Building RNA Backbone in Constant Time by Numerical Approximation

Abstract

We present a numerical approximation method designed to swiftly create RNA ribose conformations in constant time. The methods parameterization relies on the atomic coordinates of a given base along with its two neighboring phosphate groups. Such a parameterization suits three dimensional modeling engines that determine the RNA conformational search space using base operations instead of backbone sampling. These engines consider phosphate groups as part of the base rigid bodies. Reconstructing ribose conformations result in less than 1 [A] of RMSD (root-mean-square deviation) compared to original conformations derived from high-resolution X-ray crystallographic structures. By incorporating this ribose construction method into MC-Sym, a well-established RNA three dimensional modeling software, we streamline the modeling process into two phases. This enhances the search algorithms speed and improves model consistency and precision. Additionally, we employed the method to pinpoint 27 irregular ribose stereoisomers in high-resolution RNA X-ray crystal structures.