PREDICTING OLIGOMERIZATION STATES OF COILED COILS

An algorithm based on the profile method was developed that faithfully distinguishes between the amino acid sequences of dimeric and trimeri c coiled coils. Normalized sequence profiles derived from nonhomologou s, two- and three-stranded, coiled-coil sequences with unambiguous reg isters were used to assign dimer and trimer propensities to test seque nces. The difference between the dimer and trimer profile scores accur ately reflected the preferred oligomerization state. The method relied on two strategies that may be generally applicable to profile calcula tions-profile values of solvent-exposed residues and of amino acids th at were underrepresented in the database were given zero weight. Diffe rences between the dimer and trimer profiles revealed sequence pattern s that match and extend experimental studies of oligomer specification .