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Mechanisms of immunity, and of the host-pathogen interactions in general areamong the most fundamental problems of medicine, ecology, and evolutionstudies. Here, we present a microscopic, protein-level, sequence-based model ofimmune system, with explicitly defined interactions between host and pathogenproteins.. Simulations of this model show that possible outcomes of theinfection (extinction of cells, survival with complete elimination of viruses,or chronic infection with continuous coexistence of cells and viruses)crucially depend on mutation rates of the viral and immunoglobulin proteins.Infection is always lethal if the virus mutation rate exceeds a certainthreshold. Potent immunoglobulins are discovered in this model via clonalselection and affinity maturation. Surviving cells acquire lasting immunityagainst subsequent infection by the same virus strain. As a second line ofdefense cells develop apoptosis-like behavior by reducing their lifetimes toeliminate viruses. These results demonstrate the feasibility of microscopicsequence-based models of immune system, where population dynamics of theevolving B-cells is explicitly tied to the molecular properties of theirproteins.

Emergence of clonal selection and affinity maturation in an ab initio microscopic model of immunity