Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA.

José Ginés Hernández Cifre,Aarón Ayllón Benítez,José García de la Torre,Francisco Guillermo Díaz Baños

doi:10.1186/s13628-015-0025-7

José Ginés Hernández Cifre, Aarón Ayllón Benítez

Open Access

https://doi.org/10.1186/s13628-015-0025-7

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Journal: BMC biophysics	Publication Date: Dec 1, 2015
Citations: 45	License type: CC BY 4.0

Affiliation: University of Murcia

Abstract

BackgroundThe possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational scheme for predicting global properties and mimicking the internal dynamics of RNA molecules in solution. A simple coarse-grained model with one bead per nucleotide and two types of intra-molecular interactions (elastic interactions and excluded volume interactions) is used to represent the RNA chain. The elastic interactions are modeled by a set of Hooke springs that form a minimalist elastic network. The Brownian dynamics technique is employed to simulate the time evolution of the RNA conformations.ResultsThat scheme is applied to the 5S ribosomal RNA of E. Coli and the yeast phenylalanine transfer RNA. From the Brownian trajectory, several solution properties (radius of gyration, translational diffusion coefficient, and a rotational relaxation time) are calculated. For the case of yeast phenylalanine transfer RNA, the time evolution and the probability distribution of the inter-arm angle is also computed.ConclusionsThe general good agreement between our results and some experimental data indicates that the model is able to capture the tertiary structure of RNA in solution. Our simulation results also compare quite well with other numerical data. An advantage of the scheme described here is the possibility of visualizing the real time macromolecular dynamics.Electronic supplementary materialThe online version of this article (doi:10.1186/s13628-015-0025-7) contains supplementary material, which is available to authorized users.

Highlights

The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function
A bead-and-spring model for the yeast phenylalanine Transfer RNA (tRNA), yeast tRNAphe (PDB code 1EHZ), was built according to the structure sketched in Fig. 1a [45]
Each nucleotide is replaced by a bead so that the secondary structure is represented in detail

Summary

Introduction

The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. Benítez et al BMC Biophysics (2015) 8:11 it is noteworthy that the notation for ribosomal RNAs, as for some other biomacromolecules, is made in terms of a hydrodynamic property) It is well-known that tRNA and rRNA are singlestranded chains that fold unto themselves giving rise to a secondary structure that contains both ordered (essentially rigid) double-helical regions and disordered zones so-called loops (see Fig. 1). As above mentioned, dilute solution properties (hydrodynamic coefficients, scattering-related quantities, etc.) provide key information on the overall three-dimensional structure of RNA when combined with theoretical predictive models. Those models should include flexibility in order to make adequate predictions

Methods

Results

Conclusion