Isotropic reorientational eigenmode dynamics complements NMR relaxation measurements for RNA.
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Summary
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, showing that there is no separability of global and internal motions.
- Type
- article
- Published
- 2005-01-01
- Cited by
- 8
- References
- 27
- OpenAlex
- https://openalex.org/W1586504007
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:38891059
Keywords
Isotropy, Normal mode, Dynamics (music), Molecular dynamics, Relaxation (psychology)
References
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- The Dynamical Theory of Nuclear Induction
- Mapping of Spectral Density Functions Using Heteronuclear NMR Relaxation Measurements
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- A novel view of domain flexibility in E. coli adenylate kinase based on structural mode-coupling (15)N NMR relaxation.
- NMR Order Parameters of Biomolecules: A New Analytical Representation and Application to the Gaussian Axial Fluctuation Model
- Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 1. Theory and range of validity
- Solution structure of the HIV-2 TAR-argininamide complex.
- Beyond the decoupling approximation in the model free approach for the interpretation of NMR relaxation of macromolecules in solution.
- Model-free approach to the interpretation of nuclear magnetic resonance relaxation in macromolecules. 2. Analysis of experimental results
- Dynamical Theory of Nuclear Induction. II
- On the Theory of Relaxation Processes
- Reorientational eigenmode dynamics: a combined MD/NMR relaxation analysis method for flexible parts in globular proteins.
- 13C relaxation and dynamics of the purine bases in the iron responsive element RNA hairpin.
- SLOW MOTIONAL ESR IN COMPLEX FLUIDS : THE SLOWLY RELAXING LOCAL STRUCTURE MODEL OF SOLVENT CAGE EFFECTS
- Metal binding and base ionization in the U6 RNA intramolecular stem-loop structure
- Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins
- General framework for studying the dynamics of folded and nonfolded proteins by NMR relaxation spectroscopy and MD simulation.
- A structural mode-coupling approach to 15N NMR relaxation in proteins.
- Base flexibility in HIV-2 TAR RNA mapped by solution (15)N, (13)C NMR relaxation.
Cited by
- Characterizing HIV-1 Transactivation Response Element Dynamics that Govern Ligand Recognition: Direct Applications to Drug Discovery.
- Iron Responsive Element RNA Flexibility Described by NMR and Isotropic Reorientational Eigenmode Dynamics
- Pressure effects on the ensemble dynamics of ubiquitin inspected with molecular dynamics simulations and isotropic reorientational eigenmode dynamics.
- NMR studies of nucleic acid dynamics
- NMR spectroscopy on domain dynamics in biomacromolecules.
- Constructing RNA dynamical ensembles by combining MD and motionally decoupled NMR RDCs: new insights into RNA dynamics and adaptive ligand recognition
- Structural plasticity and Mg2+ binding properties of RNase P P4 from combined analysis of NMR residual dipolar couplings and motionally decoupled spin relaxation.
- Domain-elongation NMR spectroscopy yields new insights into RNA dynamics and adaptive recognition.
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