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Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at natural abundance

Summary

Dynamics of the backbone and some side chains of apo-neocarzinostatin, a 10.7 kDa carrier protein, have been studied from 13C relaxation rates R1, R2 and steady-state 13C-{1H} NOEs, measured at natural abundance. Relaxation data were obtained for 79 nonoverlapping Cα resonances and for 11 threonine Cβ single resonances. Except for three Cα relaxation rates, all data were analysed from a simple two-parameter spectral density function using the model-free approach of Lipari and Szabo. The corresponding C−H fragments exhibit fast (τe < 40 ps) restricted libration motions (S2=0.73 to 0.95). Global examination of the microdynamical parameters S2 and τe along the amino acid sequence gives no immediate correlation with structural elements. However, different trends for the three loops involved in the binding site are revealed. The β-ribbon comprising residues 37 to 47 is spatially restricted, with relatively large τe values in its hairpin region. The other β-ribbon (residues 72 to 87) and the large disordered loop ranging between residues 97–107 experience small-amplitude motions on a much faster (picosecond) time scale. The two N-terminal residues, Ala1 and Ala2, and the C-terminal residue Asn113, exhibit an additional slow motion on a subnanosecond time scale (400–500 ps). Similarly, the relaxation data for eight threonine side-chain Cβ must be interpreted in terms of a three-parameter spectral density function. They exhibit slower motions, on the nanosecond time scale (500–3000 ps). Three threonine (Thr65, Thr68, Thr81) side chains do not display a slow component, but an exchange contribution to the observed transverse relaxation rate R2 could not be excluded at these sites. The microdynamical parameters (S2, τe and R2ex) or (S infslow sup2 , S inffast sup2 and τslow) were obtained from a straightforward solution of the equations describing the relaxation data. They were calculated assuming an overall isotropic rotational correlation time τe for the protein of 5.7 ns, determined using standard procedures from R2/R1 ratios. However, it is shown that the product (1−S2)× τe is nearly independent of τe for residues not exhibiting slow motions on the nanosecond time scale. In addition, this parameter very closely follows the heteronuclear NOEs, which therefore could be good indices for local fast motions on the picosecond time scale.

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Mispelter, J., Lefèvre, C., Adjadj, É. et al. Internal motions of apo-neocarzinostatin as studied by 13C NMR methine relaxation at natural abundance. J Biomol NMR 5, 233–244 (1995). https://doi.org/10.1007/BF00211751

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Keywords

  • Neocarzinostatin
  • Backbone dynamics
  • Side-chain dynamics
  • 13C NMR relaxation