Monthly Archives: October 2018

What is the trend in diagrams of surfactant protein D

Electron microgaphs of lung, surfactant proteins A and D

The diagrams which frequent scientific publications on surfactant protein D (SP-D) are countless. I have gathered more than 27 diagrams of the SP-D dodecamer and some multimers (fuzzyballs) to see if there is conscensus in the literature about the angle between the arms of the SP-D trimers (of which there are 4) that comprise these oligomers. I have also gathered many more images of actual micrographs from publications (various methods for TEM) to see how closely the diagrams might approximate what is see in various preparations of isolated SP-D. I will mention one publication (which I have linked before) by Arroyo et al, that measures some of the angles of various multimers of SP-D and reports them in a continuous bar graph by anglular dimension.  I have done a similar kind of measurement (measuring the acute and obtuse angles of the dodecamers and less often diagrammed fuzzyballs in chart, and have also measured the dimensions suggested for the center N terminal associations. Sometimes there is no indication of the N terminal associations in diagrams, other times there is an indication, either a straight line, or lumps or circles, and in one (unfortunate diagram) as a square. The N terminal area is typically represented at about 10nm.summary of SP-D diagrams in scientific publicationsFrom the beginning of this assessment, it was obvious that some investigators tried to incorporate some actual structural elements of SP-D into their diagrams, others just copied what had been used before.  In almost all cases, the arms (composed the three SP-D molecules) have the carbohydrate recognition domains shown in a (pitiful) oval, mostly oriented at a 90 degree angle opposite of what is seen in actual protein modeling of the CRD.  So this is visually confusing, and added to this is the fact that the CRD domains are frequently not accurately sized compared to the whole of the SP-D molecule. The only explanation I can come up with, in light of very nice DRD data in the RCSB PDB, that this is just a matter of the author’s disregard for using correct graphics in scientific illustration. Two diagrams in particular are just way off base (easily found in the collection above).

Most of the literature gives the measurement of a dodecamer at about 100nm diameter, and this is the “green” circle in images below. I have placed a red dot over the images where CRD are positioned. In the diagrams above it is obvious, however, in the actual TEMs of prepared SP-D multimers it is not always obvious. But I did this for the sake of continuity between the diagrams and the actual SP-D images (a chart of images will come later).  Angles (both acute and obtuse) were calculated using an anglular dimension tool. Each angle in a multimer was measured as well as the center distance designated as the N terminal.

After calculating all values, I removed the values for two diagrams (above bottom row) that just didn’t pay any attention to the real TEMs and made their SP-D diagrams with four 90 degree angles. There was a definite trend in the diagrams (haha… copying the first guy to post a diagram likely) to have acute angles (something close to what was measured by Arroyo et al), and here measured at  45o (their SP-D dodecamer images were prepared in the pH ranges of near 7.4 and 5.5 and had acute angles of something less than 40-50o and a corresponding obtuse angle. The latter for some reason was more variable than the former. The actual measured mean in these diagrams above was in fact 45o which surprised me being so close to what is reported to the real TEMs.  Each diagram on its own seemed not very representative of what has been reported, but collectively, if one spends the time to view them all. The significance obtaining measurements of angles between the arms of SP-D oligomers relates to the possibility of using such measurements for the construction of nano-particles with SP-D as components. The most efficacious placement of the CRD needs to be calculated. And while it seems unnecessary task to use diagrams as a beginnig point…. I was hoping to point out the sometimes obvious flaws of careless diagramming, before making a similar chart of actual molecular images.

Some diagrams of SP-D are interesting

surfactant proteins A and D, Ultimate order, the cell

I have found that most of the diagrams of surfactant protein D are pretty far from reality. I found this one however that attempts to be more specific and utilizes at least some of the molecular modeling of that protein available. The RCSB PDB really doesn’t model SP-D in any complete way and while researchers have added many many variations of the carbohydrate recognition domain and the coiled coil neck region, nothing else much comes up as to the rest of the molecule.  So here is an attempt (which I have vectorized to eliminate the extraneous stuff in the diagram at least it utilizes the structures known for the trimer — from the neck up (haha). Also, it is totally confusing whether the arms are really trimers, or not, because the shape of the CRDs is relatively large compared to the whole molecule and is not tightly intertwined at the neck region (which is the way the “real” molecule is.  So Some of these arms are so spread out that there is no intertwining at the neck region whatsoever.  So this is not a good representation of the molecular structure, even though it wold suggest that it is a molecular model.  So therein lies a dilemma. 1) to make a diagram so wildly wrong that no one thinks you are making a molecularly accurate representation, or do your best, and make mistakes.  One thing for certain…mistakes get perpetuated.

What it does show  is the reasonably good approximation of the CRD, and also the curved nature of the SP-D trimeric arms which very few diagrams show but the SP-D trimers and dodecamer molecules seen by TEM show very clearly. What this diagram doesn’t do very well is look at the N terminal portion of SP-D, or show the possibility that there is a connection of the trimers at a “distance” from dead-enter, and it doesn’t indicate where the N terminal glycosylation site might be relative to the whole.  Measurements of the latter are taken from a publication by Crouch. Also, it seems that in this particular diagam the collagen-like area here is just a kind of an extended “neck”, with the wrong number of coils, and with no kink, no bend, no separate indication as to where the neck might connect to the collagen-like region. What it also does do, however, is make this particular fuzzyball in a configuration with even numbers of dodecamers (in this case 4, that is 16 arms) which would go along with the TEM images which suggest that the fuzzyballs are an aggregate of dodecamers. What it does not do is look at the possibility of open and closed, or segmented organization of the dodecamers. That would have shown up with more obtuse angles between the four dodecamers and more acute angles within each of the four dodecamer units.

Image found in the following review by Elena N. Atochina-Vasserman
I am suggesting the following structures might have been noted… just by what has been published by Crouch and other researchers on SP-D.

Toxic site –

Rants

Just saying —  The department of environmental health here at UC is not the same one that I attended first as a post doc in the 1970s or as faculty for, in the 1980s to present.  The whole university has changed: change is expected everywhere in the universe — which i understand.  But it has morphed from an institution of higher learning, into big business. The latter is not really what a university should aspire to be.

Hilarious scientific diagrams

Science and art cover illustrations, surfactant proteins A and D

I have to laugh. There are few places in the visual world where copy-cat exists more than in scientific illustrations. Working on models of real and “artistic” diagrams of SP-D I can see sthis so clearly. Copy-cat as to mis-information as well as copy-cat as to color, and misnomers as labels and size of molecular elements.  All of these diagrams are hysterical tributes to our willingness NOT to question truth. NOPE not talking politics here, but science.

Some of the clearly labeled SP-D diagrams look more like conglutinin diagrams.. than SP-D, and wouldn’t you know, when looking at shadowed conglutinin (Strang et al, Biochem J, 1986) they have a look more of SP-D with obtuse and acute angles.  In fact the latter sometimes has an interesting configuration of three acute and two obtuse angles not always mirrored. SP-D seemed to be pretty regularly mirrored.

I am planning a comparison, that is, real measurements of the angular dimensions of SP-D from “TEM” images and angular dmensions of real-copy-cat measurementsof SP-D, to see how far adrift from reality we can go, even when we have reality (yes there is likely preparation and fixation artifact in the shadowed, negatively stained and AFM images- that is not new) right under our eyes.