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Biophys J, September 2000, p. 1213-1227, Vol. 79, No. 3
and
*Center for Structural Biochemistry, Department of Bioscience at
NOVUM, Karolinska Institutet, SE-141 57 Huddinge, Sweden; and
Institute of Bioorganic Chemistry, Polish Academy of
Sciences, 61 704 Poznan, Poland
Molecular modeling and molecular dynamics have been
employed to study the conformation and flexibility of a 15-nucleotide fragment of the plant 5S rRNA containing loop D and a single uridine bulge. Two different model built initial structures were used: one with
the bulge localized inside the helical stem and another with the bulge
pointing out from the helix. Several independent 700-ps-long
trajectories in aqueous solution with Na+ conterions were
produced for each starting structure. The bulge nucleotide inside the
helix stayed in two main conformations, both of which affected the
geometry of the stem part opposite the bulge. When the bulge nucleotide
was located outside the helix, we found high base mobility and local
backbone flexibility. The dynamics of the hydrogen bond network and
conformational changes from a direct to a water mediated hydrogen bond
in the sheared G-A basepair in the tetraloop was described. Our results
correlate with lead ion induced cleavage patterns in 5S rRNA. Sites
resistant to nonspecific lead cleavage appeared in all our simulations
as the most rigid fragments independent of the localization of the bulge nucleotide.
Biophys J, September 2000, p. 1213-1227, Vol. 79, No. 3
© 2000 by the Biophysical Society 0006-3495/00/09/1213/15 $2.00
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