| Determination of the domain orientation for the solution structure of the dimer was carried out using a procedure analogous to the one described for determining the relative domain orientation in a two-domain protein fragment of a lectin. |
The coordinates of the individual domains of the domain swapped dimer CV-N were taken directly from the X-Ray coordinates, 3EZM and 1L5B. The only protons added are the HNE1 of W(49/150) and all the backbone amide protons (HN), since domain-domain orientation was based only on HN/HNE1 residual dipolar couplings.
The starting coordinates were those of two pseudo-monomer units (AB' and A'B)
extracted from the refined trigonal 1.5 X-ray structure, in which proline 51
at the junction between A and B was removed, allowing for free rotation around
this junction. We then treated AB' and A'B as two independent sub-domains.
Assuming that the orientation of the two sub-domains is fixed in solution (at
least to a first approximation), the principal axis systems, or alignment frames,
of sub-domains AB' and A'B should be equivalent to the alignment system of the
entire molecule and, vice versa, to each other. Using the residual dipolar couplings
we calculated the order tensor principal axis systems for each domain. Rotation of
pseudo sub-domain A'B around the hinge at amino acid position 51 until a superposition
of the individual coordinate frames was obtained yielded the final model of the
solution dimer. |
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