Crepe-ribbon representation for protein structures: comparison of phospholipases A2

We describe a method to generate a novel representation for protein structures called "crepe ribbons." In our representation, each piece of the ribbon was constructed using the coordinates of the backbone atoms of each individual residue. Using the internal geometries of each residue and a helix-generating algorithm, a local origin and the direction cosines of a local orthogonal system were obtained. The locus of the local origins represents the folding of the polypeptide. A color-coded origin-origin distance plot similar to that of C alpha-C alpha distance plot was generated. This plot may be used to visually compare and contrast two structures. We identified linear regions in the distribution of the local origins and assigned a secondary structure description. Parameters describing the interrelation between various secondary structure segments were calculated. We have illustrated our crepe-ribbon representation by comparing two phospholipase A2 structures in the Brookhaven National Laboratory Protein Data Bank.