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My understanding is that MHC class I and II bind to relatively short polypeptide chains (~ 20ish amino acids). I'm surprised that a non-self protein fragment that short would be distinctive enough to target for an immune response. Also, how does expressing one polypeptide chain help the immune system identify the source? Isn't it quite likely that the presented polypeptide is in the interior of a protein and would never actually be exposed to the environment until after it's been lysed? Or is it hydrophilic peptides that bind?

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