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Ribbon drawing of one yeast initiator tRNA molecule using
RIBBONS [Carson, 1987]. Note the double helical character in the
acceptor stem and anti-codon regions. Aminoacylated amino acids are
attached to the 3'-OH end of the acceptor stem. The three nucleic
acid bases that provide the base-pairing specificity for the start
codon on the messenger RNA are located at the tip of the anti-codon
loop.
Calculations of the X-ray scattering from yeast initiator
tRNA crystals. The experimental image, a, corresponds to a
1.5
rotation photograph recorded on an imaging plate set
200 mm from the crystal using 1.3 Å radiation. The red arrows
point to the streaks elongated perpendicular to the c axis, which, in
the calculated image, b, are modeled as lattice-coupled motions along
the pseudo-helix axis. The white arrow points to the very diffuse
cloud which is modeled as local intra-molecular motion in the
anti-codon arm. The corresponding unit cell orientation is shown in c
with a single tRNA molecule colored yellow and the symmetry-related
molecules and unit cell outline in blue. Magnifications of the top
right quadrant from the experimental and calculated diffraction images
are shown in d and e, respectively. The upper right hand quadrant of
each of these images shows a close correspondence in the diffuse
intensity. The magnified images have been globally rescaled slightly
to correct for the absorption seen in the lower right quadrant in
image a. The experimental diffraction and the diffuse scattering
calculations are colored such that the least intense features appear
blue, intermediate intensities pink, and the most intense features
yellow. The lack of circularly symmetric intensity in the
experimental image, a, is partially accounted for by significant
absorption.
Calculation of diffuse scattering from another tRNA crystal
orientation. The experimental image is shown in a, the calculated
image in b, and the unit cell orientation in c. The experimental
parameters are the same as in Figure 2 except that 1.17 Å radiation
was used. The parameters used in the diffuse scattering calculations
were identical to those in Figure 2. Again, the red arrows point to
the streaks elongated perpendicular to the c axis, which, in the
calculated image, b, are modeled as lattice-coupled motions along the
pseudo-helix axis, while the white arrows point to the very diffuse
clouds which are modeled as local intra-molecular motion in the
anti-codon arm.
Diffuse scattering components used in each of the
calculations, Figures 2b (row 1) and 3b (row2). Rows 1 and 2: (from
left to right) long-range lattice-coupled motion perpendicular to the
c axis , long-range lattice-coupled motion along the c axis, and
short-range motion local to the anti-codon arm. Row 3: calculated
scattering from bulk water (left) and independent atom motion
scattering (right).
Ribbon drawing of two tRNA molecules illustrating the
possible flexing behavior of tRNA derived from analysis of the
Bragg-associated diffuse scattering. Specifically, motion strongly
coupled along the pseudo-helical axis (marked by arrows), but
relatively uncorrelated with the distal half of the anti-codon arm,
results in the flexion. The motion along the direction of the arrows
has been exaggerated to demonstrate the flexing action better.
Schematic stick figure animation illustrating local motion
of base pairs in the anti-codon loop (separated by approximately 3.0
Å). This picture is based upon information derived from the
analysis of the very diffuse clouds in Figures 2a and 3a (white
arrows). This representation illustrates the local motion of the
nucleic acid bases while still preserving the approximate base-pair
separation.
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