The Proteasome

Lupas et al. (1994) predicted the secondary structure for the 20S proteasome subunits by a variety of algorithms. We took their predicted pattern of secondary structure elements and accessibility and searched the database of 780 non-redundant protein domains. Without imposing any experimental distance restraints, the method finds folds ( maps). The top scoring fold, according the the amphipathicity scoring scheme, is that of glutamine amidotransferase (PDB code 1GPH), which is structurally and functionally similar to the proteasome [Brannigan et al., 1995][Lowe et al., 1995].

A small number of weak distance restraints can make a significant difference to the results of this search. If alignment positions identified as putative active site residues by Lupas et al. , by the method of Benner and co-workers [Benner et al., 1993], are required to have axial coordinates within Å (tolerance of Å) of each other, only folds ( maps) remain, with the correct fold still at the first rank. Although distance restraints are not always available prior to 3D structure determination, our results suggest that they should be used to aid fold recognition whenever possible.