Determination of the Relative Orientation of the Two Halves of the Domain-Swapped Dimer of Cyanovirin-N in Solution Using Dipolar Couplings and Rigid Body Minimization

The HIV-inactivating protein cyanovirin-N (CVN) exists in two forms that are pH- and solvent-dependent:  a monomer which predominates at neutral pH (≥90%) and a symmetric domain-swapped dimer. We have investigated the orientation of the two halves of the domain-swapped dimer of CVN at neutral pH in solution using dipolar couplings measured in a neutral liquid crystalline bicelle medium. 1DNH dipolar couplings for the dimer were readily measured for 18 out of 101 residues, and are shown to be inconsistent with the orientation of the two halves of the dimer observed in the X-ray structure obtained from crystals grown at low pH in the presence of organic solvent. The orientation of the two halves of the domain-swapped dimer was determined by rigid body minimization, subject to the requirements of C2 symmetry. The starting coordinates for the calculations consisted of the X-ray coordinates for the two halves (with the linker residues deleted), separated by ∼45 A and placed in three different relative orientat...