Molecular Modeling - Escherichia coli 16S rRNA
Department of Biochemistry
North Carolina State University
MODELING OF INDIVIDUAL rRNA HELICES
for each secondary structure region from the Escherichia coli 16S rRNA
(58 separate) elements were constructed using the constraint satisfaction
predictive modeling program MC-SYM.
Constraints for each rRNA element consisted of the comparative secondary
structure model, chemical probing data, rRNA-rRNA crosslinking information,
coordinates from solved structures, and H-bonding conformations predicted
from patterns of base-pair covariations. Each model was subsequently energy
optimized resulting in structures with favorable geometry.
two-thirds of the structures that result from the input data are very similar
to A-form geometry. However, the presence of internal loops and bulges,
some sequences (and sequence covariants) and accessory information require
deviation from A-form geometry in the remaining instances. The structures
of more complex regions such as pseudoknots, can be predicted by this approach.
MODELING OF 16S rRNA DECODING REGION
A molecular model of how helix 28, helices 44a
and 44b and the central pseudoknot are oriented in the decoding region
was constructed based on tertiary information. UV-crosslink information
provided distance constraints while data from Fe(II)-EDTA probing experiments
was useful in orienting helices relative to solvent. Chemical modification
data was also used to determine base-pairing geometries. More indirect
data such as mRNA crosslink sites and tRNA footprinting sites were used
in the general placement of helices relative to one another.
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