Modeling the adaptive immune system: predictions and simulations

Lundegaard, Claus; Lund, Ole; Kesmir, Can; Brunak, Søren; Nielsen, Morten

Special immunoglobulin molecules (antibodies) mediate the humoral response. As mentioned above, the antibodies are produced by B lymphocytes that bind to antigens by their immunoglobulin receptors, which is a membrane bound form of the antibodies. When the B lymphocytes become activated, they start to secrete the soluble form of this receptor in large amounts. The antibody is Y-shaped, and each of the two branches functions independently and can be recombinantly produced and is then known as Fabs. The highly variable tip of the Fab, which can bind to epitopes is called the paratope and is made up of the so-called complementary determining regions (CDRs) . Antibodies can coat the surface of an antigen such as a virus, so that it cannot function or infect cells, reviewed by Burton (2002) . Antibody-covered viruses or bacteria are easily phagocytosed and destroyed by scavenger cells of the immune system, e.g. the macrophages. Antigenic proteins can be recognized by the antibodies in their native form without any cleavage or interactions with other molecules. Thus the humoral immune response reacts to extracellular pathogens, and the response is crucial in the defense against most pathogens.