Molecular Modeling - Escherichia coli 16S rRNA

Wollenzien Laboratory
Department of Biochemistry
North Carolina State University


Models 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.
Approximately 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.

MC-SYM scripts and structure files for individual 16S rRNA helices


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.

MC-SYM script and structure file for 16S rRNA decoding region model

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