Geometric Methods for Improving RNA Structure

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Geometric Methods for Improving RNA Structure

• By
• Jack Snoeyink and Xueyi Wang
• Department of Computer Science
• UNC - Chapel Hill

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Outline

• RNA Structure
• RNA Crystallography
• RNABC RNA Structure Correction
• Implementation

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Central Dogma
tRNA (adaptor in translation) rRNA (ribosome RNA,
component of ribosome) snRNA (small nuclear RNA,
component of spliceosome) snoRNA (small nucleolar
RNA, takes part in processing of rRNA) SRP RNA
(component of signal recognition particle) ..
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RNA World

• Ribosome

• RNA world hypothesis proposes that RNA was the
  first life-form on earth.
• RNA has the ability to act as both gene and
  enzyme.
• RNA has increasing industrial importance as a
  molecular tag and as an inhibitor.

From http//fig.cox.miami.edu/cmallery/
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(No Transcript)
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RNA 3D Structure

• Residue

Suite
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RNA Geometry

• Atoms bonded with carbon or phosphorus form a
  tetrahedral structure.
• Bond lengths and angles can only be adjusted in
  small ranges.
• The dihedral angles are flexible.
• Sugar rings are not planar two types of pucker
  called C2 endo and C3 endo.
• Steric clashes (collisions) occur when non-bonded
  atoms are too close.

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Ribosome

• Large ribosome subunit
• -- Chain0 2914 residues
• -- Chain9 122 residues

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Outline

• RNA Structure
• RNA Crystallography
• RNABC RNA Structure Correction
• Implementation

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RNA Crystallography

• Electron Density Map
• -- Phosphates and Bases can be clearly located.
• -- Sugar puckers can be derived.
• -- Other parts are ambiguous.

From http//campus.queens.edu/faculty/jannr/

• 2.5Å or 3Å resolution for large RNA structures is
  considered good.
• Goal Achieve correct RNA structures from
  electron density maps.

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Electron Density Map

• Image Courtesy Richardsons Lab

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All-Atom Contact Analysis

• Image Courtesy Richardsons Lab

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RNA more complex than Protein
Nucleic Acid 6 dihedrals
Amino Acid 2 dihedrals
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RNA more complex than Protein
RNA Backbone Two ends and the base plane are
fixed
Protein Side-chain One end is fixed
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Outline

• RNA Structure
• RNA Crystallography
• RNABC RNA Structure Correction
• Implementation

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Goal

• Remove steric clashes in RNA crystal structure
• -- Phosphates and Bases can be clearly located
  in the electron density map, but other parts are
  not.
• -- Satisfy bond length and angle requirements (lt
  34 s).
• -- Satisfy sugar pucker types.
• -- Avoid steric clashes.

• Difficulties
• -- Large configuration space many degrees of
  freedom
• -- Each phosphorus or base is used twice.

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Kinematics

• Forward kinematics
• -- Start from phosphate.
• -- Fit bases.

• Inverse kinematics
• -- Start from two bases.
• -- Fit the phosphate position.

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RNABC

• Use forward kinematics to remove steric clashes
  in a dinucleotide
• -- Start from three phosphates and fits two
  bases.
• -- Satisfy all the constraints.
• -- Cluster resulting conformations.
• -- Keep several valid conformations calculated
  in each dinucleotide and merge adjacent
  dinucleotides.

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Outline

• RNA Structure
• RNA Crystallography
• RNABC RNA Structure Correction
• Implementation

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Three Steps

• Step 1 Sample allowable positions of backbone
  atoms.
• -- two substeps first substep uses a rough
  sample angle (5) second substep uses a fine
  sample angle (1).
• Step 2 Construct two sugars based on sextuples
  C5, C4, C3, O3, C1, N1/9.
• -- Construct O4 and C2, examine the sugar
  pucker type, add other atoms and check steric
  clashes.

• Step 3 Cluster the allowed conformations and
  output.
• -- Clustering the conformations by the values of
  the dihedrals.

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Implementation

• Implemented using C, read pdb files using CCP4
  package.
• Some acceleration techniques
• -- Early rejection stop further calculation as
  soon as steric clashes are found or certain
  criterion are violated (e.g. the shape of sugar
  pucker).
• -- Avoid duplicate comparisons in different
  steps.
• -- Fast rejections of disallowed positions when
  calculating atoms on the sugars.

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Implementation

• Input pdb files with the residue to be adjusted.
• Output kinemage files with new conformations.
• Provide many input/output parameters, e.g.
• -- SIG choose the standard deviation range.
• -- PARAMETER define which parameter set to be
  used.
• -- PHOSPHORUS move the phosphorus to a new
  position.
• -- CONFORMNUM determine how many conformations
  need to be output.
• Solve clashes about 13 minutes.
• Can solve gt 60 of clashes now.

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Result
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The End

• Acknowledgements
• -- Prof. Jane Richardson, Prof. David Richardson,
  Laura Murray and Gary Kapral.
• -- BCB program in UNC - Chapel Hill
• -- NIH grant with the Richardson Lab
• -- NSF grant 0076984.