1. Dynamics of the intrinsically disordered protein NUPR1 in isolation and in its fuzzy complexes with DNA and prothymosin α
- Author
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José L. Neira, Bruno Rizzuti, Caterina Ricci, Juan L. Iovanna, Maria Grazia Ortore, Martina Palomino-Schätzlein, Ministerio de Economía y Competitividad (España), Ligue Nationale contre le Cancer (France), Generalitat Valenciana, Instituto de Biología Molecular y Celular [Alicante, Spain], Universidad Miguel Hernández [Elche] (UMH), CNISM, I-60131 Ancona, Italy, CNR-NANOTEC, Licryl-UOS Cosenza & CEMIF.Cal [Cosenza, Italy] (Department of Physics), Università della Calabria [Arcavacata di Rende] (Unical), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), University of Calabria [Cosenza, Italy], Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut Paoli-Calmettes, and Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Aix Marseille Université (AMU)
- Subjects
MESH: Neoplasm Proteins ,MESH: Protein Precursors ,MESH: Thymosin ,[SDV]Life Sciences [q-bio] ,Protein dynamics ,01 natural sciences ,Biochemistry ,Analytical Chemistry ,chemistry.chemical_compound ,X-Ray Diffraction ,MESH: Basic Helix-Loop-Helix Transcription Factors ,Basic Helix-Loop-Helix Transcription Factors ,30S ,0303 health sciences ,Chemistry ,Small-angle X-ray scattering ,MESH: DNA ,MESH: X-Ray Diffraction ,Energy landscape ,SAXS ,3. Good health ,Neoplasm Proteins ,MESH: Protein Domains ,Biophysics ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,010402 general chemistry ,Intrinsically disordered proteins ,03 medical and health sciences ,Protein Domains ,Scattering, Small Angle ,Molecule ,Humans ,Protein Precursors ,Molecular Biology ,MESH: Scattering, Small Angle ,030304 developmental biology ,MESH: Humans ,Mutagenesis ,DNA ,MESH: Multiprotein Complexes ,NMR ,0104 chemical sciences ,Thymosin ,Crystallography ,Fuzzy complexes ,Multiprotein Complexes - Abstract
13 pags., 7 figs., Intrinsically disordered proteins (IDPs) explore diverse conformations in their free states and, a few of them, also in their molecular complexes. This functional plasticity is essential for the function of IDPs, although their dynamics in both free and bound states is poorly understood. NUPR1 is a protumoral multifunctional IDP, activated during the acute phases of pancreatitis. It interacts with DNA and other IDPs, such as prothymosin α (ProTα), with dissociation constants of ~0.5 μM, and a 1:1 stoichiometry. We studied the structure and picosecond-to-nanosecond (ps-ns) dynamics by using both NMR and SAXS in: (i) isolated NUPR1; (ii) the NUPR1/ProTα complex; and (iii) the NUPR1/double stranded (ds) GGGCGCGCCC complex. Our SAXS findings show that NUPR1 remained disordered when bound to either partner, adopting a worm-like conformation; the fuzziness of bound NUPR1 was also pinpointed by NMR. Residues with the largest values of the relaxation rates (R, R, R and η), in the free and bound species, were mainly clustered around the 30s region of the sequence, which agree with one of the protein hot-spots already identified by site-directed mutagenesis. Not only residues in this region had larger relaxation rates, but they also moved slower than the rest of the molecule, as indicated by the reduced spectral density approach (RSDA). Upon binding, the energy landscape of NUPR1 was not funneled down to a specific, well-folded conformation, but rather its backbone flexibility was kept, with distinct motions occurring at the hot-spot region., This work was supported bySpanish Ministry of Economy and Competitiveness [CTQ2015-64445-R (to JLN) ]with European ERDF funds;by the French La Ligue Contre le Cancer, INCa, Canceropole PACA, DGOS (la bellisation SIRIC) and INSERM (to JLI). The NMR equipment used in this work has been funded by Generalitat Valenciana and co-financed with ERDF funds (OPERDF of Comunitat Valenciana 2014-2020). BR acknowledges kind hospitality in the European Magnetic Resonance Center (CERM), Sesto Fiorentino (Florence), Italy.
- Published
- 2019