RNA Pseudo-RNA Pseudo-TorsionsTorsions

Kevin Keating, Leven Wadley, Kevin Keating, Leven Wadley, and Anna Marie Pyleand Anna Marie Pyle

What are Pseudo-What are Pseudo-Torsions?Torsions?

Two torsions per Two torsions per residueresidue

Uses P, C4’Uses P, C4’ ηη ≈≈ αα++ββ++γγ θθ ≈≈ δδ++εε++ζζ

How do you use them?How do you use them?

Can plot Can plot residues on residues on 2D plot2D plot

Similar to Similar to RamachandrRamachandran plotan plot

How do you use them?How do you use them?

One pair of One pair of ηη--θθ values corresponds values corresponds to a residueto a residue (or (or θθ--ηη values to a suite) values to a suite)

Residues with similar Residues with similar ηη--θθ values values have similar structurehave similar structure Based on RMSD analysisBased on RMSD analysis

How do you use them?How do you use them?

Similar residues fall in similar areas of the plotSimilar residues fall in similar areas of the plot

What are they good for?What are they good for? Find known motifsFind known motifs Search for new motifsSearch for new motifs Compare tertiary structuresCompare tertiary structures Structure validationStructure validation

Duarte and Pyle. JMB 284 (1998), 1465-1478 Duarte, Wadley, and Pyle. NAR 31 (2003), 4755-4761 Wadley and Pyle. NAR 32 (2004), 6650-6659

The WormThe Worm

Trace Trace ηη--θθ values values along the backbonealong the backbone

Structure ComparisonStructure Comparison

Can plot the difference in Can plot the difference in ηη--θθ values values between two structuresbetween two structures

30S ribosome with/without tRNA 50S ribosome withclarithromycin vs. chloramphemicol

All-Angle AnalysisAll-Angle Analysis

Psuedo-torsional approach Psuedo-torsional approach complements other methodscomplements other methods

Agrees with rotameric analysisAgrees with rotameric analysis Examined Examined θθ--ηη values values

All-Angle AnalysisAll-Angle Analysis

All-angle analysis nearly impossible All-angle analysis nearly impossible in low resolutionin low resolution

At 3-5 Å, can’t accurately fit 6 bonds At 3-5 Å, can’t accurately fit 6 bonds into densityinto density Far easier to fit 2 bondsFar easier to fit 2 bonds

Low resolution Low resolution ηη--θθ plots almost plots almost identical to higher resolution plotsidentical to higher resolution plots

Low ResolutionLow Resolution

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

All-Angle AnalysisAll-Angle Analysis

Pseudo-torsions can’t directly Pseudo-torsions can’t directly provide precise backbone structureprovide precise backbone structure

Can indirectly provide information Can indirectly provide information about rotamerabout rotamer

ConclusionsConclusions

Psuedo-torsions useful at both high Psuedo-torsions useful at both high and low resolutionsand low resolutions

Complement all-angle methodsComplement all-angle methods Should be developed in parallel with Should be developed in parallel with

other methodsother methods Ex: solve crystal structure by first Ex: solve crystal structure by first

finding pseudo-torsionsfinding pseudo-torsions Then selecting appropriate all-angle Then selecting appropriate all-angle

rotamerrotamer