Constructing atomic-resolution RNA structural ensembles using MD and motionally decoupled NMR RDCs.
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.
Stelzer
Andrew C
AC
Department of Chemistry and Biophysics, The University of Michigan, Ann Arbor, MI 48109, USA.
Frank
Aaron T
AT
Bailor
Maximillian H
MH
Andricioaei
Ioan
I
Al-Hashimi
Hashim M
HM
D001483:Base Sequence; D002247:Carbon Isotopes / Q000737:chemistry; D015497:HIV-1 / Q000235:genetics; D009682:Magnetic Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D008969:Molecular Sequence Data; D009038:Motion; D009587:Nitrogen Isotopes / Q000737:chemistry; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry; D013997:Time Factors; D014158:Transcription, Genetic
D002247:Carbon Isotopes; D009587:Nitrogen Isotopes; D012367:RNA, Viral; D012313:RNA
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