  The immune system normally protects the human host against death by
infection. However, when an immune response is mistakenly directed at self
antigens, autoimmune disease can occur. We describe a model of protein
evolution to simulate the dynamics of the adaptive immune response to antigens.
Computer simulations of the dynamics of antibody evolution show that different
evolutionary mechanisms, namely gene segment swapping and point mutation, lead
to different evolved antibody binding affinities. Although a combination of
gene segment swapping and point mutation can yield a greater affinity to a
specific antigen than point mutation alone, the antibodies so evolved are
highly cross-reactive and would cause autoimmune disease, and this is not the
chosen dynamics of the immune system. We suggest that in the immune system a
balance has evolved between binding affinity and specificity in the mechanism
for searching the amino acid sequence space of antibodies.
