I don't think my CompSci masters degree has prepared me to answer neurobiology questions. I suspect that you'd be better served by some forum hosting phD's...
Protein mis folding has been identified in ALS, Alzheimer and Parkinson. Proteins are the work horses of cells and if they do not work correctly, well, the cell dies. This was discussed a bit in the Jackson Hole TED conference that found L-Serine could help. A link to that conference can be found in this forum thread.
I think of is like so: the workings of the cells are like jigsaw puzzles. All the pieces fit a certain way and interlock with other pieces. If a given piece (a mis-folded protein) can no longer fit into it place, we lose that function and get a damaged or dying cell.