The 3D structure of RNA backbone Xueyi Wang and Jack Snoeyink Department of Computer Science, UNCCha

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The 3D structure of RNA backboneXueyi Wang and
Jack SnoeyinkDepartment of Computer Science,
UNC-Chapel Hill
Abstract In electron density maps from x-ray
crystallography on large RNA, it is difficult to
determine the RNA backbone accurately. Usually
only the phosphate and base planes can be clearly
located, while the sugar puckers are not clear
and the zigzag parts of the backbone can barely
be seen. Our goal is to build tools to help
achieve correct RNA structure from electron
density maps. We have built a space-filling model
of RNA structure, derived Ramachandran-like plots
from analyzing the collision boundary of RNA
structures and investigated measurements (from
known phosphate and bases) to separate 42
conformations given by Richardsons lab from
observed data.
Figures above Courtesy Richardsons Lab
Complexity Each residue has six dihedrals and
each suite (defined from sugar to sugar) has
seven dihedrals, where protein backbone has only
two. Both ends of RNA backbone are fixed, where
one end of protein sidechain is fixed.
RNA backbone vs. protein backbone
RNA backbone vs. protein sidechain
Residue
Suite

• Finding Ramachandran-like plots for RNA
• Space-filling Model
• Standard RNA structure parameters (Nucleic Acid
  Database)
• Dihedrals are sampled at every 5.
• Overlaps (distances of pairs of atoms that are at
  least four bonds apart)
• -- No Clash gt vdwi vdwj - 0.2Å
• -- Small Clash lt vdwi vdwj - 0.2Å and gt
  vdwi vdwj - 0.5Å
• -- Bad Clash lt vdwi vdwj - 0.5Å
• Observed Data
• L. Murray, et al. PNAS2003.
• A-form RNA accounts for 75 of the data.
• 42 Conformations.
• 99 of backbone steric clashes are within suites.

Distribution of Dihedrals Space-filling Model
-- d C3endo 65, 94 C2endo 117,
167. -- e C3endo -200, -30 when d
94 and -245, -70 when d 65
C2endo -185, -55 when d 117 and -175,
-55 whend167 -- ? Peaks at p (60), m
(-60), and t (180),. -- a Peaks at p, m and
t. -- ß Peak at t. -- ? modet. Observed
Data (L. Murray, et al. PNAS2003) -- d
C3endo near 84 C2endo near 147 -- e
C3endo mode -150 C2endo mode-100.
-- ? Peaks at p, m, t and -140. -- a Peaks
at p, m, t and -110. -- ß Peaks at t, 110,
-135, 135 and 80. -- ? Peaks at p, m and t.
42 Conformations from Richardsons lab

• Measurements and Conformations
• Map known positions (phosphate bases) to
  C3endo and C2endo puckers.
• Map the known positions to 42 conformations.

• 18 measurements
• Distances N1--N2, P--N1, etc.
• Perpendicular distances P -- C1-N1, P -- Sugar
  Pucker
• Angles N1--P--N2, P--N1--N2, etc.

a-ß-? dihedral plot
d-e-? dihedral plot

• Results
• Separate Sugar Puckers
• Space-filling Model
• -- C3endo P -- N1-C1 gt 2.537Å C2endo P
  -- N1-C1 lt 2.313Å
• Proposed measurement from Richardsons lab
• -- C3endo P -- First Base Plane gt 2.9Å
  C2endo P -- First Base Plane lt 2.9Å

Separate all 42 conformations -- (P--Sugar2,
N1--N2 and P--N1--N2) and (P--Sugar2, C1--C2 and
P--C1--C2). Separate conformations in the
different sugar puckers -- C3endo and
C3endo (P--Sugar2, N1--N2 and P--N2--N1). --
C3endo and C2endo (P--Sugar2, N1--N2 and
P--N2--N1). -- C2endo and C3endo
(P--Sugar2, N1--N2 and P--N2). -- C2endo and
C2endo (P--Sugar2, N1--N2 and P--N2).
measurement plot
d-e-? clash plot
Sponsored by NSF (grant 0076984)
PSB 2005