Study of conformational rearrangement and refinement of structural homology models by the use of heteronuclear dipolar couplings

For an increasing fraction of proteins whose structures are being studied, sequence homology to known structures permits building of low resolution st ructural models. It is demonstrated that dipolar couplings, measured in a l iquid crystalline medium, not only can validate such structural models, but also refine them. Here, experimental H-1-N-15, H-1(alpha)-C-13(alpha), and C-13'-C-13(alpha) dipolar couplings are shown to decrease the backbone rms d between various homology models of calmodulin (CaM) and its crystal struc ture. Starting from a model of the Ca2+-saturated C-terminal domain of CaM, built from the structure of Ca2+-free recoverin on the basis of remote seq uence homology, dipolar couplings are used to decrease the rmsd between the model and the crystal structure from 5.0 to 1.25 Angstrom. A better starti ng model, built from the crystal structure of Ca2+-saturated parvalbumin, d ecreases in rmsd from 1.25 to 0.93 Angstrom. Similarly, starting from the s tructure of the Ca2+-ligated CaM N-terminal domain, experimental dipolar co uplings measured for the Ca2+-free form decrease the backbone rmsd relative to the refined solution structure of apo-CaM from 4.2 to 1.0 Angstrom.