Computational modeling of RNA 3D structures, with the aid of experimental restraints

Figures & data

Table 1. Examples of computational methods for RNA 3D structure modeling that are capable of using experimental restraints

Type	Method name	Description	Representation	Probing of conformations
Folding simulation	AMBER	Physics-based method for dynamics simulations, applicable for relatively short simulations of small molecular systems	Full-atom	Molecular dynamics
Folding simulation	DMD (Discrete Molecular Dynamics)	Coarse-grained simulation method that uses discrete molecular dynamics and a mostly physics-based energy function	Coarse-grained (3 centers / residue)	Discrete molecular dynamics
Folding simulation	SimRNA	Coarse-grained simulation method that uses Monte Carlo sampling method and a knowledge-based energy function	Coarse-grained (5 centers / residue)	Monte Carlo
Folding simulation	NAST (The Nucleic Acid Simulation Tool)	Very coarse-grained simulation method that uses molecular dynamics and relies almost completely on restraints supplied by a user	Coarse-grained (1 center / residue)	Molecular dynamics
Comparative modeling	MMB (MacroMoleculeBuilder)	A method based mostly on restraints, inferred from template structures and/or provided by a user, optimizes the structures with the function that is partially physics-based	Full-atom	Molecular dynamics
Interactive manipulation	S2S/Assemble	The method allows users to easily display, manipulate the base-base interactions, insert motifs, and eventually build a complete RNA 3D model	Full-atom	Manual
Fragment assembly	FARNA (Fragment Assembly of RNA) / FARFAR	Adaptation of the ROSETTA method for RNA structure prediction, assembles the structure from short single-stranded fragments using a Monte Carlo procedure and a hybrid physics/statistics-based scoring function, followed by full-atom refinement with a physics-based function	Full-atom	Monte Carlo
Fragment assembly	MC-Fold|MC-Sym	A method that assembles RNA structures from nucleotide cyclic motifs (NCN) with the sampling defined as a constraint satisfaction problem and evaluates the resulting conformations with a hybrid physics/statistics-based scoring function	Full-atom	Constraint satisfaction problem
Fragment assembly	RNA Composer	A method that can assemble large RNA structures from fragments taken from RNA FRABASE, using user-defined restraints, based on the machine translation principle	Full-atom	Machine translation workflow

Table 2. Low-resolution experimental methods that generate particularly useful data for computational prediction of RNA 3D structure

Type of restraints	Method	Description
Secondary structure	SHAPE (Selective 2'-Hydroxyl Acylation analyzed by Primer Extension)	Method for quantitative detection of local nucleotide flexibility. 2’-OH in flexible, unpaired nucleotides reacts preferentially with a probing reagent, forming adducts that can be identified as stops to primer extension by reverse transcriptase.
Secondary structure	DMS (dimethylsulfate footprinting)	DMS reacts with adenine at N1 and cytosine at N3. Reactive cytosines and adenines can be detected by reverse transcription and are considered as unpaired.
Secondary structure	CMCT (1-cyclohexyl-(2-morpholinoethyl)carbodiimide metho-p-toluene sulfonate)	CMCT reacts with N3 of uridine and, to a lesser extent, N1 of guanine. Reactive residues can be detected by reverse transcription and are considered as unpaired.
Secondary structure	Kethoxal	Kethoxal specifically attacks accessible N1 and N2 of guanine, and it is used for detection of unpaired guanines. The modified sites can be detected by reverse transcription.
Secondary structure + tertiary contacts	Mutate-and-map	SHAPE/DMS/CMCT chemical probing for a large number (preferably all) of point mutants of the RNA sequence. Analysis of changes in secondary structures of the set of point mutants can be used to infer tertiary contacts.
Solvent accessibility	HRP (hydroxyl radical probing)	Reports approximate backbone solvent accessibility. Solvent exposed nucleotides have high HRP reactivity.
Tertiary contacts	MOHCA (multiplexed hydroxyl radical cleavage analysis)	Enables the detection of pairs of contacting residues via random incorporation of radical cleavage agents. Contacting residues are detected from a cleavage pattern analyzed in two-dimensional gel electrophoresis.
Tertiary contacts	Cross-linking	Based on the formation of covalent bonds between spatially close regions of RNA that may be distant in sequence. Can be achieved using physical factors such as UV light or by chemical reagents.
Distances between labeled residues	FRET (Förster Resonance Energy Transfer)	Distances between fluorescent dyes linked to RNA molecule are inferred from the intensity of energy transfer.
Distances between labeled residues	ESR/EPR (Electron Spin/Paramagnetic Resonance) spectroscopy	Distances are derived from the measured spin–spin splittings for unpaired electrons localized on paramagnetic labels linked to RNA molecule
Global shape	SAXS/SANS (Small Angle X-ray/Neutron Scattering)	Provides information about the pair distance distribution within the molecule under study, which can be used to infer the particle envelope/shape.
Global shape	Cryo-EM (Cryogenic Electron Microscopy)	A 3D model is reconstructed through analysis of a very large number of 2D EM images

Figure 1. Crystal structure of Escherichia coli 5S rRNA (PDB ID: 3OAS) (A) and computational models predicted with the fragment assembly approach based on structural probing⁷⁸ (B) and manual modeling based on cryo-EM data of the 50S subunit⁷⁹ (C).

Figure 2. A model of VAI∆TS RNA structure obtained with SimRNA and built into the SAXS reconstruction using PyRy3D.⁸⁵

Figure 3. A flowchart describing relations between different types of data, computer programs, and RNA 3D structure modeling strategies.

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