Conformational Ensembles from Experimental Data and Computer Simulations

Conformational Ensembles from Experimental Data and Computer Simulations

Poster Abstracts

85-POS Board 5 Combining Molecular Dynamics and NMR to Characterize Excited States of an RNA Hairpin Sabine Reißer 1 , Peter Podbevšek 2 , Silvia Zucchelli 1 , Stefano Gustincich 1 , Giovanni Bussi 1 . 1 Scuola Internazionale Superiore di Studi Avanzati (SISSA), Trieste, Italy, 2 National Institute of Chemistry, Ljubljana, Slovenia. An inverted SINEB2 element embedded in a non-coding RNA was identified as crucial for the enhancement of mRNA translation under cellular stress [1]. Deletion studies showed, that a terminal 29 nt hairpin is important for this function. To reveal its tertiary structure, 125 NOEs were recorded from NMR experiments and translated into distance restraints for structure refinement [2]. The refined structures were used as a starting point for molecular dynamics simulations. In a replica exchange simulation with 20 replicas, the Hamiltonian (i.e. electrostatic, van-der-Waals, and dihedral potentials) of the hairpin was gradually scaled down to enhance sampling, while adaptive restraints according to the maximum-entropy principle were applied to satisfy the NOE distances as an average over the unbiased replica [3]. The resulting ensemble had an improved agreement with the NOE restraints, compared with the initially refined set of structures. A clustering analysis based on the εRMSD - a metric which measures structural similarity by analyzing base-pairing and stacking interactions [4], rather then absolute atomic coordinates like the RMSD - yielded several conformational states, some of which had shifted base pairs with respect to the initial set of structures. Averaging over the structures within one cluster, it became evident that some NOEs are satisfied in specific clusters, while not in others, leading to the conclusion that the NOE signal represents an average over different conformations exchanging rapidly on a timescale below what can be resolved by NMR. Using our approach, the population of these excited states could be quantified, and the single conformations can be studied towards their structure-function relationship. References: [1] Carrieri et al. (2012), Nature. [2] Podbevsek et al., submitted. [3] Cesari et al. (2016), JCTC. [4] Bottaro et al. (2014), NAR.

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