Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts
By Parin Sripakdeevong, Mirko Cevec, A. T. Chang, M. Erat, M. Ziegeler, Qin Zhao, G. Fox, Xiaolian Gao, S. Kennedy, R. Kierzek and 5 more. 2014
67 citations recorded by the source corpus.
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.
Subfields: Materials Chemistry, Molecular Biology
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In Materials Chemistry
- David Baker
- Jeffrey J. Gray
- Tanja Kortemme
- Frank DiMaio
- Jens Meiler
- Hahnbeom Park
- Xingjie Pan
- Santrupti Nerli
In Molecular Biology
- David Baker
- Jeffrey J. Gray
- Tanja Kortemme
- Xingjie Pan
- Jens Meiler
- Rhiju Das
- Frank DiMaio
- Brian D. Weitzner
Citations in the corpus
- Macromolecular modeling and design in Rosetta: recent methods and frameworks (2020, methodology): “As another connection of Rosetta’s RN A tools to experimental structural biology, 1 H NMR data can be used for RNA modeling via the CS-Rosetta-RNA protocol 164 .”
- Blind prediction of noncanonical RNA structure at atomic accuracy (2017, methodology): “Examples included two-strandedmotifs that required orders of magnitude higher computational expense with the prior enumerative SWA method (16), such as the most conserved domain of the signal recognition particle (1.”
- Modeling complex RNA tertiary folds with Rosetta. (2015, methodology): “…Kladwang, & Das, 2011), integration with conventional crystallographic (Chou, Sripakdeevong, Dibrov, Hermann, & Das, 2013) and NMR approaches (Sripakdeevong et al., 2014), and connections with recent single-molecule (Chou, Lipfert, & Das, 2014) and internet-scale videogame (Lee et al., 2014)…”