Remembrances of Things Past

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-C5C4-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
URB008 UPA2
Cluster 1
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
URB008 UPA2
Cluster 1
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