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Flanking Strands of Beta Turns

Flanking Strands of Beta Turns. Joe Dundas Lab Meeting 10/19/05. Motivation. Kim J et al. Protein Science 2005 Two beta turns (beta4/beta5 and beta8/beta9) of human acidic fibroblast growth factor. Turns are identical length with different conformations. No conformational change.

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Flanking Strands of Beta Turns

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  1. Flanking Strands of Beta Turns Joe Dundas Lab Meeting 10/19/05

  2. Motivation • Kim J et al. Protein Science 2005 • Two beta turns (beta4/beta5 and beta8/beta9) of human acidic fibroblast growth factor. • Turns are identical length with different conformations. • No conformational change. • Sequence swapped. • Poly-glycine substitution mutations. • Structural analysis suggests that residues flanking the turn are a primary structural determinant.

  3. Data Set • From 1770 structures (pdbselect 25%) • 1953 turns of length 4 • 1807 turns of length 5 • 1304 turns of length 6 • 760 turns of length 7 • 679 turns of length 8

  4. Turn Clusters Length 4 • All vs. all structure alignment • Hierarchical clustering (distance = rmsd) • Cut tree distance 4 • 25 clusters • Cluster 1 – 1855 members • Cut tree distance 3 • 36 clusters • Cluster 1 – 584 • Cluster 2 – 1257 • Cut tree distance 1 • 99 clusters • 6 Clusters with > 100 members

  5. Length 4 – Cut Distance 1 Cluster 3 181 members Cluster 4 287 members Cluster 2 384 members Cluster 6 125 members Cluster 8 171 members Cluster 11 170 members 1318 members in these 6 clusters = 1318/1953 = 67% of length 4 turns

  6. Turns of Length 4 Cluster 1 N terminal Strand C terminal Strand

  7. Turns of Length 4 Cluster 3 N terminal Strand C terminal Strand

  8. Turns of Length 4 Cluster 5 N terminal Strand C terminal Strand

  9. N terminal strands Cluster 1 2 3 4 5 6 2 3 4 5 6 7 0 1 Position from turn

  10. C terminal strands Cluster 1 2 3 4 5 6 0 1 2 4 3 5 6 7 Position from turn

  11. Strand Pair by Cluster Clusters 1 thru 3 1 2 3 2 3 4 5 6 7 0 1 Position from turn

  12. Strand Pair by Cluster Clusters 4 thru 6 4 5 6 2 3 4 5 6 7 0 1 Position from turn

  13. Conclusion It is possible that the sequence of the flanking strands determines the conformation of the turn rather than the sequence of the turn itself.

  14. Question It is possible that the sequence of the flanking strands determines the conformation of the turn rather than the sequence of the turn itself. Given only the sequence of two strands, is it possible to determine the orientation of the two strands relative to each other?

  15. Top View θ ρ α Side View φ β ρ Strand Angles α θ ρ β φ

  16. Future Work • Cluster based on (θ,φ,β,ρ). • Determine if there are any propensities for certain residue types at each position from the turn for each cluster. • Given only strand sequences, predict strand orientation and turn conformation.

  17. The End

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