Computer modeling 16S ribosomal RNA.

摘要

It was the goal of this research to develop and implement a rational modeling protocol which could be applied to the folding of 16S ribosomal RNA. Modeling of a DNA dodecamer and comparison with the structures of the molecule obtained by NMR and x-ray crystallography reaffirm that the results obtained by modeling are dependent on the input data set. Transfer RNA modeling is used to demonstrate the feasibility of the new protocol and to explore what levels of structural shorthand can be successfully applied. Initially, a representation is employed which replaces each all-atom nucleotide with six pseudoatoms. With an alternate replacement scheme which emphasizes the helical substructures, it is possible to reduce the size of the model to be manipulated by more than twenty-fold and still obtain good results. The modeled structures clearly occupy the same area of conformational space as that of the tRNAs which have been determined by x-ray crystallography. The 16S ribosomal RNA at the heart of the small subunit of the ribosome has been extensively studied by physical, chemical, and phylogenetic means. Once the problems produced by the size of this molecule have been addressed, applying the new computer modeling protocol is straightforward. A closely related set of conformers is consistently obtained and these structures are comparable to models which include data from outside the computer parameter set. 108 refs., 74 figs.