MULTIPLE PROTEIN-STRUCTURE ALIGNMENT

A method was developed to compare protein structures and to combine th em into a multiple structure consensus. Previous methods of multiple s tructure comparison have only concatenated pairwise alignments or prod uced a consensus structure by averaging coordinate sets. The current m ethod is a fusion of the fast structure comparison program SSAP and th e multiple sequence alignment program MULTAL. As in MULTAL, structures are progressively combined, producing intermediate consensus structur es that are compared directly to each other and all remaining single s tructures. This leads to a hierarchic ''condensation,'' continually ev aluated in the light of the emerging conserved core regions. Following the SSAP approach, all interatomic vectors were retained with well-co nserved regions distinguished by coherent vector bundles (the structur al equivalent of a conserved sequence position). Each bundle of vector s is summarized by a resultant, whereas vector coherence is captured i n an error term, which is the only distinction between conserved and v ariable positions. Resultant vectors are used directly in the comparis on, which is weighted by their error values, giving greater importance to the matching of conserved positions. The resultant vectors and the ir errors can also be used directly in molecular modeling. Application s of the method were assessed by the quality of the resulting sequence alignments, phylogenetic tree construction, and databank scanning wit h the consensus. Visual assessment of the structural superpositions an d consensus structure for various well-characterized families confirme d that the consensus had identified a reasonable core.