Daily Archives: August 22, 2022

Four dodecamers of SP-D, summary of peak number, peak height and peak width for 300 hexamers

Here is a plot of the height and width (summary of 600 different plots of SP-D trimers)

I have sorted the plots by hand into the “mean number of peaks per hexamer that was found for this same dataset”  So you see 15 peaks, you see the fifteen divided (mirror on either side of the N term peak (peach), tiny peak on the downslope of the N term (purple), peak =glycocylation peak (medium green), peak 4, unknown peak, large, and also wide (dark green), unknown small peak (peak 5, pink ), unknown low and broad peak 6, (white),  and peak 7 likely the neck domain of the hexamer (yellow), and peak 8 the CRD (orange).  This is the a mirror (n=300 plots) of the left and righ trimers (n=600). X axis is percent of width, Y axis is grayscale value 0-255.

peaks along a plot of SP-D hexamer, made with ImageJ and published AFM images of surfactant protein D

The images exported from gwyddion were not included in this dataset because of the huge difference in the grayscale values for images exported R vs RGB when plotted in ImageJ).

Peaks within each of those peaks is shown here.  The peaks which are not present all the time have a value less than 1, those with a value of more than one often have more than one peak as sorted above.  List is for a trimer…. begin in the middle of the above graph, and move to the right (and mirror to the left from the N term peak).  This means that a minimum, there are five consistent (not the published three) but five peaks found all the time. That is the widths… peak 1 (N terminal domain 26nm), peak 2, unknown peak (3nm), peak 3 (glycosylation peak 10 nm), peak 4 (undetermined function, 12nm), peak 5, undetermined function (4nm),  peak 6 (undetermined function 7nm), peak 7 (likely the neck domain that sometimes is seen sometimes covered by the CRD (4nm) and peak 8 (carbohydrate recognition domain (12nm).However, I am doing more valley determinations to provide a “background” or “baseline” for the peaks which will likely NOT be a straight line and may give information on the “slope” of peaks.