ANALYSIS OF RELATIVE POSITIONS OF RIBONUCLEOTIDE BASES IN A CRYSTAL STRUCTURE OF RIBOSOME

ABSTRACT

Relative positions of bases to bases in a crystal structure of ribosome were analyzed extensively. It was found that there is no clear relation between bases apart more than 15 Å and, thus, the relative location of bases can be analyzed within 15 Å of the reference bases. As for base pairing, major positioning was found to be due to the Watson-Crick type base pairs. Some other positions corresponding to non-Watson-Crick type base pairs were also found in some extents. As for base–base stacking, it was observed that the bases stacked to adenine base are dispersive. It was found that less non-Watson-Crick base pairs was found close to the protein binding site, suggesting that the protein components have a tendency to bind to the regular stem structures. The database of relative location of bases must be useful for improvement of structural determination and structural modeling systems.

Keywords:

• Base pair
• Base stacking
• Ribosome
• RNA
• Structure

ACKNOWLEDGMENTS

This work was supported by Grants-in-Aid for Scientific Research on Priority Areas (09278206) and High Technology Research from Ministry of Education, Science, Sports and Culture, Japan, and the “Research for the Future” Program (JSPS-RFTF97L00503) from the Japan Society for the Promotion of Science.