Additional file 4.

Analysis of proline conformational space in proteins. (A) Conformation of peptide backbones containing a single (X-P-X; X is any other non-proline residue; left panel), two (X-P-P-X; central panel), or three subsequent proline residues (X-P-P-P-X) in protein structures displayed as Ramachandran plots (data generated using the web-based server described in [64]). The relative frequency of occurrence of particular φ/ω angle is encoded by the brightness of the square at the intersection of the coordinates. The φ/ω angle combination compatible with standard α-helical conformation is indicated with a dashed purple oval (left and central panels). Single proline residues conform to α-helical geometry when present at the extreme N- and C-termini of the α-helix, thus accounting for the occurrence of single prolines in the α-helical part of the plot in the left panel. For two or three adjacent proline residues, the only conformational space is in the top left quadrant of the plot, corresponding to polyproline-specific conformations. (B) Model of the extended poly-proline stretch in the mjA' A822-P/Q823-P/S824-P triple proline substitution mutant. The triple substitution mutant displays approximately 150% of activity in comparison to the wildtype enzyme (Figure 4B). The three proline substitutions are shown as yellow stick models and T821 is shown in red as a reference point pointing towards the catalytic site. The structure shown here was constructed using the M. jannaschii Bridge Helix sequence and conforms to the typical φ/ω angle combinations observed in α-helices and in polyproline structures. The structure is not necessarily an accurate model, but serves to demonstrate the increased local flexibility due to the presence of three subsequent proline residues. The model was created with Abalone http://www.biomolecular-modeling.com/Abalone/index.html webcite.

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Weinzierl BMC Biology 2010 8:134   doi:10.1186/1741-7007-8-134