ArticleProtein science : a publication of the Protein Society2008
Modeling of protein binary complexes using structural mass spectrometry data.
Article in Protein science : a publication of the Protein Society, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- In silico study of some selective phytochemicals against a hypothetical SARS-CoV-2 spike RBD using molecular docking tools.Computers in biology and medicine · 2021Article
- Covalent Labeling with Diethylpyrocarbonate for Studying Protein Higher-Order Structure by Mass Spectrometry.Journal of visualized experiments : JoVE · 2021Article
- Methods for Molecular Modelling of Protein Complexes.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Using X-ray Footprinting and Mass Spectrometry to Study the Structure and Function of Membrane Proteins.Protein and peptide letters · 2019Review
- Covalent labeling-mass spectrometry with non-specific reagents for studying protein structure and interactions.Methods (San Diego, Calif.) · 2018Review
- The ClusPro web server for protein-protein docking.Nature protocols · 2017Article
- Theoretical modeling of multiprotein complexes by iSPOT: Integration of small-angle X-ray scattering, hydroxyl radical footprinting, and computational docking.Journal of structural biology · 2016Article
- Synchrotron X-ray footprinting as a method to visualize water in proteins.Journal of synchrotron radiation · 2016Article
- Experiment-Guided Molecular Modeling of Protein-Protein Complexes Involving GPCRs.Methods in molecular biology (Clifton, N.J.) · 2015Article
- Development of a microsecond X-ray protein footprinting facility at the Advanced Light Source.Journal of synchrotron radiation · 2014Article
- Synchrotron X-ray footprinting on tour.Journal of synchrotron radiation · 2014Article
- Structural mass spectrometry of proteins using hydroxyl radical based protein footprinting.Analytical chemistry · 2011Article
- Modeling of the DNA-binding site of yeast Pms1 by mass spectrometry.DNA repair · 2011Article
- A combined global and local approach to elucidate spatial organization of the Mycobacterial ParB-parS partition assembly.Biochemistry · 2011Article
- Fast photochemical oxidation of proteins for comparing structures of protein-ligand complexes: the calmodulin-peptide model system.Analytical chemistry · 2011Article
- Visualizing water molecules in transmembrane proteins using radiolytic labeling methods.Biochemistry · 2010Review
- Outcome of a workshop on applications of protein models in biomedical research.Structure (London, England : 1993) · 2009Article
- Quantifying protein interface footprinting by hydroxyl radical oxidation and molecular dynamics simulation: application to galectin-1.Journal of the American Society for Mass Spectrometry · 2008Article
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2 authors.
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Abstract
In this article, we describe a general approach to modeling the structure of binary protein complexes using structural mass spectrometry data combined with molecular docking. In the first step, hydroxyl radical mediated oxidative protein footprinting is used to identify residues that experience conformational reorganization due to binding or participate in the binding interface. In the second step, a three-dimensional atomic structure of the complex is derived by computational modeling. Homology modeling approaches are used to define the structures of the individual proteins if footprinting detects significant conformational reorganization as a function of complex formation. A three-dimensional model of the complex is constructed from these binary partners using the ClusPro program, which is composed of docking, energy filtering, and clustering steps. Footprinting data are used to incorporate constraints-positive and/or negative-in the docking step and are also used to decide the type of energy filter-electrostatics or desolvation-in the successive energy-filtering step. By using this approach, we examine the structure of a number of binary complexes of monomeric actin and compare the results to crystallographic data. Based on docking alone, a number of competing models with widely varying structures are observed, one of which is likely to agree with crystallographic data. When the docking steps are guided by footprinting data, accurate models emerge as top scoring. We demonstrate this method with the actin/gelsolin segment-1 complex. We also provide a structural model for the actin/cofilin complex using this approach which does not have a crystal or NMR structure.
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