  Mechanisms of immunity, and of the host-pathogen interactions in general are
among the most fundamental problems of medicine, ecology, and evolution
studies. Here, we present a microscopic, protein-level, sequence-based model of
immune system, with explicitly defined interactions between host and pathogen
proteins.. Simulations of this model show that possible outcomes of the
infection (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 certain
threshold. Potent immunoglobulins are discovered in this model via clonal
selection and affinity maturation. Surviving cells acquire lasting immunity
against subsequent infection by the same virus strain. As a second line of
defense cells develop apoptosis-like behavior by reducing their lifetimes to
eliminate viruses. These results demonstrate the feasibility of microscopic
sequence-based models of immune system, where population dynamics of the
evolving B-cells is explicitly tied to the molecular properties of their
proteins.
