A Probabilistic Model of RNA Conformational Space

Abstract

The increasing importance of non-coding RNA in biology and medicine has led to a growing interest in the problem of RNA 3-D structure prediction. As is the case for proteins, RNA 3-D structure prediction methods require two key ingredients: an accurate energy function and a conformational sampling procedure. Both are only partly solved problems. Here, we focus on the problem of conformational sampling. The current state of the art solution is based on fragment assembly methods, which construct plausible conformations by stringing together short fragments obtained from experimental structures. However, the discrete nature of the fragments necessitates the use of carefully tuned, unphysical energy functions, and their non-probabilistic nature impairs unbiased sampling. We offer a solution to the sampling problem that removes these important limitations: a probabilistic model of RNA structure that allows efficient sampling of RNA conformations in continuous space, and with associated probabilities. We show that the model captures several key features of RNA structure, such as its rotameric nature and the distribution of the helix lengths. Furthermore, the model readily generates native-like 3-D conformations for 9 out of 10 test structures, solely using coarse-grained base-pairing information. In conclusion, the method provides a theoretical and practical solution for a major bottleneck on the way to routine prediction and simulation of RNA structure and dynamics in atomic detail.

Author Summary

The importance of RNA in biology and medicine has increased immensely over the last several years, due to the discovery of a wide range of important biological processes that are under the guidance of non-coding RNA. As is the case with proteins, the function of an RNA molecule is encoded in its three-dimensional (3-D) structure, which in turn is determined by the molecule's sequence. Therefore, interest in the computational prediction of the 3-D structure of RNA from sequence is great. One of the main bottlenecks in routine prediction and simulation of RNA structure and dynamics is sampling, the efficient generation of RNA-like conformations, ideally in a mathematically and physically sound way. Current methods require the use of unphysical energy functions to amend the shortcomings of the sampling procedure. We have developed a mathematical model that describes RNA's conformational space in atomic detail, without the shortcomings of other sampling methods. As an illustration of its potential, we describe a simple yet efficient method to sample conformations that are compatible with a given secondary structure. An implementation of the sampling method, called BARNACLE, is freely available.