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Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.

Research paper by Andrew C AC Stelzer, Aaron T AT Frank, Maximillian H MH Bailor, Ioan I Andricioaei, Hashim M HM Al-Hashimi

Indexed on: 25 Aug '09Published on: 25 Aug '09Published in: Methods



Abstract

A broad structural landscape often needs to be characterized in order to fully understand how regulatory RNAs perform their biological functions at the atomic level. We present a protocol for visualizing thermally accessible RNA conformations at atomic-resolution and with timescales extending up to milliseconds. The protocol combines molecular dynamics (MD) simulations with experimental residual dipolar couplings (RDCs) measured in partially aligned (13)C/(15)N isotopically enriched elongated RNA samples. The structural ensembles generated in this manner provide insights into RNA dynamics and its role in functionally important transitions.