I thought this was a rather unlovely picture of a dodecamer which i cut and pasted from a pixelated image which was part of a SP-D publication and a figure from Hartshorn et al. The original crop and imageJ LUT plot is shown along with the images processed in ImageJ (filters>unsharp mask> 20 px radius, 50% mask and then 10 px gaussian blur). The smoothness of the LUT plot was greatly enhanced, and the number of peaks in this seemingly unhelpful original image turned out to be very close to the LUT plots that have been obtained for Arroyo et al’s AFM images of SP-D.
Middle and bottom image left = processed image and trace lines in ImageJ. Plots from the unprocessed and processed images superimposed. They are basically identical but the processed images is smooth. In this particular dodecamer the relative difference in the N termini peak height and the glycosylation peak on either side, if one were to theorhetically divide the N termini peak into quarters, a peak this size might mean that the glycosylation of only a single molecule of the trimer is glycosylated or none. ( I have not seen this proposed before, but peak height at the site of the glycosylation site should be quantifiable and relate to the amount of glycosylation. Does anyone have an opinion on why one would expect glycosylation to be an all or none phenomenon – that is, all three molecules in the trimer? does anyone entertain the idea that it could be on a scale of 1-12?
I am really pleased to see a consistent 3 peaks on either side of the N termini, with just a hint of the new peak that shows up very near the margins of the N termini peak. (see previous posts and pictures on this site).
Either 1 or 2 peaks can occur in the CRD section of the molecule. so the two peaks at the left hand side of all four plots seems to be related to the head and neck domains and the irregularity of their positions in most micrographs.