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

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.

SUBMITTER: Sripakdeevong P

PROVIDER: S-EPMC3985481 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature

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

Sripakdeevong Parin P Cevec Mirko M Chang Andrew T AT Erat Michèle C MC Ziegeler Melanie M Zhao Qin Q Fox George E GE Gao Xiaolian X Kennedy Scott D SD Kierzek Ryszard R Nikonowicz Edward P EP Schwalbe Harald H Sigel Roland K O RK Turner Douglas H DH Das Rhiju R

Nature methods 20140302 4

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- ...[more]

PMID: 24584194

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