Strategy for the study of paramagnetic proteins with slow electronic relaxation rates by NMR spectroscopy: Application to oxidized human [2Fe-2S] ferredoxin

NMR studies of paramagnetic proteins are hampered by the rapid relaxation of nuclei near the paramagnetic center, which prevents the application of conventional methods to investigations of the most interesting regions of such molecules. This problem is particularly acute in systems with slow electronic relaxation rates. We present a strategy that can be used with a protein with slow electronic relaxation to identify and assign resonances from nuclei near the paramagnetic center. Oxidized human [2Fe-2S] ferredoxin (adrenodoxin) was used to test the approach. The strategy involves six steps: (1) NMR signals from H-1, C-13, and N-15 nuclei unaffected or minimally affected by paramagnetic effects are assigned by standard multinuclear two- and three-dimensional (2D and 3D) spectroscopic methods with protein samples labeled uniformly with C-13 and N-15. (2) The very broad, hyperfine-shifted signals from carbons in the residues that ligate the metal center are classified by amino acid and atom type by selective C-13 labeling and one-dimensional (1D) C-13 NMR spectroscopy. (3) Spin systems involving carbons near the paramagnetic center that are broadened but not hyperfine-shifted are elucidated by C-13{C-13} constant time correlation spectroscopy (CT-COSY). (4) Signals from amide nitrogens affected by the paramagnetic center are assigned to amino acid type by selective N-15 labeling and 1D N-15 NMR spectroscopy. (5) Sequence-specific assignments of these carbon and nitrogen signals are determined by 1D C-13{N-15} difference decoupling experiments. (6) Signals from 1H nuclei in these spin systems are assigned by paramagnetic-optimized 2D and 3D H-1{C-13} experiments. For oxidized human ferredoxin, this strategy led to assignments (to amino acid and atom type) for 88% of the carbons in the [2Fe-2S] cluster-binding loops (residues 43-58 and 89-94). These included complete carbon spin-system assignments for eight of the 22 residues and partial assignments for each of the others. Sequence-specific assignments were determined for the backbone N-15 signals from nine of the 22 residues and ambiguous assignments for five of the others.