Figure 3

Structure and sequence based alignments of Staphostatins with putative inhibitors from Bacteroides fragilis. Panel A is a sequence alignment generated with T-coffee. Superimposed on this are secondary structure predictions for all 5 proteins, generated with GorIV [46]. Residues with secondary structure assigned as coil, β-strand, and α-helix are back-highlighted in yellow, red and blue respectively. The glycine residue conserved in Staphostatins is marked with a vertical black arrowhead. Panel B is a sequence alignment of Staphostatin A (1OH1A [56]) and Staphostatin B (1NYCB [14]). The sequence based alignment was generated with T-coffee. This alignment is coloured, as for panel A, according to secondary structure determined from the crystal structures of the two inhibitors. For clarity the spacing is preserved from panel A. These alignments suggest that GorIV is over-predicting helical content in the staphostatins.