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.