SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

Abstract

RNA molecules play fundamental roles in cellular processes. Their function and interactions with other biomolecules are dependent on the ability to form complex three-dimensional (3D) structures. However, experimental determination of RNA 3D structures is laborious and challenging, and therefore, the majority of known RNAs remain structurally uncharacterized. Here, we present SimRNA: a new method for computational RNA 3D structure prediction, which uses a coarse-grained representation, relies on the Monte Carlo method for sampling the conformational space, and employs a statistical potential to approximate the energy and identify conformations that correspond to biologically relevant structures. SimRNA can fold RNA molecules using only sequence information, and, on established test sequences, it recapitulates secondary structure with high accuracy, including correct prediction of pseudoknots. For modeling of complex 3D structures, it can use additional restraints, derived from experimental or computational analyses, including information about secondary structure and/or long-range contacts. SimRNA also can be used to analyze conformational landscapes and identify potential alternative structures.

Figure 1.

Reduced representation of RNA structure in SimRNA including the relationships between various base and backbone terms. (A) An example of an RNA structure (GCAA tetraloop, PDB id: 1zih) shown in reduced representation where green represents the backbone and red represents the base moieties. (B) Examples of reduced representation for the adenosine and uridine residues, with base level 1 and level 2 representation shown as red and blue points, respectively. (C) The backbone section including the vectors that orient the base relative to the backbone. (D) Level 3, the central layer (slice) of the 3D grid for the reference base, where the orange region represents the excluded volume of atoms of the base (repulsive region) and the purple region is an example of the attractive interactions between A and U in the central layer, including base-pairing around the Watson–Crick edge (the largest purple cloud), around the Hoogsteen edge (the second largest purple cloud) and the sugar edge (small purple cloud at the bottom of the diagram). It is worth noting that even though the red triangle covers only part of the base, the 3D grid approximates the volume of all atoms of the base. (E) Representation of the bond lengths, flat angles and pseudotorsion angles η and θ.

Figure 2.

Examples of the Monte Carlo move set. During a simulation, each new conformation is generated as a small modification of a previous conformation: (A) a change in the conformation of the base in the local backbone coordinates; (B) a change in the backbone position of the C4′ atom; (C) a change in the backbone position of P atom; (D) a change in the position of two subsequent atoms of the backbone; and (E) a change in the direction of a fragment of the backbone.

Figure 3.

Distance restraints implemented in SimRNA. (A) immobilization of one atom; (B) flexible pinning of one atom; (C) flexible tethering of two atoms; (D) canonical base-pairing of two residues.

Figure 4.

An example of the energy landscape generated in the course of a set of SimRNA simulations. Results are shown for the gene 32 messenger RNA pseudoknot of bacteriophage T2 (PDB id: 2tpk). The upper panel illustrates the relationship between the distance to the reference structure (expressed in RMSD), and the energy of a given conformation (calculated according to the SimRNA statistical potential). Each conformation recorded in the course of the simulation is represented by one dot; where the dots are colored (red to purple to black) according to the conformation's similarity to other conformations. Structures that have many similar conformations are colored red, and structures that have rather unique conformations are colored in black, purple being in-between. The starting conformation is indicated by (S), the reference structure determined by X-ray crystallography is indicated by (C), an example intermediate structure is indicated by (I), and the top three clusters are indicated by (1), (2) and (3). The bottom panel illustrates the tertiary and secondary structure of these conformations. RNA molecules are colored by a spectrum from blue (5′ terminus) to red (3′ terminus) and the secondary structure is shown in dot-bracket format.