using structure
Category Archives: Ultimate order, the cell
Plotting peaks in a hexamer of a “fuzzy ball” multimer of SP-D
Plotting peaks in a hexamer of a “fuzzy ball” multimer of SP-D are problematic at best, and the plots that most coincide with the hexamer plots from dodecamers are “V” shaped tracings making the boundaries of the N term domain peaks hard to define. It is a decision that needs to be made, that is whether to go back to measuring hexamers “within the fuzzy balls” is important to completeing a writeup on SP-D trimer (hexamer) peak number, size, and shape.
Eight dodecamers: SP-D – neck peak height and valley
Six dodecamers: SP-D – peak height (peak 7)
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
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.
Six dodecamers of surfactant protein D, N termini junction grayscale peak – width
Four dodecamers: Peak height for peak 4 in SP-D trimers
Same format for peak height as other peaks, and this peak is just lateral to the glycosylation peak in SP-D, when counting begins at the N term peak.
Four dodecamers: peak 5 width (nm)
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.
Four dodecamers of surfactant protein D: peak 4 width
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.
Four dodecamers: peak width and incidence of the neck domain in AFM images of SP-D
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.
