Quantitative φ torsion angle analysis in Desulfovibrio vulgaris flavodoxin based on six φ related 3J couplings

Quantitative phi-dihedral angle determinations of non-glycine and non-proline residues in Desulfovibrio vulgaris flavodoxin are carried out on the exclusive basis of (3)J coupling constants. In total 124 (3)J(H)N(H)alpha, 123 (3)J(H)N(C'i), 118 (3)J(H)N(C)beta, 117 (3)JC'Hi-l alpha 109 (3)JC'Ci-l'(i), and 103 (3)JC'Hi-l beta values form the experimental basis for translating J coupling data into geometry information using various combinations of Karplus parameters given in the literature. In addition, each backbone torsional angle phi is adjusted assuming different models of local geometry, either a rigid torsion, a Gaussian distribution centered at a distinct angle, or a two-site jump model. Numerical optimization is followed by a statistical significance evaluation to assess the results. It is found that experimental coupling constants of most of the residues involved in secondary structure elements agree best with those predicted from rigid local conformations. For dihedral angles in loop regions, mobility effects are not negligible, and a single torsion (Glu 42) is likely to adopt two distinct adjustments. However, alpha-helix conformations with -60 degrees < phi < -45 degrees give rise to an alternate solution with phi=+170 degrees with similar statistical significance when using the four traditionally determined proton-involved (3)J couplings. This ambiguity is efficiently avoided only when taking advantage of the complete data set comprising six available experimental 3J coupling constants and of the degeneracy intrinsic to the Karplus relation. The optimized phi conformations are compared with reference values from the crystal structure of flavodoxin.