Figure 1.

Alignment of two proteins with a conformational change and a polypeptide chain folding back onto itself. For two hypothetical proteins with homologous structures (protein 1 and protein 2), with two domains (one consisting of stretches A1 and A2 and one consisting of stretch B in sequence space) moving with respect to one another around a hinge, the aligned parts of the sequence are shown at the top, while the mapping of the alignment onto structures is shown with the same colours in the bottom of the figure. The alignment of proteins of such topology (e.g. GroEL) poses two problems: (1) the treatment of large conformational changes involving the motion of domains around hinge-regions (closed form of protein 1 versus open form of protein 2) and (2) the recognition of domains that are continuous in space but discontinuous in sequence (domain A of protein 1 and protein 2 consisting of parts of the N- (A1) and C-termini (A2)).