Title : “Deciphering RNA conformational dynamics in solution using computer simulations and experimental data” 

From :  Molecular and Statistical and Biophysics Group of SISSA  – Trieste, Italy 

When :  Friday, February 21st 

Where :  CNR Conference Room  – Research Area NA1 ( Naples )

Host :  Host: Dr. Andrea Beccari  |  Tel. 081/6132339; e-mail: ndrea.Beccari@dompe.com 



RNA molecules are crucial characters of the cellular machinery. While their historical relevance stems from being the intermediate carrier of the genetic information from the DNA to functional proteins, it is now clear that they are also active players in regulation and signaling processes. To exert these biological functions, they need to adopt a well-defined structural organization, which in turn allows establishing interactions with specific molecular partners (1). Despite experimental techniques such as fluorescence spectroscopy and small-angle x-ray scattering (SAXS) are well suited to achieve a structural characterization, their outcome data are generated as time and ensemble averages and produce low resolution information. As such, interpreting them unambiguously is not always straightforward. Therefore, combining the available experimental data with an atomic-level perspective, as provided by molecular dynamics (MD) simulations, can be of remarkable support.

We apply this framework to the GTPase-associated center (GAC), an RNA molecule found in the 23S ribosomal subunit, where it is involved in protein translation. To associate with its ribosomal protein partner L11 and thus play its function, GAC must adopt a complex tertiary structure. In particular, recent SAXS experiments reported on GAC structural flexibility in response to ions of different nature in the buffer solution (2), noticing that Mg2+ can stabilize the folded state, while K+ favored less compact and more extended conformations. Using these experimental data as a reference, we performed MD simulations and predicted SAXS spectra from the sampled structures. Through this procedure, we thus aim at providing an atomic-level view of the conformations adopted by GAC along its folding pathway.

(1) Al-Hashimi, H.M. and Walter, N.G. Curr. Opin. Struct. Biol. , 2008 , 18(3), 321-329.

(2) Welty, R., Pabit, S.A., Katz, A.M., Calvey, G.D., Pollack, L., Hall, K.B. RNA , 2018 , 24(12), 1828-38.