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

Background

The 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.

Results

That 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.

Conclusions

The 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 material

The online version of this article (doi:10.1186/s13628-015-0025-7) contains supplementary material, which is available to authorized users.

Photon cross-correlation spectroscopy to 10-ns resolution

We describe a low-cost modification based on the research of Arecchi et al. [Opt. Commun. 3, 284-288 (1971)] on a standard photon correlation spectroscopy setup for measuring small (approximately equal 1%) and fast (resolution, approximately equal 10 ns) light fluctuations. Details of the electronics and optics permit the apparatus to be easily reproduced. Careful tests show that spurious correlations of <or=1% can be achieved with standard detectors only when taking precautions with the electronics. Moreover, measurements on latex spheres, ellipsoids, and protein solutions show that fast and very small light fluctuations ( approximately equal 1-5%) can be studied versus scattering vector and light polarization.