Reconstruction of symmetry deviations: a procedure to analyze partially decorated F-actin and other incomplete structures

The absolute value of individual differences (AVID) procedure is a method to map variations within images arising from deviations in symmetry. We devised this procedure to analyze images of actin filaments decorated with actin-binding proteins (ABPs). In three-dimensional maps of such actin complexes, ABPs often appear weak (i.e. they have low density) relative to actin. Because the 3D map represents an average taken over equivalent positions in the helix, the final density at the position of the ABP represents an average of the densities at all ABP sites. If there is either incomplete binding or a conformational variability of the bound ABP, the average density will be lowered. By the same argument, the variation of density at these sites will be increased. The aim of the AVID procedure is to calculate the density variations within partially decorated filaments and thereby attempt to locate the bound protein. We tested the AVID procedure with model data and then applied it to electron micrographs of F-actin decorated with an actin-binding domain of fimbrin known as N375 [Hanein et al., J. Cell Biol. 139 (1997) 387–396]. The AVID maps have peaks at the site where N375 binds. Because it excludes the layer line data, the AVID procedure uses data that are independent of the data used for 3D reconstruction and difference mapping. It therefore provides an independent way to localize the bound subunit without the need for a map of undecorated actin. Moreover, the difficulties of scaling maps are minimized. This procedure could also be applied to structures with non-helical symmetry.