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Remembrances of Things Past

Remembrances of Things Past. Comparison of RNA conformers with very small RNA crystal structures. Clustered the conformers Compared with dinucleoside phosphates High resolution With and without ligands. RMSD Clustering. Hierarchical clustering using ‘complete linkages’

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Remembrances of Things Past

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  1. Remembrances of Things Past

  2. Comparison of RNA conformers with very small RNA crystal structures • Clustered the conformers • Compared with dinucleoside phosphates • High resolution • With and without ligands

  3. RMSD Clustering • Hierarchical clustering using ‘complete linkages’ • Cluster data set included: • 38 model dinucleotides representing the diversity of RNA conformation space (earlier version) • 7 high resolution dinucleoside phosphate crystal structures • Clustered families based on backbone RMSD

  4. RMSD clustering P-O5’-C5’-C4-’C3-O3’-P-O5’-C5’C4’-C3’-O3’ No base atoms included in calculations

  5. RMSD Cluster Results ARNA DRB006 CGPF

  6. All A RNA-like conformers

  7. Subtle backbone changes affect base geometry and function

  8. RMSD Cluster Results Cluster 2 Cluster 1 URB008 UPA2

  9. UpA 2 an open conformation

  10. UpA 2 like conformers

  11. RMSD Cluster Results DRB003 ApU - 9AA URB008 UPA1 URB003 ApA - Ca++

  12. UpA1helix turner

  13. UpA1 like conformerssmall backbone changes make big structural changes

  14. RMSD Cluster Resultsdinucleotide backbone DRB003 ApU - 9AA URB008 UPA1 Cluster 2 Cluster 1 URB008 UPA2 DRB006 CGPF ARNA URB003 ApA - Ca4

  15. RMSD Cluster Resultssuite backbone URB008 UPA1 DRB006 CGPF DRB003 ApU - 9AA URB008 UPA2 URB003 ApA - Ca4 ARNA

  16. RMSD Cluster Results backbone plus chi DRB003 ApU - 9AA URB008 UPA1 ARNA DRB006 CGPF URB008 UPA2 URB003 ApA - Ca4

  17. myRNAdb • MySQL relational database of ~1000 RNA containing structures in NDB/PDB • Uses core schema based on mmCIF/PDB Exchange Dictionary • Includes base-pair and base-pair step geometries and RNA SCOR annotation • Warehouse style tables for mining nucleotide, dinucleotide and trinucleotide features. • Python tools for loading, access and analysis

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