RNA Pseudo-Torsions Kevin Keating, Leven Wadley, and Anna Marie Pyle

What are Pseudo-Torsions? Two torsions per residue Two torsions per residue Uses P, C4’ Uses P, C4’ η ≈ α+β+γ η ≈ α+β+γ θ ≈ δ+ε+ζ θ ≈ δ+ε+ζ

How do you use them? Can plot residues on 2D plot Similar to Ramachandran plot

How do you use them? One pair of η-θ values corresponds to a residue One pair of η-θ values corresponds to a residue (or θ-η values to a suite) (or θ-η values to a suite) Residues with similar η-θ values have similar structure Residues with similar η-θ values have similar structure Based on RMSD analysis Based on RMSD analysis

How do you use them? Similar residues fall in similar areas of the plot Similar residues fall in similar areas of the plot

What are they good for? Find known motifs Find known motifs Search for new motifs Search for new motifs Compare tertiary structures Compare tertiary structures Structure validation Structure validation Duarte and Pyle. JMB 284 (1998), Duarte, Wadley, and Pyle. NAR 31 (2003), Wadley and Pyle. NAR 32 (2004),

The Worm Trace η-θ values along the backbone

Structure Comparison Can plot the difference in η-θ values between two structures Can plot the difference in η-θ values between two structures 30S ribosome with/without tRNA 50S ribosome with clarithromycin vs. chloramphemicol

All-Angle Analysis Psuedo-torsional approach complements other methods Psuedo-torsional approach complements other methods Agrees with rotameric analysis Agrees with rotameric analysis Examined θ-η values Examined θ-η values

All-Angle Analysis All-angle analysis nearly impossible in low resolution All-angle analysis nearly impossible in low resolution At 3-5 Å, can’t accurately fit 6 bonds into density At 3-5 Å, can’t accurately fit 6 bonds into density Far easier to fit 2 bonds Far easier to fit 2 bonds Low resolution η-θ plots almost identical to higher resolution plots Low resolution η-θ plots almost identical to higher resolution plots

Low Resolution ≤ 3.0 Å 4.5 Å structure of 30S ribosome (1I95)

All-Angle Analysis Pseudo-torsions can’t directly provide precise backbone structure Pseudo-torsions can’t directly provide precise backbone structure Can indirectly provide information about rotamer Can indirectly provide information about rotamer

Conclusions Psuedo-torsions useful at both high and low resolutions Psuedo-torsions useful at both high and low resolutions Complement all-angle methods Complement all-angle methods Should be developed in parallel with other methods Should be developed in parallel with other methods Ex: solve crystal structure by first finding pseudo-torsions Ex: solve crystal structure by first finding pseudo-torsions Then selecting appropriate all-angle rotamer Then selecting appropriate all-angle rotamer