Experimentally exploring the conformational space sampled by domain reorientation in calmodulin

Abstract

The conformational space sampled by the two-domain protein calmodulin has been explored by an approach based on four sets of NMR observables obtained on Tb(3+)- and Tm(3+)-substituted proteins. The observables are the pseudocontact shifts and residual dipolar couplings of the C-terminal domain when lanthanide substitution is at the N-terminal domain. Each set of observables provides independent information on the conformations experienced by the molecule. It is found that not all sterically allowed conformations are equally populated. Taking the N-terminal domain as the reference, the C-terminal domain preferentially resides in a region of space inscribed in a wide elliptical cone. The axis of the cone is tilted by approximately 30 degrees with respect to the direction of the N-terminal part of the interdomain helix, which is known to have a flexible central part in solution. The C-terminal domain also undergoes rotation about the axis defined by the C-terminal part of the interdomain helix. Neither the extended helix conformation initially observed in the solid state for free calcium calmodulin nor the closed conformation(s) adopted by calcium calmodulin either alone or in its adduct(s) with target peptide(s) is among the most preferred ones. These findings are unique, both in terms of structural information obtained on a biomolecule that samples multiple conformations and in terms of the approach developed to achieve the results. The same approach is in principle applicable to other multidomain proteins, as well as to multiple interaction modes between two macromolecular partners.

Fig. 1.

Relative orientation of the N-terminal and C-terminal domains in CaM as early observed by x-ray in the absence of target peptides (A; extended conformation) and as observed in the presence of target peptides (B; closed conformation). Labels N4 and C1 indicate the fourth helix of the N-terminal domain and the first helix of the C-terminal domain, respectively.

Fig. 2.

Calculated vs. observed values of pcs of N-terminal nuclei for the terbium(III) (•) and thulium(III) (▪) derivatives. The directions of the χ tensor axes are indicated, and the magnetic susceptibility anisotropies are reported.

Fig. 3.

Calculated vs. observed values of rdc of C-terminal HN for the terbium(III) (•) and thulium(III) (▪) derivatives. Each set of data was fit separately by using fantaorient.

Fig. 4.

Distribution of the rdc values calculated for all conformations by using the Bax structure and the magnetic susceptibility anisotropy values obtained from the experimental rdc of the N-terminal domain (A), from the experimental rdc of the C-terminal domain (B), and from the average rdc of the C-terminal domain obtained from sterically allowed uniformly sampled conformations (C).

Fig. 5.

Cone containing the three conformations of the C-terminal domain (only the first two helices are shown), which provide pcs and rdc with an average in good fit with the experimental data.