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Publication . Article . 2006

The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation

Yaroslava G. Yingling; Bruce A. Shapiro;
Open Access
Published: 01 Oct 2006
Publisher: Zenodo
Abstract

In this study, the three-dimensional structure of the wild-type human telomerase RNA pseudoknot was predicted via molecular modeling. The wild-type pseudoknot structure is then compared to the recent NMR solution structure of the telomerase pseudoknot, which does not contain the U177 bulge. The removal of the bulge from the pseudoknot structure results in higher stability and significant reduction of activity of telomerase. We show that the effect of the bulge on the structure results in a significant transformation of the pseudoknot junction region where the starting base pairs are disrupted and unique triple base pairs are formed. We found that the formation of the junction region is greatly influenced by interactions of the U177 bulge with loop residues and rotation of residue A174. Moreover, this is the first study to our knowledge where a structure as complex as the pseudoknot has been solved by purely theoretical methods.

Subjects by Vocabulary

Microsoft Academic Graph classification: Base pair Pseudoknot Bulge Wild type RNA Telomerase Molecular dynamics Biophysics Biology Molecular model Genetics

Medical Subject Headings: viruses

Subjects

Materials Chemistry, Computer Graphics and Computer-Aided Design, Physical and Theoretical Chemistry, Spectroscopy

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