Deriving shape space parameters from immunological data

Derek J. Smith, Stephanie Forrest, Ron R. Hightower, Alan S. Perelson

Research output: Contribution to journalArticlepeer-review

52 Scopus citations


We present a method for deriving shape space parameters that are consistent with immunological data, and illustrate the method by deriving shape space parameters for a model of cross-reactive memory. Cross-reactive memory responses occur when the immune system is primed by one strain of a pathogen and challenged with a related, but different, strain. Much of the nature of a cross-reactive response is determined by the quantity and distribution of the memory cells, raised to the primary antigen, that cross-react with the secondary antigen. B cells with above threshold affinity for an antigen lie in a region of shape space that we call a ball of stimulation. In a cross-reactive response, the intersection of the balls of stimulation of the primary and secondary antigens contains the cross-reactive B cells and thus determines the degree of cross-reactivity between the antigens. We derive formulas for the volume of intersection of balls of stimulation in different shape spaces and show that the parameters of shape space, such as its dimensionality, have a large impact on the number of B cells in the intersection. The application of our method for deriving shape space parameters indicates that, for Hamming shape spaces, 20 to 25 dimensions, a three or four letter alphabet, and balls of stimulation of radius five or six, are choices that match the experimental data. For Euclidean shape spaces, five to eight dimensions and balls of stimulation with radius about 20% of the radius of the whole space, match the experimental data.

Original languageEnglish (US)
Pages (from-to)141-150
Number of pages10
JournalJournal of Theoretical Biology
Issue number2
StatePublished - Nov 21 1997
Externally publishedYes

ASJC Scopus subject areas

  • Statistics and Probability
  • Modeling and Simulation
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Agricultural and Biological Sciences(all)
  • Applied Mathematics


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