RNA Backbone Rotamers: Introduction and Updates

Laura Weston Murray

July 27, 2008

ROC Meeting, Berlin

Outline

• Background information on RNA backbone consensus conformers

• Applications and collaborations• Dataset update (in progress)

A Series of Tubes

1Q9A 1JJ2

Classification Consensus

• Selected and quality-filtered dataset• Nomenclature to translate among

residue, dinucleotide, suite descriptions• Applied and cross-referenced methods

– 7D visualization– Pseudo-electron density contours– Multi-dimensional binning– Pseudotorsion analysis

Selection and Quality Filtering

• Dataset selection – resolution (3Å and better)

– variety

• B-factor– local reliability

• Sterics– Eliminate the impossible

1a

1a

#a

4s

5z

1a1a

1a

1a

1a

1e

1a

Applications

• Motif identification and description– But Gary will tell you more about that one.

• PHENIX• RNABC• Ribosome

Applications

• Motif identification and description– But Gary will tell you more about that one.

• PHENIX• RNABC• Ribosome

Applications

• Motif identification and description– But Gary will tell you more about that one.

• PHENIX• RNABC• Ribosome

RNABC: RNA Backbone Correction

Original

dihedral

RNABC conformation

RNABC correction

50S 1941-2

Applications

• Motif identification and description– But Gary will tell you more about that one.

• PHENIX• RNABC• Ribosome

RNA08

RNA03 RNA05 RNA08 est.

Files 132 171 200

Residues 86369486 15000

Acknowledgements

Richardson Lab Rutgers-Prague Georgia Tech Yale

Jane Richardson Helen Berman Loren Williams Anna-Marie Pyle

David Richardson Bohdan Schneider Eli Hershkovitz John Westbrook

Gary Kapral Zdenek Moravek Kevin Keating

Bryan Arendall David Micallef

Lizbeth Videau Daniela Hamova

Ian Davis

Funding

NIH HHMI NSF ROC