Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts

Parin Sripakdeevong; Mirko Cevec; Andrew T Chang; Michèle C Erat; Melanie Ziegeler; Qin Zhao; George E Fox; Xiaolian Gao; Scott D Kennedy; Ryszard Kierzek; Edward P Nikonowicz; Harald Schwalbe; Roland K O Sigel; Douglas H Turner; Rhiju Das

doi:10.1038/nmeth.2876

Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts

Nat Methods. 2014 Apr;11(4):413-6. doi: 10.1038/nmeth.2876. Epub 2014 Mar 2.

Authors

Affiliations

¹ Biophysics Program, Stanford University, Stanford, California, USA.
² Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University Frankfurt, Frankfurt, Germany.
³ Department of Biochemistry and Cell Biology, Rice University, Houston, Texas, USA.
⁴ 1] Department of Biochemistry, University of Oxford, Oxford, UK. [2] Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland.
⁵ Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA.
⁶ Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA.
⁷ Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA.
⁸ Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
⁹ Institute of Inorganic Chemistry, University of Zurich, Zurich, Switzerland.
¹⁰ Department of Chemistry, University of Rochester, Rochester, New York, USA.
¹¹ 1] Biophysics Program, Stanford University, Stanford, California, USA. [2] Department of Biochemistry, Stanford University, Stanford, California, USA. [3] Department of Physics, Stanford University, Stanford, California, USA.

Abstract

Structured noncoding RNAs underlie fundamental cellular processes, but determining their three-dimensional structures remains challenging. We demonstrate that integrating ¹H NMR chemical shift data with Rosetta de novo modeling can be used to consistently determine high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 'blind' targets, chemical-shift Rosetta for RNA (CS-Rosetta-RNA) recovered experimental structures with high accuracy (0.6-2.0 Å all-heavy-atom r.m.s. deviation) in 18 cases.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Animals
Nuclear Magnetic Resonance, Biomolecular / methods*
Nucleotide Motifs*
RNA, Untranslated / chemistry*

Substances

RNA, Untranslated

Abstract

Publication types

MeSH terms

Substances

Grants and funding