Isotropic reorientational eigenmode dynamics complements NMR relaxation measurements for RNA. 2005

Scott A Showalter, and Kathleen B Hall
Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouro 63110, USA.

(13)C NMR relaxation measurements alone are often not sufficient to describe the motions of small RNA molecules in solution. In the case where the global tumbling time of the RNA is on the same time scale as its internal motions, standard Lipari-Szabo analysis becomes inadequate, and other methods must be used to describe the dynamics. Here, molecular dynamics simulations of the iron-responsive element (IRE) RNA hairpin are analyzed using isotropic reorientational eigenmode dynamics (iRED) to provide a picture of the motions of the RNA. The results show that indeed there is no separability of global and internal motions, and thus the order parameters determined from experimental data cannot be quantitatively accurate. iRED analysis also identifies correlated motions, providing a new picture of the dynamics of the IRE loop.

UI MeSH Term Description Entries
D009682 Magnetic Resonance Spectroscopy Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING). In Vivo NMR Spectroscopy,MR Spectroscopy,Magnetic Resonance,NMR Spectroscopy,NMR Spectroscopy, In Vivo,Nuclear Magnetic Resonance,Spectroscopy, Magnetic Resonance,Spectroscopy, NMR,Spectroscopy, Nuclear Magnetic Resonance,Magnetic Resonance Spectroscopies,Magnetic Resonance, Nuclear,NMR Spectroscopies,Resonance Spectroscopy, Magnetic,Resonance, Magnetic,Resonance, Nuclear Magnetic,Spectroscopies, NMR,Spectroscopy, MR
D012313 RNA A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed) RNA, Non-Polyadenylated,Ribonucleic Acid,Gene Products, RNA,Non-Polyadenylated RNA,Acid, Ribonucleic,Non Polyadenylated RNA,RNA Gene Products,RNA, Non Polyadenylated

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