ArticleJournal of biomolecular NMR2008
Self-consistent residual dipolar coupling based model-free analysis for the robust determination of nanosecond to microsecond protein dynamics.
Article in Journal of biomolecular NMR, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed.
- Extending the detectable time window of fast protein dynamics usingJournal of biomolecular NMR · 2025Article
- Structure-Based Experimental Datasets for Benchmarking Protein Simulation Force Fields [Article v1.0].Living journal of computational molecular science · 2025Article
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Protein Allostery at Atomic Resolution.Angewandte Chemie (International ed. in English) · 2020Article
- Enhancing NMR derived ensembles with kinetics on multiple timescales.Journal of biomolecular NMR · 2020Article
- Ensembles of a small number of conformations with relative populations.Journal of biomolecular NMR · 2015Article
- Side Chain Conformational Distributions of a Small Protein Derived from Model-Free Analysis of a Large Set of Residual Dipolar Couplings.Journal of the American Chemical Society · 2015Article
- Information content of long-range NMR data for the characterization of conformational heterogeneity.Journal of biomolecular NMR · 2015Article
- Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding.Scientific reports · 2015Article
- Structural heterogeneity in microcrystalline ubiquitin studied by solid-state NMR.Protein science : a publication of the Protein Society · 2015Article
- New look at hemoglobin allostery.Chemical reviews · 2015Review
- NMR studies of dynamic biomolecular conformational ensembles.Progress in nuclear magnetic resonance spectroscopy · 2015Review
- Extensive conformational heterogeneity within protein cores.The journal of physical chemistry. B · 2014Article
- ORIUM: optimized RDC-based Iterative and Unified Model-free analysis.Journal of biomolecular NMR · 2014Article
- Improved cross validation of a static ubiquitin structure derived from high precision residual dipolar couplings measured in a drug-based liquid crystalline phase.Journal of the American Chemical Society · 2014Article
- Enhancing the quality of protein conformation ensembles with relative populations.Journal of biomolecular NMR · 2014Article
- Nanosecond time scale motions in proteins revealed by high-resolution NMR relaxometry.Journal of the American Chemical Society · 2013Article
- Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin.Journal of biomolecular NMR · 2013Article
- CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data.Journal of computational chemistry · 2013Article
- Measuring dynamic and kinetic information in the previously inaccessible supra-τ(c) window of nanoseconds to microseconds by solution NMR spectroscopy.Molecules (Basel, Switzerland) · 2013Review
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11 authors.
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Abstract
Residual dipolar couplings (RDCs) provide information about the dynamic average orientation of inter-nuclear vectors and amplitudes of motion up to milliseconds. They complement relaxation methods, especially on a time-scale window that we have called supra-tau(c) (tau(c) < supra-tau(c) < 50 micros). Here we present a robust approach called Self-Consistent RDC-based Model-free analysis (SCRM) that delivers RDC-based order parameters-independent of the details of the structure used for alignment tensor calculation-as well as the dynamic average orientation of the inter-nuclear vectors in the protein structure in a self-consistent manner. For ubiquitin, the SCRM analysis yields an average RDC-derived order parameter of the NH vectors <S2(rdc)>0.72 +/- 0.02 compared to <S2(LS)> = 0.778 +/- 0.003 for the Lipari-Szabo order parameters, indicating that the inclusion of the supra-tau(c) window increases the averaged amplitude of mobility observed in the sub-supra-tau(c) window by about 34%. For the beta-strand spanned by residues Lys48 to Leu50, an alternating pattern of backbone NH RDC order parameter S2(rdc)(NH) = (0.59, 0.72, 0.59) was extracted. The backbone of Lys48, whose side chain is known to be involved in the poly-ubiquitylation process that leads to protein degradation, is very mobile on the supra-tau(c) time scale (S2(rdc)(NH) = 0.59 +/- 0.03), while it is inconspicuous (S2(LS)(NH)= 0.82) on the sub-tau(c) as well as on micros-ms relaxation dispersion time scales. The results of this work differ from previous RDC dynamics studies of ubiquitin in the sense that the results are essentially independent of structural noise providing a much more robust assessment of dynamic effects that underlie the RDC data.
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