Arroyo et al published a plot (height) of a particular SP-D hexamer and I have used this image to see whether some processing will increase the amount of information available. The image below sums up the comparison. Firstly, using the micron marker they provided and using the node (crux) rich vector line they used for their “height” plot, I could not replicate how they arrived at the dimensions of the molecule (the plot says about 150 nm but my analysis comes up with just 116nm (using their line and their micron marker). My line and their micron marker comes up with a slightly higher nm assignment of the molecule (about 123.8nm). In addition the diameter of a circle (which works pretty well at finding the arm length of dodecamers) doesn’t come up with a good estimate of the size of the hexamer (here is comes in at about 133nm).
I exported their image as a whole, cut it into 1nm slices and centered the slices then exported as a tiff and plotted the LUT tables in ImageJ and arrived at a similar plot to theirs. I also made plots of just the Ntermini with the first collagen-like domain peaks on either side, and each arm independently. The plots are basically similar, but my plot centered gives a more informative analysis of potentially important peaks in the collagen-like domain on either side of the Ntermini.
Plots and comparisons are in the image. My plot (orange, bottom figure, with a red plot overlying where each arm of the hexamer is adjusted to half of the total width of the molecule.
Their plot is replicated from their publication, and a my red plot with cut, centered, plotted and arm length evened up is overlying their original plot. It is obvious that the Ntermini in the “center” of the molecule are somewhat flattened… that peak should in fact be higher than the first peak in the collagen-like domains on either side. Maybe another hexamer will show better results. HOWEVER, that said, there are still three obvious peaks in both arms of the collagen-like domains as well as something that might be a fourth peak.
haha… here is a thought about why the Ntermini peak is smaller than the collagen-like domain peak 1….. in comparison to the dodecamer…. half as many Ntermini – that is just TWO overlapping so it is understandable that this peak does not reach as high.
