ArticleThe journal of physical chemistry. B2010
Referencing strategy for the direct comparison of nuclear magnetic resonance and molecular dynamics motional parameters in RNA.
Article in The journal of physical chemistry. B, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- MD2NMR: Linking molecular dynamics with NMR relaxation.Biophysical journal · 2026Article
- Hierarchical multi-timescale structural dynamics of the disordered N-terminal of p53.Nature communications · 2026Article
- G34R cancer mutation alters the conformational ensemble and dynamics of the histone H3.3 tails.Nucleic acids research · 2026Article
- Structural and computational studies of HIV-1 RNA.RNA biology · 2024Review
- Point mutations in SARS-CoV-2 variants induce long-range dynamical perturbations in neutralizing antibodies.Chemical science · 2022Article
- Slowdown of Interhelical Motions Induces a Glass Transition in RNA.Biophysical journal · 2015Article
- On the Possibility of Facilitated Diffusion of Dendrimers Along DNA.The journal of physical chemistry. B · 2015Article
- Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore.Nucleic acids research · 2014Article
- NMR studies of nucleic acid dynamics.Journal of magnetic resonance (San Diego, Calif. : 1997) · 2013Article
- A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed.Journal of the American Chemical Society · 2013Article
- Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.Biochemistry · 2012Article
- Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch.Nucleic acids research · 2012Article
- Synergistic applications of MD and NMR for the study of biological systems.Journal of biomedicine & biotechnology · 2012Review
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Authors and funding
4 authors.
Funding
Abstract
Nuclear magnetic resonance (NMR) spectroscopy and molecular dynamics (MD) simulations are both techniques that can be used to characterize the structural dynamics of biomolecules and their underlying time scales. Comparison of relaxation parameters obtained through each methodology allows for cross validation of techniques and for complementarity in the analysis of dynamics. Here we present a combined NMR/MD study of the dynamics of HIV-1 transactivation response (TAR) RNA. We compute relaxation constants (R(1), R(2), and NOE) and model-free parameters (S(2) and tau) from a 65 ns molecular dynamics (MD) trajectory and compare them with the respective parameters measured in a domain-elongation NMR experiment. Using the elongated domain as the frame of reference for all computed parameters allows for a direct comparison between experiment and simulation. We see good agreement for many parameters and gain further insight into the nature of the local and global dynamics of TAR, which are found to be quite complex, spanning multiple time scales. For the few cases where agreement is poor, comparison of the dynamical parameters provides insight into the limits of each technique. We suggest a frequency-matching procedure that yields an upper bound for the time scale of dynamics to which the NMR relaxation experiment is sensitive.
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