Conformational Ensembles from Experimental Data and Computer Simulations

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Conformational Ensembles from Experimental Data
and Computer Simulations Poster Abstracts
122
85-POS Board 5
Combining Molecular Dynamics and NMR to Characterize Excited States of an RNA
Hairpin
Sabine Reißer1, Peter Podbevšek2, Silvia Zucchelli1, Stefano Gustincich1, Giovanni Bussi 1.
1Scuola 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.