Values with and without the “0” missing peaks are given for all peak plots, and for individual dodecamers as well. To me it makes no sense to show the values with undetectable peaks, but it is here (along with the number of times the peaks dont show.
Six dodecamers: SP-D – N termini junction peak width. The N term peak is a merge of the right and left hand sides of the trimeric mirrors of the peak measurements. The N term peak width was measured on mirror-trimers from the peak height, but these two values were merged to form the width of a complete N term peak width, not just half. Top set of numbers is for all individual measurements (left) and the individual dodecamer values (right) as separate means. Individual values for each of the 6 dodecamers = bottom set of values.
i dont know why molecule named 80 has an N term peak that is so thin… but i checked and it seems to be correct.
Peak 5 of the trimers of surfactant protein D is shown this post. The peak number is counted with the N termini junction peak as peak 1 and moving in a mirrored direction from that point toward the CRD peak. Peak 1 (N termini junction, well described, obvious and tallest); tiny peak (peak 2, not currently described, small, and between peak 1 and the alledged glycosylation peak); peak 3, the described glycosylation peak; peak 4 (lateral to the glycosylation peak, detected very frequently, large, and not as tall as the glycosylation peak); Peak 5, below, is not tall, and quite thin, but detected frequently enough to make it a likely event.
This peak, consistently appears, (98.8% of the time – 5/392) plots in a combined dataset, the old and the new (shown below). The fourth peak (N term peak=peak 1, tiny peak=peak 2, glycosylation peak=peak 3, and this peak lies lateral to the glycosylation peaks. It appears to have a lower peak height, and a little broader peak width. Data below, calculated two ways, the summation of the old and new dataset using four dodecamers, shows that calculating them in these two ways matters very very little (p=.9281). The peak width is about 11.9nm in width.
A peak in the hexamer plots where the “neck domain” of SP-D likely appears is registered about 78% of the time (135/172 plots) in the new 4 dodecamer dataset, and about 68% of the time (151/222 plots) in the old – four dodecamer dataset. This particular peak shows up as a slightly lower peak when the CRD domains dont quite cover this region. In molecular models (the neck and CRD domains are currently the only molecular models that I have found, show that the CRD are sort of “floppy” and sometimes appear to cover, or partially cover the neck domain. This arrangement is very apparent in the AFM images, and drawing the line which is to be used to plot the grayscale values of is highly dependent upon the imput of the observer. I plotted these lines trying to pick a center portion of the hexamers not varying the plot line to include or eliminate the influence of neck domain.
peak width for the neck domain is about 5 nm, but keep in mind this peak shows up under the CRD domain(s) about 70% of the time only.
The first rhythm and order I think i found as a graduate student in anatomy (light microscopy of cartilege) was the order of the beginning of long bone development in mice. Back then, (as in 50 years ago) many journals didn’t have cover images. At this time, dissolving all my records, publications, micrographs from the finite universe, I made this cover for one very lovely design in nature. I attach a very bad phone phot of the publication (not even I, its author, was willing to spend the highway robbery that some journal websites ask for an almost equally fuzzy scanned image of the original).
Here is my suggested cover, half century down the pike, and a free link to a terrible scanned pdf of the paper.
This is an often hidden portion of the SP-D trimer, as it can be hidden under the CRD domain which can flop around and lie in different positions during processing. It seems that this peak will be something around 5 nm (top figure) depending upon how the CRD domains have obscured it. It might not have any subpeaks (the mode for this peak is 1 and it seems reasonable for this relatively tightly wound helical neck portion of the trimers (bottom figure).
It will be interesting what adding four more measurements to this dataset will confirm or refute. It is nice that the small N of four (composed of 50 to 100 separate grayscale plots of trimers (from a tracing of the hexamer) after image and signal processing, show some consensus.