Structures: Folding Patterns and Sequence Patterns

  • Alexander Kister
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5542)

Abstract

Two crucial problems of protein folding are considered here. First, the hypothesis, that all proteins with an identical SSS, regardless of degree of sequence identity among sequences have common sequence pattern. To find conserved positions and create a sequences pattern a new algorithm of the structure-based multiple sequences alignment was developed. An essential feature of the algorithm is that the alignment is based on residues that form hydrogen bond contacts between strands in protein structures. It was shown that SSS-specific sequence patterns have very high sensitivity for identifying protein structure and can be used for SSS prediction without any prior structural information. Second, the rules by which secondary structure elements – beta strands come together into supersecondary structure (SSS) – folding patterns. Knowledge of these patterns that uncover the spatial arrangement of strands will likely prove useful in protein structure prediction.

Keywords

Beta-sandwich proteins supersecondary structure protein folding protein structure classification protein structure prediction sequence alignment 

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References

  1. 1.
    Sela, M., White Jr., F.H., Anfinsen, C.B.: Reductive Cleavage of Disulfide Bridges in Ribonuclease. Science 125, 691–692 (1957)CrossRefPubMedGoogle Scholar
  2. 2.
    Anfinsen, C.: Principles that Govern the Folding of Protein Chains. Science 181, 223–230 (1973)CrossRefPubMedGoogle Scholar
  3. 3.
    Xiang, Z.: Advances in homology protein structure modeling. Curr. Protein Pept. Sci. 7, 217–227 (2006)CrossRefPubMedPubMedCentralGoogle Scholar
  4. 4.
    Dalton, J., Jackson, R.: n evaluation of automated homology modelling methods at low target template sequence similarity. Bioinformatics 3, 1901–1908 (2007)CrossRefGoogle Scholar
  5. 5.
    Gunalski, K.: Comparative modeling for protein structure prediction. Curr. Opin. Struct. Biol. 16, 172–177 (2006)CrossRefGoogle Scholar
  6. 6.
    Pugalenthi, G., Tang, K., Suganthan, P.N., Chakrabarti, C.: Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. Bioinformatics 25, 204–210 (2008)CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Kister, A.E., Fokas, A.S., Papatheodorou, T.S., Gelfand, I.M.: Strict rules determine arrangements of strands in sandwich proteins. Proc. Natl. Acad. Sci. USA 103, 4107–4110 (2006)CrossRefPubMedPubMedCentralGoogle Scholar
  8. 8.
    Chiang, Y.S., Gelfand, T.I., Kister, A.E., Gelfand, I.M.: New classification of supersecondary structures of sandwich-like proteins uncovers strict patterns of strand assemblage. Proteins 68(4), 915–921 (2007)CrossRefPubMedGoogle Scholar
  9. 9.
    Levitt, M., Chothia, C.: Structural patterns in globular proteins. Nature 261, 552–558 (1976)CrossRefPubMedGoogle Scholar
  10. 10.
    Sternberg, M.J.E., Thornton, J.M.: On the conformation of proteins: the handedness of the b-strand-a-helix-b-strand unit. J. Mol. Biol. 105, 367–382 (1976)CrossRefPubMedGoogle Scholar
  11. 11.
    Cohen, F.E., Sternberg, M.J.E., Taylor, W.R.: Analysis of the tertiary structure of protein beta-sheet sandwiches. J. Mol. Biol. 148, 253–272 (1981)CrossRefPubMedGoogle Scholar
  12. 12.
    Michalopoulos, I., Torrance, G.M., Gilbert, D.R., Westhead, D.R.: TOPS: an enhanced database of protein structural topology. Nucleic Acids Res. 32, D251–D254 (2004)CrossRefGoogle Scholar
  13. 13.
    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)PubMedGoogle Scholar
  14. 14.
    Orengo, C.A., Michie, A.D., Jones, D.T., Swindells, M.B., Thornton, J.M.: CATH: A Hierarchic Classification of Protein Domain Structures. Structure 5, 1093–1108 (1997)CrossRefPubMedGoogle Scholar
  15. 15.
    Rice, P., Longden, I., Bleasby, A.: EMBOSS: The European Molecular Biology Open Software Suite Trends in Genetics 16, 276–277 (2000)PubMedGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2009

Authors and Affiliations

  • Alexander Kister
    • 1
  1. 1.Department of Health InformaticsSHRP, University of Medicine and Dentistry of New JerseyNewarkUSA

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