Science Buddies: "Ask an Expert"

Hi,

I've been reading about amyloids the past couple of days - just for curiosity's sake, though if I can work with it somehow I might turn it into a science project!

I've been reading about how these amyloids play a major part in Alzheimer's and many other diseases and conditions. I have a couple of questions about them though (forgive me if my questions do not make sense biologically or are not correct in any way, my internet sources may not have been of the highest quality!):

1) how are amyloids formed both in vivo and in vitro?
2) how do amyloids denature/unfold both in vivo and in vitro?
3) what makes amyloids "chemically sticky"?
4) how do protein peptides convert to amyloid fibers?
5) why is the partially denatured form susceptible to joining together with other amyloids to form plaques etc.?

Also, if this does turn out to be a project worth doing can you offer any other advice/tips/information on this subject? Also, if it does end up being a project, I have quite a few months to work on it

Thanks heaps in advance!

Hi Barney77,

Those are really good questions about a very interesting topic. In fact, several aspects of your questions are being researched in Alheizmer's/amyloid labs.

The general cause of amyloid formation is that a protein becomes unfolded or misfolded. When this happens, segments of hydrophobic amino acids (that is, those that don't like water) that are usually hidden on the inside of the protein structure get exposed to the outside. These exposed hydrophobic elements are what make the protein "chemically sticky", and the result is that the proteins start sticking very tightly to each other. One way to think of this is to imagine what would happen if you poured some oil into a bottle of water and shook it up. Right after you got done shaking, the oil would be in a bunch of very small droplets in the water. As you let it sit, all of those droplets will coalesce into a single layer of oil that separates itself from the water. When there are a lot of "oily" proteins in a watery cell, they also want to stick together in one mass, which is one way in which amyloids form.

In vivo, it isn't always known what causes the amyloid-forming proteins to become misfolded in the first place. Sometimes (as is the case with Huntington's disease), a genetic mutation causes the protein to be misfolded. Other times protein misfolding can be caused by general cellular stress, which may cause the protein folding mechanism to be compromised. In vitro, folded proteins can be denatured by either harsh chemicals or by subjecting them to ultrasonic frequencies. For amyloid-prone proteins, that forced denaturation can drive them to aggregate into amyloids.

When thinking about a project with amyloid proteins, it may not be advisable to work directly with amyloid proteins since they can be dangerous to work with. If you'd really like to pursue that route, the best bet would be to contact a lab at a local university who does amyloid work. A more viable direction for you project might be to make it a computational project. There are several web-based amyloid prediction sites (http://bioinfo.protres.ru/fold-amyloid/oga.cgi) that might be the basis for an amyloid project.

I hope this was helpful. Good luck.

Caleb

Awesome, thank you so much Caleb! That answered my questions perfectly! I am really interested in amyloids, even more so now I understand them more.
Thanks, I didn't know they could be dangerous either, so if I do go down that track, I probably will contact the uni or the Menzies centre maybe One more question - why are they dangerous?

Thanks heaps for your help, tips & link! I'd also just like to say thanks for that fact that even though I'm only in grade nine, you didn't completely ignore the idea of a science project to do with something complicated like this.

Thanks again
Barney77

I'm glad the information was helpful for you.

The reason amyloid can be dangerous to work with is that certain amyloid proteins (known as prions) can be infectious if you ingest them. You may have heard of Mad Cow Disease, which results from cows eating food that contained prion proteins. Not all amyloid proteins are infectious, so the danger depends on which amyloid protein you're studying. Nevertheless, doing experiments with amyloid proteins is probably better done under the guidance of someone with amyloid research experience. Here's a nice overview of some of the infectious prion diseases:
http://learn.genetics.utah.edu/content/ ... es/prions/

Let us know how the project goes!

Caleb

Oh ok, if I do decide to conduct an experiment with amyloid, I definitely will seek out someone with experience I remember reading somewhere about prions - and that link is really cool! Also, yet another question! Could you please explain what the first link you provided is and how it works? I'm just trying to get everything straight to decide whether I think I should consider this for my project!

Thanks heaps once again!

Barney77

The first link is an algorithm that predicts how likely peptides are to aggregate into amyloids. After I gave you that link, I found a better web interface for the same thing: tango.crg.es After you register for free, you can input a protein sequence (uniprot.org is a good place to look up protein sequences) and hit "calculate". It spits out a bunch of numbers, but the key numbers are in the "beta aggregation" column. That number is a score (on a scale of 0-100%) for how likely each amino acid residue is to aggregate. According to the handbook: "As a rule of the thumb any segment with an aggregation tendency above 5% over 5-6 residues is a potential aggregating segment."

I would suggest starting with the sequence for amyloid beta, the protein involved in Alzheimer's Disease. You should see lots of high beta aggregation scores for that one.

Caleb

Wow that is so cool, I had no clue that kind of thing even existed! Thanks heaps, I'll try it out today with amyloid beta to get my head around it and then go from there Thanks again,

Barney77