title: A dynamical study of antibody-antigen encounter reactions.
abstract: The effects of internal dynamics in diffusion-driven encounters between macro-molecules represent a problem of broad relevance in molecular biology. In this view, we investigate a typical antigen-antibody reaction chain, based on a coarse-grained mechanical model parameterized directly upon results from single-molecule experiments. We demonstrate that the internal dynamics is a crucial factor in the encounter process. To describe our numerical results, we formulate a simple, intuitive theoretical framework, and we develop it analytically. This enables us to show that the inner dynamics of antibody molecules results in a cooperative behavior of their individual sub-units. Along the same lines, we also investigate the case of double binding to multi-valent antigens. Our results quantify the enhancement of avidity afforded by the double binding in excellent agreement with the available experimental data.
authors.affiliation: Dipartimento di Fisica, Università di Firenze, V. G. Sansone 1, 50019 Firenze, Italy. bongini@fi.infn.it
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Bongini
authors.forename: Duccio
authors.initials: D
authors.lastname: Fanelli
authors.forename: Francesco
authors.initials: F
authors.lastname: Piazza
authors.forename: Paolo
authors.initials: P
authors.lastname: De Los Rios
authors.forename: Michel
authors.initials: M
authors.lastname: Sanner
authors.forename: Ulf
authors.initials: U
authors.lastname: Skoglund
mesh_terms: D000818:Animals; D000906:Antibodies / Q000737:chemistry* / Q000276:immunology; D000915:Antibody Affinity; D000936:Antigen-Antibody Complex / Q000737:chemistry* / Q000276:immunology; D000937:Antigen-Antibody Reactions; D000941:Antigens / Q000737:chemistry* / Q000276:immunology; D001666:Binding Sites, Antibody; D003198:Computer Simulation; D007700:Kinetics; D008956:Models, Chemical; D018448:Models, Immunological; D011485:Protein Binding
chemical_list: D000906:Antibodies; D000936:Antigen-Antibody Complex; D000941:Antigens