system
Given the following post, respond as if you're commenting on Reddit:
human
What makes misfolding a protein dangerous? Why are prions functionally different from their original form?
gpt
There is nothing inherently dangerous about misfolded proteins. Proteins misfold all the time. All proteins start out as a somewhat 1 dimensional string of amino acids and then sample many different conformational states before reaching their "folded" state. Even then, a folded state is not necessarily static, nor is it necessarily unique. 

Function of a protein is very much related to the structure of the protein because function is chemically determined, and the chemistry a given protein can do is precisely controlled by the arrangement of its amino acids (or the electrons within them). This is a general tenet of all chemistry, not just biochemistry, since we classify molecules based on their structure. So, if for a protein to perform its function, a nitrogen from amino acid 23 has to be able to hydrogen bond to a substrate which then has to hydrogen bond 2 angtroms away at a 30 degree angle to an oxygen in amino acid 347, then if the protein does not allow for that specific arrangement, the chemistry will not be performed.

The proteins in all cells start out unfolded, sample some states, and in general adopt a folded conformation. The folded conformation may not be the most energetically favorable one, but it is usually a local energy minimum. Over time, since the temperature of all living systems is well above 0K, the protein may jigger to a different state that may be more energetically favorable but may not be the functional conformation. There are mechanisms in all cells to slowly degrade proteins, and often to even find proteins that look misfolded and degrade those preferentially. Meanwhile, new proteins are synthesized from the remnants of old ones.

What makes prions unique, is 3 things. First, the prion conformation is incredibly hardy. It is in a very deep energy well, which means it is very difficult to unfold it. So when the protein ends up in that state, it is likely to remain there and never fold properly again. Second, the prion state often exposes hydrophobic residues such that it acts as a nucleation site for more unfolding. So when a prion is around the properly folded protein, it facilitates the misfolding of the other protein into the prion confirmation. And lastly, the combination of the first 2 issues makes the prion able to be transmitted from cell to cell or even dead tissue to living tissue. 

If you take into account all of the various proteins that exist, prions are very very very rare, but once they show up, they are difficult to get rid of.