ArticleJournal of structural biology2016
Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking.
Article in Journal of structural biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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20 citing papers in PubMed, 35 citations in OpenAlex.
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- Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery.Biomolecules · 2023Review
- Incorporation of DThe journal of physical chemistry. B · 2022Article
- Recent advances in structural characterization of biomacromolecules in foodsFrontiers in nutrition · 2022Review
- New system for archiving integrative structures.Acta crystallographica. Section D, Structural biology · 2021Article
- Structural Proteomics Methods to Interrogate the Conformations and Dynamics of Intrinsically Disordered Proteins.Frontiers in chemistry · 2021Review
- Hybrid methods for combined experimental and computational determination of protein structure.The Journal of chemical physics · 2020Review
- Mass Spectrometry-Based Protein Footprinting for Higher-Order Structure Analysis: Fundamentals and Applications.Chemical reviews · 2020Review
- Protein Footprinting: Auxiliary Engine to Power the Structural Biology Revolution.Journal of molecular biology · 2020Review
- Zinc-finger protein CNBP alters the 3-D structure of lncRNA Braveheart in solution.Nature communications · 2020Article
- Reporting on the future of integrative structural biology ORAU workshop.Frontiers in bioscience (Landmark edition) · 2020Article
- Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures.Structure (London, England : 1993) · 2019Article
- Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR.Current opinion in structural biology · 2019Review
- A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.Structure (London, England : 1993) · 2019Article
- Tracking Higher Order Protein Structure by Hydrogen-Deuterium Exchange Mass Spectrometry.Protein and peptide letters · 2019Review
- Fast Photochemical Oxidation of Proteins Coupled with Mass Spectrometry.Protein and peptide letters · 2019Review
- Multidomain architecture of estrogen receptor reveals interfacial cross-talk between its DNA-binding and ligand-binding domains.Nature communications · 2018Article
- Implementing fast photochemical oxidation of proteins (FPOP) as a footprinting approach to solve diverse problems in structural biology.Methods (San Diego, Calif.) · 2018Review
- Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions.Methods (San Diego, Calif.) · 2018Review
- Rosetta Protein Structure Prediction from Hydroxyl Radical Protein Footprinting Mass Spectrometry Data.Analytical chemistry · 2018Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
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Abstract
Structural determination of protein-protein complexes such as multidomain nuclear receptors has been challenging for high-resolution structural techniques. Here, we present a combined use of multiple biophysical methods, termed iSPOT, an integration of shape information from small-angle X-ray scattering (SAXS), protection factors probed by hydroxyl radical footprinting, and a large series of computationally docked conformations from rigid-body or molecular dynamics (MD) simulations. Specifically tested on two model systems, the power of iSPOT is demonstrated to accurately predict the structures of a large protein-protein complex (TGFβ-FKBP12) and a multidomain nuclear receptor homodimer (HNF-4α), based on the structures of individual components of the complexes. Although neither SAXS nor footprinting alone can yield an unambiguous picture for each complex, the combination of both, seamlessly integrated in iSPOT, narrows down the best-fit structures that are about 3.2Å and 4.2Å in RMSD from their corresponding crystal structures, respectively. Furthermore, this proof-of-principle study based on the data synthetically derived from available crystal structures shows that the iSPOT-using either rigid-body or MD-based flexible docking-is capable of overcoming the shortcomings of standalone computational methods, especially for HNF-4α. By taking advantage of the integration of SAXS-based shape information and footprinting-based protection/accessibility as well as computational docking, this iSPOT platform is set to be a powerful approach towards accurate integrated modeling of many challenging multiprotein complexes.
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