25-30 August 2019
Henry Ford Building
Europe/Berlin timezone

Exact distance measurement and spatial sampling in RNA

Not scheduled
Harnack House and Henry Ford Building

Harnack House and Henry Ford Building

Board: 493
Poster Posters


Prof. Beat Vogeli (Assistant Professor, University of Colorado, Denver)


RNA does not only translate the genetic code into proteins, but also carries out important cellular functions. Understanding such functions requires knowledge of the structure and dynamics at atomic resolution. Almost half of the published RNA structures have been solved by NMR, but as a result of severe resonance overlap and low proton density, high-resolution RNA structures are rarely obtained from NOE data alone. Instead, additional semi-empirical restraints and labor-intensive techniques are required for structural averages, while there are only a few experimentally derived ensembles representing dynamics.
We have replaced the standard NOE-based procedure for protein structure determination by an approach that employs tight averaged distance restraints derived from exact NOEs (eNOEs). We have recently shown that our protocol is also able to define a 14-mer RNA tetraloop structure at high resolution without other restraints. Here, we redefine the limits of the eNOE methodology in terms of retrieving spatial sampling and the RNA size amenable to such studies:
We use eNOEs to calculate a two-state structure of the tetraloop. Then, we demonstrate that a molecular dynamics trajectory generated without experimental restraints features a distinct and previously unknown low-populated state that improves the agreement with the eNOEs.
Since fully sampled NOESY buildup series can take 10 days or more to acquire, eNOE studies are both expensive and problematic in the case of unstable samples. We investigate the fidelity of eNOE restraints recorded with non-uniform sampling (NUS) of the indirect dimensions. NUS imparts negligible errors on the eNOE distances down to 10% sampling, but there is a noticeable decrease in the eNOE yield below 40%.
Our innovations to the eNOE protocol may open an avenue to obtain high-resolution structural ensembles of small RNA with moderate experimental efforts and average structures of larger RNA.

Primary authors

Prof. Beat Vogeli (Assistant Professor, University of Colorado, Denver) Mr Parker Nichols (Research Assistant, University of Colorado, Denver) Morkos Henen (RC1-South, 9th floor) Ms Alexandra Born (Ph.D. Student, University of Colorado, Denver) Dr Dean Strotz (ETH Zürich) Prof. Peter Güntert (ETH Zürich) Dr Sandro Bottaro (Instituto Italiano di Tecnologia, Genova, Italy) Prof. Michele Parrinello (Instituto Italiano di Tecnologia, Genova, Italy) Prof. Kresten Lindorff-Larsen (University of Copenhagen) Dr Frank Delaglio (Institute for Bioscience and Biotechnology Research, National Institute of Standards and Technology and the University of Maryland, Rockville, Maryland)

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