ArticleJournal of biomolecular NMR2008
A structure refinement protocol combining NMR residual dipolar couplings and small angle scattering restraints.
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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Molecular insights on CALX-CBD12 interdomain dynamics from MD simulations, RDCs, and SAXS.Biophysical journal · 2021Article
- Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints.Structure (London, England : 1993) · 2019Article
- Combining NMR and small angle X-ray scattering for the study of biomolecular structure and dynamics.Archives of biochemistry and biophysics · 2017Review
- Sampling Enrichment toward Target Structures Using Hybrid Molecular Dynamics-Monte Carlo Simulations.PloS one · 2016Article
- Tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by NMR, SAXS, chemical crosslinking, and functional studies.Biochimica et biophysica acta · 2015Review
- Uniqueness of models from small-angle scattering data: the impact of a hydration shell and complementary NMR restraints.Acta crystallographica. Section D, Biological crystallography · 2015Article
- Structural characterization of a flexible two-domain protein in solution using small angle X-ray scattering and NMR data.Structure (London, England : 1993) · 2014Article
- Using small angle solution scattering data in Xplor-NIH structure calculations.Progress in nuclear magnetic resonance spectroscopy · 2014Review
- The dynamic duo: combining NMR and small angle scattering in structural biology.Protein science : a publication of the Protein Society · 2014Review
- An overview of tools for the validation of protein NMR structures.Journal of biomolecular NMR · 2014Review
- Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex.Journal of biomolecular NMR · 2013Article
- MaxOcc: a web portal for maximum occurrence analysis.Journal of biomolecular NMR · 2012Article
- A simple procedure to evaluate the efficiency of bio-macromolecular rigid-body refinement by small-angle scattering.European biophysics journal : EBJ · 2012Article
- High-resolution membrane protein structure by joint calculations with solid-state NMR and X-ray experimental data.Journal of biomolecular NMR · 2011Article
- Nuclear magnetic resonance analysis of protein-DNA interactions.Journal of the Royal Society, Interface · 2011Review
- Minireview: structural insights into early folding events using continuous-flow time-resolved small-angle X-ray scattering.Biopolymers · 2011Review
- Structure of the K-turn U4 RNA: a combined NMR and SANS study.Nucleic acids research · 2010Article
- Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation.Biophysical journal · 2010Article
- Effect of interdomain dynamics on the structure determination of modular proteins by small-angle scattering.European biophysics journal : EBJ · 2010Article
- Small-angle scattering for structural biology--expanding the frontier while avoiding the pitfalls.Protein science : a publication of the Protein Society · 2010Review
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Authors and funding
6 authors.
Funding
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Abstract
We present the implementation of a target function based on Small Angle Scattering data (Gabel et al. Eur Biophys J 35(4):313-327, 2006) into the Crystallography and NMR Systems (CNS) and demonstrate its utility in NMR structure calculations by simultaneous application of small angle scattering (SAS) and residual dipolar coupling (RDC) restraints. The efficiency and stability of the approach are demonstrated by reconstructing the structure of a two domain region of the 31 kDa nuclear export factor TAP (TIP-associated protein). Starting with the high resolution X-ray structures of the two individual TAP domains, the translational and orientational domain arrangement is refined simultaneously. We tested the stability of the protocol against variations of the SAS target parameters and the number of RDCs and their uncertainties. The activation of SAS restraints results in an improved translational clustering of the domain positions and lifts part of the fourfold degeneracy of their orientations (associated with a single alignment tensor). The resulting ensemble of structures reflects the conformational space that is consistent with the experimental SAS and RDC data. The SAS target function is computationally very efficient. SAS restraints can be activated at different levels of precision and only a limited SAS angular range is required. When combined with additional data from chemical shift perturbation, paramagnetic relaxation enhancement or mutational analysis the SAS refinement is an efficient approach for defining the topology of multi-domain and/or multimeric biomolecular complexes in solution based on available high resolution structures (NMR or X-ray) of the individual domains.
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