by Andre on 18 May 2006
I’ve posted data from experiments in the past, but it’s always been to illustrate the kinds of things I work on or to share a method. This time, I want advice. You can also consider this a test of using weblogs as a collaborative tool, something I’m told is common in the humanities but seems to be extremely rare in science (but not unheard of—see Evolgen and Science and Politics).
Here’s the story so far.
I’ve started doing some experiments on vimentin, a ~45 nm long helical protein that serves as an intermediate filament in some cells’ cytoskeletons. See the Wikipedia entry on vimentin for all the background you need about the protein.
The data I want to talk about are really a side product from the main experiments I was doing but I think they are neat and I would like to learn more about them.
Here’s how they were generated. First, I put a drop of the protein/water solution onto freshly cleaved mica, a common substrate for AFM experiments, and let it sit for a few minutes so that the protein could adsorb to the surface. Next, I added some buffer solution to increase the ionic strength of the sample. This should cause the vimentin to self-assemble into fibers. Finally, the sample was allowed to dry slowly in air. When I took an image the next morning I got the image shown at the top (this image is 40 microns on a side).
I did the same thing, but dried the sample more quickly by blowing some nitrogen over it and I got the image shown at the bottom (this image is 10 microns on a side):
This reminded me of the undergrad lab I did on diffusion limited aggregation. For that experiment, I used a flat circular electrochemical cell to aggregate zinc from solution. Different solute concentrations give different patterns. This “phase diagram” is discussed even in the earliest papers. Depending on the voltage and concentration of zinc sulfate you can form dendrites (like I saw with vimentin) or fractal “stringy” stuctures.
The last piece of information I would like to bring to your attention (purely for motivation) is that Alzheimer’s disease and other neurodegenerative disorders result from the formation of protein aggregates of beta amyloid, a protein that can also form fibrils.
So, I’ve laid out the puzzle and now I have some questions for you readers (especially any nonlinear science types… you know who you are). Is the aggregation of small fibers any different from the aggregation of little balls? Can you convince me to do some related experiments to flesh out the story? Will we cure Alzheimer’s or other protein aggregation related diseases by understanding this problem better? :)