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PRE-driven protein NMR structures: an alternative approach in highly paramagnetic systems.
- Source :
-
The FEBS journal [FEBS J] 2021 May; Vol. 288 (9), pp. 3010-3023. Date of Electronic Publication: 2020 Nov 23. - Publication Year :
- 2021
-
Abstract
- Metalloproteins play key roles across biology, and knowledge of their structure is essential to understand their physiological role. For those metalloproteins containing paramagnetic states, the enhanced relaxation caused by the unpaired electrons often makes signal detection unfeasible near the metal center, precluding adequate structural characterization right where it is more biochemically relevant. Here, we report a protein structure determination by NMR where two different sets of restraints, one containing Nuclear Overhauser Enhancements (NOEs) and another containing Paramagnetic Relaxation Enhancements (PREs), are used separately and eventually together. The protein PioC from Rhodopseudomonas palustris TIE-1 is a High Potential Iron-Sulfur Protein (HiPIP) where the [4Fe-4S] cluster is paramagnetic in both oxidation states at room temperature providing the source of PREs used as alternative distance restraints. Comparison of the family of structures obtained using NOEs only, PREs only, and the combination of both reveals that the pairwise root-mean-square deviation (RMSD) between them is similar and comparable with the precision within each family. This demonstrates that, under favorable conditions in terms of protein size and paramagnetic effects, PREs can efficiently complement and eventually replace NOEs for the structural characterization of small paramagnetic metalloproteins and de novo-designed metalloproteins by NMR. DATABASES: The 20 conformers with the lowest target function constituting the final family obtained using the full set of NMR restraints were deposited to the Protein Data Bank (PDB ID: 6XYV). The 20 conformers with the lowest target function obtained using NOEs only (PDB ID: 7A58) and PREs only (PDB ID: 7A4L) were also deposited to the Protein Data Bank. The chemical shift assignments were deposited to the BMRB (code 34487).<br /> (© 2020 Federation of European Biochemical Societies.)
- Subjects :
- Bacterial Proteins chemistry
Bacterial Proteins genetics
Binding Sites
Electrons
Iron-Sulfur Proteins chemistry
Iron-Sulfur Proteins genetics
Magnetic Resonance Imaging
Magnetic Resonance Spectroscopy
Metalloproteins chemistry
Metalloproteins genetics
Models, Molecular
Photosynthetic Reaction Center Complex Proteins chemistry
Photosynthetic Reaction Center Complex Proteins genetics
Rhodopseudomonas chemistry
Bacterial Proteins ultrastructure
Iron-Sulfur Proteins ultrastructure
Metalloproteins ultrastructure
Photosynthetic Reaction Center Complex Proteins ultrastructure
Protein Conformation
Rhodopseudomonas ultrastructure
Subjects
Details
- Language :
- English
- ISSN :
- 1742-4658
- Volume :
- 288
- Issue :
- 9
- Database :
- MEDLINE
- Journal :
- The FEBS journal
- Publication Type :
- Academic Journal
- Accession number :
- 33124176
- Full Text :
- https://doi.org/10.1111/febs.15615