Theoretical Search for RNA Folding Nuclei

Leonid Pereyaslavets,Oxana Galzitskaya

doi:10.3390/e17117827

Abstract

The functions of RNA molecules are defined by their spatial structure, whose folding is regulated by numerous factors making RNA very similar to proteins. Prediction of RNA folding nuclei gives the possibility to take a fresh look at the problems of the multiple folding pathways of RNA molecules and RNA stability. The algorithm previously developed for prediction of protein folding nuclei has been successfully applied to ~150 various RNA structures: hairpins, tRNAs, structures with pseudoknots, and the large structured P4-P6 domain of the Tetrahymena group I intron RNA. The calculated Φ-values for tRNA structures agree with the experimental data obtained earlier. According to the experiment the nucleotides of the D and T hairpin loops are the last to be involved in the tRNA tertiary structure. Such agreement allowed us to do a prediction for an example of large structured RNA, the P4-P6 RNA domain. One of the advantages of our method is that it allows us to make predictions about the folding nucleus for nontrivial RNA motifs: pseudoknots and tRNA.

Highlights

The spatial structure and folding of RNA molecules is currently the subject of many investigations [1,2].In the folding process, the RNA strand, like a protein globule, passes through numerous intermediate states able to play a key role in the kinetics of the process
It was supposed for a long time that RNA folding is a hierarchical process: the secondary structure is formed first, and only tertiary interactions are formed stabilizing the spatial structure, but using the SHAPE approach it has been recently shown that tRNA folds in a non-hierarchical manner, with non-native conformations accumulated during the folding as observed in experiments [24] and RNA
The analysis of Φ-values for 103 tRNA molecules whose structures were obtained in bound and unbound states makes it reasonable to suppose that the anticodon hairpin is incorporated in the folding nucleus, while nucleotide residues in the region of Dand T-hairpin loops are the last to be involved in the tRNA structure

Summary

Introduction

The spatial structure and folding of RNA molecules is currently the subject of many investigations [1,2]. 2′-Hydroxyl Acylation analyzed by Primer Extension (SHAPE)—allows for the identification of mobile nucleotides in RNA molecules of any size [23] It was supposed for a long time that RNA folding (unfolding) is a hierarchical process: the secondary structure is formed first, and only tertiary interactions are formed stabilizing the spatial structure, but using the SHAPE approach it has been recently shown that tRNA folds in a non-hierarchical manner, with non-native conformations accumulated during the folding as observed in experiments [24] and RNA secondary and tertiary interactions are formed mutually. The analysis of Φ-values for 103 tRNA molecules whose structures were obtained in bound and unbound states makes it reasonable to suppose that the anticodon hairpin is incorporated in the folding nucleus, while nucleotide residues in the region of Dand T-hairpin loops are the last to be involved in the tRNA structure. One of the advantages of our method is that we can predict the folding nucleus for any structure even with pseudoknots if its spatial structure is in the PDB or NDB databases

Theory

10.80 Å dmax

Estimation of Free Energy and Calculation of Folding Nuclei

Prediction of Folding Nuclei for tRNAs

Prediction of Folding Nuclei for RNA Structures with Hairpin and Pseudoknots

Conclusions