Popular Science Summary
We are all familiar with the idea that living organisms are made of atoms and molecules. But not everyone knows that one of those molecules that are crucial for our lives are proteins. And no, they aren’t just something we have to eat. Proteins are an essential molecule which form our cells, together with fat, sugars, and nucleic acids. Proteins are the workforce of the cell, carrying out most of the active duties, from moving other molecules, to cutting them or gluing them, giving the cells a “skeleton”, and so on. We don’t just eat them, we also produce them, as we need them constantly to perform their duties in the cell.
A crucial aspect for a protein to work well is its folding. You can think of it as a sheet of paper that you need to fold into the appropriate shape for its function, like making a paper plane if you want it to fly. Each protein has a specific fold, and that fold is made exactly for the function the protein has. That is the case to such an extent, that some improperly folded proteins are the cause of some diseases. On the other hand, there are some proteins that prefer to be unfolded instead and be a “flat sheet of paper”. But if you just have a bunch of flat sheets of paper, isn’t it tempting to just stack them neatly on top of each other? Well, that’s what these proteins do. These proteins, called amyloid proteins, are proteins we produce in our everyday life, and they perform functions we need for having a normal life. However, they have a tendency to clump together and aggregate into very neat and ordered helixlike structures. These structures are called fibrils. Many neurodegenerative diseases, such as Alzheimer’s or Parkinson’s, are characterized by the presence of small deposits in the brain, which are formed by amyloid fibrils. And the most interesting thing is that there are many different amyloid proteins, and each of them can be associated to different diseases. This implies that there is something about this aggregation process that they all follow that somehow is connected to the diseases.
This led scientists to study amyloid proteins and their aggregation into fibrils, with the hopes of understanding how the disease is caused and how is it connected to these proteins. Recently, they found out that the proteins alone, one by one, or the fibrils by themselves, don’t harm cells too much. Instead, they found that more disordered intermediate species, formed by a bunch of units put together, are actually toxic. This makes the study of these intermediate species, called amyloid oligomers, crucial to understand how the protein behaves and how it is associated with the disease. However, they are just the middle stage of a transition between single proteins and fibrils, so, as one would guess, they are very transient and short lived. Due to that, conventional techniques fail to capture them, and methods have to be developed explicitly for their measurement.
In this thesis, we focus on the optimization of two amyloid oligomer measuring methods, called PICUP and µFFE. For PICUP, we have built a machine to make the 17 reaction as fast as possible to freeze amyloid oligomers in the position they are in the moment of reaction. In doing so, we have understood a lot of key aspects of the reaction, as well as gaining information on what parts of the protein are in contact with each other when they are in an oligomer together. With µFFE, we can count the number of oligomers on a sample. Using this, we have evaluated different factors and how they affect oligomer population. All in all, we have improved some previously existing methods and/or given them a new niche focus, which has allowed us to learn a lot about oligomers, hopefully taking the amyloid field a small step closer to understanding the connection between protein and disease.
