We have talked about the major histocompatibility complex (MHC) and how this is gives us our identities and allows use to distinguish ourselves from invaders into the body.
The T cell has a molecule that allows it to see its target. This is called the T cell receptor. There are many variants and this allows them to recognise alot (a billion billion) of targets
These come together so the T cell receptor recognises a linear sequence of amino acids and the MHC (=HLA).
There are twenty different amino acids that protiens are made from and T cells recognise 9-13 amino acids in a sequence. Some of the amino acids bind to the HLA and others bind to the T cell receptor. It is possible that a T cell that recognises a virus or bacteria could also react with a brain protein.
Each circle (above) is an amino acid the different colours represent different amino acids, white ones mean their identity are not important. Responses to Bacteria/virus 2 could cross-react with the brain protien. This is known as Molecular mimicry and is defined as the theoretical possibility that sequence similarities between foreign and self-peptides are sufficient to result in the cross-activation of autoreactive (autoimmune) T or B cells by pathogen-derived peptides.