Images such as this one (from Arroyo et al) show perplexing differences in the lengths of trimeric arms. I measured these, and plotted their peaks and clearly the plot on the right hand side of the molecule (in this image) is quite expected. peaks 1, 2, 3 for the collagen like domain and a nice often lumpy CRD, and a neck region that is somewhat low height (brightness), but can show up as a small peak. The left hand side gives pause to what actually constitutes the Ntermini junction. It looks as if there are two Ntermini side by side not end to end. Even then however, the peaks along the other domains of the SP-D molecule just are not present in this image to the left of the bright peak.

Image shows (top) Arroyo’s original image, green bar at 100nm from their bar marker, my outline of the portion of the SP-D dodecamer cut out for LUT plots, then cut into 1nm vertical slices, ungrouped, centered horizontally, resulting two trimmed arms of the dodecamer. This image was exported as a grayscale tif  and imported into ImageJ, with rectangle from end to end used for plot analysis  of grayscale brightness (blue line with brightness (0-255) on the left. Peaks are named N, collagen-like domain peaks 1, 2, 3 and the least bright portion of the coiled coil neck domain (not labeled) and the CRDs on left and right but there is no assurance that the N terminal is not seen as two peaks one in each of the longer arms.  There is little bilateral symmetry in this dodecamer. A possible real-time shortening of the arms on the left of the image might result from the molecule lying over itself, or some error in protein production or defect in processing for AFM.

One comment against deep bending of the two arms of the dodecamer on the left hand side of the image is that the CRD on the left is actually brighter (higher) in the AFM image than the CRD on the right hand side of the image. But, the 1 and 2 peaks of the collagen-like domain may overlap making for a very high peak and very bright….  guess?

This plays into the dilemma whether to equalize the two arms of the dodecamer when doing morphometry or not to equalize them.