Integrating NMR and simulations reveals motions in the UUCG tetraloop.

Kresten Lindorff-Larsen,Beat Vögeli,Michele Parrinello,Parker J Nichols,Sandro Bottaro

doi:10.1093/nar/gkaa399

Abstract

We provide an atomic-level description of the structure and dynamics of the UUCG RNA stem–loop by combining molecular dynamics simulations with experimental data. The integration of simulations with exact nuclear Overhauser enhancements data allowed us to characterize two distinct states of this molecule. The most stable conformation corresponds to the consensus three-dimensional structure. The second state is characterized by the absence of the peculiar non-Watson–Crick interactions in the loop region. By using machine learning techniques we identify a set of experimental measurements that are most sensitive to the presence of non-native states. We find that although our MD ensemble, as well as the consensus UUCG tetraloop structures, are in good agreement with experiments, there are remaining discrepancies. Together, our results show that (i) the MD simulation overstabilize a non-native loop conformation, (ii) eNOE data support its presence with a population of ≈10% and (iii) the structural interpretation of experimental data for dynamic RNAs is highly complex, even for a simple model system such as the UUCG tetraloop.

Highlights

RNA loops are structural elements that cap A-form double helices, and as such are fundamental structural units in RNA molecules
Our results show that (i) the molecular dynamics (MD) simulation overstabilize a non-native loop conformation, (ii) exact NOE measurements (eNOEs) data support its presence with a population of ≈10% and (iii) the structural interpretation of experimental data for dynamic RNAs is highly complex, even for a simple model system such as the UUCG tetraloop
Based on our extensive MD simulations and integrating them with exact nuclear Overhauser effects (NOE) data, we report the free energy landscape of a prototype stem-loop RNA 14-mer known as the UUCG tetraloop

Summary

Introduction

RNA loops are structural elements that cap A-form double helices, and as such are fundamental structural units in RNA molecules. The great majority of known RNA tetraloops have the sequence GNRA or UNCG, where N is any nucleotide and R is guanine or adenine [2]. Their small size, together with their biological relevance, has made these systems primary targets for nuclear magnetic resonance (NMR) spectroscopy, X-raycrystallography, and atomistic molecular dynamics (MD) simulation studies [3,4,5]. The UUCG tetraloop has been long known to be highly stable, and both crystallographic and NMR studies suggest that this tetraloop adopts a well-defined three dimensional structure including a characteristic trans-SugarWatson (tSW) interaction between U6 and G9 [6,7] (Figure 1). The UUCG tetraloop is used to stabilize the secondary structure of larger RNA molecules without interacting with other RNAs or proteins [8]

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Results

Conclusion