Daily Archives: July 17, 2022

Hexamer and individual peak widths (nm) for four dodecamers of SP-D

As separate trimers, and as hexamers peak width summaries, regardless of how they are sorted seem to be consistent for these first four image and signal processed dodecamers of SP-D.  A model for further peak counting using these parameters for an intelligent signal processing approach might be interesting. The 8 peaks per trimer (15 peaks per hexamer as N is counted as one peak in each trimer and becomes the odd center peak in hexamers) widths are given below.

N, tiny peak, and glycosylation peak(s) proximity in some SP-D dodecamers

AFM images (from rhSP-D at pH 7.4 Arroyo et al) of SP-D are informative and numerous and during a careful analysis of them it seems pretty obvious that there are a significant number of occasions where there is a close “sticking” together of the strands of the trimer from the N termini junction, through the tiny peak on either side of the N peak and up to the glycosylation (often including it) peak(s)(plural here because there are a significant number of imaging and signal processing applications that count more than one peak in the area considered the glycosylation peak).
Here are two images (labels on each show the number of nm diameter, the length in nm of each of the hexamers, and arrows that show where the trimers from two hexamers are in close association. I scanned 83 images from the images of Arroyo et al, and found that such an association (which in order to be visualized with any confidence requires that the dodecamer to be lying such that the rest of the trimer-arms are separated, thus not just overlapping — overlapping trimer arms were not included in the count of closely associated N, tiny peak, and glycosylation peak associations.
I have also given a number (my reference number for the set of thumbnail images, and the set of dodecamers to which some measurements have been applied.
Any reason for such a close association between trimers in that specific location is not known by me, comments welcome. 100 nm bar is given for your “enjoyment”,  green nm measurements correspond to green segmented tracing through the center of the hexamer to which it refers, same for red segmented line and nm values.  Diameter values (orange) are made in ImageJ, and requires that three of the four carbohydrate recognition domains be touched.  It is easy to see that once past the glycosylation peaks, the arms of each trimer are separate. On the bottom image, the trimers are close on the top half of the micrograph, but not the bottom half, as the glycosylation peaks are separate. (42 dodecamers, of 86 total, show N, tiny peak, glycosylation peak closeness on one or both sides of the dodecamer.)