1. Exploring the Conformational and Binding Dynamics of HMGA2·DNA Complexes Using Trapped Ion Mobility Spectrometry–Mass Spectrometry
- Author
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Kevin Jeanne Dit Fouque, Sarah N. Sipe, Alyssa Garabedian, German Mejia, Linjia Su, Md Lokman Hossen, Prem P. Chapagain, Fenfei Leng, Jennifer S. Brodbelt, and Francisco Fernandez-Lima
- Subjects
Mammals ,Tandem Mass Spectrometry ,Structural Biology ,HMGA2 Protein ,Ion Mobility Spectrometry ,Animals ,DNA ,Article ,Spectroscopy - Abstract
The mammalian high mobility group protein AT-hook 2 (HMGA2) is an intrinsically disordered DNA-binding protein expressed during embryogenesis. In the present work, the conformational and binding dynamics of HMGA2 and HMGA2 in complex with a 22-nt (DNA(22)) and a 50-nt (DNA(50)) AT-rich DNA hairpin were investigated using trapped ion mobility spectrometry–mass spectrometry (TIMS–MS) under native starting solvent conditions (e.g., 100 mM aqueous NH(4)Ac) and collision-induced unfolding/dissociation (CIU/CID) as well as solution fluorescence anisotropy to assess the role of the DNA ligand when binding to the HMGA2 protein. CIU-TIMS–CID-MS/MS experiments showed a significant reduction of the conformational space and charge-state distribution accompanied by an energy stability increase of the native HMGA2 upon DNA binding. Fluorescence anisotropy experiments and CIU-TIMS–CID-MS/MS demonstrated for the first time that HMGA2 binds with high affinity to the minor groove of AT-rich DNA oligomers and with lower affinity to the major groove of AT-rich DNA oligomers (minor groove occupied by a minor groove binder Hoechst 33258). The HMGA2·DNA22 complex (18.2 kDa) 1:1 and 1:2 stoichiometry suggests that two of the AT-hook sites are accessible for DNA binding, while the other AT-hook site is probably coordinated by the C-terminal motif peptide (CTMP). The HMGA2 transition from disordered to ordered upon DNA binding is driven by the interaction of the three basic AT-hook residues with the minor and/or major grooves of AT-rich DNA oligomers.
- Published
- 2022