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Publication Detail
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
  • Publication Type:
    Journal article
  • Publication Sub Type:
    Journal Article
  • Authors:
    Edwards YJK, Perkins SJ
  • Publication date:
  • Pagination:
    277, 285
  • Journal:
    Journal of Molecular Biology
  • Volume:
  • Issue:
  • Status:
  • Print ISSN:
The fold of the von Willebrand Factor type A domain (vWF-A) was predicted to be similar to an α/β doubly wound fold in the GTP-binding domain of ras-p21, despite the lack of sequence or functional similarity. This was subsequently confirmed by the vWF-A crystal structure from complement receptor type 3. The prediction is now reviewed. The vWF-A secondary structure was predicted with 62 to 75% accuracy and 12 of the 13 secondary structure elements were identified correctly. Accessibility predictions were 69 to 71% accurate. The fold recognition analysis was confirmed, but was much improved by averaging the results from 70 complete vWF-A sequences. The related folds of ras-p21 and flavodoxin scored highly. In addition, both the mapping of the predicted vWF-A secondary structure elements with those in 12 known α/β folds and two Asp residues at the C-terminal ends of two adjacent β-strands matched well with ras-p21 and flavodoxin. The predicted Mg2+-binding site, two disulphide bridges and the secondary structure topology were largely accurate. The exception is the reversal of a β-hairpin at one end of the central β-sheet. We conclude that non-homologous folds with dissimilar functions can be predicted from sequence data with reasonable accuracy, and that the accuracy in this case was principally limited at the periphery of the fold.
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