ArticleJournal of the American Chemical Society2011
Determination of the structures of symmetric protein oligomers from NMR chemical shifts and residual dipolar couplings.
Article in Journal of the American Chemical Society, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Recent Advances in NMR Protein Structure Prediction with ROSETTA.International journal of molecular sciences · 2023Review
- The Importance of Weakly Co-Evolving Residue Networks in Proteins is Revealed by Visual Analytics.Frontiers in bioinformatics · 2022Article
- Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches.International journal of molecular sciences · 2021Review
- Structure of membrane diacylglycerol kinase in lipid bilayers.Communications biology · 2021Article
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
- Computational design of closely related proteins that adopt two well-defined but structurally divergent folds.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Integrative Protein Modeling in RosettaNMR from Sparse Paramagnetic Restraints.Structure (London, England : 1993) · 2019Article
- Disordered region of H3K9 methyltransferase Clr4 binds the nucleosome and contributes to its activity.Nucleic acids research · 2019Article
- CS-ROSETTA.Methods in enzymology · 2019Article
- Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data.Analytical chemistry · 2018Article
- The PROSECCO server for chemical shift predictions in ordered and disordered proteins.Journal of biomolecular NMR · 2017Article
- Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.Biochemistry · 2016Review
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Structure determination of helical filaments by solid-state NMR spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A community resource of experimental data for NMR / X-ray crystal structure pairs.Protein science : a publication of the Protein Society · 2016Review
- Structure of the α-crystallin domain from the redox-sensitive chaperone, HSPB1.Journal of biomolecular NMR · 2015Article
- Article
- A hybrid NMR/SAXS-based approach for discriminating oligomeric protein interfaces using Rosetta.Proteins · 2015Article
- Integrating solid-state NMR and computational modeling to investigate the structure and dynamics of membrane-associated ghrelin.PloS one · 2015Article
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9 authors.
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Abstract
Symmetric protein dimers, trimers, and higher-order cyclic oligomers play key roles in many biological processes. However, structural studies of oligomeric systems by solution NMR can be difficult due to slow tumbling of the system and the difficulty in identifying NOE interactions across protein interfaces. Here, we present an automated method (RosettaOligomers) for determining the solution structures of oligomeric systems using only chemical shifts, sparse NOEs, and domain orientation restraints from residual dipolar couplings (RDCs) without a need for a previously determined structure of the monomeric subunit. The method integrates previously developed Rosetta protocols for solving the structures of monomeric proteins using sparse NMR data and for predicting the structures of both nonintertwined and intertwined symmetric oligomers. We illustrated the performance of the method using a benchmark set of nine protein dimers, one trimer, and one tetramer with available experimental data and various interface topologies. The final converged structures are found to be in good agreement with both experimental data and previously published high-resolution structures. The new approach is more readily applicable to large oligomeric systems than conventional structure-determination protocols, which often require a large number of NOEs, and will likely become increasingly relevant as more high-molecular weight systems are studied by NMR.
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